private void exportSimulationToFile(Simulation simulation, string moBiFile)
{
_lazyLoadTask.Load(simulation);
if (simulation.IsImported)
{
throw new PKSimException(PKSimConstants.Error.CannotExportAnImportedSimulation);
}
var configuration = _buildConfigurationTask.CreateFor(simulation, shouldValidate: true, createAgingDataInSimulation: false);
var moBiSimulation = _simulationMapper.MapFrom(simulation, configuration, shouldCloneModel: false);
updateObserverForAllFlag(moBiSimulation);
updateRepresentationInfo(moBiSimulation);
updateFormulaIdIn(moBiSimulation);
var simulationTransfer = new SimulationTransfer
{
Simulation = moBiSimulation,
JournalPath = _journalRetriever.JournalFullPath
};
var currentProject = _projectRetriever.CurrentProject;
if (currentProject != null)
{
simulationTransfer.AllObservedData = simulation.UsedObservedData.Select(o => currentProject.ObservedDataBy(o.Id)).ToList();
simulationTransfer.Favorites = currentProject.Favorites;
}
_simulationPersistor.Save(simulationTransfer, moBiFile);
}
private void exportToDirectory(ISimulation simulation, string exportDirectory)
{
var fileName = createFilePathFor(simulation, exportDirectory, Constants.Filter.XML_EXTENSION);
var modelCoreSimulation = _simulationToModelCoreSimulationMapper.MapFrom(simulation, shouldCloneModel: false);
_simModelExporter.ExportSimModelXml(modelCoreSimulation, fileName);
}
private Task runSimulation(IndividualSimulation simulation, bool exportAll, bool raiseEvents, bool checkForNegativeValues)
{
//Should be done outside of the Task.Run to ensure that any event that might be raised by this action won't cause threading issue
updatePersistableFor(simulation, exportAll);
return(Task.Run(() =>
{
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(simulation, shouldCloneModel: false);
var simRunOptions = new SimulationRunOptions
{
SimModelExportMode = SimModelExportMode.Optimized,
CheckForNegativeValues = checkForNegativeValues
};
var simResults = _simModelManager.RunSimulation(modelCoreSimulation, simRunOptions);
if (!simResults.Success)
{
return;
}
_simulationResultsSynchronizer.Synchronize(simulation, simResults.Results);
simulation.ClearPKCache();
if (raiseEvents)
{
_eventPublisher.PublishEvent(new SimulationResultsUpdatedEvent(simulation));
}
}));
}
private ISimModelBatch createSimModelBatch(ISimulation simulation)
{
var simModelBatch = _simModelBatchFactory.Create();
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(simulation, shouldCloneModel: true);
_timeGridUpdater.UpdateSimulationTimeGrid(modelCoreSimulation, _parameterIdentification.Configuration.RemoveLLOQMode, _parameterIdentification.AllDataRepositoryMappedFor(simulation));
_outputSelectionUpdater.UpdateOutputsIn(modelCoreSimulation, _parameterIdentification.AllOutputsMappedFor(simulation));
simModelBatch.InitializeWith(modelCoreSimulation, _parameterIdentification.PathOfOptimizedParameterBelongingTo(simulation), simulationResultsName: Captions.ParameterIdentification.SimulationResultsForRun(RunResult.Index));
return(simModelBatch);
}
protected override void Context()
{
_eventPublisher = A.Fake <IEventPublisher>();
_sensitivityAnalysisVariationDataCreator = A.Fake <ISensitivityAnalysisVariationDataCreator>();
_populationRunner = A.Fake <IPopulationRunner>();
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_runResultCalculator = A.Fake <ISensitivityAnalysisRunResultCalculator>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
