public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
protected override void Context()
{
_view = A.Fake <ISimulationModelSelectionView>();
_categoryCalculationMethodDTOMapper = A.Fake <ICalculationMethodToCategoryCalculationMethodDTOMapper>();
_modelPropertiesTask = A.Fake <IModelPropertiesTask>();
_modelConfigurationRepository = A.Fake <IModelConfigurationRepository>();
_modelPropertiesMapper = A.Fake <IModelConfigurationDTOToModelPropertiesMapper>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_simulation = A.Fake <Simulation>();
_species = A.Fake <Species>();
_individual = A.Fake <Individual>();
_modelProperties = A.Fake <ModelProperties>();
_modelConfiguration = A.Fake <ModelConfiguration>();
_modelConfiguration.ModelName = "4Comp";
_originData = new OriginData();
_modelProperties.ModelConfiguration = _modelConfiguration;
_simulation.ModelProperties = _modelProperties;
_simulation.ModelConfiguration = _modelConfiguration;
A.CallTo(() => _simulation.BuildingBlock <ISimulationSubject>()).Returns(_individual);
_individual.OriginData = _originData;
_originData.Species = _species;
A.CallTo(() => _modelPropertiesTask.Update(A <ModelProperties> ._, A <ModelProperties> ._, _originData)).Returns(_modelProperties);
sut = new SimulationModelSelectionPresenter(_view, _modelConfigurationRepository, _modelPropertiesTask, _modelPropertiesMapper, _representationInfoRepository, _categoryCalculationMethodDTOMapper);
}
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 SimulationModelSelectionPresenter(ISimulationModelSelectionView view, IModelConfigurationRepository modelConfigurationRepository,
IModelPropertiesTask modelPropertiesTask, IModelConfigurationDTOToModelPropertiesMapper modelPropertiesMapper,
IRepresentationInfoRepository representationInfoRepository, ICalculationMethodToCategoryCalculationMethodDTOMapper categoryCalculationMethodDTOMapper)
: base(view)
{
_modelConfigurationRepository = modelConfigurationRepository;
_modelPropertiesTask = modelPropertiesTask;
_modelPropertiesMapper = modelPropertiesMapper;
_representationInfoRepository = representationInfoRepository;
_categoryCalculationMethodDTOMapper = categoryCalculationMethodDTOMapper;
}
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;
}
public SimulationMapper(
SolverSettingsMapper solverSettingsMapper,
OutputSchemaMapper outputSchemaMapper,
OutputSelectionsMapper outputSelectionsMapper,
CompoundPropertiesMapper compoundPropertiesMapper,
ParameterMapper parameterMapper,
AdvancedParameterMapper advancedParameterMapper,
EventMappingMapper eventMappingMapper,
ObserverSetMappingMapper observerSetMappingMapper,
SimulationTimeProfileChartMapper simulationTimeProfileChartMapper,
PopulationAnalysisChartMapper populationAnalysisChartMapper,
ProcessMappingMapper processMappingMapper,
ISimulationFactory simulationFactory,
IExecutionContext executionContext,
ISimulationModelCreator simulationModelCreator,
ISimulationBuildingBlockUpdater simulationBuildingBlockUpdater,
IModelPropertiesTask modelPropertiesTask,
ISimulationRunner simulationRunner,
ISimulationParameterOriginIdUpdater simulationParameterOriginIdUpdater,
ILogger logger,
IContainerTask containerTask,
IEntityPathResolver entityPathResolver
)
{
_solverSettingsMapper = solverSettingsMapper;
_outputSchemaMapper = outputSchemaMapper;
_outputSelectionsMapper = outputSelectionsMapper;
_compoundPropertiesMapper = compoundPropertiesMapper;
_parameterMapper = parameterMapper;
_advancedParameterMapper = advancedParameterMapper;
_eventMappingMapper = eventMappingMapper;
_observerSetMappingMapper = observerSetMappingMapper;
_simulationTimeProfileChartMapper = simulationTimeProfileChartMapper;
_populationAnalysisChartMapper = populationAnalysisChartMapper;
_processMappingMapper = processMappingMapper;
_simulationFactory = simulationFactory;
