public override void GlobalContext() { base.GlobalContext(); _transporterContainerTemplateRepository = IoC.Resolve <ITransporterContainerTemplateRepository>(); var allTransporters = _transporterContainerTemplateRepository.TransportersFor(_individual.Species.Name, CoreConstants.Organ.Brain); var influxBBB = allTransporters.Where(x => x.MembraneLocation == MembraneLocation.BloodBrainBarrier) .FirstOrDefault(x => x.TransportType == TransportType.Influx); _transporter = _transporterFactory.CreateFor(_individual).DowncastTo <IndividualTransporter>().WithName("TRANS"); var transportContainer = _transporter.ExpressionContainer(CoreConstants.Organ.Brain).DowncastTo <TransporterExpressionContainer>(); transportContainer.UpdatePropertiesFrom(influxBBB); _individual.AddMolecule(_transporter); _transportProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.ACTIVE_TRANSPORT_SPECIFIC_MM) .DowncastTo <PartialProcess>()); _transportProcess.Name = "My Transport Process"; _compound.AddProcess(_transportProcess); _simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith(_individual, _compound, _protocol) .DowncastTo <IndividualSimulation>(); _simulation.CompoundPropertiesList.First() .Processes .TransportAndExcretionSelection .AddPartialProcessSelection(new EnzymaticProcessSelection { CompoundName = _compound.Name, ProcessName = _transportProcess.Name, MoleculeName = _transporter.Name }); DomainFactoryForSpecs.AddModelToSimulation(_simulation); }
protected override void Context() { _expressionParameterMapper = A.Fake <IExpressionParameterMapper <TransporterExpressionParameterDTO> >(); _transporterContainerTemplateRepository = A.Fake <ITransporterContainerTemplateRepository>(); _transporterDirectionRepository = A.Fake <ITransportDirectionRepository>(); sut = new IndividualTransporterToTransporterExpressionDTOMapper(_expressionParameterMapper, _transporterDirectionRepository, _transporterContainerTemplateRepository); }
public TransportContainerUpdater( ITransporterContainerTemplateRepository transporterContainerTemplateRepository, IEventPublisher eventPublisher) { _transporterContainerTemplateRepository = transporterContainerTemplateRepository; _eventPublisher = eventPublisher; }
protected override void Context() { _view = A.Fake <IIndividualTransporterExpressionsView>(); _parameterTask = A.Fake <IEditParameterPresenterTask>(); _moleculeTask = A.Fake <IMoleculeExpressionTask <Individual> >(); _transporterMapper = A.Fake <IIndividualTransporterToTransporterExpressionDTOMapper>(); _transportRepository = A.Fake <ITransporterContainerTemplateRepository>(); _moleculePropertiesPresenter = A.Fake <IIndividualMoleculePropertiesPresenter <Individual> >(); sut = new IndividualTransporterExpressionsPresenter <Individual>(_view, _parameterTask, _moleculeTask, _transporterMapper, _transportRepository, _moleculePropertiesPresenter); }
public IndividualTransporterToTransporterExpressionDTOMapper( IExpressionParameterMapper <TransporterExpressionParameterDTO> expressionParameterMapper, ITransportDirectionRepository transportDirectionRepository, ITransporterContainerTemplateRepository transporterContainerTemplateRepository ) { _expressionParameterMapper = expressionParameterMapper; _transportDirectionRepository = transportDirectionRepository; _transporterContainerTemplateRepository = transporterContainerTemplateRepository; }
public UsedMoleculeRepository( IPKSimProjectRetriever projectRetriever, IOntogenyRepository ontogenyRepository, IMoleculeParameterRepository moleculeParameterRepository, ITransporterContainerTemplateRepository transporterContainerTemplateRepository) { _projectRetriever = projectRetriever; _ontogenyRepository = ontogenyRepository; _moleculeParameterRepository = moleculeParameterRepository; _transporterContainerTemplateRepository = transporterContainerTemplateRepository; }
public IndividualTransporterExpressionsPresenter(IIndividualTransporterExpressionsView view, IEditParameterPresenterTask parameterTask, IMoleculeExpressionTask <TSimulationSubject> moleculeExpressionTask, IIndividualTransporterToTransporterExpressionDTOMapper transporterExpressionDTOMapper, ITransporterContainerTemplateRepository transporterContainerTemplateRepository, IIndividualMoleculePropertiesPresenter <TSimulationSubject> moleculePropertiesPresenter) : base(view, parameterTask) { _moleculeExpressionTask = moleculeExpressionTask; _transporterExpressionDTOMapper = transporterExpressionDTOMapper; _moleculePropertiesPresenter = moleculePropertiesPresenter; _transporterContainerTemplateRepository = transporterContainerTemplateRepository; AddSubPresenters(_moleculePropertiesPresenter); view.AddMoleculePropertiesView(_moleculePropertiesPresenter.View); }
