protected override void Context()
{
_populationSimulationSettingsPresenter = A.Fake <IPopulationSimulationSettingsPresenter>();
_applicationController = A.Fake <IApplicationController>();
_projectRetriever = A.Fake <IPKSimProjectRetriever>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
_project = A.Fake <PKSimProject>();
_compound1 = A.Fake <Compound>();
_individual = A.Fake <Individual>();
_human = new Species().WithName(CoreConstants.Species.HUMAN);
_rat = new Species().WithName(CoreConstants.Species.RAT);
_mouse = new Species().WithName(CoreConstants.Species.MOUSE);
A.CallTo(() => _individual.Species).Returns(_human);
_populationSimulation = A.Fake <PopulationSimulation>();
A.CallTo(() => _populationSimulation.Compounds).Returns(new[] { _compound1 });
A.CallTo(() => _populationSimulation.Individual).Returns(_individual);
_keyPathMapper = A.Fake <IKeyPathMapper>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_userSettings = A.Fake <ICoreUserSettings>();
_originalSettings = new OutputSelections();
A.CallTo(() => _populationSimulation.OutputSelections).Returns(_originalSettings);
_populationSimulation.Model = new Model();
_populationSimulation.Model.Root = new Container();
_compound1.Name = "DRUG";
var organism = new Organism();
var peripheralVenousBlood = new Container().WithName(CoreConstants.Organ.PeripheralVenousBlood);
var venousBlood = new Container().WithName(CoreConstants.Organ.VenousBlood);
var venousBloodPlasma = new Container().WithName(CoreConstants.Compartment.Plasma).WithParentContainer(venousBlood);
var drugPeripheralBlood = new Container().WithName(_compound1.Name);
var drugVenousBlood = new Container().WithName(_compound1.Name);
var periperhalVenousBloodObserver = new Observer {
Name = CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD
};
drugPeripheralBlood.Add(periperhalVenousBloodObserver);
var venousBloodObserver = new Observer {
Name = CoreConstants.Observer.CONCENTRATION
};
drugVenousBlood.Add(venousBloodObserver);
peripheralVenousBlood.Add(drugPeripheralBlood);
venousBloodPlasma.Add(drugVenousBlood);
organism.Add(peripheralVenousBlood);
organism.Add(venousBlood);
_populationSimulation.Model.Root.Add(organism);
A.CallTo(() => _projectRetriever.Current).Returns(_project);
A.CallTo(() => _applicationController.Start <ISimulationOutputSelectionPresenter <PopulationSimulation> >()).Returns(_populationSimulationSettingsPresenter);
sut = new SimulationSettingsRetriever(_applicationController, _projectRetriever, _entityPathResolver, _keyPathMapper, _userSettings, _simulationPersistableUpdater);
A.CallTo(() => _entityPathResolver.PathFor(periperhalVenousBloodObserver)).Returns("PERIPHERAL_OBSERVER");
A.CallTo(() => _entityPathResolver.PathFor(venousBloodObserver)).Returns("VENOUS_BLOOD_OBSERVER");
}
protected override void Context()
{
base.Context();
_individual = A.Fake<Individual>();
var originData = new OriginData();
originData.Population = new SpeciesPopulation();
A.CallTo(() => _individual.OriginData).Returns(originData);
var organism = new Organism();
var ga = DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(Constants.Parameters.GESTATIONAL_AGE);
ga.Info.MinValue = 24;
ga.Info.MaxValue = 25;
organism.Add(ga);
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.MEAN_WEIGHT));
A.CallTo(() => _individual.IsPreterm).Returns(true);
A.CallTo(() => _individual.Organism).Returns(organism);
}
protected override void Context()
{
sut = new ExpressionContainersRetriever();
var objectPathFactory = new ObjectPathFactoryForSpecs();
var entityPathResolver = new EntityPathResolverForSpecs();
_liver.Add(_intLiver);
