public ExpressionContainerMapper( ParameterMapper parameterMapper, ITransportContainerUpdater transportContainerUpdater, ILogger logger) { _parameterMapper = parameterMapper; _transportContainerUpdater = transportContainerUpdater; _logger = logger; }
public MoleculeParameterTask( IMoleculeParameterRepository moleculeParameterRepository, ITransportContainerUpdater transportContainerUpdater, IOntogenyRepository ontogenyRepository, IOntogenyTask ontogenyTask) { _moleculeParameterRepository = moleculeParameterRepository; _transportContainerUpdater = transportContainerUpdater; _ontogenyRepository = ontogenyRepository; _ontogenyTask = ontogenyTask; }
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() { _transportContainerUpdater = A.Fake <ITransportContainerUpdater>(); _ontogenyRepository = A.Fake <IOntogenyRepository>(); _ontogenyTask = A.Fake <IOntogenyTask>(); _moleculeParameterRepository = A.Fake <IMoleculeParameterRepository>(); sut = new MoleculeParameterTask(_moleculeParameterRepository, _transportContainerUpdater, _ontogenyRepository, _ontogenyTask); _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 MoleculeExpressionTask(IApplicationController applicationController, IExecutionContext executionContext, IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver, IMoleculeToQueryExpressionSettingsMapper queryExpressionSettingsMapper, IContainerTask containerTask, IProteinExpressionsDatabasePathManager proteinExpressionsDatabasePathManager, IOntogenyRepository ontogenyRepository, ITransportContainerUpdater transportContainerUpdater, ISimulationSubjectExpressionTask <TSimulationSubject> simulationSubjectExpressionTask, IOntogenyTask <TSimulationSubject> ontogenyTask, IMoleculeParameterTask moleculeParameterTask) { _applicationController = applicationController; _executionContext = executionContext; _individualMoleculeFactoryResolver = individualMoleculeFactoryResolver; _queryExpressionSettingsMapper = queryExpressionSettingsMapper; _containerTask = containerTask; _proteinExpressionsDatabasePathManager = proteinExpressionsDatabasePathManager; _ontogenyRepository = ontogenyRepository; _transportContainerUpdater = transportContainerUpdater; _simulationSubjectExpressionTask = simulationSubjectExpressionTask; _ontogenyTask = ontogenyTask; _moleculeParameterTask = moleculeParameterTask; }
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); }