protected override void Context()
{
base.Context();
_rootContainer = CreateContainer(null, "Sim", ContainerType.Simulation);
var organism = CreateContainer(_rootContainer, "Organism");
var liver = CreateContainer(organism, "Liver");
var plasma = CreateContainer(liver, "Plasma", ContainerType.Compartment);
_moleculeAmount = new MoleculeAmount().WithName("ABC").WithParentContainer(plasma);
}
public void TestSerializationMoleculeAmountWithFixedValue()
{
MoleculeAmount x1 = CreateObject <MoleculeAmount>().WithName("Monica").WithDimension(DimensionLength);
x1.Persistable = true;
x1.Value = 2.3;
x1.ScaleDivisor = 0.345;
IMoleculeAmount x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualMoleculeAmount(x2, x1);
}
public void TestSerializationQuantityAndContainerWithConstantFormula()
{
MoleculeAmount x1 = CreateObject <MoleculeAmount>().WithName("Monica").WithDimension(DimensionLength);
x1.IsFixedValue = false;
x1.Persistable = false;
x1.Formula = CreateObject <ConstantFormula>().WithDimension(DimensionLength).WithValue(23.4);
x1.Mode = ContainerMode.Logical;
Parameter p1 = CreateObject <Parameter>().WithName("Quentin").WithDimension(DimensionLength);
x1.Add(p1);
IQuantityAndContainer x2 = SerializeAndDeserialize(x1);
AssertForSpecs.AreEqualQuantityAndContainer(x2, x1);
}
protected override void Context()
{
base.Context();
var organsim = new Container().WithName(Constants.ORGANISM);
var kidney = new Container().WithName(CoreConstants.Organ.KIDNEY).WithParentContainer(organsim);
var urine = new Container().WithName(CoreConstants.Compartment.URINE).WithParentContainer(kidney);
var lumen = new Container().WithName(CoreConstants.Organ.LUMEN).WithParentContainer(organsim);
var feces = new Container().WithName(CoreConstants.Compartment.FECES).WithParentContainer(lumen);
var gallBladder = new Container().WithName(CoreConstants.Organ.GALLBLADDER).WithParentContainer(organsim);
_moleculeUrine = new MoleculeAmount().WithName("DRUG")
.WithParentContainer(urine);
_moleculeUrine.Persistable = false;
_moleculeFeces = new MoleculeAmount().WithName("DRUG")
.WithParentContainer(feces);
_moleculeFeces.Persistable = false;
_moleculeGallBladder = new MoleculeAmount().WithName("DRUG")
.WithParentContainer(gallBladder);
_moleculeGallBladder.Persistable = false;
_urineConcentrationObserver = new Observer().WithName(CoreConstants.Observer.CONCENTRATION_IN_CONTAINER);
_urineConcentrationObserver.Persistable = true;
_moleculeUrine.Add(_urineConcentrationObserver);
_fecesConcentrationObserver = new Observer().WithName(CoreConstants.Observer.CONCENTRATION_IN_CONTAINER);
_fecesConcentrationObserver.Persistable = true;
_moleculeFeces.Add(_fecesConcentrationObserver);
var compound = new Compound().WithName("DRUG");
_individualSimulation = new IndividualSimulation();
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("Id", PKSimBuildingBlockType.Compound)
{
BuildingBlock = compound
});
_individualSimulation.Model = new OSPSuite.Core.Domain.Model {
Root = new Container {
organsim
}
};
}
protected override void Context()
{
_entityPathResolver = new EntityPathResolverForSpecs();
_representationInfoRepository = new RepresentationInfoRepositoryForSpecs();
sut = new PKSimPathToPathElementsMapper(_representationInfoRepository, _entityPathResolver);
_organism = new Organism();
_venousBlood = new Organ().WithName(CoreConstants.Organ.VenousBlood).WithParentContainer(_organism);
_liver = new Organ().WithName(CoreConstants.Organ.Liver).WithParentContainer(_organism);
_kidney = new Organ().WithName(CoreConstants.Organ.Kidney).WithParentContainer(_organism);
_liverInt = new Compartment().WithName(CoreConstants.Compartment.Interstitial).WithParentContainer(_liver);
_liverCell = new Compartment().WithName(CoreConstants.Compartment.Intracellular).WithParentContainer(_liver);
_kidneyUrine = new Compartment().WithName(CoreConstants.Compartment.URINE).WithParentContainer(_kidney);
_gallBladder = new Organ().WithName(CoreConstants.Organ.Gallbladder).WithParentContainer(_organism);
_lumen = new Organ().WithName(CoreConstants.Organ.Lumen).WithParentContainer(_organism);
_peripheralVenousBlood = new Container().WithName(CoreConstants.Organ.PeripheralVenousBlood).WithParentContainer(_organism);
_smallIntestine = new Organ().WithName(CoreConstants.Organ.SmallIntestine).WithParentContainer(_organism);
_mucosa = new Compartment().WithName(CoreConstants.Compartment.Mucosa).WithParentContainer(_smallIntestine);
_mucosa_duo = new Compartment().WithName(CoreConstants.Compartment.Duodenum).WithParentContainer(_mucosa);
_mucosa_duo_interstitial = new Compartment().WithName(CoreConstants.Compartment.Interstitial).WithParentContainer(_mucosa_duo);
_events = new Container().WithName(Constants.EVENTS);
_eventGroup = new EventGroup().WithName("E1").WithParentContainer(_events);
_plasma = new Compartment().WithName(CoreConstants.Compartment.Plasma).WithParentContainer(_venousBlood);
_drugContainerVenousBlood = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_venousBlood);
_drugContainerPeripheralVenousBlood = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_peripheralVenousBlood);
_drugContainerGallBladder = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_gallBladder);
