protected override void Context() { _objectBaseFactory = A.Fake <IObjectBaseFactory>(); _simulationBuildingBlockUpdater = A.Fake <ISimulationBuildingBlockUpdater>(); _simulationModelCreator = A.Fake <ISimulationModelCreator>(); _simulationParametersUpdater = A.Fake <ISimulationParametersUpdater>(); _modelPropertiesTask = A.Fake <IModelPropertiesTask>(); _cloner = A.Fake <ICloner>(); _diagramModelFactory = A.Fake <IDiagramModelFactory>(); _interactionTask = A.Fake <IInteractionTask>(); _individual = A.Fake <Individual>(); _compounds = new List <Compound>(); A.CallTo(() => _individual.BuildingBlockType).Returns(PKSimBuildingBlockType.Individual); _population = A.Fake <Population>(); A.CallTo(() => _population.BuildingBlockType).Returns(PKSimBuildingBlockType.Population); _originData = new OriginData(); _modelProperties = A.Fake <ModelProperties>(); _individualSimulation = A.Fake <IndividualSimulation>(); _populationSimulation = A.Fake <PopulationSimulation>(); _objectIdResetter = A.Fake <IObjectIdResetter>(); _compoundPropertiesUpdater = A.Fake <ICompoundPropertiesUpdater>(); A.CallTo(() => _objectBaseFactory.Create <IndividualSimulation>()).Returns(_individualSimulation); A.CallTo(() => _objectBaseFactory.Create <PopulationSimulation>()).Returns(_populationSimulation); _individual.OriginData = _originData; A.CallTo(() => _individual.Organism).Returns(A.Fake <Organism>()); sut = new SimulationFactory(_objectBaseFactory, _simulationBuildingBlockUpdater, _simulationModelCreator, _objectIdResetter, _compoundPropertiesUpdater, _simulationParametersUpdater, _modelPropertiesTask, _cloner, _diagramModelFactory, _interactionTask); }
public MoleculesAndReactionsCreator(IObjectBaseFactory objectBaseFactory, IMoleculeBuilderFactory moleculeBuilderFactory, IParameterIdUpdater parameterIdUpdater, IProcessToProcessBuilderMapper processBuilderMapper, IParameterSetUpdater parameterSetUpdater, IIndividualEnzymeFactory individualEnzymeFactory, IIndividualTransporterFactory individualTransporterFactory, IModelContainerMoleculeRepository modelContainerMoleculeRepo, IStaticReactionRepository staticReactionRepository, IMoleculeCalculationRetriever moleculeCalculationRetriever, IInteractionKineticUpdater interactionKineticUpdater, IInteractionTask interactionTask ) { _objectBaseFactory = objectBaseFactory; _moleculeBuilderFactory = moleculeBuilderFactory; _parameterIdUpdater = parameterIdUpdater; _processBuilderMapper = processBuilderMapper; _parameterSetUpdater = parameterSetUpdater; _individualEnzymeFactory = individualEnzymeFactory; _individualTransporterFactory = individualTransporterFactory; _modelContainerMoleculeRepo = modelContainerMoleculeRepo; _staticReactionRepository = staticReactionRepository; _moleculeCalculationRetriever = moleculeCalculationRetriever; _interactionKineticUpdater = interactionKineticUpdater; _interactionTask = interactionTask; _allMoleculeNames = new List <string>(); _moleculeWithTurnoverReactions = new List <IMoleculeBuilder>(); }
protected override void Context() { _spatialStructureFactory = A.Fake <IMoBiSpatialStructureFactory>(); _interactionTaskContext = A.Fake <IInteractionTaskContext>(); _interactionTask = A.Fake <IInteractionTask>(); A.CallTo(() => _interactionTaskContext.InteractionTask).Returns(_interactionTask); sut = new EditTaskForContainer(_interactionTaskContext, _spatialStructureFactory); }
protected EditTaskFor(IInteractionTaskContext interactionTaskContext) { _interactionTaskContext = interactionTaskContext; _applicationController = interactionTaskContext.ApplicationController; _interactionTask = interactionTaskContext.InteractionTask; _context = interactionTaskContext.Context; ObjectName = _interactionTaskContext.GetTypeFor <T>(); }