_liver.Add(_cellLiver);
_liver.Add(_plsLiver);
_liver.Add(_bcLiver);
_liver.Add(_endoLiver);
_kidney.Add(_intKidney);
_kidney.Add(_cellKidney);
_kidney.Add(_plsKidney);
_kidney.Add(_bcKidney);
_kidney.Add(_endoKidney);
_lumen.Add(_duodenum);
_organism.Add(_liver);
_organism.Add(_kidney);
_organism.Add(_lumen);
_protein = new IndividualEnzyme();
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.BloodCells)
}.WithName(CoreConstants.Compartment.BloodCells));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.Plasma)
}.WithName(CoreConstants.Compartment.Plasma));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = objectPathFactory.CreateObjectPathFrom(CoreConstants.Compartment.VascularEndothelium)
}.WithName(CoreConstants.Compartment.VascularEndothelium));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_liver)
}.WithName(CoreConstants.Organ.Liver));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_kidney)
}.WithName(CoreConstants.Organ.Kidney));
_protein.Add(new MoleculeExpressionContainer {
OrganPath = entityPathResolver.ObjectPathFor(_lumen), GroupName = CoreConstants.Groups.GI_LUMEN, ContainerName = _duodenum.Name
}.WithName(CoreConstants.ContainerName.LumenSegmentNameFor("Duodenum")));
}
protected override void Context()
{
base.Context();
_originData = new OriginData {
Species = new Species {
Name = "A", Icon = "B"
}, SpeciesPopulation = A.Fake <SpeciesPopulation>()
};
_individual = new Individual();
_organism = new Organism();
_neighborhoods = A.Fake <IContainer>();
_rootContainer = new RootContainer();
A.CallTo(() => _entityBaseFactory.Create <IRootContainer>()).Returns(_rootContainer);
A.CallTo(() => _entityBaseFactory.Create <Individual>()).Returns(_individual);
A.CallTo(() => _entityBaseFactory.Create <Organism>()).Returns(_organism);
A.CallTo(() => _entityBaseFactory.Create <IContainer>()).Returns(_neighborhoods);
_valueOrigin = new ValueOrigin {
Method = ValueOriginDeterminationMethods.InVitro, Source = ValueOriginSources.Database
};
_originData.UpdateValueOriginFrom(_valueOrigin);
_originData.Age = 10;
_originData.AgeUnit = _age.DisplayUnit.Name;
_organism.Add(_age);
_originData.GestationalAge = 40;
_originData.GestationalAgeUnit = _gestationalAge.DisplayUnit.Name;
_organism.Add(_gestationalAge);
_originData.Height = 170;
_originData.HeightUnit = _height.DisplayUnit.Name;
_organism.Add(_height);
_originData.Weight = 170;
_originData.WeightUnit = _weight.DisplayUnit.Name;
_organism.Add(_weight);
_originData.BMI = 170;
_originData.BMIUnit = _bmi.DisplayUnit.Name;
_organism.Add(_bmi);
}
protected override void Context()
{
base.Context();
_individual = new Individual {
Root = new RootContainer()
};
var organism = new Organism();
_individual.Add(organism);
var ageParameter = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.AGE);
organism.Add(ageParameter);
var gaParameter = DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.GESTATIONAL_AGE);
organism.Add(gaParameter);
var ageValues = new ParameterValues(_entityPathResolver.PathFor(ageParameter));
ageValues.Add(1);
ageValues.Add(2);
var gaValues = new ParameterValues(_entityPathResolver.PathFor(gaParameter));
gaValues.Add(30);
gaValues.Add(40);
_population = new RandomPopulation {
Settings = new RandomPopulationSettings {
BaseIndividual = _individual, NumberOfIndividuals = 2
}
};
_population.IndividualValuesCache.Add(ageValues);
_population.IndividualValuesCache.Add(gaValues);
_population.IndividualValuesCache.IndividualIds.AddRange(new [] { 1, 2 });
A.CallTo(() => _ontogenyRepository.OntogenyFactorFor(_ontogeny, CoreConstants.Groups.ONTOGENY_LIVER, 1, 30, _population.RandomGenerator)).Returns(10);
