protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_advancedParameterFactory = A.Fake <IAdvancedParameterFactory>();
_logger = A.Fake <ILogger>();
_advancedParameter = new AdvancedParameter
{
DistributedParameter = DomainHelperForSpecs.NormalDistributedParameter(10, 5),
ParameterPath = "ParameterPath",
Name = "ParameterName"
};
_originalSeed = _advancedParameter.Seed;
sut = new AdvancedParameterMapper(_parameterMapper, _advancedParameterFactory, _entityPathResolver, _logger);
_meanSnapshot = new Parameter
{
Name = _advancedParameter.DistributedParameter.MeanParameter.Name,
};
_deviationSnapshot = new Parameter
{
Name = _advancedParameter.DistributedParameter.DeviationParameter.Name,
};
A.CallTo(() => _parameterMapper.MapToSnapshot(_advancedParameter.DistributedParameter.MeanParameter)).Returns(_meanSnapshot);
A.CallTo(() => _parameterMapper.MapToSnapshot(_advancedParameter.DistributedParameter.DeviationParameter)).Returns(_deviationSnapshot);
return(Task.FromResult(true));
}
protected override Task Context()
{
_qualificationStepRunnerFactory = A.Fake <IQualificationStepRunnerFactory>();
_logger = A.Fake <ILogger>();
sut = new QualiticationPlanRunner(_qualificationStepRunnerFactory, _logger);
return(_completed);
}
public LogWatcher(ILogger logger, LogWatcherOptions logWatcherOptions)
{
_logger = logger;
_logWatcherOptions = logWatcherOptions;
_fileSystemWatchers = new List <FileSystemWatcher>();
configureFileSystemWatcher(_logWatcherOptions.LogFile);
subscribe();
}
protected override Task Context()
{
_logger = A.Fake <ILogger>();
sut = new DescriptorConditionMapper(_logger);
_inContainer = new InContainerCondition("CONT");
_notInContainer = new NotInContainerCondition("NOT_CONT");
_matchAllCondition = new MatchAllCondition();
_notMatchAllCondition = new NotMatchTagCondition("NOT_MATCH");
_notMatchCondition = new MatchTagCondition("MATCH");
return(_completed);
}
protected override Task Context()
{
_calculationMethodRepository = A.Fake <ICalculationMethodRepository>();
_calculationMethodCategoryRepository = A.Fake <ICalculationMethodCategoryRepository>();
_logger = A.Fake <ILogger>();
sut = new CalculationMethodCacheMapper(_calculationMethodRepository, _calculationMethodCategoryRepository, _logger);
_singleCategory = new CalculationMethodCategory {
Name = "Multiple"
};
_multipleCategory = new CalculationMethodCategory {
Name = "Single"
};
_calculationMethodWithMultipleOptions = new CalculationMethod
{
Name = "CM1",
DisplayName = "CM1",
Category = _multipleCategory.Name
};
_calculationMethodWithSingleOption = new CalculationMethod
{
Name = "CM2",
DisplayName = "CM2",
Category = _singleCategory.Name
};
_anotherCalculationMethodInMultipleOptions = new CalculationMethod
{
Name = "Another CM",
Category = _multipleCategory.Name
};
A.CallTo(() => _calculationMethodRepository.All()).Returns(new [] { _calculationMethodWithMultipleOptions, _anotherCalculationMethodInMultipleOptions, _calculationMethodWithSingleOption, });
_singleCategory.Add(_calculationMethodWithSingleOption);
_multipleCategory.Add(_calculationMethodWithMultipleOptions);
_multipleCategory.Add(_anotherCalculationMethodInMultipleOptions);
_calculationMethodCache = new CalculationMethodCache();
_calculationMethodCache.AddCalculationMethod(_calculationMethodWithMultipleOptions);
_calculationMethodCache.AddCalculationMethod(_calculationMethodWithSingleOption);
A.CallTo(() => _calculationMethodCategoryRepository.FindBy(_singleCategory.Name)).Returns(_singleCategory);
A.CallTo(() => _calculationMethodCategoryRepository.FindBy(_multipleCategory.Name)).Returns(_multipleCategory);
return(Task.FromResult(true));
