protected override void Context()
{
base.Context();
A.CallTo(() => _executionContext.Resolve <IParameterTask>()).Returns(sut);
_relativeExpressionParameter = new Parameter
{
BuildingBlockType = PKSimBuildingBlockType.Individual,
Formula = new ConstantFormula(0.0),
GroupName = CoreConstants.Groups.RELATIVE_EXPRESSION,
Name = CoreConstants.Parameters.REL_EXP
};
_relativeExpressionParameterNorm = new Parameter
{
BuildingBlockType = PKSimBuildingBlockType.Individual,
Formula = new ConstantFormula(0.0),
GroupName = CoreConstants.Groups.RELATIVE_EXPRESSION,
Name = CoreConstants.Parameters.REL_EXP_NORM
};
var expressionContainer = new MoleculeExpressionContainer {
Name = "Plasma"
};
expressionContainer.Add(_relativeExpressionParameter);
expressionContainer.Add(_relativeExpressionParameterNorm);
var molecule = new IndividualEnzyme {
expressionContainer
};
}
protected override void Context()
{
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_geneExpressionsDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
_applicationController = A.Fake <IApplicationController>();
sut = new EditMoleculeTask <Individual>(_moleculeExpressionTask, _applicationController);
_expressionProfileSelectionPresenter = A.Fake <IExpressionProfileSelectionPresenter>();
A.CallTo(() => _applicationController.Start <IExpressionProfileSelectionPresenter>()).Returns(_expressionProfileSelectionPresenter);
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_individual = new Individual {
OriginData = new OriginData {
Species = new Species {
Name = "Human", DisplayName = "Human"
}
}
};
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
}
protected override void Context()
{
base.Context();
_displayName = "tutu";
_expressionContainer = new MoleculeExpressionContainer().WithName("tralal");
_expressionContainer.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
A.CallTo(() => _representationInfoRepository.DisplayNameFor(_expressionContainer)).Returns(_displayName);
}
protected override void Context()
{
base.Context();
_enzyme = new IndividualEnzyme {
Name = "CYP"
};
_container1 = new MoleculeExpressionContainer().WithName("EXP1");
_container2 = new MoleculeExpressionContainer().WithName("EXP2");
_enzyme.AddChildren(_container1, _container2);
}
private IEnumerable <IContainer> compartmentFor(Organism organism, MoleculeExpressionContainer expressionContainer, string defaultCompartment)
{
var usedCompartment = expressionContainer.IsLumen ? expressionContainer.ContainerName : defaultCompartment;
var compartment = expressionContainer.CompartmentPath(usedCompartment).Resolve <IContainer>(organism);
if (compartment == null)
{
return(Enumerable.Empty <IContainer>());
}
return(new[] { compartment });
}
protected override void Context()
{
_expressionContainer = new MoleculeExpressionContainer().WithName("tralal");
_expressionContainer.Add(A.Fake <IParameter>().WithName(CoreConstants.Parameters.REL_EXP));
_anotherContainer = new MoleculeExpressionContainer().WithName("AnotherContainer");
sut = new IndividualEnzyme();
_referenceConcentration = A.Fake <IParameter>().WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION);
sut.Add(_referenceConcentration);
sut.Add(_expressionContainer);
sut.Add(_anotherContainer);
}
protected override void Context()
{
_individual = new Individual();
_individual.OriginData = new OriginData();
_individual.OriginData.Species = new Species().WithName("Human");
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_proteinExpressionPresenter = A.Fake <IProteinExpressionsPresenter>();
_simpleMoleculePresenter = A.Fake <ISimpleMoleculePresenter>();
_querySettingsMapper = A.Fake <IMoleculeToQueryExpressionSettingsMapper>();
_applicationController = A.Fake <IApplicationController>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_containerTask = A.Fake <IContainerTask>();
_geneExpressionsDatabasePathManager = A.Fake <IGeneExpressionsDatabasePathManager>();
A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter);
