protected override Task Context()
{
_classificationMapper = A.Fake <ClassificationMapper>();
_snapshotMapper = A.Fake <ISnapshotMapper>();
_executionContext = A.Fake <IExecutionContext>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_simulationMapper = A.Fake <SimulationMapper>();
_simulationComparisonMapper = A.Fake <SimulationComparisonMapper>();
_parameterIdentificationMapper = A.Fake <ParameterIdentificationMapper>();
_classificationSnapshotTask = A.Fake <IClassificationSnapshotTask>();
_qualificationPlanMapper = A.Fake <QualificationPlanMapper>();
_creationMetaDataFactory = A.Fake <ICreationMetaDataFactory>();
_logger = A.Fake <ILogger>();
sut = new ProjectMapper(
_simulationMapper,
_simulationComparisonMapper,
_parameterIdentificationMapper,
_qualificationPlanMapper,
_executionContext,
_classificationSnapshotTask,
_lazyLoadTask,
_creationMetaDataFactory,
_logger);
A.CallTo(() => _executionContext.Resolve <ISnapshotMapper>()).Returns(_snapshotMapper);
_individual = new Individual().WithName("IND");
_compound = new Compound().WithName("COMP");
_event = new PKSimEvent().WithName("EVENT");
_formulation = new Formulation().WithName("FORM");
_protocol = new SimpleProtocol().WithName("PROTO");
_population = new RandomPopulation().WithName("POP");
_observerSet = new ObserverSet().WithName("OBS_SET");
_observedData = new DataRepository().WithName("OD");
_parameterIdentification = new OSPSuite.Core.Domain.ParameterIdentifications.ParameterIdentification().WithName("PI").WithId("PI_ID");
_classifiableObservedData = new ClassifiableObservedData {
Subject = _observedData
};
_classification = new Classification {
ClassificationType = ClassificationType.ObservedData
}.WithName("OD Classification");
_simulationComparison = new IndividualSimulationComparison().WithName("COMP").WithId("SimComp");
_simulation = new IndividualSimulation().WithName("IND_SIM").WithId("IndSim");
_qualificationPlan = new QualificationPlan().WithName("QP").WithId("QP_ID");
_project = new PKSimProject();
_project.AddBuildingBlock(_individual);
_project.AddBuildingBlock(_compound);
_project.AddBuildingBlock(_event);
_project.AddBuildingBlock(_formulation);
_project.AddBuildingBlock(_protocol);
_project.AddBuildingBlock(_population);
_project.AddBuildingBlock(_observerSet);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_simulation);
_project.AddClassifiable(_classifiableObservedData);
_project.AddClassification(_classification);
_project.AddSimulationComparison(_simulationComparison);
_project.AddParameterIdentification(_parameterIdentification);
_project.AddQualificationPlan(_qualificationPlan);
_compoundSnapshot = new Snapshots.Compound();
_individualSnapshot = new Snapshots.Individual();
_eventSnapshot = new Event();
_observerSetSnapshot = new Snapshots.ObserverSet();
_formulationSnapshot = new Snapshots.Formulation();
_protocolSnapshot = new Snapshots.Protocol();
_populationSnapshot = new Snapshots.Population();
_observedDataSnapshot = new Snapshots.DataRepository();
_parameterIdentificationSnapshot = new ParameterIdentification();
_observedDataClassificationSnapshot = new Snapshots.Classification();
_simulationComparisonSnapshot = new SimulationComparison();
_simulationClassificationSnapshot = new Snapshots.Classification();
_comparisonClassificationSnapshot = new Snapshots.Classification();
_parameterIdentificationClassificationSnapshot = new Snapshots.Classification();
_qualificationPlanClassificationSnapshot = new Snapshots.Classification();
_qualificationPlanSnapshot = new Snapshots.QualificationPlan();
_simulationSnapshot = new Simulation();
A.CallTo(() => _snapshotMapper.MapToSnapshot(_compound)).Returns(_compoundSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_individual)).Returns(_individualSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_event)).Returns(_eventSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_formulation)).Returns(_formulationSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_protocol)).Returns(_protocolSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_population)).Returns(_populationSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_observedData)).Returns(_observedDataSnapshot);