}
protected override Task Context()
{
_parameterIdentificationConfigurationMapper = A.Fake <ParameterIdentificationConfigurationMapper>();
_outputMappingMapper = A.Fake <OutputMappingMapper>();
_identificationParameterMapper = A.Fake <IdentificationParameterMapper>();
_parameterIdentificationAnalysisMapper = A.Fake <ParameterIdentificationAnalysisMapper>();
_objectBaseFactory = A.Fake <IObjectBaseFactory>();
_logger = A.Fake <ILogger>();
_project = new PKSimProject();
_simulation = new IndividualSimulation().WithName("S1");
_project.AddBuildingBlock(_simulation);
_parameterIdentification = new ModelParameterIdentification();
_snapshotParameterIndentificationConfiguration = new ParameterIdentificationConfiguration();
_snapshotOutputMapping = new Snapshots.OutputMapping();
_outputMapping = new OutputMapping();
_parameterIdentification.AddSimulation(_simulation);
_parameterIdentification.AddOutputMapping(_outputMapping);
_identificationParameter = new IdentificationParameter {
Name = "IP"
};
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_snapshotIdentificationParameter = new Snapshots.IdentificationParameter();
_snapshotParameterIdentificationAnalysis = new ParameterIdentificationAnalysis();
_parameterIdentificationAnalysis = A.Fake <ISimulationAnalysis>();
_parameterIdentification.AddAnalysis(_parameterIdentificationAnalysis);
sut = new ParameterIdentificationMapper(
_parameterIdentificationConfigurationMapper,
_outputMappingMapper,
_identificationParameterMapper,
_parameterIdentificationAnalysisMapper,
_objectBaseFactory,
_logger
);
A.CallTo(() => _parameterIdentificationConfigurationMapper.MapToSnapshot(_parameterIdentification.Configuration)).Returns(_snapshotParameterIndentificationConfiguration);
A.CallTo(() => _outputMappingMapper.MapToSnapshot(_outputMapping)).Returns(_snapshotOutputMapping);
A.CallTo(() => _identificationParameterMapper.MapToSnapshot(_identificationParameter)).Returns(_snapshotIdentificationParameter);
A.CallTo(() => _parameterIdentificationAnalysisMapper.MapToSnapshot(_parameterIdentificationAnalysis)).Returns(_snapshotParameterIdentificationAnalysis);
return(_completed);
}
protected override Task Context()
{
_parameterIdentificationEngineFactory = A.Fake <IParameterIdentificationEngineFactory>();
_transferOptimizedParametersToSimulationsTask = A.Fake <ITransferOptimizedParametersToSimulationsTask>();
_logger = A.Fake <ILogger>();
sut = new RunParameterIdentificationQualificationStepRunner(_parameterIdentificationEngineFactory, _transferOptimizedParametersToSimulationsTask, _logger);
_parameterIdentification = new ParameterIdentification();
_runParameterIdentificationStep = new RunParameterIdentificationQualificationStep
{
ParameterIdentification = _parameterIdentification
};
_parameterIdentificationEngine = A.Fake <IParameterIdentificationEngine>();
A.CallTo(() => _parameterIdentificationEngineFactory.Create()).Returns(_parameterIdentificationEngine);
return(_completed);
}
protected override Task Context()
{
_logger = A.Fake <ILogger>();
_workspacePersitor = A.Fake <IWorkspacePersistor>();
_workspace = A.Fake <IWorkspace>();
_simulationExporter = A.Fake <ISimulationExporter>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
sut = new ExportSimulationRunner(_logger, _workspacePersitor, _workspace, _simulationExporter, _lazyLoadTask);
_project = new PKSimProject();
_simulation1 = createSimulationWithResults(_simulation1Name);
_simulation2 = createSimulationWithResults(_simulation2Name);
A.CallTo(() => _workspacePersitor.LoadSession(_workspace, _projectFileName)).Invokes(x => { _workspace.Project = _project; });
return(_completed);