_drugContainerInLumen = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_lumen);
_drugContainerInLiverCell = new Container().WithName(_drugName).WithContainerType(ContainerType.Molecule).WithParentContainer(_liverCell);
_drug = new MoleculeAmount().WithName(_drugName).WithParentContainer(_plasma);
_drugUrineKidney = new MoleculeAmount().WithName(_drugName).WithParentContainer(_kidneyUrine);
_applications = new Container().WithName(Constants.APPLICATIONS);
_application1 = new EventGroup().WithName("App").WithParentContainer(_applications).WithContainerType(ContainerType.EventGroup);
_formulation = new Container().WithName("F1").WithParentContainer(_application1);
_neighborhoods = new Container().WithName(Constants.NEIGHBORHOODS);
_liverCellToLiverIntNeighborhood = new Neighborhood {
FirstNeighbor = _liverInt, SecondNeighbor = _liverCell
}.WithParentContainer(_neighborhoods);
_concentrationDimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_fractionDimension = DomainHelperForSpecs.FractionDimensionForSpecs();
}
protected override void Context()
{
base.Context();
var root = new Container().WithName("Root").WithId("Root");
sut.Root = root;
_molecule = new MoleculeAmount().WithName("Molecule");
var globalMoleculeContainer = new Container().WithName("toto").WithContainerType(ContainerType.Molecule);
_parameterUnderMolecule = new Parameter().WithName("Param").WithFormula(new ConstantFormula(400));
_parameterUnderAnotherContainer = new Parameter().WithName("Param").WithFormula(new ConstantFormula(400));
globalMoleculeContainer.Add(_parameterUnderMolecule);
sut.Root.Add(_molecule);
sut.Root.Add(globalMoleculeContainer);
var anotherContainer = new Container().WithName("anotherContainer");
sut.Root.Add(anotherContainer);
anotherContainer.Add(_parameterUnderAnotherContainer);
_aParameterWithoutParent = new Parameter().WithName("_aParameterWithoutParent").WithFormula(new ConstantFormula(400));
}
protected override void Context()
{
_organism = new Container().WithName(Constants.ORGANISM);
_liver = new Container().WithName("Liver");
_kidney = new Container().WithName("Kidney");
_liverIntracellular = new Container().WithName(INTRACELLULAR);
_kidneyIntracellular = new Container().WithName(INTRACELLULAR);
_liverRelExp = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("Relative expression (normalized)");
_volumeLiver = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.VOLUME);
_volumeLiver.Formula = new ExplicitFormula("1+2");
_volumeOrganism = DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(Constants.Parameters.VOLUME);
_volumeLiverCell = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.VOLUME);
_liverIntracellularSubContainer = new Container().WithName("Intracellular Sub Container");
_volumeKidneyCell = DomainHelperForSpecs.ConstantParameterWithValue(3).WithName(Constants.Parameters.VOLUME);
_gfr = DomainHelperForSpecs.NormalDistributedParameter(3).WithName("GFR");
_volumeKidney = DomainHelperForSpecs.ConstantParameterWithValue(14).WithName(Constants.Parameters.VOLUME);
_height = DomainHelperForSpecs.ConstantParameterWithValue(175).WithName("Height");
_weight = DomainHelperForSpecs.ConstantParameterWithValue(75).WithName("Weight");
_paramWithRHS = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName("RHSParam");
_paramWithRHS.RHSFormula = new ExplicitFormula();
_clearance = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName("CL");
_organism.AddChildren(_liver, _kidney, _height, _weight, _volumeOrganism, _paramWithRHS);
_liver.AddChildren(_liverIntracellular, _volumeLiver);
_liverIntracellular.AddChildren(_volumeLiverCell, _liverIntracellularSubContainer, _liverRelExp);
_liverIntracellularSubContainer.Add(_clearance);
_kidney.AddChildren(_kidneyIntracellular, _volumeKidney);
_kidneyIntracellular.AddChildren(_volumeKidneyCell, _gfr);
_liverIntracellularMoleculeAmount = new MoleculeAmount().WithName("Drug");
_liverIntracellular.Add(_liverIntracellularMoleculeAmount);
_simulation = A.Fake <ISimulation>();
_simulation.Model.Root = _organism;
}
protected override void Context()
{
base.Context();
var root = new Container().WithName("Root").WithId("Root");
sut.Root = root;
_quantityWithMolWeight = new MoleculeAmount().WithName("Molecule");
var quantityWithMolWeightContainer = new Container().WithName(_quantityWithMolWeight.Name).WithContainerType(ContainerType.Molecule);
quantityWithMolWeightContainer.Add(new Parameter().WithName(Constants.Parameters.MOL_WEIGHT).WithFormula(new ConstantFormula(400)));
_parameterUnderMoleculeWithMolWeight = new Parameter().WithName("Concentration");
quantityWithMolWeightContainer.Add(_parameterUnderMoleculeWithMolWeight);
_quantityWithoutMolWeight = new MoleculeAmount().WithName("Molecule2");
var quantityWithoutMolWeightContainer = new Container().WithName(_quantityWithoutMolWeight.Name);
_parameterUnderMoleculeWithoutMolWeight = new Parameter().WithName("Concentration");
quantityWithoutMolWeightContainer.Add(_parameterUnderMoleculeWithoutMolWeight);
sut.Root.Add(quantityWithMolWeightContainer);
sut.Root.Add(quantityWithoutMolWeightContainer);
}
protected override void Context()
{
sut = new MoleculeAmount {
Name = "TOTO"
};
}
