public ObserverMapper(
DescriptorConditionMapper descriptorConditionMapper,
ExplicitFormulaMapper explicitFormulaMapper,
MoleculeListMapper moleculeListMapper,
IObjectBaseFactory objectBaseFactory,
IDimensionRepository dimensionRepository,
IOSPSuiteLogger logger)
{
_descriptorConditionMapper = descriptorConditionMapper;
_explicitFormulaMapper = explicitFormulaMapper;
_moleculeListMapper = moleculeListMapper;
_objectBaseFactory = objectBaseFactory;
_dimensionRepository = dimensionRepository;
_logger = logger;
}
public ParameterIdentificationMapper(
ParameterIdentificationConfigurationMapper parameterIdentificationConfigurationMapper,
OutputMappingMapper outputMappingMapper,
IdentificationParameterMapper identificationParameterMapper,
ParameterIdentificationAnalysisMapper parameterIdentificationAnalysisMapper,
IObjectBaseFactory objectBaseFactory,
IOSPSuiteLogger logger
)
{
_parameterIdentificationConfigurationMapper = parameterIdentificationConfigurationMapper;
_outputMappingMapper = outputMappingMapper;
_identificationParameterMapper = identificationParameterMapper;
_parameterIdentificationAnalysisMapper = parameterIdentificationAnalysisMapper;
_objectBaseFactory = objectBaseFactory;
_logger = logger;
}
public LoadSimulationFromSnapshotPresenter(
ILoadFromSnapshotView view,
ILogPresenter logPresenter,
ISnapshotTask snapshotTask,
IDialogCreator dialogCreator,
IObjectTypeResolver objectTypeResolver,
IOSPSuiteLogger logger,
IEventPublisher eventPublisher,
SimulationMapper simulationMapper,
IPKSimProjectRetriever projectRetriever,
IStartOptions startOptions
) : base(view, logPresenter, snapshotTask, dialogCreator, objectTypeResolver, logger, eventPublisher, startOptions)
{
_simulationMapper = simulationMapper;
_projectRetriever = projectRetriever;
}
protected override Task Context()
{
_snapshotTask = A.Fake <ISnapshotTask>();
_jsonSerializer = A.Fake <IJsonSerializer>();
_workspace = A.Fake <ICoreWorkspace>();
_workspacePersistor = A.Fake <IWorkspacePersistor>();
_exportSimulationRunner = A.Fake <IExportSimulationRunner>();
_logger = A.Fake <IOSPSuiteLogger>();
_dataRepositoryTask = A.Fake <IDataRepositoryExportTask>();
_markdownReporterTask = A.Fake <IMarkdownReporterTask>();
sut = new QualificationRunner(_snapshotTask, _jsonSerializer, _workspace, _workspacePersistor, _exportSimulationRunner, _dataRepositoryTask, _markdownReporterTask, _logger);
_runOptions = new QualificationRunOptions();
_qualificationConfiguration = new QualifcationConfiguration();
return(_completed);
}
protected override Task Context()
{
_parameterIdentificationEngineFactory = A.Fake <IParameterIdentificationEngineFactory>();
_transferOptimizedParametersToSimulationsTask = A.Fake <ITransferOptimizedParametersToSimulationsTask>();
_logger = A.Fake <IOSPSuiteLogger>();
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);
}
public SnapshotRunPresenter(ISnapshotRunView view,
SnapshotRunner batchRunner,
IDialogCreator dialogCreator,
ILogPresenter logPresenter,
IOSPSuiteLogger batchLogger,
ISingleFolderSnapshotPresenter singleFolderSnapshotPresenter,
IFolderListSnapshotPresenter folderListSnapshotPresenter) : base(view, batchRunner, dialogCreator, logPresenter, batchLogger)
{
_singleFolderSnapshotPresenter = singleFolderSnapshotPresenter;
_folderListSnapshotPresenter = folderListSnapshotPresenter;
AddSubPresenters(_singleFolderSnapshotPresenter, _folderListSnapshotPresenter);
_view.AddSingleFolderView(_singleFolderSnapshotPresenter.View);
_view.AddFolderListView(_folderListSnapshotPresenter.View);
selectSnapshotPresenter(_singleFolderSnapshotPresenter);
_singleFolderSnapshotPresenter.StatusChanged += (o, e) => updateView();
_folderListSnapshotPresenter.StatusChanged += (o, e) => updateView();
}
public CompoundProcessMapper(
ParameterMapper parameterMapper,
IRepresentationInfoRepository representationInfoRepository,
ICompoundProcessRepository compoundProcessRepository,
ICloner cloner,
ISpeciesRepository speciesRepository,
ICompoundProcessTask compoundProcessTask,
IOSPSuiteLogger logger