A.CallTo(() => _applicationController.Start <ISimpleMoleculePresenter>()).Returns(_simpleMoleculePresenter);
_moleculeParameterTask = A.Fake <IMoleculeParameterTask>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.REL_EXP_NORM));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.REL_EXP_NORM));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.CreateFor(_individual)).Returns(_molecule);
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
sut = new MoleculeExpressionTask <Individual>(_applicationController, _executionContext,
_individualMoleculeFactoryResolver, _querySettingsMapper,
_containerTask, _geneExpressionsDatabasePathManager,
_ontogenyRepository, _transportContainerUpdater, _subjectExpressionTask, _ontogenyTask, _moleculeParameterTask);
}
protected override void Context()
{
base.Context();
_protein = A.Fake <IndividualProtein>();
_protein.QueryConfiguration = "toto";
_exp1 = new MoleculeExpressionContainer().WithName("exp1");
_exp2 = new MoleculeExpressionContainer().WithName("exp2");
_expInfo1 = A.Fake <ExpressionContainerInfo>();
_expInfo2 = A.Fake <ExpressionContainerInfo>();
A.CallTo(() => _protein.AllExpressionsContainers()).Returns(new[] { _exp1, _exp2 });
_proteinContent = 10;
A.CallTo(() => _protein.ReferenceConcentration).Returns(DomainHelperForSpecs.ConstantParameterWithValue(_proteinContent));
A.CallTo(() => _expressionContainerMapper.MapFrom(_exp1)).Returns(_expInfo1);
A.CallTo(() => _expressionContainerMapper.MapFrom(_exp2)).Returns(_expInfo2);
}
public void UpdateProperties(ExpressionContainerDTO expressionDTO, MoleculeExpressionContainer expressionContainer)
{
var group = _groupRepository.GroupByName(expressionContainer.GroupName);
var groupInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.GROUP, expressionContainer.GroupName);
var containerInfo = _representationInfoRepository.InfoFor(RepresentationObjectType.CONTAINER, expressionContainer.ContainerName);
expressionDTO.GroupingPathDTO = groupInfo.ToPathElement();
expressionDTO.ContainerPathDTO = containerInfo.ToPathElement();
expressionDTO.Sequence = group.Sequence;
expressionDTO.RelativeExpressionParameter =
_parameterMapper.MapFrom(expressionContainer.RelativeExpressionParameter, expressionDTO,
x => x.RelativeExpression, x => x.RelativeExpressionParameter);
expressionDTO.RelativeExpressionNormParameter =
_parameterMapper.MapFrom(expressionContainer.RelativeExpressionNormParameter, expressionDTO,
x => x.RelativeExpressionNorm, x => x.RelativeExpressionNormParameter);
}
protected override void Context()
{
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_ontogeny = new DatabaseOntogeny {
Name = "toto"
};
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyRepository = A.Fake <IOntogenyRepository>();
var proteinFactory = A.Fake <IIndividualMoleculeFactory>();
_expressionProfileUpdater = A.Fake <IExpressionProfileUpdater>();
_moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1");
_moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
_moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2");
_moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameters.REL_EXP));
A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory);
_molecule = new IndividualEnzyme {
Name = "CYP3A4"
};
_molecule.Add(_moleculeContainer1);
_molecule.Add(_moleculeContainer2);
A.CallTo(() => proteinFactory.AddMoleculeTo(_individual, A <string> ._)).Returns(_molecule);
A.CallTo(() => _ontogenyRepository.AllFor(_individual.Species.Name)).Returns(new[] { _ontogeny, new DatabaseOntogeny {
Name = "tralala"
}, });
A.CallTo(() => _executionContext.Resolve <IOntogenyRepository>()).Returns(_ontogenyRepository);
_subjectExpressionTask = new IndividualExpressionTask(_executionContext);
sut = new MoleculeExpressionTask <Individual>(
_executionContext,
_individualMoleculeFactoryResolver,
_subjectExpressionTask,
_expressionProfileUpdater
);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _logger);
_relativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular;
_bloodCellsExpressionContainer = new TransporterExpressionContainer().WithName(CoreConstants.Compartment.BLOOD_CELLS);
