public void AddDataRepository(ModelDataRepository dataRepository)
{
if (dataRepository != null)
{
_dataRepositories.Add(dataRepository);
}
}
protected override async Task Context()
{
await base.Context();
_runOptions.Validate = true;
_expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME);
_expectedObsDataPath = _qualificationConfiguration.ObservedDataFolder;
DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath);
DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s;
_observedData = DomainHelperForSpecs.ObservedData().WithName("OBS");
_project.AddObservedData(_observedData);
}
protected override async Task Context()
{
await base.Context();
_snapshot = await sut.MapToSnapshot(_individualSimulation, _project);
var individualSimulation = new IndividualSimulation
{
Properties = _simulationProperties,
SimulationSettings = _settings,
Model = _model
};
individualSimulation.AddUsedBuildingBlock(new UsedBuildingBlock("IndTemplateId", PKSimBuildingBlockType.Individual)
{
Name = _individual.Name,
BuildingBlock = _individual
});
_modelProperties = new ModelProperties();
A.CallTo(() => _modelPropertiesTask.DefaultFor(_individual.OriginData, _snapshot.Model)).Returns(_modelProperties);
A.CallTo(() => _simulationFactory.CreateFrom(_individual, A <IReadOnlyList <Compound> > ._, _modelProperties, null)).Returns(individualSimulation);
_outputSelection = new OSPSuite.Core.Domain.OutputSelections();
_outputSelection.AddOutput(new QuantitySelection("PATH", QuantityType.BaseGrid));
A.CallTo(() => _outputSelectionMapper.MapToModel(_snapshot.OutputSelections, individualSimulation)).Returns(_outputSelection);
_solver = new SolverSettings();
A.CallTo(() => _solverSettingsMapper.MapToModel(_snapshot.Solver)).Returns(_solver);
_outputSchema = new OutputSchema();
A.CallTo(() => _outputSchemaMapper.MapToModel(_snapshot.OutputSchema)).Returns(_outputSchema);
A.CallTo(() => _curveChartMapper.MapToModel(_snapshotSimulationTimeProfile, A <SimulationAnalysisContext> ._))
.Invokes(x => _context = x.GetArgument <SimulationAnalysisContext>(1))
.Returns(_simulationTimeProfile);
//ensure that run will be performed
_snapshot.HasResults = true;
_calculatedDataRepository = DomainHelperForSpecs.ObservedData("Calculated");
A.CallTo(() => _simulationRunner.RunSimulation(individualSimulation, A <SimulationRunOptions> ._))
.Invokes(x => { individualSimulation.DataRepository = _calculatedDataRepository; });
A.CallTo(() => _eventMappingMapper.MapToModel(_eventSelection, _project)).Returns(_eventMapping);
A.CallTo(() => _observerSetMappingMapper.MapToModel(_observerSetSelection, _project)).Returns(_observerSetMapping);
}
protected override Task Context()
{
_parameterIdentificationAnalysisChartMapper = A.Fake <ParameterIdentificationAnalysisChartMapper>();
_dataRepositoryMapper = A.Fake <DataRepositoryMapper>();
_idGenerator = A.Fake <IIdGenerator>();
sut = new ParameterIdentificationAnalysisMapper(_parameterIdentificationAnalysisChartMapper, _dataRepositoryMapper, _idGenerator);
_parameterIdentificationAnalysis = new T().WithName("Chart");
_chartSnapshot = new CurveChart();
_localRepository = DomainHelperForSpecs.ObservedData();
_snapshotLocalRepository = new Snapshots.DataRepository();
A.CallTo(() => _dataRepositoryMapper.MapToSnapshot(_localRepository)).Returns(_snapshotLocalRepository);
_parameterIdentification = new ParameterIdentification();
_project = new PKSimProject();
_parameterIdentificationContext = new ParameterIdentificationContext(_parameterIdentification, _project);
return(_completed);
}
protected override async Task Context()
{
await base.Context();
_expectedOutputPath = Path.Combine(_qualificationConfiguration.OutputFolder, PROJECT_NAME);
DirectoryHelper.DirectoryExists = s => string.Equals(s, _expectedOutputPath);
DirectoryHelper.DeleteDirectory = (s, b) => _deletedDirectory = s;
_simulationName = "S1";
_simulation = new Simulation {
Name = _simulationName
};
_individualSimulation = new IndividualSimulation {
Name = _simulationName
};
_input = new Input {
Project = PROJECT_NAME, Name = _simulationName, SectionId = 2, Type = PKSimBuildingBlockType.Simulation, SectionLevel = 5
};
_expectedSimulationPath = Path.Combine(_expectedOutputPath, _simulationName);
_simulationExport = new SimulationMapping {
Project = PROJECT_NAME, Simulation = _simulationName, Path = _expectedSimulationPath
};
_simulationExports = new[] { _simulationExport };
A.CallTo(() => _exportSimulationRunner.ExportSimulationsIn(_project, A <ExportRunOptions> ._))
.Invokes(x => _exportOptions = x.GetArgument <ExportRunOptions>(1))
.Returns(_simulationExports);
_observedData = DomainHelperForSpecs.ObservedData().WithName("OBS");
_project.AddObservedData(_observedData);
_projectSnapshot.Simulations = new[] { _simulation };
_expectedObservedDataXlsFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.XLSX_EXTENSION}");
_expectedObservedDataCsvFullPath = Path.Combine(_qualificationConfiguration.ObservedDataFolder, $"{_observedData.Name}{Constants.Filter.CSV_EXTENSION}");
_expectedInputFullPath = Path.Combine(_qualificationConfiguration.InputsFolder, PROJECT_NAME, PKSimBuildingBlockType.Simulation.ToString(), $"{_simulationName}{CoreConstants.Filter.MARKDOWN_EXTENSION}");
A.CallTo(() => _jsonSerializer.Serialize(A <QualificationMapping> ._, _qualificationConfiguration.MappingFile))
.Invokes(x => _mapping = x.GetArgument <QualificationMapping>(0));
_project.AddBuildingBlock(_individualSimulation);
_qualificationConfiguration.Inputs = new[] { _input };
_qualificationConfiguration.Simulations = new[] { _simulationName, };
_runOptions.Run = true;
}
protected override Task Context()
{
_curveOptionsMapper = A.Fake <CurveOptionsMapper>();
sut = new ObservedDataCollectionMappper(_curveOptionsMapper);
_observedDataRepository = DomainHelperForSpecs.ObservedData("ID").WithName("ObsData");
_observedDataCollection = new Model.PopulationAnalyses.ObservedDataCollection();
_observedDataCollection.ApplyGroupingToObservedData = true;
_observedDataCollection.AddObservedData(_observedDataRepository);
_firstObservedDataColumn = _observedDataRepository.ObservationColumns().First();
_observedDataCurveOptions = new ObservedDataCurveOptions
{
Caption = "Obs Data Caption",
ColumnId = _firstObservedDataColumn.Id
};
_observedDataCollection.AddCurveOptions(_observedDataCurveOptions);
_snapshotCurveOptions = new CurveOptions();
A.CallTo(() => _curveOptionsMapper.MapToSnapshot(_observedDataCurveOptions.CurveOptions)).Returns(_snapshotCurveOptions);
return(_completed);
}
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);
}
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");
_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.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();
_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(() => _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);
}
private void addObservedDataToProject(ModelProject project, ModelDataRepository repository)
{
addClassifiableToProject <ClassifiableObservedData, ModelDataRepository>(project, repository, project.AddObservedData);
}