public ObservedDataTask(IDataImporter dataImporter, IDimensionFactory dimensionFactory, IMoBiContext context, IDialogCreator dialogCreator, IInteractionTask interactionTask, IDataRepositoryTask dataRepositoryTask, IContainerTask containerTask, IObjectTypeResolver objectTypeResolver) : base(dialogCreator, context, dataRepositoryTask, containerTask, objectTypeResolver) { _dataImporter = dataImporter; _mobiDialogCreator = dialogCreator; _interactionTask = interactionTask; _dimensionFactory = dimensionFactory; _context = context; _molWeightDimension = dimensionFactory.Dimension(AppConstants.DimensionNames.MOL_WEIGHT); }
public override void GlobalContext() { base.GlobalContext(); _compoundProcessRepo = IoC.Resolve <ICompoundProcessRepository>(); _interactionTask = IoC.Resolve <IInteractionTask>(); var cloner = IoC.Resolve <ICloneManager>(); var enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>(); var transporterFactory = IoC.Resolve <IIndividualTransporterFactory>(); var inhibitor = DomainFactoryForSpecs.CreateStandardCompound().WithName("Inhibitor"); var protocol2 = DomainFactoryForSpecs.CreateStandardIVBolusProtocol().WithName("IV2"); var allPartialProcesses = PartialProcesses.ToList(); foreach (var metaTemplate in allPartialProcesses) { var moleculeName = "Molecule_" + metaTemplate.Name; if (metaTemplate as EnzymaticProcess != null) { var individualProtein = enzymeFactory.CreateFor(_individual).WithName(moleculeName); _individual.AddMolecule(individualProtein.DowncastTo <IndividualEnzyme>().WithName(moleculeName)); } else { var individualProtein = transporterFactory.CreateFor(_individual).WithName(moleculeName); _individual.AddMolecule(individualProtein.DowncastTo <IndividualTransporter>().WithName(moleculeName)); } var process = cloner.Clone(metaTemplate).DowncastTo <PartialProcess>(); process.Name = "Process " + moleculeName; process.MoleculeName = moleculeName; _compound.AddProcess(process); var inhibitionTemplate = _compoundProcessRepo.ProcessByName <InteractionProcess>(InhibitionProcessName); var inhibitionProcess = cloner.Clone(inhibitionTemplate); inhibitionProcess.Name = "InhibitionProcess " + moleculeName; inhibitionProcess.MoleculeName = moleculeName; inhibitor.AddProcess(inhibitionProcess); } _simulation = DomainFactoryForSpecs.CreateModelLessSimulationWith( _individual, new[] { _compound, inhibitor }, new[] { _protocol, protocol2 }).DowncastTo <IndividualSimulation>(); foreach (var inhibitionProcess in inhibitor.AllProcesses <InteractionProcess>()) { var interactionSelection = new InteractionSelection { CompoundName = inhibitor.Name, MoleculeName = inhibitionProcess.MoleculeName, ProcessName = inhibitionProcess.Name }; _simulation.InteractionProperties.AddInteraction(interactionSelection); } DomainFactoryForSpecs.AddModelToSimulation(_simulation); }
public ModelObserverQuery(IObjectBaseFactory objectBaseFactory, IObserverBuilderRepository observerBuilderRepository, ICloneManagerForBuildingBlock cloneManager, IDimensionRepository dimensionRepository, IObjectPathFactory objectPathFactory, IInteractionTask interactionTask) { _objectBaseFactory = objectBaseFactory; _observerBuilderRepository = observerBuilderRepository; _cloneManager = cloneManager; _dimensionRepository = dimensionRepository; _objectPathFactory = objectPathFactory; _interactionTask = interactionTask; }