sut = new SensitivityAnalysisEngine(_eventPublisher, _sensitivityAnalysisVariationDataCreator, _populationRunner, _modelCoreSimulationMapper, _runResultCalculator, _simulationPersistableUpdater);
_sensitivityAnalysis = A.Fake <SensitivityAnalysis>();
_modelCoreSimulation = A.Fake <IModelCoreSimulation>();
A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_sensitivityAnalysis.Simulation, true)).Returns(_modelCoreSimulation);
}
private Task runSimulation(IndividualSimulation simulation, SimulationRunOptions simulationRunOptions)
{
return(Task.Run(() =>
{
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(simulation, shouldCloneModel: false);
var simResults = _simModelManager.RunSimulation(modelCoreSimulation, simulationRunOptions);
if (!simResults.Success)
{
return;
}
_simulationResultsSynchronizer.Synchronize(simulation, simResults.Results);
updateResultsName(simulation);
simulation.ClearPKCache();
raiseEvent(new SimulationResultsUpdatedEvent(simulation));
}));
}
public async Task <PopulationRunResults> RunAsync(PopulationSimulation populationSimulation, SimulationRunOptions simulationRunOptions)
{
_progressUpdater = _progressManager.Create();
_progressUpdater.Initialize(populationSimulation.NumberOfItems, PKSimConstants.UI.Calculating);
var begin = SystemTime.UtcNow();
try
{
var populationData = _populationExporter.CreatePopulationDataFor(populationSimulation);
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(populationSimulation, shouldCloneModel: false);
var runOptions = new RunOptions {
NumberOfCoresToUse = _userSettings.MaximumNumberOfCoresToUse
};
_eventPublisher.PublishEvent(new SimulationRunStartedEvent());
var populationRunResults = await _populationRunner.RunPopulationAsync(modelCoreSimulation, runOptions, populationData, populationSimulation.AgingData.ToDataTable());
_simulationResultsSynchronizer.Synchronize(populationSimulation, populationRunResults.Results);
_populationSimulationAnalysisSynchronizer.UpdateAnalysesDefinedIn(populationSimulation);
_eventPublisher.PublishEvent(new SimulationResultsUpdatedEvent(populationSimulation));
return(populationRunResults);
}
catch (OperationCanceledException)
{
simulationTerminated();
return(null);
}
catch (Exception)
{
simulationTerminated();
throw;
}
finally
{
var end = SystemTime.UtcNow();
var timeSpent = end - begin;
_eventPublisher.PublishEvent(new SimulationRunFinishedEvent(populationSimulation, timeSpent));
}
}
public async Task RunAsync(PopulationSimulation populationSimulation)
{
_progressUpdater = _progressManager.Create();
_progressUpdater.Initialize(populationSimulation.NumberOfItems, PKSimConstants.UI.Calculating);
_populationRunner.NumberOfCoresToUse = _userSettings.MaximumNumberOfCoresToUse;
//make sure that thread methods always catch and handle any exception,
//otherwise we risk unplanned application termination
var begin = SystemTime.UtcNow();
try
{
var populationData = _populationExporter.CreatePopulationDataFor(populationSimulation);
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(populationSimulation, shouldCloneModel: false);
_simulationPersistableUpdater.UpdatePersistableFromSettings(populationSimulation);
_eventPublisher.PublishEvent(new SimulationRunStartedEvent());
var populationRunResults = await _populationRunner.RunPopulationAsync(modelCoreSimulation, populationData, populationSimulation.AgingData.ToDataTable());
_simulationResultsSynchronizer.Synchronize(populationSimulation, populationRunResults.Results);
_populationSimulationAnalysisSynchronizer.UpdateAnalysesDefinedIn(populationSimulation);
_eventPublisher.PublishEvent(new SimulationResultsUpdatedEvent(populationSimulation));