) : base(parameterMapper)
{
_representationInfoRepository = representationInfoRepository;
_compoundProcessRepository = compoundProcessRepository;
_cloner = cloner;
_speciesRepository = speciesRepository;
_compoundProcessTask = compoundProcessTask;
_logger = logger;
}
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,
IOSPSuiteLogger 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;
}
public static void AddException(this IOSPSuiteLogger logger, Exception exception, string categoryName = null)
{
//Info message only => Should be shown as warning in log
if (exception.IsInfoException())
{
logger.AddWarning(exception.ExceptionMessage(addContactSupportInfo: false), categoryName);
}
// Not an info message but an exception thrown by the suite. Error without stack trace
else if (exception.IsOSPSuiteException())
{
logger.AddError((exception.ExceptionMessage(addContactSupportInfo: false)), categoryName);
}
// this is bad => Stack trace
else
{
logger.AddError(exception.ExceptionMessageWithStackTrace(false), categoryName);
}
}
public QualificationRunner(ISnapshotTask snapshotTask,
IJsonSerializer jsonSerializer,
ICoreWorkspace workspace,
IWorkspacePersistor workspacePersistor,
IExportSimulationRunner exportSimulationRunner,
IDataRepositoryExportTask dataRepositoryExportTask,
IMarkdownReporterTask markdownReporterTask,
IOSPSuiteLogger logger
)
{
_snapshotTask = snapshotTask;
_jsonSerializer = jsonSerializer;
_workspace = workspace;
_workspacePersistor = workspacePersistor;
_logger = logger;
_exportSimulationRunner = exportSimulationRunner;
_dataRepositoryExportTask = dataRepositoryExportTask;
_markdownReporterTask = markdownReporterTask;
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_identificationParameterFactory = A.Fake <IIdentificationParameterFactory>();
_logger = A.Fake <IOSPSuiteLogger>();
_identificationParameterTask = A.Fake <IIdentificationParameterTask>();
sut = new IdentificationParameterMapper(_parameterMapper, _identificationParameterFactory, _identificationParameterTask, _logger);
_identificationParameter = new IdentificationParameter
{
IsFixed = true,
UseAsFactor = true,
Scaling = Scalings.Linear
};
_startValueParameter = DomainHelperForSpecs.ConstantParameterWithValue().WithName(Constants.Parameters.START_VALUE);
_identificationParameter.Add(_startValueParameter);
_identificationParameter.Name = "PARAM";
_parameter1 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P1");
_parameter2 = DomainHelperForSpecs.ConstantParameterWithValue().WithName("P2");
_simulation = A.Fake <Simulation>().WithName("S");
_simulation.Model.Root = new Container {
_parameter1, _parameter2
};
_identificationParameter.Scaling = Scalings.Linear;
_parameterSelection1 = new ParameterSelection(_simulation, _parameter1.Name);
_parameterSelection2 = new ParameterSelection(_simulation, _parameter2.Name);
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_snapshotStartValueParameter = new Parameter();
A.CallTo(() => _parameterMapper.MapToSnapshot(_startValueParameter)).Returns(_snapshotStartValueParameter);
_project = new PKSimProject();
_project.AddBuildingBlock(_simulation);
_snapshotContext = new SnapshotContext(_project, ProjectVersions.Current);
_parameterIdentification = new ParameterIdentification();
_parameterIdentificationContext = new ParameterIdentificationContext(_parameterIdentification, _snapshotContext);
return(_completed);
}
protected override void Context()
{
_view = A.Fake <ILoadFromSnapshotView>();
_snapshotTask = A.Fake <ISnapshotTask>();
_dialogCreator = A.Fake <IDialogCreator>();
_objectTypeResolver = A.Fake <IObjectTypeResolver>();
_logger = A.Fake <IOSPSuiteLogger>();
_eventPublisher = A.Fake <IEventPublisher>();
_logPresenter = A.Fake <ILogPresenter>();
_startOptions = A.Fake <IStartOptions>();
A.CallTo(() => _view.BindTo(A <LoadFromSnapshotDTO> ._))
.Invokes(x => _loadFromSnapshotDTO = x.GetArgument <LoadFromSnapshotDTO>(0));
A.CallTo(() => _logPresenter.CanClose).Returns(true);
A.CallTo(() => _objectTypeResolver.TypeFor <Individual>()).Returns(_objectType);