protected override void Context() { _interactionTaskContext = A.Fake <IInteractionTaskContext>(); _interactionTask = A.Fake <IInteractionTask>(); A.CallTo(() => _interactionTaskContext.InteractionTask).Returns(_interactionTask); _builder = new ApplicationBuilder(); sut = new EditTasksForEventGroupBuilder <IApplicationBuilder>(_interactionTaskContext); A.CallTo(() => _interactionTask.ForbiddenNamesFor(_builder)).Returns(new List <string> { _builderName }); }
protected InteractionKineticUpdaterSpecificationBase(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask, InteractionType interactionType, string kiNumeratorParameter, string kiDenominatorParameter, string kiNumeratorAlias, string kiDenominatorAlias, string inhibitorAlias) { _objectPathFactory = objectPathFactory; _dimensionRepository = dimensionRepository; _interactionTask = interactionTask; _interactionType = interactionType; _kineticModifications = modificationsFrom(interactionType); _kiNumeratorParameter = kiNumeratorParameter; _kiDenominatorParameter = kiDenominatorParameter; _kiNumeratorAlias = kiNumeratorAlias; _kiDenominatorAlias = kiDenominatorAlias; _inhibitorAlias = inhibitorAlias; }
public GlobalPKAnalysisTask(IParameterFactory parameterFactory, IProtocolToSchemaItemsMapper protocolToSchemaItemsMapper, IProtocolFactory protocolFactory, IGlobalPKAnalysisRunner globalPKAnalysisRunner, IPKAnalysisTask pkAnalysisTask, IPKCalculationOptionsFactory pkCalculationOptionsFactory, IVSSCalculator vssCalculator, IInteractionTask interactionTask, ICloner cloner) { _parameterFactory = parameterFactory; _protocolToSchemaItemsMapper = protocolToSchemaItemsMapper; _protocolFactory = protocolFactory; _globalPKAnalysisRunner = globalPKAnalysisRunner; _pkAnalysisTask = pkAnalysisTask; _pkCalculationOptionsFactory = pkCalculationOptionsFactory; _vssCalculator = vssCalculator; _interactionTask = interactionTask; _cloner = cloner; }
protected override void Context() { _interactionTaskContext = A.Fake <IInteractionTaskContext>(); _editTasks = A.Fake <IEditTaskFor <IMoleculeBuilder> >(); _calculation = A.Fake <ICoreCalculationMethodRepository>(); _dimensionRetriever = A.Fake <IReactionDimensionRetriever>(); _parameterFactory = A.Fake <IParameterFactory>(); _formulaTask = A.Fake <IMoBiFormulaTask>(); sut = new InteractionTasksForMoleculeBuilder(_interactionTaskContext, _editTasks, _dimensionRetriever, _parameterFactory, _calculation, _formulaTask); _interactionTask = A.Fake <IInteractionTask>(); _context = A.Fake <IMoBiContext>(); A.CallTo(() => _interactionTaskContext.InteractionTask).Returns(_interactionTask); A.CallTo(() => _interactionTaskContext.Context).Returns(_context); }
public ObservedDataTask( IDataImporter dataImporter, IDimensionFactory dimensionFactory, IMoBiContext context, IDialogCreator dialogCreator, IInteractionTask interactionTask, IDataRepositoryExportTask dataRepositoryTask, IContainerTask containerTask, IObjectTypeResolver objectTypeResolver) : base(dialogCreator, context, dataRepositoryTask, containerTask, objectTypeResolver) { _dataImporter = dataImporter; _mobiDialogCreator = dialogCreator; _interactionTask = interactionTask; _dimensionFactory = dimensionFactory; _context = context; }
public SimulationFactory(IObjectBaseFactory objectBaseFactory, ISimulationBuildingBlockUpdater simulationBuildingBlockUpdater, ISimulationModelCreator simulationModelCreator, IObjectIdResetter objectIdResetter, ICompoundPropertiesUpdater compoundPropertiesUpdater, ISimulationParametersUpdater simulationParametersUpdater, IModelPropertiesTask modelPropertiesTask, ICloner cloner, IDiagramModelFactory diagramModelFactory, IInteractionTask interactionTask) { _objectBaseFactory = objectBaseFactory; _simulationBuildingBlockUpdater = simulationBuildingBlockUpdater; _simulationModelCreator = simulationModelCreator; _objectIdResetter = objectIdResetter; _compoundPropertiesUpdater = compoundPropertiesUpdater; _simulationParametersUpdater = simulationParametersUpdater; _modelPropertiesTask = modelPropertiesTask; _cloner = cloner; _diagramModelFactory = diagramModelFactory; _interactionTask = interactionTask; }
