protected override void Context() { _moleculeParameterFactory = A.Fake <IMoleculeParameterRepository>(); _advancedParmeterFactory = A.Fake <IAdvancedParameterFactory>(); _advancedParametersTask = A.Fake <IAdvancedParametersTask>(); _executionContext = A.Fake <IExecutionContext>(); sut = new MoleculeParameterVariabilityCreator(_advancedParmeterFactory, _moleculeParameterFactory, _advancedParametersTask, _executionContext); _randomPopulation = new RandomPopulation { Settings = new RandomPopulationSettings() }; _randomPopulation.SetAdvancedParameters(new AdvancedParameterCollection()); var individual = A.Fake <Individual>(); _molecule1 = DomainHelperForSpecs.DefaultIndividualMolecule().WithName("CYP1"); _molecule2 = DomainHelperForSpecs.DefaultIndividualMolecule().WithName("CYP2"); A.CallTo(() => individual.AllMolecules()).Returns(new[] { _molecule1, _molecule2 }); _randomPopulation.Settings.BaseIndividual = individual; A.CallTo(() => _advancedParametersTask.AddAdvancedParameter(A <IAdvancedParameter> ._, _randomPopulation)) .Invokes(x => { var advancedParameter = x.GetArgument <IAdvancedParameter>(0); _randomPopulation.AddAdvancedParameter(advancedParameter); }) .Returns(new AddAdvancedParameterToContainerCommand(A.Fake <IAdvancedParameter>(), _randomPopulation, _executionContext)); }
public MoleculeParameterVariabilityCreator(IAdvancedParameterFactory advancedParameterFactory, IMoleculeParameterRepository moleculeParameterRepository, IAdvancedParametersTask advancedParametersTask, IExecutionContext executionContext) { _advancedParameterFactory = advancedParameterFactory; _moleculeParameterRepository = moleculeParameterRepository; _advancedParametersTask = advancedParametersTask; _executionContext = executionContext; }
protected override void Context() { _moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>(); sut = new MoleculeParameterTask(_moleculeParameterRepository); _molecule = new IndividualEnzyme { Name = "CYP3A4" }; _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameters.REFERENCE_CONCENTRATION)); _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameters.HALF_LIFE_LIVER)); _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameters.HALF_LIFE_INTESTINE)); }
public MoleculeParameterTask( IMoleculeParameterRepository moleculeParameterRepository, ITransportContainerUpdater transportContainerUpdater, IOntogenyRepository ontogenyRepository, IOntogenyTask ontogenyTask) { _moleculeParameterRepository = moleculeParameterRepository; _transportContainerUpdater = transportContainerUpdater; _ontogenyRepository = ontogenyRepository; _ontogenyTask = ontogenyTask; }
public UsedMoleculeRepository( IPKSimProjectRetriever projectRetriever, IOntogenyRepository ontogenyRepository, IMoleculeParameterRepository moleculeParameterRepository, ITransporterContainerTemplateRepository transporterContainerTemplateRepository) { _projectRetriever = projectRetriever; _ontogenyRepository = ontogenyRepository; _moleculeParameterRepository = moleculeParameterRepository; _transporterContainerTemplateRepository = transporterContainerTemplateRepository; }
protected override void Context() { _individual = new Individual(); _individual.OriginData = new OriginData(); _individual.OriginData.Species = new Species().WithName("Human"); _ontogeny = new DatabaseOntogeny { Name = "toto" }; _molecule = new IndividualEnzyme { Name = "CYP3A4" }; _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>(); _moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>(); _proteinExpressionDbPathManager = A.Fake <IProteinExpressionsDatabasePathManager>(); A.CallTo(() => _applicationController.Start <IProteinExpressionsPresenter>()).Returns(_proteinExpressionPresenter); A.CallTo(() => _applicationController.Start <ISimpleMoleculePresenter>()).Returns(_simpleMoleculePresenter); _ontogenyRepository = A.Fake <IOntogenyRepository>(); var proteinFactory = A.Fake <IIndividualMoleculeFactory>(); _moleculeContainer1 = new MoleculeExpressionContainer().WithName("C1"); _moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp)); _moleculeContainer1.