A.CallTo(() => _snapshotMapper.MapToSnapshot(_observerSet)).Returns(_observerSetSnapshot);
A.CallTo(() => _simulationMapper.MapToSnapshot(_simulation, _project)).Returns(_simulationSnapshot);
A.CallTo(() => _simulationComparisonMapper.MapToSnapshot(_simulationComparison)).Returns(_simulationComparisonSnapshot);
A.CallTo(() => _parameterIdentificationMapper.MapToSnapshot(_parameterIdentification, _project)).Returns(_parameterIdentificationSnapshot);
A.CallTo(() => _qualificationPlanMapper.MapToSnapshot(_qualificationPlan)).Returns(_qualificationPlanSnapshot);
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableObservedData>(_project)).Returns(new[] { _observedDataClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableSimulation>(_project)).Returns(new[] { _simulationClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableComparison>(_project)).Returns(new[] { _comparisonClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableParameterIdentification>(_project)).Returns(new[] { _parameterIdentificationClassificationSnapshot });
A.CallTo(() => _classificationSnapshotTask.MapClassificationsToSnapshots <ClassifiableQualificationPlan>(_project)).Returns(new[] { _qualificationPlanClassificationSnapshot });
return(_completed);
}
public override void GlobalContext()
{
base.GlobalContext();
_observedData = DomainHelperForSpecs.ObservedData();
_sim1 = new IndividualSimulation
{
Id = "Sim1",
Name = "Sim1",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim1.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_sim2 = new IndividualSimulation
{
Id = "Sim2",
Name = "Sim2",
IsLoaded = true,
Model = new Model {
Root = new Container()
}
};
_sim2.Model.Root.Add(new Container {
new Parameter().WithName("P")
}.WithName("Liver"));
_objectBaseRepository = IoC.Resolve <IWithIdRepository>();
var workspace = IoC.Resolve <ICoreWorkspace>();
_project = IoC.Resolve <PKSimProject>();
workspace.Project = _project;
_objectBaseRepository.Register(_sim1);
_objectBaseRepository.Register(_sim2);
_project.AddObservedData(_observedData);
_project.AddBuildingBlock(_sim1);
_project.AddBuildingBlock(_sim2);
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.AddSimulation(_sim1);
_parameterIdentification.AddSimulation(_sim2);
_outputMapping = new OutputMapping
{
WeightedObservedData = new WeightedObservedData(_observedData),
OutputSelection = new SimulationQuantitySelection(_sim1, new QuantitySelection("A|B", QuantityType.Metabolite)),
Weight = 5,
Scaling = Scalings.Log
};
_outputMapping.WeightedObservedData.Weights[1] = 10;
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = DomainHelperForSpecs.IdentificationParameter(min: 1, max: 10, startValue: 5);
_parameterSelection1 = new ParameterSelection(_sim1, new QuantitySelection("Liver|P", QuantityType.Parameter));
_parameterSelection2 = new ParameterSelection(_sim2, new QuantitySelection("Liver|P", QuantityType.Parameter));
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_identificationParameter.Scaling = Scalings.Linear;
_parameterIdentification.Configuration.AlgorithmProperties = new OptimizationAlgorithmProperties("AA");
_parameterIdentification.AlgorithmProperties.Add(new ExtendedProperty <double> {
Name = "Toto", Value = 5
});
_runResult = new ParameterIdentificationRunResult();
_parameterIdentification.AddResult(_runResult);
_parameterIdentification.AddAnalysis(new ParameterIdentificationPredictedVsObservedChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationTimeProfileChart());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualHistogram());
_parameterIdentification.AddAnalysis(new ParameterIdentificationResidualVsTimeChart());
GlobalBecause();
}
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 <IOSPSuiteLogger>();
_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 = "IndTemplateId"
};
_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", Id = "PopTemplateId"
};
_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, A <CompoundProcessSnapshotContext> .That.Matches(x => x.Process == _inductionProcess))).Returns(_interactionSelection);
return(_completed);
}