public override void GlobalContext()
{
base.GlobalContext();
_individual = new Individual();
_originData = new OriginData();
_neighborhoods = new Container().WithName(Constants.NEIGHBORHOODS);
_individual.OriginData = _originData;
_individual.Add(_organism);
_individual.Add(_neighborhoods);
_originData.Species = new Species();
A.CallTo(() => _speciesContainerQuery.SubContainersFor(_originData.Species, _individual)).Returns(new[] { _organism });
A.CallTo(() => _speciesContainerQuery.SubContainersFor(_originData.Species, _organism)).Returns(new[] { _organ });
A.CallTo(() => _speciesContainerQuery.SubContainersFor(_originData.Species, _organ)).Returns(new[] { _compartment });
A.CallTo(() => _speciesContainerQuery.SubContainersFor(_originData.Species, _compartment)).Returns(new List <IContainer>());
A.CallTo(() => _speciesContainerQuery.SubContainersFor(_originData.Species, _neighborhoods)).Returns(new List <IContainer>());
}
protected override void Context()
{
base.Context();
_individual = new Individual();
var neighborhoods = A.Fake <IContainer>().WithName(Constants.NEIGHBORHOODS);
_neighborhood1 = A.Fake <INeighborhood>();
_neighborhood2 = A.Fake <INeighborhood>();
A.CallTo(() => neighborhoods.GetChildren <INeighborhood>()).Returns(new[] { _neighborhood1, _neighborhood2 });
_individual.Add(neighborhoods);
}
protected override void Context()
{
base.Context();
_para1 = A.Fake <IParameter>().WithName("P1");
A.CallTo(() => _para1.IsChangedByCreateIndividual).Returns(true);
_para2 = A.Fake <IParameter>().WithName("P2");
A.CallTo(() => _para2.IsChangedByCreateIndividual).Returns(true);
_para3 = A.Fake <IParameter>().WithName("P3");
A.CallTo(() => _para3.IsChangedByCreateIndividual).Returns(false);
_pathPara1 = "tralal";
_pathPara2 = "tutu";
_individual = new Individual();
_individual.OriginData = A.Fake <OriginData>();
_individual.OriginData.Gender = A.Fake <Gender>();
A.CallTo(() => _entityPathResolver.PathFor(_para1)).Returns(_pathPara1);
A.CallTo(() => _entityPathResolver.PathFor(_para2)).Returns(_pathPara2);
A.CallTo(() => _entityPathResolver.PathFor(_para2)).Returns(_pathPara2);
_individual.Add(_para1);
_individual.Add(_para2);
_individual.Add(_para3);
}
protected override void Context()
{
_withIdRepository = A.Fake <IWithIdRepository>();
sut = new BuildingBlockRetriever(_withIdRepository);
_objectWithoutParent = A.Fake <IEntity>();
_objectWithParent = A.Fake <IEntity>();
_objectWithoutParent.ParentContainer = null;
_container = new Compartment();
_container.Add(_objectWithParent);
_individual = new Individual();
_individual.Add(_container);
}
protected override void Context()
{
_view = A.Fake <IIndividualParametersView>();
_parameterGroupPresenter = A.Fake <IParameterGroupsPresenter>();
A.CallTo(() => _parameterGroupPresenter.View).Returns(A.Fake <IParameterGroupsView>());
_organism = A.Fake <Organism>();
_individual = new Individual();
_individual.Add(_organism);
_individualPresenter = A.Fake <IIndividualPresenter>();
A.CallTo(() => _individualPresenter.Individual).Returns(_individual);
sut = new IndividualParametersPresenter(_view, _parameterGroupPresenter);
sut.InitializeWith(_individualPresenter);
}
protected override void Context()
{
base.Context();
_para1 = A.Fake <IParameter>().WithName("P1");
A.CallTo(() => _para1.IsChangedByCreateIndividual).Returns(true);
_para2 = A.Fake <IParameter>().WithName("P2");
A.CallTo(() => _para2.IsChangedByCreateIndividual).Returns(true);
_para3 = A.Fake <IParameter>().WithName("P3");
A.CallTo(() => _para3.IsChangedByCreateIndividual).Returns(false);
_pathPara1 = "tata";
_pathPara2 = "tutu";
_individual = new Individual();
_individual.OriginData = new OriginData
{
Gender = new Gender().WithName("TOTO"),
Population = new SpeciesPopulation(),
};
A.CallTo(() => _entityPathResolver.PathFor(_para1)).Returns(_pathPara1);
A.CallTo(() => _entityPathResolver.PathFor(_para2)).Returns(_pathPara2);
A.CallTo(() => _entityPathResolver.PathFor(_para2)).Returns(_pathPara2);
_individual.Add(_para1);
_individual.Add(_para2);
_individual.Add(_para3);
}
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);
}
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);
}