}
protected override Task Context()
{
_entitiesInContainerRetriever = A.Fake <IEntitiesInContainerRetriever>();
_logger = A.Fake <ILogger>();
sut = new OutputSelectionsMapper(_entitiesInContainerRetriever, _logger);
_quantitySelection1 = new QuantitySelection("PATH1", QuantityType.Drug);
_quantitySelection2 = new QuantitySelection("PATH2", QuantityType.Observer);
_outputSelections = new OutputSelections();
_outputSelections.AddOutput(_quantitySelection1);
_outputSelections.AddOutput(_quantitySelection2);
_simulation = new IndividualSimulation();
_allQuantities = new PathCacheForSpecs <IQuantity>();
A.CallTo(() => _entitiesInContainerRetriever.QuantitiesFrom(_simulation)).Returns(_allQuantities);
return(Task.FromResult(true));
}
protected override Task Context()
{
_tableFormulaMapper = A.Fake <TableFormulaMapper>();
_valueOriginMapper = A.Fake <ValueOriginMapper>();
_entityPathResolver = A.Fake <IEntityPathResolver>();
_logger = A.Fake <ILogger>();
sut = new ParameterMapper(_tableFormulaMapper, _valueOriginMapper, _entityPathResolver, _logger);
//5 mm is the value
_parameter = DomainHelperForSpecs.ConstantParameterWithValue(10)
.WithName("P1")
.WithDescription("P1 description")
.WithDimension(DomainHelperForSpecs.LengthDimensionForSpecs());
_parameter.DisplayUnit = _parameter.Dimension.Unit("mm");
_snapshotValueOrigin = new ValueOrigin();
A.CallTo(() => _valueOriginMapper.MapToSnapshot(_parameter.ValueOrigin)).Returns(_snapshotValueOrigin);
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);
}
protected override Task Context()
{
_calculationMethodCacheMapper = A.Fake <CalculationMethodCacheMapper>();
_processMappingMapper = A.Fake <ProcessMappingMapper>();
_logger = A.Fake <ILogger>();
_project = new PKSimProject();
_calculationMethodSnapshot = new CalculationMethodCache();
sut = new CompoundPropertiesMapper(_calculationMethodCacheMapper, _processMappingMapper, _logger);
_compoundGroupSelectionOneAlternative = new CompoundGroupSelection
{
AlternativeName = "ALT1",
GroupName = "ALTERNATIVE_GROUP_1"
};
_compoundGroupSelectionTwoAlternatives = new CompoundGroupSelection
{
AlternativeName = "ALT2",
GroupName = "ALTERNATIVE_GROUP_2"
};
_compound = new Compound
{
Name = "COMP",
};
_protocol = new SimpleProtocol
{
Name = "PROTOCOL"
};
_parameterAlternativeGroupWithOneAlternative = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionOneAlternative.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives = new ParameterAlternativeGroup {
Name = _compoundGroupSelectionTwoAlternatives.GroupName
};
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT1"
});
_parameterAlternativeGroupWithTwoAlternatives.AddAlternative(new ParameterAlternative {
Name = "ALT2"
});
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithOneAlternative);
_compound.AddParameterAlternativeGroup(_parameterAlternativeGroupWithTwoAlternatives);
_compoundProperties = new Model.CompoundProperties();
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionOneAlternative);
_compoundProperties.AddCompoundGroupSelection(_compoundGroupSelectionTwoAlternatives);
_compoundProperties.Compound = _compound;
_enzymaticProcess = new EnzymaticProcess {
Name = "EnzymaticProcess"
};
_anotherEnzymaticProcess = new EnzymaticProcess {
Name = "AnotherEnzymaticProcess", MoleculeName = "CYP3A4"
};
_specificBindingProcess = new SpecificBindingPartialProcess {
Name = "SpecificBinding"
};
_gfrTransportProcess = new SystemicProcess {
Name = "Transport", SystemicProcessType = SystemicProcessTypes.GFR
};
_hepaticEnzymaticProcess = new SystemicProcess {
Name = "Plasma Clearance", SystemicProcessType = SystemicProcessTypes.Hepatic
