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() { _expressionContainer = new MoleculeExpressionContainer().WithName("tralal"); _expressionContainer.Add(A.Fake <IParameter>().WithName(CoreConstants.Parameters.REL_EXP)); _expressionContainer.Add(A.Fake <IParameter>().WithName(CoreConstants.Parameters.REL_EXP_NORM)); _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() { _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() { _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 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); }
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); }