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)
{
}