A.CallTo(() => _ontogenyRepository.OntogenyFactorFor(_ontogeny, CoreConstants.Groups.ONTOGENY_LIVER, 2, 40, _population.RandomGenerator)).Returns(11);
A.CallTo(() => _ontogenyRepository.OntogenyFactorFor(_ontogeny, CoreConstants.Groups.ONTOGENY_DUODENUM, 1, 30, _population.RandomGenerator)).Returns(20);
A.CallTo(() => _ontogenyRepository.OntogenyFactorFor(_ontogeny, CoreConstants.Groups.ONTOGENY_DUODENUM, 2, 40, _population.RandomGenerator)).Returns(21);
}
protected override void Because()
{
_sim = new IndividualSimulation().WithName("Tralala");
_organism = new Organism().WithName(Constants.ORGANISM);
_sim.Add(_organism);
_organ = new Organ().WithName("Liver");
_organism.Add(_organ);
_entityPathResolver = new EntityPathResolverForSpecs();
}
protected override void Context()
{
_defaultIndividualRetriever = A.Fake <IDefaultIndividualRetriever>();
_speciesRepository = A.Fake <ISpeciesRepository>();
_simulationFactory = A.Fake <ISimulationFactory>();
_parameterFactory = A.Fake <IParameterFactory>();
_protocolFactory = A.Fake <IProtocolFactory>();
sut = new VSSCalculator(_defaultIndividualRetriever, _speciesRepository, _simulationFactory, _parameterFactory, _protocolFactory);
_species1 = new Species().WithId("Human");
_species2 = new Species().WithId("Dog");
A.CallTo(() => _speciesRepository.All()).Returns(new[] { _species1, _species2 });
_simulation = A.Fake <Simulation>();
var organism = new Organism();
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameter.HCT));
A.CallTo(() => _simulation.Individual.Organism).Returns(organism);
}
protected override void Context()
{
base.Context();
_population = A.Fake <RandomPopulation>().WithName("POP");
A.CallTo(() => _population.NumberOfItems).Returns(7);
_baseIndividual = A.Fake <Individual>();
_cloneIndividual = A.Fake <Individual>();
var organism = new Organism();
A.CallTo(() => _cloneIndividual.Organism).Returns(organism);
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(40).WithName(CoreConstants.Parameters.WEIGHT));
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(50).WithName(CoreConstants.Parameters.HEIGHT));
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(60).WithName(CoreConstants.Parameters.BMI));
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(70).WithName(CoreConstants.Parameters.AGE));
organism.Add(DomainHelperForSpecs.ConstantParameterWithValue(80).WithName(Constants.Parameters.GESTATIONAL_AGE));
_constParam1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1");
_constParam2 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P2");
//create a reference to another parameter to ensure that formula parameter are not overwritten if nothing has changed
_formulaParameter = new PKSimParameter().WithName("P3").WithFormula(new ExplicitFormula("P2*2"));
_formulaParameter.Formula.AddObjectPath(new FormulaUsablePath("..", "P2").WithAlias("P2"));
var container1 = new Container {
_constParam1, _constParam2, _formulaParameter
};
_indParam1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName("P1");
_indParam2 = DomainHelperForSpecs.ConstantParameterWithValue(2).WithName("P2");
_indParam3 = new PKSimParameter().WithName("P3").WithFormula(new ExplicitFormula("P2*2"));
_indParam3.Formula.AddObjectPath(new FormulaUsablePath("..", "P2").WithAlias("P2"));
_indParam4 = DomainHelperForSpecs.ConstantParameterWithValue(4).WithName("P4");
var container2 = new Container {
_indParam1, _indParam2, _indParam3, _indParam4
};
A.CallTo(() => _executionContext.Clone(_baseIndividual)).Returns(_cloneIndividual);
A.CallTo(() => _population.FirstIndividual).Returns(_baseIndividual);