sut = new LoadFromSnapshotPresenter <Individual>(_view, _logPresenter, _snapshotTask, _dialogCreator, _objectTypeResolver, _logger, _eventPublisher, _startOptions);
}
protected override Task Context()
{
_logger = A.Fake <IOSPSuiteLogger>();
_workspacePersistor = A.Fake <IWorkspacePersistor>();
_workspace = A.Fake <ICoreWorkspace>();
_simulationExporter = A.Fake <ISimulationExporter>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
sut = new ExportSimulationRunner(_logger, _workspacePersistor, _workspace, _simulationExporter, _lazyLoadTask);
_project = new PKSimProject {
Name = _projectName
};
_simulation1 = createSimulationWithResults(_simulation1Name);
_simulation2 = createSimulationWithResults(_simulation2Name);
A.CallTo(() => _workspacePersistor.LoadSession(_workspace, _projectFileName)).Invokes(x => { _workspace.Project = _project; });
return(_completed);
}
protected override Task Context()
{
_entitiesInContainerRetriever = A.Fake <IEntitiesInContainerRetriever>();
_logger = A.Fake <IOSPSuiteLogger>();
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 <IOSPSuiteLogger>();
_containerTask = new ContainerTaskForSpecs();
sut = new ParameterMapper(_tableFormulaMapper, _valueOriginMapper, _entityPathResolver, _logger, _containerTask);
//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()
{
_parameterMapper = A.Fake <ParameterMapper>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new ExpressionContainerMapper(_parameterMapper, _logger);
_relativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_moleculeExpressionContainer = new MoleculeExpressionContainer().WithName("EXP");
_moleculeExpressionContainer.Add(_relativeExpressionParameter);
_transporterRelativeExpressionParameter =
DomainHelperForSpecs.ConstantParameterWithValue(0, isDefault: true).WithName(CoreConstants.Parameters.REL_EXP);
_transporterExpressionContainer = new TransporterExpressionContainer().WithName("TRANS");
_transporterExpressionContainer.TransportDirection = TransportDirectionId.InfluxInterstitialToIntracellular;
_bloodCellsExpressionContainer = new TransporterExpressionContainer().WithName(CoreConstants.Compartment.BLOOD_CELLS);
_bloodCellsExpressionContainer.TransportDirection = TransportDirectionId.BiDirectionalBloodCellsPlasma;
_transporterExpressionContainer.Add(_transporterRelativeExpressionParameter);
_individual = new Individual {
OriginData = new OriginData {
Species = new Species().WithName("Human")
}
};
_expressionContainerMapperContext = new ExpressionContainerMapperContext(new SnapshotContext())
{
};
_enzyme = new IndividualEnzyme {
_moleculeExpressionContainer
};
_transporter = new IndividualTransporter {
_transporterExpressionContainer, _bloodCellsExpressionContainer
};
return(_completed);
}
public LoadFromSnapshotPresenter(
ILoadFromSnapshotView view,
ILogPresenter logPresenter,
ISnapshotTask snapshotTask,
IDialogCreator dialogCreator,
IObjectTypeResolver objectTypeResolver,
IOSPSuiteLogger logger,
IEventPublisher eventPublisher,
IStartOptions startOptions) : base(view)
{
_snapshotTask = snapshotTask;
_dialogCreator = dialogCreator;
_objectTypeResolver = objectTypeResolver;
_logger = logger;
_logPresenter = logPresenter;
_eventPublisher = eventPublisher;
AddSubPresenters(_logPresenter);
_view.Caption = PKSimConstants.UI.LoadObjectFromSnapshot(typeToLoad);
_view.AddLogView(_logPresenter.BaseView);
_view.BindTo(_loadFromSnapshotDTO);
_view.RunSimulationsSwitchVisible = startOptions.IsDeveloperMode;
}
public ProjectMapper(
SimulationMapper simulationMapper,
SimulationComparisonMapper simulationComparisonMapper,
ParameterIdentificationMapper parameterIdentificationMapper,
QualificationPlanMapper qualificationPlanMapper,
IExecutionContext executionContext,
IClassificationSnapshotTask classificationSnapshotTask,
ILazyLoadTask lazyLoadTask,
ICreationMetaDataFactory creationMetaDataFactory,
IOSPSuiteLogger logger)
{
_simulationMapper = simulationMapper;
_simulationComparisonMapper = simulationComparisonMapper;