_executionContext = executionContext;
_simulationModelCreator = simulationModelCreator;
_simulationBuildingBlockUpdater = simulationBuildingBlockUpdater;
_modelPropertiesTask = modelPropertiesTask;
_simulationRunner = simulationRunner;
_simulationParameterOriginIdUpdater = simulationParameterOriginIdUpdater;
_logger = logger;
_containerTask = containerTask;
_entityPathResolver = entityPathResolver;
}
protected override Task Context()
{
_solverSettingsMapper = A.Fake <SolverSettingsMapper>();
_outputSchemaMapper = A.Fake <OutputSchemaMapper>();
_outputSelectionMapper = A.Fake <OutputSelectionsMapper>();
_parameterMapper = A.Fake <ParameterMapper>();
_compoundPropertiesMapper = A.Fake <CompoundPropertiesMapper>();
_advancedParameterMapper = A.Fake <AdvancedParameterMapper>();
_eventMappingMapper = A.Fake <EventMappingMapper>();
_observerSetMappingMapper = A.Fake <ObserverSetMappingMapper>();
_curveChartMapper = A.Fake <SimulationTimeProfileChartMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_simulationFactory = A.Fake <ISimulationFactory>();
_executionContext = A.Fake <IExecutionContext>();
_simulationModelCreator = A.Fake <ISimulationModelCreator>();
_simulationBuildingBlockUpdater = A.Fake <ISimulationBuildingBlockUpdater>();
_modelPropertiesTask = A.Fake <IModelPropertiesTask>();
_simulationRunner = A.Fake <ISimulationRunner>();
_populationAnalysisChartMapper = A.Fake <PopulationAnalysisChartMapper>();
_simulationParameterOriginIdUpdater = A.Fake <ISimulationParameterOriginIdUpdater>();
_logger = A.Fake <ILogger>();
_containerTask = A.Fake <IContainerTask>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
sut = new SimulationMapper(_solverSettingsMapper, _outputSchemaMapper,
_outputSelectionMapper, _compoundPropertiesMapper, _parameterMapper,
_advancedParameterMapper, _eventMappingMapper, _observerSetMappingMapper, _curveChartMapper,
_populationAnalysisChartMapper, _processMappingMapper,
_simulationFactory, _executionContext, _simulationModelCreator,
_simulationBuildingBlockUpdater, _modelPropertiesTask,
_simulationRunner, _simulationParameterOriginIdUpdater,
_logger, _containerTask, _entityPathResolver
);
_project = new PKSimProject();
_individual = new Individual {
Name = "IND", Id = "IND"
};
_compound = new Compound {
Name = "COMP", Id = "COMP"
};
_observerSet = new ObserverSet {
Name = "OBS_SET", Id = "OBS_SET"
};
_protocol = new SimpleProtocol {
Name = "PROT", Id = "PROT"
};
_inductionProcess = new InductionProcess().WithName("Interaction process");
_compound.AddProcess(_inductionProcess);
_event = new PKSimEvent {
Name = "Event"
};
_population = new RandomPopulation()
{
Name = "POP"
};
_observedData = new DataRepository("OBS_ID").WithName("OBS");
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(_compound);
_project.AddBuildingBlock(_event);
_project.AddBuildingBlock(_population);
_project.AddBuildingBlock(_observerSet);
_project.AddObservedData(_observedData);
_simulationProperties = new SimulationProperties
{
ModelProperties = new ModelProperties
{
ModelConfiguration = new ModelConfiguration {
ModelName = "4Comp"
}
}
};
_interactionSelection = new InteractionSelection {
ProcessName = _inductionProcess.Name
};
_noInteractionSelection = new InteractionSelection {
MoleculeName = "CYP2D6"
};
_simulationProperties.InteractionProperties.AddInteraction(_interactionSelection);
_simulationProperties.InteractionProperties.AddInteraction(_noInteractionSelection);
_settings = new SimulationSettings();
_rootContainer = new Container().WithName("Sim");
_model = new OSPSuite.Core.Domain.Model {
Root = _rootContainer
};
_individualSimulation = new IndividualSimulation
{
Name = "S1",
Properties = _simulationProperties,
SimulationSettings = _settings,
Description = "Simulation Description",
Model = _model
};