_bloodCellsExpressionContainer.TransportDirection = TransportDirectionId.BiDirectionalBloodCellsPlasma;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext(new SnapshotContext())
{
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer, _bloodCellsExpressionContainer
};
return(_completed);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_transportContainerUpdater = A.Fake <ITransportContainerUpdater>();
_logger = A.Fake <ILogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _transportContainerUpdater, _logger);
_relativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter = DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.MembraneLocation = MembraneLocation.Apical;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new Model.OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext
{
SimulationSubject = _individual
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer
};
return(_completed);
}
protected override void Context()
{
base.Context();
_protein = A.Fake <IndividualProtein>();
_protein.QueryConfiguration = "toto";
_exp1 = new MoleculeExpressionContainer().WithName("exp1");
_exp2 = new MoleculeExpressionContainer().WithName("exp2");
_relExp1 = DomainHelperForSpecs.ConstantParameterWithValue(1);
_relExp2 = DomainHelperForSpecs.ConstantParameterWithValue(2);
var allExpressions = new Cache <string, IParameter> {
{ _exp1.Name, _relExp1 }, { _exp2.Name, _relExp2 }
};
A.CallTo(() => _individual.AllExpressionParametersFor(_protein)).Returns(allExpressions);
_proteinContent = 10;
A.CallTo(() => _protein.ReferenceConcentration).Returns(DomainHelperForSpecs.ConstantParameterWithValue(_proteinContent));
A.CallTo(() => _representationInfoRepository.ContainerInfoFor(_exp1.Name)).Returns(new RepresentationInfo {
DisplayName = "disp1"
});
A.CallTo(() => _representationInfoRepository.ContainerInfoFor(_exp2.Name)).Returns(new RepresentationInfo {
DisplayName = "disp2"
});
}
private IEnumerable <IContainer> allContainersFor(Organism organism, IndividualMolecule molecule, IEnumerable <IContainer> allContainers, MoleculeExpressionContainer expressionContainer)
{
if (molecule.MoleculeType == QuantityType.Transporter)
{
return(allContainersForTransporter(organism, molecule.DowncastTo <IndividualTransporter>(), allContainers, expressionContainer.DowncastTo <TransporterExpressionContainer>()));
}
var protein = molecule.DowncastTo <IndividualProtein>();
//plasma always generated
if (expressionContainer.IsPlasma())
{
return(allPlasmaCompartmentsOf(allContainers));
}
switch (protein.TissueLocation)
{
case TissueLocation.ExtracellularMembrane:
if (expressionContainer.IsBloodCell())
{
return(allPlasmaCompartmentsOf(allContainers));
}
if (expressionContainer.IsVascularEndothelium())
{
if (protein.MembraneLocation == MembraneLocation.Apical)
{
return(allPlasmaCompartmentsOf(allContainers));
}
return(allInterstitialCompartmentsOf(allContainers));
}
return(compartmentFor(organism, expressionContainer, CoreConstants.Compartment.Interstitial));
case TissueLocation.Intracellular:
if (expressionContainer.IsBloodCell())
{
return(allBloodCellsCompartmentsOf(allContainers));
}
if (expressionContainer.IsVascularEndothelium())
{
if (protein.IntracellularVascularEndoLocation == IntracellularVascularEndoLocation.Endosomal)
{
return(allEndosomeCompartmentsOf(allContainers));
}
return(allInterstitialCompartmentsOf(allContainers));
}
return(compartmentFor(organism, expressionContainer, CoreConstants.Compartment.Intracellular));
case TissueLocation.Interstitial:
if (expressionContainer.IsBloodCell())
{
return(allBloodCellsCompartmentsOf(allContainers));
}
if (expressionContainer.IsVascularEndothelium())
{
return(allInterstitialCompartmentsOf(allContainers));
}
return(compartmentFor(organism, expressionContainer, CoreConstants.Compartment.Interstitial));
default:
throw new ArgumentOutOfRangeException();
}
}
private void updateReferenceToIndividualParametersForSurrogateContainer(Individual individual, IndividualMolecule molecule, MoleculeExpressionContainer expressionContainer, IContainer globalMoleculeContainer)
