END_TEST
START_TEST (test_SpatialExtension_read_L3V1V1_defaultNS)
{
string file = TestDataDirectory;
file += "/read_L3V1V1_defaultNS.xml";
SBMLDocument *document = readSBMLFromFile(file.c_str());
string sbmlDoc = writeSBMLToStdString(document);
Model *model = document->getModel();
//document->printErrors();
fail_unless(model != NULL);
//fail_unless(document->getNumErrors() == 0);
// model : compartment
fail_unless(model->getNumCompartments() == 1);
Compartment *comp = model->getCompartment(0);
// compartment : compartmentMapping
SpatialCompartmentPlugin* cplugin = static_cast<SpatialCompartmentPlugin*>(comp->getPlugin("spatial"));
fail_unless(cplugin != NULL);
CompartmentMapping *cMapping = cplugin->getCompartmentMapping();
if (cMapping->isSetId()) {
fail_unless(cMapping->getId() == "compMap1");
fail_unless(cMapping->getDomainType() == "dtype1");
fail_unless(cMapping->getUnitSize() == 1);
}
// model : species 1
fail_unless(model->getNumSpecies() == 2);
Species *sp = model->getSpecies(0);
SpatialSpeciesPlugin* srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
fail_unless(srplugin != NULL);
fail_unless(srplugin->getIsSpatial() == true);
// model : species 2
sp = model->getSpecies(1);
srplugin = static_cast<SpatialSpeciesPlugin*>(sp->getPlugin("spatial"));
fail_unless(srplugin != NULL);
fail_unless(srplugin->getIsSpatial() == true);
// model : parameters (species diffusion, advection coeffs, species boundary conditions, coordinate components from Geometry
fail_unless(model->getNumParameters() == 5);
// parameter 0 : diffusionCoefficient
Parameter *param = model->getParameter(0);
SpatialParameterPlugin* pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_DIFFUSIONCOEFFICIENT);
DiffusionCoefficient *diffCoeff = pplugin->getDiffusionCoefficient();
fail_unless(diffCoeff->getVariable() == "ATPc");
fail_unless(diffCoeff->isSetCoordinateReference1());
fail_unless(diffCoeff->getCoordinateReference1() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
// parameter 1 : advectionCoefficient
param = model->getParameter(1);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_ADVECTIONCOEFFICIENT);
AdvectionCoefficient *advCoeff = pplugin->getAdvectionCoefficient();
fail_unless(advCoeff->getVariable() == "ATPc");
fail_unless(advCoeff->getCoordinate() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
// parameter 2 : boundaryCondition X
param = model->getParameter(2);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
fail_unless(pplugin->isSpatialParameter() == true);
fail_unless(pplugin->getType() == SBML_SPATIAL_BOUNDARYCONDITION);
BoundaryCondition *bc = pplugin->getBoundaryCondition();
fail_unless(bc->getVariable() == "ATPc");
fail_unless(bc->getCoordinateBoundary() == "Xmin");
fail_unless(bc->getType() == SPATIAL_BOUNDARYKIND_DIRICHLET);
// parameter 3 : SpatialSymbolReference (coordinateComponent from geometry)
param = model->getParameter(3);
pplugin = static_cast<SpatialParameterPlugin*>(param->getPlugin("spatial"));
fail_unless(pplugin != NULL);
SpatialSymbolReference *spSymRef = pplugin->getSpatialSymbolReference();
fail_unless(spSymRef->getSpatialRef() == "coordComp1");
// model : reaction
fail_unless(model->getNumReactions() == 1);
Reaction *rxn = model->getReaction(0);
SpatialReactionPlugin* rplugin = static_cast<SpatialReactionPlugin*>(rxn->getPlugin("spatial"));
fail_unless(rplugin != NULL);
fail_unless(rplugin->getIsLocal() == true);
// get the Geometry
SpatialModelPlugin* mplugin = static_cast<SpatialModelPlugin*>(model->getPlugin("spatial"));
fail_unless(mplugin != NULL);
Geometry *geometry = mplugin->getGeometry();
fail_unless(geometry != NULL);
fail_unless(geometry->getPackageName() == "spatial");
fail_unless(geometry->getCoordinateSystem() == SPATIAL_GEOMETRYKIND_CARTESIAN);
// geometry coordinateComponent
fail_unless(geometry->getNumCoordinateComponents() == 1);
fail_unless(geometry->getListOfCoordinateComponents()->getPackageName() == "spatial");
CoordinateComponent* coordComp = geometry->getCoordinateComponent(0);
fail_unless(coordComp->getId() == "coordComp1");
fail_unless(coordComp->getType() == SPATIAL_COORDINATEKIND_CARTESIAN_X);
fail_unless(coordComp->getUnit() == "umeter");
fail_unless(coordComp->getPackageName() == "spatial");
// boundaryMin and boundayMax within coordinateComponent
Boundary *minX = coordComp->getBoundaryMin();
fail_unless(minX->getId() == "Xmin");
fail_unless(minX->getValue() == 0);
fail_unless(minX->getPackageName() == "spatial");
Boundary *maxX = coordComp->getBoundaryMax();
fail_unless(maxX->getId() == "Xmax");
fail_unless(maxX->getValue() == 10);
