protected override void Context() { _sourceIndividual = A.Fake <Individual>(); _ontogenyTask = A.Fake <IOntogenyTask <Individual> >(); _cloner = A.Fake <ICloner>(); _targetIndividual = DomainHelperForSpecs.CreateIndividual(); sut = new IndividualExpressionsUpdater(_ontogenyTask, _cloner); }
protected override void Context() { _view = A.Fake <IOntogenySelectionView>(); _ontogenyRepository = A.Fake <IOntogenyRepository>(); _ontogenyTask = A.Fake <IOntogenyTask <Individual> >(); _commandRegister = A.Fake <ICommandCollector>(); _allOntogenies = new List <Ontogeny>(); A.CallTo(() => _ontogenyRepository.AllFor(CoreConstants.Species.Human)).Returns(_allOntogenies); sut = new OntogenySelectionPresenter <Individual>(_view, _ontogenyRepository, _ontogenyTask); sut.InitializeWith(_commandRegister); }
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 MoleculeMapper( ParameterMapper parameterMapper, ExpressionContainerMapper expressionContainerMapper, OntogenyMapper ontogenyMapper, IIndividualMoleculeFactoryResolver individualMoleculeFactoryResolver, IExecutionContext executionContext, IOntogenyTask <ModelIndividual> ontogenyTask, IMoleculeParameterTask moleculeExpressionTask ) : base(parameterMapper) { _expressionContainerMapper = expressionContainerMapper; _individualMoleculeFactoryResolver = individualMoleculeFactoryResolver; _executionContext = executionContext; _ontogenyTask = ontogenyTask; _moleculeExpressionTask = moleculeExpressionTask; _ontogenyMapper = ontogenyMapper; }
public ExpressionProfileMapper( ParameterMapper parameterMapper, ExpressionContainerMapper expressionContainerMapper, OntogenyMapper ontogenyMapper, IOntogenyTask ontogenyTask, IMoleculeExpressionTask <ModelIndividual> moleculeExpressionTask, IExpressionProfileFactory expressionProfileFactory, IMoleculeParameterTask moleculeParameterTask ) { _parameterMapper = parameterMapper; _expressionContainerMapper = expressionContainerMapper; _ontogenyTask = ontogenyTask; _moleculeExpressionTask = moleculeExpressionTask; _expressionProfileFactory = expressionProfileFactory; _moleculeParameterTask = moleculeParameterTask; _ontogenyMapper = ontogenyMapper; }
public ExpressionProfileUpdater( IParameterSetUpdater parameterSetUpdater, IContainerTask containerTask, IOntogenyTask ontogenyTask, ICloner cloner, IPKSimProjectRetriever projectRetriever, ILazyLoadTask lazyLoadTask, IParameterIdUpdater parameterIdUpdater, IExecutionContext executionContext, IDiseaseStateImplementationFactory diseaseStateImplementationFactory) { _parameterSetUpdater = parameterSetUpdater; _containerTask = containerTask; _ontogenyTask = ontogenyTask; _cloner = cloner; _projectRetriever = projectRetriever; _lazyLoadTask = lazyLoadTask; _parameterIdUpdater = parameterIdUpdater; _executionContext = executionContext; _diseaseStateImplementationFactory = diseaseStateImplementationFactory; }
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>(); _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); }
public OntogenySelectionPresenter(IOntogenySelectionView view, IOntogenyRepository ontogenyRepository, IOntogenyTask ontogenyTask) : base(view) { _ontogenyTask = ontogenyTask; _allOntogenies = ontogenyRepository.AllFor(CoreConstants.Species.HUMAN); }
public IndividualExpressionsUpdater(IOntogenyTask <Individual> ontogenyTask, ICloner cloner) { _ontogenyTask = ontogenyTask; _cloner = cloner; }
public OntogenySelectionPresenter(IOntogenySelectionView view, IOntogenyRepository ontogenyRepository, IOntogenyTask <TSimulationSubject> ontogenyTask) : base(view) { _ontogenyTask = ontogenyTask; _allOntogenies = ontogenyRepository.AllFor(CoreConstants.Species.Human); }