//put explicit formula first
A.CallTo(() => _population.AllVectorialParameters(_entityPathResolver)).Returns(new[] { _formulaParameter, _constParam1, _constParam2 });
A.CallTo(() => _cloneIndividual.GetAllChildren <IParameter>()).Returns(new[] { _indParam1, _indParam2, _indParam3, _indParam4 });
A.CallTo(() => _entityPathResolver.PathFor(_constParam1)).Returns("PATH1");
A.CallTo(() => _entityPathResolver.PathFor(_constParam2)).Returns("PATH2");
A.CallTo(() => _entityPathResolver.PathFor(_formulaParameter)).Returns("PATH3");
A.CallTo(() => _entityPathResolver.PathFor(_indParam1)).Returns("PATH1");
A.CallTo(() => _entityPathResolver.PathFor(_indParam2)).Returns("PATH2");
A.CallTo(() => _entityPathResolver.PathFor(_indParam3)).Returns("PATH3");
A.CallTo(() => _entityPathResolver.PathFor(_indParam4)).Returns("PATH4");
A.CallTo(() => _population.AllValuesFor("PATH1")).Returns(new[] { 10d, 11, 12, 13, 14, 15, 16 });
A.CallTo(() => _population.AllValuesFor("PATH2")).Returns(new[] { 20d, 21, 22, 23, 24, 25, 26 });
A.CallTo(() => _population.AllValuesFor("PATH3")).Returns(new[] { 40d, 42, 44, 46, 48, 50, 52 });
_templateIndividual1.Name = "POP-3";
_addIndividualCommand = A.Fake <IPKSimCommand>();
A.CallTo(() => _individualTask.AddToProject(_cloneIndividual, false, false)).Returns(_addIndividualCommand);
A.CallTo(() => _executionContext.AddToHistory(A <ICommand> ._))
.Invokes(x => _overallCommand = x.GetArgument <ICommand>(0));
}
public static Individual CreateIndividual()
{
var originData = new OriginData();
originData.SubPopulation = new SubPopulation();
originData.Species = new Species().WithName("Species");
originData.Gender = new Gender().WithName("Gender");
originData.SpeciesPopulation = new SpeciesPopulation().WithName("Population");
var pvv = new ParameterValueVersion().WithName("PVVName");
var category = new ParameterValueVersionCategory().WithName("CategoryName");
category.Add(pvv);
originData.SubPopulation.AddParameterValueVersion(pvv);
var organism = new Organism().WithName("Organism").WithId("OrganismId");
var organLiver = new Organ().WithName(CoreConstants.Organ.Liver).WithId("LiverId");
organLiver.OrganType = OrganType.Liver;
var periportal = new Compartment().WithName(CoreConstants.Compartment.Periportal).WithId("PeriportalId");
periportal.Add(new Container().WithName(CoreConstants.Compartment.Intracellular).WithId("PeriportalIntracellular"));
var pericentral = new Compartment().WithName(CoreConstants.Compartment.Pericentral).WithId("PericentralId");
pericentral.Add(new Container().WithName(CoreConstants.Compartment.Intracellular).WithId("PericentralIntracellular"));
organLiver.Add(periportal);
organLiver.Add(pericentral);
var organKidney = new Organ().WithName(CoreConstants.Organ.Kidney).WithId("KidneyId");
organKidney.OrganType = OrganType.Kidney;
organKidney.Add(new Compartment {
Visible = true
}.WithName(CoreConstants.Compartment.Plasma).WithId("KidneyPlasma"));
var lumen = new Organ().WithName("GiTract").WithId("GiTract");
lumen.OrganType = OrganType.Lumen;
var duodenum = new Compartment().WithName("Duodenum").WithId("Duodenum");
var caecum = new Compartment().WithName("Caecum").WithId("Caecum");
var dimension = Constants.Dimension.NO_DIMENSION;
var parameterLiver = new PKSimParameter().WithName("PLiver").WithId("PLiverId").WithFormula(new ExplicitFormula("1").WithId("1")).WithDimension(dimension);
parameterLiver.Info = new ParameterValueMetaData {
DefaultValue = 1
};
var parameterKidney = new PKSimParameter().WithName("PKidney").WithId("PKidneyId").WithFormula(new ExplicitFormula("2").WithId("2")).WithDimension(dimension);