protected override void Context() { _dataImporter = A.Fake <IDataImporter>(); _dimensionFactory = A.Fake <IDimensionFactory>(); _context = A.Fake <IMoBiContext>(); _dialogCreator = A.Fake <IDialogCreator>(); _dataRepository = new DataRepository { new BaseGrid("", DimensionFactoryForSpecs.Factory.Dimension("Time")) }; _interactionTask = A.Fake <IInteractionTask>(); _dataRepositoryTask = A.Fake <IDataRepositoryTask>(); _containerTask = A.Fake <IContainerTask>(); _objectTypeResolver = A.Fake <IObjectTypeResolver>(); sut = new ObservedDataTask(_dataImporter, _dimensionFactory, _context, _dialogCreator, _interactionTask, _dataRepositoryTask, _containerTask, _objectTypeResolver); _project = new MoBiProject(); A.CallTo(() => _context.Project).Returns(_project); A.CallTo(() => _context.CurrentProject).Returns(_project); }
public InteractionTaskContext(IMoBiContext context, IMoBiApplicationController applicationController, IInteractionTask interactionTask, IActiveSubjectRetriever activeSubjectRetriever, IUserSettings userSettings, IDisplayUnitRetriever displayUnitRetriever, IDialogCreator dialogCreator, ICommandTask commandTask, IObjectTypeResolver objectTypeResolver, IMoBiFormulaTask moBiFormulaTask, IMoBiConfiguration configuration, DirectoryMapSettings directoryMapSettings) { DialogCreator = dialogCreator; Context = context; ApplicationController = applicationController; InteractionTask = interactionTask; ActiveSubjectRetriever = activeSubjectRetriever; UserSettings = userSettings; DisplayUnitRetriever = displayUnitRetriever; _commandTask = commandTask; _objectTypeResolver = objectTypeResolver; _configuration = configuration; _directoryMapSettings = directoryMapSettings; MoBiFormulaTask = moBiFormulaTask; }
protected override void Context() { _objectPathFactory = new ObjectPathFactoryForSpecs(); _dimensionRepository = A.Fake <IDimensionRepository>(); _interactionTask = new InteractionTask(); sut = new UncompetitiveInhibitionKineticUpdaterSpecification(_objectPathFactory, _dimensionRepository, _interactionTask); _simulation = A.Fake <Simulation>(); _competitiveInhibition = new InhibitionProcess { InteractionType = InteractionType.CompetitiveInhibition }.WithName("CompetitiveInhibition"); _uncompetitiveInhibition1 = new InhibitionProcess { InteractionType = InteractionType.UncompetitiveInhibition }.WithName("UncompetitiveInhibition1"); _uncompetitiveInhibition2 = new InhibitionProcess { InteractionType = InteractionType.UncompetitiveInhibition }.WithName("UncompetitiveInhibition2"); _interactionProperties = new InteractionProperties(); A.CallTo(() => _simulation.InteractionProperties).Returns(_interactionProperties); _compound1 = new Compound().WithName("Compound1"); _compound1.AddProcess(_competitiveInhibition); _compound2 = new Compound().WithName("Compound2"); _compound2.AddProcess(_uncompetitiveInhibition1); _compound2.AddProcess(_uncompetitiveInhibition2); A.CallTo(() => _simulation.Compounds).Returns(new[] { _compound1, _compound2 }); _interactionProperties.AddInteraction(new InteractionSelection { MoleculeName = _moleculeName, ProcessName = _competitiveInhibition.Name, CompoundName = _compound1.Name }); _interactionProperties.AddInteraction(new InteractionSelection { MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition1.Name, CompoundName = _compound2.Name }); _interactionProperties.AddInteraction(new InteractionSelection { MoleculeName = _moleculeName, ProcessName = _uncompetitiveInhibition2.Name, CompoundName = _compound2.Name }); }