_parameterIdentificationMapper = parameterIdentificationMapper;
_qualificationPlanMapper = qualificationPlanMapper;
_classificationSnapshotTask = classificationSnapshotTask;
_lazyLoadTask = lazyLoadTask;
_creationMetaDataFactory = creationMetaDataFactory;
_logger = logger;
//required to load the snapshot mapper via execution context to avoid circular references
_snapshotMapper = new Lazy <ISnapshotMapper>(executionContext.Resolve <ISnapshotMapper>);
}
protected override Task Context()
{
_parameterMapper = A.Fake <ParameterMapper>();
_representationInfoRepository = A.Fake <IRepresentationInfoRepository>();
_compoundProcessRepository = A.Fake <ICompoundProcessRepository>();
_cloner = A.Fake <ICloner>();
_speciesRepository = A.Fake <ISpeciesRepository>();
_compoundProcessTask = A.Fake <ICompoundProcessTask>();
_logger = A.Fake <IOSPSuiteLogger>();
sut = new CompoundProcessMapper(_parameterMapper, _representationInfoRepository, _compoundProcessRepository, _cloner, _speciesRepository, _compoundProcessTask, _logger);
_enzymaticProcess = new EnzymaticProcess
{
Name = "Enzymatic Process",
Description = "Process description",
InternalName = "A",
DataSource = "B",
MetaboliteName = "Meta"
};
//Same description as DB
A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcess.InternalName)).Returns(_enzymaticProcess.Description);
_enzymaticProcessWithSpecies = new EnzymaticProcessWithSpecies
{
Name = "Enzymatic process with species",
Description = "toto",
Species = new Species().WithName("Human"),
InternalName = "C",
DataSource = "D",
};
A.CallTo(() => _representationInfoRepository.DescriptionFor(RepresentationObjectType.PROCESS, _enzymaticProcessWithSpecies.InternalName)).Returns("Process description");
return(Task.FromResult(true));
}
protected override Task Context()
{
sut = new OutputMappingMapper(_logger);
_simulation = A.Fake <Simulation>().WithName("S");
_output = new Observer().WithName("OBS");
_simulation.Model.Root = new Container {
_output
};
_logger = A.Fake <IOSPSuiteLogger>();
_dataRepository = DomainHelperForSpecs.ObservedData("OBS_DATA");
_outputMapping = new OutputMapping
{
Scaling = Scalings.Log,
Weight = 5,
OutputSelection = new SimulationQuantitySelection(_simulation, new QuantitySelection(_output.Name, QuantityType.Observer)),
WeightedObservedData = new WeightedObservedData(_dataRepository)
};
_outputMapping.WeightedObservedData.Weights[1] = 2f;
return(_completed);
}
public CLIEntityValidationTask(IEntityValidator entityValidator, IExecutionContext executionContext, IOSPSuiteLogger logger)
{
_entityValidator = entityValidator;
_executionContext = executionContext;
_logger = logger;
}
public static void AddError(this IOSPSuiteLogger logger, string message, string categoryName = null) => addToLog(logger, message, LogLevel.Error, categoryName);
public DataImporter(IImporter importer, IOSPSuiteLogger logger, IDimensionFactory dimensionFactory) : base(importer, dimensionFactory)
{
_logger = logger;
}
public static void AddDebug <T>(this IOSPSuiteLogger logger, string message) => addToLog <T>(logger, message, LogLevel.Debug);
public RunSimulationQualificationStepRunner(ISimulationRunner simulationRunner, IOSPSuiteLogger logger) : base(logger)
{
_simulationRunner = simulationRunner;
}
public static void AddException <T>(this IOSPSuiteLogger logger, Exception exception) => logger.AddException(exception, typeof(T).Name);
public QualificationStepMapper(IOSPSuiteLogger logger)
{
_logger = logger;
}
private static void addToLog(IOSPSuiteLogger logger, string message, LogLevel logLevel, string category)
{
logger?.AddToLog(message, logLevel, category);
}
public CompoundPropertiesMapper(CalculationMethodCacheMapper calculationMethodCacheMapper, ProcessMappingMapper processMappingMapper, IOSPSuiteLogger logger)
{
_calculationMethodCacheMapper = calculationMethodCacheMapper;
_processMappingMapper = processMappingMapper;
_logger = logger;
}
private static void addToLog <T>(IOSPSuiteLogger logger, string message, LogLevel logLevel)
{
logger.AddToLog(message, logLevel, typeof(T).Name);
}
