protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_moleculeMapper = A.Fake <MoleculeMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
sut = new IndividualMapper(_parameterMapper, _moleculeMapper, _originDataMapper, _individualFactory);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Liver, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.Kidney, "PKidney");
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_enzyme = new IndividualEnzyme
{
Name = "Enz",
};
_individual.AddMolecule(_enzyme);
_transporter = new IndividualTransporter
{
Name = "Trans",
};
_individual.AddMolecule(_transporter);
_enzymeSnapshot = new Molecule {
Type = QuantityType.Enzyme
};
_transporterSnapshot = new Molecule {
Type = QuantityType.Transporter
};
A.CallTo(() => _moleculeMapper.MapToSnapshot(_enzyme)).Returns(_enzymeSnapshot);
A.CallTo(() => _moleculeMapper.MapToSnapshot(_transporter)).Returns(_transporterSnapshot);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > .That.Contains(_parameterKidney))).Returns(new[] { _localizedParameterKidney });
return(_completed);
}
public DefaultIndividualRetriever(
ISpeciesRepository speciesRepository,
IIndividualFactory individualFactory,
OriginDataMapper originDataMapper
)
{
_speciesRepository = speciesRepository;
_individualFactory = individualFactory;
_originDataMapper = originDataMapper;
}
internal MatlabIndividualFactory(
OriginDataMapper originDataMapper,
IIndividualFactory individualFactory,
IIndividualToIndividualPropertiesMapper individualPropertiesMapper,
IOntogenyFactorsRetriever ontogenyFactorsRetriever,
IEntityPathResolver entityPathResolver)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualPropertiesMapper = individualPropertiesMapper;
_ontogenyFactorsRetriever = ontogenyFactorsRetriever;
_entityPathResolver = entityPathResolver;
}
public StarterRelativeExpressionPresenter(
IStarterRelativeExpressionView view,
OriginDataMapper originDataMapper,
IIndividualFactory individualFactory,
IIndividualEnzymeFactory individualEnzymeFactory, IIndividualEnzymeExpressionsPresenter <Individual> individualEnzymeExpressionsPresenter) : base(view)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualEnzymeFactory = individualEnzymeFactory;
_individualEnzymeExpressionsPresenter = individualEnzymeExpressionsPresenter;
AddSubPresenters(individualEnzymeExpressionsPresenter);
InitializeWith(new PKSimMacroCommand());
}
public IndividualFactory(
OriginDataMapper originDataMapper,
ICoreIndividualFactory individualFactory,
IIndividualToIndividualValuesMapper individualValuesMapper,
IOntogenyFactorsRetriever ontogenyFactorsRetriever,
IEntityPathResolver entityPathResolver,
IContainerTask containerTask)
{
_originDataMapper = originDataMapper;
_individualFactory = individualFactory;
_individualValuesMapper = individualValuesMapper;
_ontogenyFactorsRetriever = ontogenyFactorsRetriever;
_entityPathResolver = entityPathResolver;
_containerTask = containerTask;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionProfileMapper = A.Fake <ExpressionProfileMapper>();
_dimensionRepository = A.Fake <IDimensionRepository>();
_individualFactory = A.Fake <IIndividualFactory>();
_originDataMapper = A.Fake <OriginDataMapper>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <ModelIndividual> >();
sut = new IndividualMapper(_parameterMapper, _expressionProfileMapper, _originDataMapper, _individualFactory, _moleculeExpressionTask);
_individual = DomainHelperForSpecs.CreateIndividual();
_individual.Name = "Ind";
_individual.Description = "Model Description";
var kidney = _individual.EntityAt <IContainer>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY);
_parameterLiver = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.LIVER, "PLiver");
_parameterKidney = _individual.EntityAt <IParameter>(Constants.ORGANISM, CoreConstants.Organ.KIDNEY, "PKidney");
_parameterKidneyRelExp = DomainHelperForSpecs.ConstantParameterWithValue().WithName(CoreConstants.Parameters.REL_EXP);
_parameterKidneyRelExp.DefaultValue = 10;
kidney.Add(_parameterKidneyRelExp);
_parameterLiver.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.ValueDiffersFromDefault().ShouldBeFalse();
_parameterKidney.Value = 40;
_parameterKidney.ValueDiffersFromDefault().ShouldBeTrue();
_parameterKidneyRelExp.Value = 50;
_parameterKidneyRelExp.ValueDiffersFromDefault().ShouldBeTrue();
_expressionProfile1 = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>(moleculeName: "Enz");
_expressionProfile2 = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>(moleculeName: "Trans");
_individual.AddExpressionProfile(_expressionProfile1);
_individual.AddExpressionProfile(_expressionProfile2);
_originDataSnapshot = new OriginData();
A.CallTo(() => _originDataMapper.MapToSnapshot(_individual.OriginData)).Returns(_originDataSnapshot);
_localizedParameterKidney = new LocalizedParameter {
Path = "Organism|Kidney|PKidney"
};
A.CallTo(() => _parameterMapper.LocalizedParametersFrom(A <IEnumerable <IParameter> > ._))
.Invokes(x => _mappedParameters = x.GetArgument <IEnumerable <IParameter> >(0).ToList())
.Returns(new[] { _localizedParameterKidney });
return(_completed);
}
protected override void Context()
{
_speciesRepository = A.Fake <ISpeciesRepository>();
_originDataTask = A.Fake <IOriginDataTask>();
_individualModelTask = A.Fake <IIndividualModelTask>();
_male = new Gender().WithName(CoreConstants.Gender.Male);
_female = new Gender().WithName(CoreConstants.Gender.Female);
_human = new Species().WithName(CoreConstants.Species.Human);
_icrp = new SpeciesPopulation {
IsHeightDependent = true, IsAgeDependent = true
}.WithName(CoreConstants.Population.ICRP);
_anotherPop = new SpeciesPopulation().WithName("Another Pop");
_cmForHuman = new CalculationMethod();
_cmForHuman.AddSpecies(_human.Name);
_icrp.AddGender(_male);
_human.AddPopulation(_icrp);
_category = new CalculationMethodCategory();
_category.Add(_cmForHuman);
A.CallTo(() => _speciesRepository.All()).Returns(new[] { _human });
A.CallTo(() => _originDataTask.AllCalculationMethodCategoryFor(_human)).Returns(new[] { _category });
_batchOriginData = new OriginData();
sut = new OriginDataMapper(_speciesRepository, _originDataTask, _individualModelTask);
}