protected override void Context() { _interactionTaskContext = A.Fake <IInteractionTaskContext>(); _context = A.Fake <IMoBiContext>(); _project = A.Fake <IMoBiProject>(); _amountObserver = A.Fake <IAmountObserverBuilder>(); _amountObserverBuilderWithForbiddenName = new AmountObserverBuilder { Name = "forbidden name" }; _buildingBlock = new ObserverBuildingBlock { _amountObserverBuilderWithForbiddenName, _amountObserver }; _interactionTask = A.Fake <IInteractionTask>(); A.CallTo(() => _context.CurrentProject).Returns(_project); A.CallTo(() => _interactionTaskContext.Context).Returns(_context); A.CallTo(() => _project.ObserverBlockCollection).Returns(new[] { _buildingBlock }); A.CallTo(() => _interactionTaskContext.InteractionTask).Returns(_interactionTask); sut = new EditTasksForAmountObserverBuilder(_interactionTaskContext); }
protected override void Context() { _vssCalculator = A.Fake <IVSSCalculator>(); _parameterFactory = A.Fake <IParameterFactory>(); _protocolMapper = A.Fake <IProtocolToSchemaItemsMapper>(); _protocolFactory = A.Fake <IProtocolFactory>(); _globalPKAnalysisRunner = A.Fake <IGlobalPKAnalysisRunner>(); _pkCalculationOptionsFactory = A.Fake <IPKCalculationOptionsFactory>(); _pkAnalysisTask = A.Fake <IPKAnalysesTask>(); _interactionTask = A.Fake <IInteractionTask>(); _cloner = A.Fake <ICloner>(); sut = new GlobalPKAnalysisTask(_parameterFactory, _protocolMapper, _protocolFactory, _globalPKAnalysisRunner, _pkAnalysisTask, _pkCalculationOptionsFactory, _vssCalculator, _interactionTask, _cloner); var baseGrid = new BaseGrid("time", A.Fake <IDimension>()); _peripheralVenousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, _compoundName); _venousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.VENOUS_BLOOD, CoreConstants.Compartment.PLASMA, CoreConstants.Observer.CONCENTRATION_IN_CONTAINER, _compoundName); _individual = A.Fake <Individual>(); _species = new Species(); A.CallTo(() => _individual.Species).Returns(_species); _compound = new Compound().WithName(_compoundName); _compoundProperties = new CompoundProperties { Compound = _compound }; _protocol = new SimpleProtocol(); _compoundProperties.ProtocolProperties.Protocol = _protocol; _simulation = new IndividualSimulation { Properties = new SimulationProperties() }; _simulation.Properties.AddCompoundProperties(_compoundProperties); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompId", PKSimBuildingBlockType.Compound) { BuildingBlock = _compound }); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndividualId", PKSimBuildingBlockType.Individual) { BuildingBlock = _individual }); _simulation.DataRepository = new DataRepository { _venousBloodPlasma, _peripheralVenousBloodPlasma }; _simulation.SimulationSettings = new SimulationSettings(); _simulation.OutputSchema = new OutputSchema(); _simulation.OutputSchema.AddInterval(new OutputInterval { DomainHelperForSpecs.ConstantParameterWithValue(100).WithName(Constants.Parameters.END_TIME) }); _simulation.Model = new OSPSuite.Core.Domain.Model { Root = new Container() }; _eventGroup = new EventGroup(); _application1 = new Container().WithName("App1").WithContainerType(ContainerType.Application); _application1.Add(new MoleculeAmount().WithName(_compoundName)); _application1.