};
_compound.AddProcess(_enzymaticProcess);
_compound.AddProcess(_specificBindingProcess);
_compound.AddProcess(_gfrTransportProcess);
_compound.AddProcess(_hepaticEnzymaticProcess);
_enzymaticPartialProcessSelection = new EnzymaticProcessSelection {
ProcessName = _enzymaticProcess.Name
};
_noEnzymaticSystemicProcessSelection = new SystemicProcessSelection {
ProcessType = SystemicProcessTypes.Hepatic
};
_specificBindingPartialProcessSelection = new ProcessSelection {
ProcessName = _specificBindingProcess.Name
};
_transportSystemicProcessSelection = new SystemicProcessSelection {
ProcessName = _gfrTransportProcess.Name, ProcessType = _gfrTransportProcess.SystemicProcessType,
};
_noEnzymaticPartialProcessSelection = new EnzymaticProcessSelection {
MoleculeName = _anotherEnzymaticProcess.MoleculeName
};
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_enzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddPartialProcessSelection(_noEnzymaticPartialProcessSelection);
_compoundProperties.Processes.MetabolizationSelection.AddSystemicProcessSelection(_noEnzymaticSystemicProcessSelection);
_compoundProperties.Processes.SpecificBindingSelection.AddPartialProcessSelection(_specificBindingPartialProcessSelection);
_compoundProperties.Processes.TransportAndExcretionSelection.AddSystemicProcessSelection(_transportSystemicProcessSelection);
_snapshotProcess1 = new CompoundProcessSelection {
Name = _enzymaticPartialProcessSelection.ProcessName
};
_snapshotProcess2 = new CompoundProcessSelection {
Name = _specificBindingPartialProcessSelection.ProcessName
};
_snapshotProcess3 = new CompoundProcessSelection {
Name = _transportSystemicProcessSelection.ProcessName
};
_snapshotProcess4 = new CompoundProcessSelection {
SystemicProcessType = _noEnzymaticSystemicProcessSelection.ProcessType.SystemicProcessTypeId.ToString()
};
_snapshotProcess5 = new CompoundProcessSelection {
MoleculeName = _noEnzymaticPartialProcessSelection.MoleculeName
};
_formulation = new Formulation
{
Id = "123456"
};
_compoundProperties.ProtocolProperties.Protocol = _protocol;
_compoundProperties.ProtocolProperties.AddFormulationMapping(new FormulationMapping
{
FormulationKey = "F1",
TemplateFormulationId = _formulation.Id
});
_project.AddBuildingBlock(_formulation);
A.CallTo(() => _calculationMethodCacheMapper.MapToSnapshot(_compoundProperties.CalculationMethodCache)).Returns(_calculationMethodSnapshot);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_enzymaticPartialProcessSelection)).Returns(_snapshotProcess1);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_specificBindingPartialProcessSelection)).Returns(_snapshotProcess2);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_transportSystemicProcessSelection)).Returns(_snapshotProcess3);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticSystemicProcessSelection)).Returns(_snapshotProcess4);
A.CallTo(() => _processMappingMapper.MapToSnapshot(_noEnzymaticPartialProcessSelection)).Returns(_snapshotProcess5);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess1, _enzymaticProcess)).Returns(_enzymaticPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess2, _specificBindingProcess)).Returns(_specificBindingPartialProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess3, _gfrTransportProcess)).Returns(_transportSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess4, A <NotSelectedSystemicProcess> ._)).Returns(_noEnzymaticSystemicProcessSelection);
A.CallTo(() => _processMappingMapper.MapToModel(_snapshotProcess5, A <EnzymaticProcess> ._)).Returns(_noEnzymaticPartialProcessSelection);
return(_completed);
}