{
string relExpName;
if (expressionContainer.IsBloodCell())
{
relExpName = CoreConstants.Parameters.REL_EXP_BLOOD_CELL;
}
else if (expressionContainer.IsPlasma())
{
relExpName = CoreConstants.Parameters.REL_EXP_PLASMA;
}
else if (expressionContainer.IsVascularEndothelium())
{
relExpName = CoreConstants.Parameters.REL_EXP_VASC_ENDO;
}
else
{
return;
}
var relExpNormName = CoreConstants.Parameters.NormParameterFor(relExpName);
updateFromIndividualParameter(globalMoleculeContainer.Parameter(relExpName), expressionContainer.RelativeExpressionParameter, individual, molecule);
updateFromIndividualParameter(globalMoleculeContainer.Parameter(relExpNormName), expressionContainer.RelativeExpressionNormParameter, individual, molecule);
}
private void updateReferenceToIndividualParametersForStandardContainer(Individual individual, IndividualMolecule molecule, MoleculeExpressionContainer expressionContainer, IList <IContainer> allOrganismContainers, PathCache <IMoleculeAmount> moleculeAmountPath)
{
var allContainers = _expressionContainersRetriever.AllContainersFor(individual.Organism, allOrganismContainers, molecule, expressionContainer);
foreach (var container in allContainers)
{
var amount = amountFor(container, molecule, moleculeAmountPath);
if (amount == null)
{
continue;
}
updateFromIndividualParameter(amount.Parameter(CoreConstants.Parameters.REL_EXP), expressionContainer.RelativeExpressionParameter, individual, molecule);
updateFromIndividualParameter(amount.Parameter(CoreConstants.Parameters.REL_EXP_NORM), expressionContainer.RelativeExpressionNormParameter, individual, molecule);
}
}
public ExpressionContainerInfo MapFrom(MoleculeExpressionContainer moleculeExpressionContainer)
{
return(new ExpressionContainerInfo(moleculeExpressionContainer.Name,
_representationInfoRepository.DisplayNameFor(moleculeExpressionContainer),
moleculeExpressionContainer.RelativeExpression));
}
private void addContainerExpression(ProteinExpressionDTO proteinExpressionDTO, IndividualProtein protein, MoleculeExpressionContainer moleculeExpressionContainer)
{
var expressionDTO = new ExpressionContainerDTO {
MoleculeName = protein.Name, ContainerName = moleculeExpressionContainer.Name
};
_expressionContainerDTOUpdater.UpdateProperties(expressionDTO, moleculeExpressionContainer);
proteinExpressionDTO.AddProteinExpression(expressionDTO);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionContainerMapper = A.Fake <ExpressionContainerMapper>();
_executionContext = A.Fake <IExecutionContext>();
_individualMoleculeFactoryResolver = A.Fake <IIndividualMoleculeFactoryResolver>();
_ontogenyMapper = A.Fake <OntogenyMapper>();
_ontogenyTask = A.Fake <IOntogenyTask <Individual> >();
_individualMoleculeParametersTask = A.Fake <IMoleculeParameterTask>();
sut = new MoleculeMapper(_parameterMapper, _expressionContainerMapper,
_ontogenyMapper, _individualMoleculeFactoryResolver, _executionContext, _ontogenyTask, _individualMoleculeParametersTask);
_ontogeny = new DatabaseOntogeny
{
Name = "Ontogeny"
};
_enzyme = new IndividualEnzyme
{
Name = "Enzyme",
Description = "Help",
Ontogeny = _ontogeny,
};
_transporter = new IndividualTransporter
{
Name = "Transporter",
Description = "Help"
};
_otherProtein = new IndividualOtherProtein
{
Name = "OtherProtein",
Description = "Help"
};
_enzymeGlobalParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_enzymeGlobalParameterSnapshot = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_enzymeGlobalParameter)).Returns(_enzymeGlobalParameterSnapshot);
_expressionContainer1 = new MoleculeExpressionContainer {
Name = "Exp Container1"
};
_expressionContainer2 = new MoleculeExpressionContainer {
Name = "Exp Container2"
};
_enzyme.AddChildren(_expressionContainer1, _expressionContainer2, _enzymeGlobalParameter);
_relativeExpressionParameter1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNorm1 = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer1.Add(_relativeExpressionParameter1);