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.START_TIME)); _application2 = new Container().WithName("App2").WithContainerType(ContainerType.Application); _application2.Add(DomainHelperForSpecs.ConstantParameterWithValue(10).WithName(Constants.Parameters.START_TIME)); _application2.Add(new MoleculeAmount().WithName(_compoundName)); _simulation.Model.Root.Add(_eventGroup); _eventGroup.Add(_application1); _venousBloodPK = new PKValues(); _venousBloodPK.AddValue(Constants.PKParameters.Vss, 10); _venousBloodPK.AddValue(Constants.PKParameters.Vd, 11); _venousBloodPK.AddValue(Constants.PKParameters.CL, 12); _venousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 13); _venousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 14); _peripheralVenousBloodPK = new PKValues(); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vss, 21); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vd, 22); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.CL, 23); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 24); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 25); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max, 26); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max_tDLast_tDEnd, 27); A.CallTo(() => _pkAnalysisTask.CalculatePK(_venousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_venousBloodPK); A.CallTo(() => _pkAnalysisTask.CalculatePK(_peripheralVenousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_peripheralVenousBloodPK); A.CallTo(() => _parameterFactory.CreateFor(A <string> ._, A <double> ._, A <string> ._, PKSimBuildingBlockType.Simulation)) .ReturnsLazily(s => new PKSimParameter().WithName((string)s.Arguments[0]) .WithDimension(A.Fake <IDimension>()) .WithFormula(new ConstantFormula((double)s.Arguments[1]))); }
protected RenameTask(IInteractionTask interactionTask, IMoBiContext context) { _interactionTask = interactionTask; _context = context; }
public CompetitiveInhibitionsKineticUpdaterSpecification(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask) : base(objectPathFactory, dimensionRepository, interactionTask, InteractionType.CompetitiveInhibition, kiNumeratorAlias: CoreConstants.Alias.COMPETITIVE_INHIBITION_KI, kiNumeratorParameter: CoreConstants.Parameters.KI, kiDenominatorAlias: CoreConstants.Alias.COMPETITIVE_INHIBITION_KI, kiDenominatorParameter: CoreConstants.Parameters.KI, inhibitorAlias: CoreConstants.Alias.COMPETITIVE_INHIBITION_I, kWaterAlias: CoreConstants.Alias.COMPETITIVE_INHIBITION_K_WATER) { }
public IrreversibleInhibitionKineticUpdaterSpecification(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask) : base(objectPathFactory, dimensionRepository, interactionTask, InteractionType.IrreversibleInhibition, kiNumeratorAlias: CoreConstants.Alias.IRREVERSIBLE_INHIBITION_KI, kiNumeratorParameter: CoreConstants.Parameters.KI, kiDenominatorAlias: CoreConstants.Alias.IRREVERSIBLE_INHIBITION_KI, kiDenominatorParameter: CoreConstants.Parameters.KI, inhibitorAlias: CoreConstants.Alias.IRREVERSIBLE_INHIBITION_I) { }