}
catch (OperationCanceledException)
{
simulationTerminated();
}
catch (Exception ex)
{
_exceptionManager.LogException(ex);
simulationTerminated();
}
finally
{
var end = SystemTime.UtcNow();
var timeSpent = end - begin;
_eventPublisher.PublishEvent(new SimulationRunFinishedEvent(populationSimulation, timeSpent));
}
}
public async Task StartAsync(SensitivityAnalysis sensitivityAnalysis, SensitivityAnalysisRunOptions runOptions)
{
_sensitivityAnalysis = sensitivityAnalysis;
_eventPublisher.PublishEvent(new SensitivityAnalysisStartedEvent(sensitivityAnalysis));
try
{
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(sensitivityAnalysis.Simulation, shouldCloneModel: true);
_simulationPersistableUpdater.UpdateSimulationPersistable(modelCoreSimulation);
var variationData = _sensitivityAnalysisVariationDataCreator.CreateForRun(sensitivityAnalysis);
var runResults = await _populationRunner.RunPopulationAsync(modelCoreSimulation, runOptions, variationData.ToDataTable());
sensitivityAnalysis.Results = await calculateSensitivityBasedOn(sensitivityAnalysis, variationData, runResults, runOptions);
_eventPublisher.PublishEvent(new SensitivityAnalysisResultsUpdatedEvent(sensitivityAnalysis));
}
finally
{
_eventPublisher.PublishEvent(new SensitivityAnalysisTerminatedEvent(sensitivityAnalysis));
_sensitivityAnalysis = null;
}
}
protected override void Context()
{
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
_residualCalculatorFactory = A.Fake <IResidualCalculatorFactory>();
_timeGridUpdater = A.Fake <ITimeGridUpdater>();
_simModelBatchFactory = A.Fake <ISimModelBatchFactory>();
_optimizationAlgorithmMapper = A.Fake <IParameterIdentificationAlgorithmToOptmizationAlgorithmMapper>();
_outputSelectionUpdater = A.Fake <IOutputSelectionUpdater>();
_coreUserSettings = A.Fake <ICoreUserSettings>();
_jacobianMatrixCalculator = A.Fake <IJacobianMatrixCalculator>();
_coreUserSettings.MaximumNumberOfCoresToUse = 2;
sut = new ParameterIdentificationRun(_residualCalculatorFactory, _timeGridUpdater, _simModelBatchFactory, _modelCoreSimulationMapper,
_optimizationAlgorithmMapper, _outputSelectionUpdater, _coreUserSettings, _jacobianMatrixCalculator);
_simulation = A.Fake <ISimulation>();
_parameter1 = A.Fake <IParameter>();
_parameter1.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameter1.Value = 15;
_parameter2 = A.Fake <IParameter>();
_parameter2.Value = 35;
_parameter2.Dimension = DomainHelperForSpecs.ConcentrationDimensionForSpecs();
_parameterIdentification = new ParameterIdentification();
_parameterIdentification.Configuration.LLOQMode = LLOQModes.OnlyObservedData;
_parameterIdentification.Configuration.RemoveLLOQMode = RemoveLLOQModes.NoTrailing;
_parameterIdentification.AddSimulation(_simulation);
_parameterSelection1 = ParameterSelectionFor(_parameter1, "ParameterPath1");
_parameterSelection2 = ParameterSelectionFor(_parameter2, "ParameterPath2");
_identificationParameter = DomainHelperForSpecs.IdentificationParameter("IdParam", min: 10, max: 20, startValue: 15);
_identificationParameter.AddLinkedParameter(_parameterSelection1);
_identificationParameter.AddLinkedParameter(_parameterSelection2);
_modelCoreSimulation = A.Fake <IModelCoreSimulation>();
A.CallTo(() => _modelCoreSimulationMapper.MapFrom(_simulation, true)).Returns(_modelCoreSimulation);
_outputMapping = A.Fake <OutputMapping>();
A.CallTo(() => _outputMapping.UsesSimulation(_simulation)).Returns(true);
A.CallTo(() => _outputMapping.WeightedObservedData.ObservedData).Returns(DomainHelperForSpecs.ObservedData());