parameterKidney.Info = new ParameterValueMetaData {
DefaultValue = 2
};
var parameterOrganism = new PKSimParameter().WithName(ParameterInOrganism).WithId("POrganismId").WithFormula(new ExplicitFormula("3").WithId("3")).WithDimension(dimension);
parameterOrganism.Info = new ParameterValueMetaData {
DefaultValue = 3
};
organLiver.Add(parameterLiver);
organKidney.Add(parameterKidney);
organism.Add(organLiver);
organism.Add(organKidney);
organism.Add(lumen);
organism.Add(parameterOrganism);
lumen.Add(duodenum);
lumen.Add(caecum);
var individual = new Individual {
OriginData = originData
}.WithName("Individual").WithId("IndividualId");
individual.Add(organism);
return(individual);
}
public static Individual CreateIndividual(string speciesName = "Species")
{
var originData = new OriginData
{
SubPopulation = new SubPopulation(),
Species = new Species {
DisplayName = speciesName, Id = speciesName
}.WithName(speciesName),
Gender = new Gender().WithName("Gender"),
Population = new SpeciesPopulation().WithName("Population"),
};
var pvv = new ParameterValueVersion().WithName("PVVName");
var category = new ParameterValueVersionCategory().WithName("CategoryName");
category.Add(pvv);
originData.SubPopulation.AddParameterValueVersion(pvv);
var organism = new Organism().WithName(Constants.ORGANISM).WithId("OrganismId");
var organLiver = new Organ().WithName(CoreConstants.Organ.LIVER).WithId("LiverId");
organLiver.OrganType = OrganType.TissueOrgansNotInGiTract;
var periportal = new Compartment().WithName(CoreConstants.Compartment.PERIPORTAL).WithId("PeriportalId");
periportal.Add(new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithId("PeriportalIntracellular"));
var pericentral = new Compartment().WithName(CoreConstants.Compartment.PERICENTRAL).WithId("PericentralId");
pericentral.Add(new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithId("PericentralIntracellular"));
organLiver.Add(periportal);
organLiver.Add(pericentral);
var organKidney = new Organ().WithName(CoreConstants.Organ.KIDNEY).WithId("KidneyId");
organKidney.OrganType = OrganType.TissueOrgansNotInGiTract;
organKidney.Add(new Compartment {
Visible = true
}.WithName(CoreConstants.Compartment.PLASMA).WithId("KidneyPlasma"));
var lumen = new Organ().WithName("GiTract").WithId("GiTract");
lumen.OrganType = OrganType.Lumen;
var duodenum = new Compartment().WithName("Duodenum").WithId("Duodenum");
var caecum = new Compartment().WithName("Caecum").WithId("Caecum");
var dimension = Constants.Dimension.NO_DIMENSION;
var parameterLiver = new PKSimParameter().WithName("PLiver").WithId("PLiverId").WithFormula(new ExplicitFormula("1").WithId("1")).WithDimension(dimension);
parameterLiver.Info = new ParameterValueMetaData {
DefaultValue = 1
};
var parameterKidney = new PKSimParameter().WithName("PKidney").WithId("PKidneyId").WithFormula(new ExplicitFormula("2").WithId("2")).WithDimension(dimension);
parameterKidney.Info = new ParameterValueMetaData {
DefaultValue = 2
};
var parameterOrganism = new PKSimParameter().WithName(ParameterInOrganism).WithId("POrganismId").WithFormula(new ExplicitFormula("3").WithId("3")).WithDimension(dimension);
parameterOrganism.Info = new ParameterValueMetaData {
DefaultValue = 3
};
organLiver.Add(parameterLiver);
organKidney.Add(parameterKidney);
organism.Add(organLiver);
organism.Add(organKidney);
organism.Add(lumen);
organism.Add(parameterOrganism);
lumen.Add(duodenum);
lumen.Add(caecum);
var individual = new Individual {
OriginData = originData
}.WithName("Individual").WithId("IndividualId");
individual.Add(organism);
return(individual);
}