_expressionContainer1.Add(_relativeExpressionParameterNorm1);
_relativeExpressionParameterNotSet = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP);
_relativeExpressionParameterNotSetNorm = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP_NORM);
_expressionContainer2.Add(_relativeExpressionParameterNotSet);
_expressionContainer2.Add(_relativeExpressionParameterNotSetNorm);
_relativeExpressionContainerSnapshot1 = new ExpressionContainer();
_relativeExpressionContainerSnapshot2 = new ExpressionContainer();
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer1)).Returns(_relativeExpressionContainerSnapshot1);
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer2)).Returns(_relativeExpressionContainerSnapshot2);
_snapshotOntogeny = new Snapshots.Ontogeny();
A.CallTo(() => _ontogenyMapper.MapToSnapshot(_ontogeny)).Returns(_snapshotOntogeny);
_individual = new Individual();
return(_completed);
}
public IEnumerable <IContainer> AllContainersFor(Organism organism, IEnumerable <IContainer> allOrganismContainers, IndividualMolecule molecule, MoleculeExpressionContainer expressionContainer)
{
return(allContainersFor(organism, molecule, allOrganismContainers, expressionContainer));
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_expressionContainerMapper = A.Fake <ExpressionContainerMapper>();
_expressionProfileFactory = A.Fake <IExpressionProfileFactory>();
_ontogenyMapper = A.Fake <OntogenyMapper>();
_ontogenyTask = A.Fake <IOntogenyTask>();
_moleculeExpressionTask = A.Fake <IMoleculeExpressionTask <Individual> >();
_moleculeParameterTask = A.Fake <IMoleculeParameterTask>();
sut = new ExpressionProfileMapper(
_parameterMapper,
_expressionContainerMapper,
_ontogenyMapper,
_ontogenyTask,
_moleculeExpressionTask,
_expressionProfileFactory,
_moleculeParameterTask);
_ontogeny = new DatabaseOntogeny
{
Name = "Ontogeny"
};
_expressionProfileEnzyme = DomainHelperForSpecs.CreateExpressionProfile <IndividualEnzyme>("Enzyme");
_expressionProfileEnzyme.Molecule.Ontogeny = _ontogeny;
_expressionProfileEnzyme.Description = "Help";
_expressionProfileTransporter = DomainHelperForSpecs.CreateExpressionProfile <IndividualTransporter>("Transporter");
_expressionProfileTransporter.Description = "Help";
_expressionProfileOtherProtein = DomainHelperForSpecs.CreateExpressionProfile <IndividualOtherProtein>("OtherProtein");
_enzymeGlobalParameter = DomainHelperForSpecs.ConstantParameterWithValue(5, isDefault: true)
.WithName(CoreConstants.Parameters.HALF_LIFE_LIVER);
_enzymeGlobalParameterSnapshot = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_enzymeGlobalParameter)).Returns(_enzymeGlobalParameterSnapshot);
_expressionContainer1 = new MoleculeExpressionContainer {
Name = "Exp Container1"
};
_expressionContainer2 = new MoleculeExpressionContainer {
Name = "Exp Container2"
};
_expressionProfileEnzyme.Individual.AddChildren(_expressionContainer1, _expressionContainer2, _enzymeGlobalParameter);
_expressionProfileEnzyme.Molecule.DowncastTo <IndividualEnzyme>().Localization = Localization.Intracellular | Localization.BloodCellsMembrane;
_relativeExpressionParameter1 = DomainHelperForSpecs.ConstantParameterWithValue(0.5).WithName(CoreConstants.Parameters.REL_EXP);
_expressionContainer1.Add(_relativeExpressionParameter1);
_relativeExpressionParameterNotSet = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.REL_EXP);
_expressionContainer2.Add(_relativeExpressionParameterNotSet);
_relativeExpressionContainerSnapshot1 = new ExpressionContainer();
_relativeExpressionContainerSnapshot2 = new ExpressionContainer();
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer1)).Returns(_relativeExpressionContainerSnapshot1);
A.CallTo(() => _expressionContainerMapper.MapToSnapshot(_expressionContainer2)).Returns(_relativeExpressionContainerSnapshot2);
_snapshotOntogeny = new Snapshots.Ontogeny();
A.CallTo(() => _ontogenyMapper.MapToSnapshot(_ontogeny)).Returns(_snapshotOntogeny);
_individual = new Individual();
return(_completed);
}