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" } }); }
protected override void Context() { _repository = A.Fake<ITransporterContainerTemplateRepository>(); _eventPublisher = A.Fake<IEventPublisher>(); sut = new TransportContainerUpdater(_repository, _eventPublisher); }
protected override void Context() { _repository = A.Fake <ITransporterContainerTemplateRepository>(); _eventPublisher = A.Fake <IEventPublisher>(); _transportDirectionRepository = A.Fake <ITransportDirectionRepository>(); sut = new TransportContainerUpdater(_repository, _eventPublisher); _fractionExpressedApical = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL); _fractionExpressedApicalMucosa = DomainHelperForSpecs.ConstantParameterWithValue(0).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL); _fractionExpressedApicalBone = DomainHelperForSpecs.ConstantParameterWithValue(1).WithName(CoreConstants.Parameters.FRACTION_EXPRESSED_APICAL); //Indicates that this parameter should not be visible to the user and therefore remains unchanged _fractionExpressedApicalBone.Visible = false; _individual = A.Fake <ISimulationSubject>(); _individual.Species.Name = _species; _transporter = new IndividualTransporter { TransportType = TransportType.Efflux, Name = "toto" }; var organism = new Organism(); var mucosa = new Container().WithName(CoreConstants.Compartment.MUCOSA).WithParentContainer(organism); var liver = new Container().WithName(CoreConstants.Organ.LIVER).WithParentContainer(organism); var liverCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(liver); var kidney = new Container().WithName(CoreConstants.Organ.KIDNEY).WithParentContainer(organism); var kidneyCell = new Container().WithName(CoreConstants.Compartment.INTRACELLULAR).WithParentContainer(kidney); var bone = new Container().WithName(CoreConstants.Organ.BONE).WithParentContainer(organism); var boneInterstitial = new Container().WithName(CoreConstants.Compartment.INTERSTITIAL).WithParentContainer(bone); _transporterWithTemplate = new TransporterExpressionContainer { TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular } .WithParentContainer(liverCell); _transporterWithoutTemplate = new TransporterExpressionContainer { TransportDirection = TransportDirectionId.EffluxIntracellularToInterstitial } .WithParentContainer(kidneyCell); _transporterInMucosa = new TransporterExpressionContainer { TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular } .WithParentContainer(mucosa); _transporterInBone = new TransporterExpressionContainer { TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular } .WithParentContainer(boneInterstitial); _transporterInMucosa.Add(_fractionExpressedApicalMucosa); _transporterWithoutTemplate.Add(_fractionExpressedApical); _transporterInBone.Add(_fractionExpressedApicalBone); A.CallTo(() => _individual.AllMoleculeContainersFor <TransporterExpressionContainer>(_transporter)) .Returns(new[] { _transporterWithTemplate, _transporterWithoutTemplate, _transporterInMucosa, _transporterInBone }); _transporterContainerTemplate = new TransporterContainerTemplate { TransportType = TransportType.Influx }; _allTransporterTemplates.Add(_transporterContainerTemplate); A.CallTo(() => _repository.HasTransporterTemplateFor(_species, _transporter.Name)).Returns(true); A.CallTo(() => _repository.TransportTypeFor(_species, _transporter.Name)).Returns(TransportType.Influx); A.CallTo(() => _repository.TransportersFor(_species, liver.Name, _transporter.Name)).Returns(_allTransporterTemplates); A.CallTo(() => _repository.TransportersFor(_species, kidney.Name, _transporter.Name)).Returns(new List <TransporterContainerTemplate>()); }
public IndividualTransporterFactory(IObjectBaseFactory objectBaseFactory, IParameterFactory parameterFactory, IObjectPathFactory objectPathFactory, IEntityPathResolver entityPathResolver, ITransporterContainerTemplateRepository transporterContainerTemplateRepository) : base(objectBaseFactory, parameterFactory, objectPathFactory, entityPathResolver) { _transporterContainerTemplateRepository = transporterContainerTemplateRepository; }