protected override void Context() { _vssCalculator = A.Fake <IVSSCalculator>(); _parameterFactory = A.Fake <IParameterFactory>(); _protocolMapper = A.Fake <IProtocolToSchemaItemsMapper>(); _protocolFactory = A.Fake <IProtocolFactory>(); _globalPKAnalysisRunner = A.Fake <IGlobalPKAnalysisRunner>(); _pkCalculationOptionsFactory = A.Fake <IPKCalculationOptionsFactory>(); _pkAnalysisTask = A.Fake <IPKAnalysesTask>(); _interactionTask = A.Fake <IInteractionTask>(); _cloner = A.Fake <ICloner>(); sut = new GlobalPKAnalysisTask(_parameterFactory, _protocolMapper, _protocolFactory, _globalPKAnalysisRunner, _pkAnalysisTask, _pkCalculationOptionsFactory, _vssCalculator, _interactionTask, _cloner); var baseGrid = new BaseGrid("time", A.Fake <IDimension>()); _peripheralVenousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.PeripheralVenousBlood, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, CoreConstants.Observer.PLASMA_PERIPHERAL_VENOUS_BLOOD, _compoundName); _venousBloodPlasma = CalculationColumnFor(baseGrid, CoreConstants.Organ.VenousBlood, CoreConstants.Compartment.Plasma, CoreConstants.Observer.CONCENTRATION_IN_CONTAINER, _compoundName); _individual = A.Fake <Individual>(); _species = new Species(); A.CallTo(() => _individual.Species).Returns(_species); _compound = new Compound().WithName(_compoundName); _compoundProperties = new CompoundProperties { Compound = _compound }; _simulationSchemaItems = new List <SchemaItem>(); _protocol = new SimpleProtocol(); _compoundProperties.ProtocolProperties.Protocol = _protocol; A.CallTo(() => _protocolMapper.MapFrom(_protocol)).Returns(_simulationSchemaItems); _simulation = new IndividualSimulation { Properties = new SimulationProperties() }; _simulation.Properties.AddCompoundProperties(_compoundProperties); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompId", PKSimBuildingBlockType.Compound) { BuildingBlock = _compound }); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndividualId", PKSimBuildingBlockType.Individual) { BuildingBlock = _individual }); _simulation.DataRepository = new DataRepository { _venousBloodPlasma, _peripheralVenousBloodPlasma }; _venousBloodPK = new PKValues(); _venousBloodPK.AddValue(Constants.PKParameters.Vss, 10); _venousBloodPK.AddValue(Constants.PKParameters.Vd, 11); _venousBloodPK.AddValue(Constants.PKParameters.CL, 12); _venousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 13); _venousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 14); _peripheralVenousBloodPK = new PKValues(); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vss, 21); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.Vd, 22); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.CL, 23); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf, 24); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.AUC_inf_tD1_norm, 25); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max, 26); _peripheralVenousBloodPK.AddValue(Constants.PKParameters.C_max_tDLast_tDEnd, 27); A.CallTo(() => _pkAnalysisTask.CalculatePK(_venousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_venousBloodPK); A.CallTo(() => _pkAnalysisTask.CalculatePK(_peripheralVenousBloodPlasma, A <PKCalculationOptions> ._)).Returns(_peripheralVenousBloodPK); A.CallTo(() => _parameterFactory.CreateFor(A <string> ._, A <double> ._, A <string> ._, PKSimBuildingBlockType.Simulation)) .ReturnsLazily(s => new PKSimParameter().WithName((string)s.Arguments[0]) .WithDimension(A.Fake <IDimension>()) .WithFormula(new ConstantFormula((double)s.Arguments[1]))); }
public MixedInhibitionKineticUpdaterSpecification(IObjectPathFactory objectPathFactory, IDimensionRepository dimensionRepository, IInteractionTask interactionTask) : base(objectPathFactory, dimensionRepository, interactionTask, InteractionType.MixedInhibition, kiNumeratorAlias: CoreConstants.Alias.MIXED_COMPETITIVE_INHIBITION_KI, kiNumeratorParameter: CoreConstants.Parameter.KI_C, kiDenominatorAlias: CoreConstants.Alias.MIXED_UNCOMPETITIVE_INHIBITION_KI, kiDenominatorParameter: CoreConstants.Parameter.KI_U, inhibitorAlias: CoreConstants.Alias.MIXED_COMPETIVE_INHIBITION_I) { }