_simulationTimeProfile = new SimulationTimeProfileChart();
_snapshotSimulationTimeProfile = new CurveChart();
_individualSimulation.AddAnalysis(_simulationTimeProfile);
A.CallTo(() => _curveChartMapper.MapToSnapshot(_simulationTimeProfile)).Returns(_snapshotSimulationTimeProfile);
_populationSimulation = new PopulationSimulation
{
Properties = _simulationProperties,
SimulationSettings = _settings,
Model = _model
};
_advancedParameterCollection = new AdvancedParameterCollection();
_populationSimulationAnalysisChart = new BoxWhiskerAnalysisChart();
_populationSimulation.SetAdvancedParameters(_advancedParameterCollection);
_populationSimulation.AddAnalysis(_populationSimulationAnalysisChart);
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual
});
_snapshotPopulationAnalysisChart = new Snapshots.PopulationAnalysisChart();
A.CallTo(() => _populationAnalysisChartMapper.MapToSnapshot(_populationSimulationAnalysisChart)).Returns(_snapshotPopulationAnalysisChart);
_snapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_interactionSelection)).Returns(_snapshotInteraction);
_snapshotInteraction.CompoundName = _compound.Name;
_snapshotInteraction.Name = _inductionProcess.Name;
_noSelectionSnapshotInteraction = new CompoundProcessSelection();
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noInteractionSelection)).Returns(_noSelectionSnapshotInteraction);
_noSelectionSnapshotInteraction.MoleculeName = _noInteractionSelection.MoleculeName;
_compoundProperties = new CompoundProperties();
_snapshotCompoundProperties = new Snapshots.CompoundProperties {
Name = _compound.Name
};
_individualSimulation.Properties.AddCompoundProperties(_compoundProperties);
_eventMapping = new EventMapping();
_individualSimulation.EventProperties.AddEventMapping(_eventMapping);
_observerSetMapping = new ObserverSetMapping();
_individualSimulation.ObserverSetProperties.AddObserverSetMapping(_observerSetMapping);
A.CallTo(() => _compoundPropertiesMapper.MapToSnapshot(_compoundProperties, _project)).Returns(_snapshotCompoundProperties);
_eventSelection = new EventSelection
{
Name = _event.Name,
};
_observerSetSelection = new ObserverSetSelection
{
Name = _observerSet.Name,
};
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
BuildingBlock = _individual,
Altered = true
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("CompTemplateId", PKSimBuildingBlockType.Compound)
{
BuildingBlock = _compound
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ProtTemplateId", PKSimBuildingBlockType.Protocol)
{
BuildingBlock = _protocol
});
_individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("ObserveSetTemplateId", PKSimBuildingBlockType.ObserverSet)
{
BuildingBlock = _observerSet
});
_populationSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("PopTemplateId", PKSimBuildingBlockType.Population)
{
BuildingBlock = _population
});
_individualSimulation.AddUsedObservedData(_observedData);
A.CallTo(() => _eventMappingMapper.MapToSnapshot(_eventMapping, _project)).Returns(_eventSelection);
A.CallTo(() => _observerSetMappingMapper.MapToSnapshot(_observerSetMapping, _project)).Returns(_observerSetSelection);
_outputSelectionSnapshot = new OutputSelections();
A.CallTo(() => _outputSelectionMapper.MapToSnapshot(_individualSimulation.OutputSelections)).Returns(_outputSelectionSnapshot);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotInteraction, _inductionProcess)).Returns(_interactionSelection);
return(_completed);
}
public Converter50To513(IModelPropertiesTask modelPropertiesTask, IDimensionConverter dimensionConverter)
{
_modelPropertiesTask = modelPropertiesTask;
_dimensionConverter = dimensionConverter;
}
public ModelPropertiesMapper(IModelPropertiesTask modelPropertiesTask, IBatchLogger batchLogger)
{
_modelPropertiesTask = modelPropertiesTask;
_batchLogger = batchLogger;
}