fail_unless(maxX->getPackageName() == "spatial");
// geometry domainType
fail_unless(geometry->getNumDomainTypes() == 1);
fail_unless(geometry->getListOfDomainTypes()->getPackageName() == "spatial");
DomainType *domainType = geometry->getDomainType(0);
fail_unless(domainType->getId() == "dtype1");
fail_unless(domainType->getSpatialDimensions() == 3);
fail_unless(domainType->getPackageName() == "spatial");
// geometry domains
fail_unless(geometry->getNumDomains() == 2);
fail_unless(geometry->getListOfDomains()->getPackageName() == "spatial");
Domain* domain = geometry->getDomain(0);
fail_unless(domain->getId() == "domain1");
fail_unless(domain->getDomainType() == "dtype1");
//fail_unless(domain->getImplicit() == false);
//fail_unless(domain->getShapeId() == "circle");
fail_unless(domain->getPackageName() == "spatial");
// interiorPoints in Domain
fail_unless(domain->getNumInteriorPoints() == 1);
fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial");
InteriorPoint* interiorPt = domain->getInteriorPoint(0);
fail_unless(interiorPt->getCoord1() == 1);
fail_unless(interiorPt->getPackageName() == "spatial");
// second domain in geometry
domain = geometry->getDomain(1);
fail_unless(domain->getId() == "domain2");
fail_unless(domain->getDomainType() == "dtype1");
//fail_unless(domain->getImplicit() == false);
//fail_unless(domain->getShapeId() == "square");
fail_unless(domain->getPackageName() == "spatial");
// Domain : interiorPoints
fail_unless(domain->getNumInteriorPoints() == 1);
fail_unless(domain->getListOfInteriorPoints()->getPackageName() == "spatial");
interiorPt = domain->getInteriorPoint(0);
fail_unless(interiorPt->getCoord1() == 5);
fail_unless(interiorPt->getPackageName() == "spatial");
// geometry adjacentDomains
fail_unless(geometry->getNumAdjacentDomains() == 1);
fail_unless(geometry->getListOfAdjacentDomains()->getPackageName() == "spatial");
AdjacentDomains* adjDomain = geometry->getAdjacentDomains(0);
fail_unless(adjDomain->getId() == "adjDomain1");
fail_unless(adjDomain->getDomain1() == "domain1");
fail_unless(adjDomain->getDomain2() == "domain2");
fail_unless(adjDomain->getPackageName() == "spatial");
// geometry : geometryDefinitions
fail_unless(geometry->getNumGeometryDefinitions() == 2);
fail_unless(geometry->getListOfGeometryDefinitions()->getPackageName() == "spatial");
GeometryDefinition *gd = geometry->getGeometryDefinition(0);
AnalyticGeometry *analyticGeom = static_cast<AnalyticGeometry*>(gd);
fail_unless(analyticGeom->getId() == "analyticGeom1");
fail_unless(analyticGeom->getPackageName() == "spatial");
// AnalyticGeometry : analyticVolumes
fail_unless(analyticGeom->getNumAnalyticVolumes() == 1);
fail_unless(analyticGeom->getListOfAnalyticVolumes()->getPackageName() == "spatial");
AnalyticVolume* av = analyticGeom->getAnalyticVolume(0);
fail_unless(av->getId() == "analyticVol1");
fail_unless(av->getDomainType() == "dtype1");
fail_unless(av->getFunctionType() == SPATIAL_FUNCTIONKIND_LAYERED);
fail_unless(av->getOrdinal() == 1);
fail_unless(av->getPackageName() == "spatial");
// ??????Math????
// geometry : sampledFieldGeometry
gd = geometry->getGeometryDefinition(1);
SampledFieldGeometry* sfGeom = static_cast<SampledFieldGeometry*>(gd);
fail_unless(sfGeom->getId() == "sampledFieldGeom1");
fail_unless(sfGeom->getPackageName() == "spatial");
// sampledFieldGeometry : SampledVolumes
fail_unless(sfGeom->getNumSampledVolumes() == 1);
fail_unless(sfGeom->getListOfSampledVolumes()->getPackageName() == "spatial");
SampledVolume* sv = sfGeom->getSampledVolume(0);
fail_unless(sv->getId() == "sv_1");
fail_unless(sv->getDomainType() == "dtype1");
fail_unless(sv->getSampledValue() == 128);
fail_unless(sv->getMinValue() == 0);
fail_unless(sv->getMaxValue() == 255);
fail_unless(sv->getPackageName() == "spatial");
// sampledFieldGeometry : SampledField
SampledField* sf = geometry->getSampledField( sfGeom->getSampledField() );
fail_unless(sf->getId() == "sampledField1");
fail_unless(sf->getDataType() == SPATIAL_DATAKIND_UINT8);
fail_unless(sf->getInterpolationType() == SPATIAL_INTERPOLATIONKIND_LINEAR);
fail_unless(sf->getCompression() == SPATIAL_COMPRESSIONKIND_UNCOMPRESSED);
fail_unless(sf->getNumSamples1() == 4);
fail_unless(sf->getNumSamples2() == 4);
fail_unless(sf->getNumSamples3() == 2);
fail_unless(sf->getPackageName() == "spatial");
// sampledField : ImageData
fail_unless(sf->getSamplesLength() == 32);
int* samples = new int[sf->getSamplesLength()];
sf->getSamples(samples);
fail_unless(samples[0] == 0);
string s2 = writeSBMLToStdString(document);
fail_unless(sbmlDoc==s2);
delete document;
delete[] samples;
}