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm)); _moleculeContainer2 = new MoleculeExpressionContainer().WithName("C2"); _moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(5).WithName(CoreConstants.Parameter.RelExp)); _moleculeContainer2.Add(DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameter.RelExpNorm)); A.CallTo(() => _individualMoleculeFactoryResolver.FactoryFor <IndividualProtein>()).Returns(proteinFactory); A.CallTo(() => proteinFactory.CreateFor(_individual)).Returns(_molecule); _molecule.Add(_moleculeContainer1); _molecule.Add(_moleculeContainer2); _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(CoreConstants.Parameter.REFERENCE_CONCENTRATION)); _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(20).WithName(CoreConstants.Parameter.HALF_LIFE_LIVER)); _molecule.Add(DomainHelperForSpecs.ConstantParameterWithValue(30).WithName(CoreConstants.Parameter.HALF_LIFE_INTESTINE)); 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, _proteinExpressionDbPathManager, _ontogenyRepository, _transportContainerUpdater, _moleculeParameterRepository, _subjectExpressionTask, _ontogenyTask); }
protected override void Context() { _project = new PKSimProject(); _projectRetriever = A.Fake <IPKSimProjectRetriever>(); _transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>(); A.CallTo(() => _projectRetriever.Current).Returns(_project); _compound1 = A.Fake <Compound>(); _compound1.IsLoaded = false; _compound2 = new Compound { IsLoaded = true }; _compound2.AddProcess(new EnzymaticProcess { MoleculeName = "ProjA", Name = "P1" }); _compound2.AddProcess(new EnzymaticProcess { MoleculeName = "ProjC", Name = "P2" }); _compound2.AddProcess(new EnzymaticProcess { MoleculeName = "ProjB", Name = "P3" }); _ontogenyRepository = A.Fake <IOntogenyRepository>(); _moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>(); _expressionProfile = A.Fake <ExpressionProfile>(); _expressionProfile.IsLoaded = true; A.CallTo(() => _expressionProfile.MoleculeName).Returns("ProjE"); _project.AddBuildingBlock(_compound1); _project.AddBuildingBlock(_compound2); _project.AddBuildingBlock(_expressionProfile); sut = new UsedMoleculeRepository(_projectRetriever, _ontogenyRepository, _moleculeParameterRepository, _transporterContainerTemplateRepository); var molParam1 = new MoleculeParameter { MoleculeName = "DbB" }; var molParam2 = new MoleculeParameter { MoleculeName = "DbA" }; A.CallTo(() => _moleculeParameterRepository.All()).Returns(new[] { molParam1, molParam2 }); A.CallTo(() => _transporterContainerTemplateRepository.AllTransporterNames).Returns(new[] { "ATRANS1", "TRANS2" }); A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.HUMAN)).Returns(new[] { new DatabaseOntogeny { Name = "OntoC" } }); }
public MoleculeExpressionTask(IApplicationController applicationController, IExecutionContext executionContext, IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver, IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper, IContainerTask containerTask, IProteinExpressionsDatabasePathManager proteinExpressionsDatabasePathManager, IOntogenyRepository ontogenyRepository, ITransportContainerUpdater transportContainerUpdater, IMoleculeParameterRepository moleculeParameterRepository, ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask, IOntogenyTask <TSimulationSubject> ontogenyTask) { _applicationController = applicationController; _executionContext = executionContext; _individualMoleculeFactoryResolver = individualMoleculeFactoryResolver; _queryExpressionSettingsMapper = queryExpressionSettingsMapper; _containerTask = containerTask; _proteinExpressionsDatabasePathManager = proteinExpressionsDatabasePathManager; _ontogenyRepository = ontogenyRepository; _transportContainerUpdater = transportContainerUpdater; _moleculeParameterRepository = moleculeParameterRepository; _simulationSubjectExpressionTask = simulationSubjectExpressionTask; _ontogenyTask = ontogenyTask; }
public MoleculeParameterTask(IMoleculeParameterRepository moleculeParameterRepository) { _moleculeParameterRepository = moleculeParameterRepository; }