public ProtocolChartPresenter(IProtocolChartView view, IProtocolToSchemaItemsMapper schemaItemsMapper, ISchemaItemToSchemaItemDTOMapper schemaItemDTOMapper, IDimensionRepository dimensionRepository) : base(view) { _schemaItemsMapper = schemaItemsMapper; _schemaItemDTOMapper = schemaItemDTOMapper; _dimensionRepository = dimensionRepository; }
protected override void Context() { _simulation = new IndividualSimulation { Properties = new SimulationProperties(), SimulationSettings = new SimulationSettings(), ModelConfiguration = new ModelConfiguration() }; _individual = new Individual().WithName("MyIndividual"); _speciesPopulation = new SpeciesPopulation(); _individual.OriginData = new OriginData { SpeciesPopulation = _speciesPopulation }; _compound = A.Fake <Compound>().WithName("MyCompound"); _protocol = A.Fake <SimpleProtocol>().WithName("MyProtocol"); _formulation = A.Fake <Formulation>().WithName("Formulation"); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Individual", PKSimBuildingBlockType.Individual) { BuildingBlock = _individual }); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Compound", PKSimBuildingBlockType.Compound) { BuildingBlock = _compound }); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Protocol", PKSimBuildingBlockType.Protocol) { BuildingBlock = _protocol }); _simulation.AddUsedBuildingBlock(new UsedBuildingBlock("Formulation", PKSimBuildingBlockType.Formulation) { BuildingBlock = _formulation }); _protocolToProtocolSchemaItemMapper = A.Fake <IProtocolToSchemaItemsMapper>(); sut = new SimulationConfigurationValidator(_protocolToProtocolSchemaItemMapper); _speciesPopulation.IsHeightDependent = false; _schemaItem = A.Fake <SchemaItem>(); _doseUnit = A.Fake <Unit>(); _schemaItem.Dose.DisplayUnit = _doseUnit; _protocolProperties = new ProtocolProperties(); _formulationMapping = new FormulationMapping { FormulationKey = "F1", Formulation = _formulation }; _simulation.Properties.AddCompoundProperties(new CompoundProperties { Compound = _compound, ProtocolProperties = _protocolProperties }); A.CallTo(() => _protocolToProtocolSchemaItemMapper.MapFrom(_protocol)).Returns(new [] { _schemaItem }); }
public ProtocolChartPresenter( IProtocolChartView view, IProtocolToSchemaItemsMapper schemaItemsMapper, ISchemaItemToSchemaItemDTOMapper schemaItemDTOMapper, IDimensionRepository dimensionRepository, IApplicationSettings applicationSettings) : base(view) { _schemaItemsMapper = schemaItemsMapper; _schemaItemDTOMapper = schemaItemDTOMapper; _dimensionRepository = dimensionRepository; _applicationSettings = applicationSettings; }
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; }
public EventBuildingBlockCreator(IObjectBaseFactory objectBaseFactory, IProtocolToSchemaItemsMapper schemaItemsMapper, IApplicationFactory applicationFactory, IFormulationFromMappingRetriever formulationFromMappingRetriever, ICloneManagerForBuildingBlock cloneManagerForBuildingBlock, IParameterIdUpdater parameterIdUpdater, IParameterSetUpdater parameterSetUpdater, IEventGroupRepository eventGroupRepository) { _objectBaseFactory = objectBaseFactory; _schemaItemsMapper = schemaItemsMapper; _applicationFactory = applicationFactory; _formulationFromMappingRetriever = formulationFromMappingRetriever; _cloneManagerForBuildingBlock = cloneManagerForBuildingBlock; _parameterIdUpdater = parameterIdUpdater; _parameterSetUpdater = parameterSetUpdater; _eventGroupRepository = eventGroupRepository; }
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 SimulationConfigurationValidator(IProtocolToSchemaItemsMapper schemaItemsMapper) { _schemaItemsMapper = schemaItemsMapper; }
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]))); }