_parameterIdentification.AddOutputMapping(_outputMapping);
_simModelBatch = A.Fake <ISimModelBatch>();
A.CallTo(() => _simModelBatchFactory.Create()).Returns(_simModelBatch);
_parameterIdentification.AddIdentificationParameter(_identificationParameter);
_residualCalculator = A.Fake <IResidualCalculator>();
A.CallTo(_residualCalculatorFactory).WithReturnType <IResidualCalculator>().Returns(_residualCalculator);
_algorithm = A.Fake <IOptimizationAlgorithm>();
A.CallTo(() => _optimizationAlgorithmMapper.MapFrom(_parameterIdentification.AlgorithmProperties)).Returns(_algorithm);
_cancellationTokenSource = new CancellationTokenSource();
_cancellationToken = _cancellationTokenSource.Token;
_runInitializer = A.Fake <IParameterIdentifcationRunInitializer>();
A.CallTo(() => _runInitializer.InitializeRun()).ReturnsAsync(_parameterIdentification);
PerformExtraInitializationSteps();
sut.InitializeWith(_runInitializer);
}
public void ExportForCluster(PopulationSimulation populationSimulation)
{
_lazyLoadTask.Load(populationSimulation);
if (settingsRequired(populationSimulation))
{
var outputSelections = _simulationSettingsRetriever.SettingsFor(populationSimulation);
if (outputSelections == null)
{
return;
}
populationSimulation.OutputSelections.UpdatePropertiesFrom(outputSelections, _cloner);
}
FileSelection populationExport;
using (var presenter = _applicationController.Start <ISelectFilePresenter>())
{
populationExport = presenter.SelectDirectory(PKSimConstants.UI.ExportForClusterSimulationTitle, Constants.DirectoryKey.SIM_MODEL_XML);
}
if (populationExport == null)
{
return;
}
var populationFolder = populationExport.FilePath;
var existingFiles = Directory.GetFiles(populationFolder);
if (existingFiles.Any())
{
if (_dialogCreator.MessageBoxYesNo(PKSimConstants.UI.DeleteFilesIn(populationFolder)).Equals(ViewResult.No))
{
return;
}
existingFiles.Each(FileHelper.DeleteFile);
}
var fileName = populationSimulation.Name;
var modelFileFullPath = Path.Combine(populationFolder, $"{fileName}.xml");
var agingFileFullPath = Path.Combine(populationFolder, $"{fileName}{CoreConstants.Population.TableParameterExport}.csv");
var outputDeffinitionFileFullPath = Path.Combine(populationFolder, $"{fileName}{CoreConstants.Population.OutputDefinitionExport}.csv");
//Model
_simModelExporter.Export(_modelCoreSimulationMapper.MapFrom(populationSimulation, shouldCloneModel: false), modelFileFullPath);
// Outputs
var outputSelection = populationSimulation.OutputSelections;
exportOutputDefiniton(outputSelection, outputDeffinitionFileFullPath);
//all values
var dataTable = CreatePopulationDataFor(populationSimulation);
dataTable.ExportToCSV(Path.Combine(populationFolder, $"{fileName}.csv"), comments: getProjectMetaInfo(populationExport.Description));
//all aging data
var agingData = populationSimulation.AgingData.ToDataTable();
if (agingData.Rows.Count > 0)
{
agingData.ExportToCSV(agingFileFullPath, comments: getProjectMetaInfo(populationExport.Description));
}
}
public Task ExportSimulationToSimModelXmlAsync(Simulation simulation, string fileName)
{
return(Task.Run(() => _simModelExporter.Export(_coreSimulationMapper.MapFrom(simulation, shouldCloneModel: false), fileName)));
}
public Task ExportSimulationToCppAsync(Simulation simulation, string outputFolder)
{
_lazyLoadTask.Load(simulation);
return(Task.Run(() => _simModelExporter.ExportCppCode(_coreSimulationMapper.MapFrom(simulation, shouldCloneModel: false), outputFolder, FormulaExportMode.Formula)));
}
