public async Task RunAsync(IndividualSimulation individualSimulation, SimulationRunOptions simulationRunOptions)
{
_shouldRaiseEvents = simulationRunOptions.RaiseEvents;
initializeProgress();
_simModelManager.SimulationProgress += simulationProgress;
//make sure that thread methods always catch and handle any exception,
//otherwise we risk unplanned application termination
var begin = SystemTime.UtcNow();
try
{
raiseEvent(new SimulationRunStartedEvent());
await runSimulation(individualSimulation, simulationRunOptions);
}
catch (Exception)
{
terminated();
throw;
}
finally
{
var end = SystemTime.UtcNow();
var timeSpent = end - begin;
raiseEvent(new SimulationRunFinishedEvent(individualSimulation, timeSpent));
}
}
private async Task exportSimulation(Simulation simulation, ExportRunOptions exportRunOptions)
{
var outputFolder = Path.Combine(exportRunOptions.OutputFolder, simulation.Name);
DirectoryHelper.CreateDirectory(outputFolder);
var simulationRunOptions = new SimulationRunOptions();
_lazyLoadTask.Load(simulation);
_lazyLoadTask.LoadResults(simulation);
if (!simulation.OutputSelections.HasSelection)
{
_logger.AddWarning($"Simulation '{simulation.Name}' does not have any selected output and will not be exported");
return;
}
if (exportRunOptions.RunSimulation)
{
await _simulationExporter.RunAndExport(simulation, outputFolder, simulationRunOptions, exportRunOptions.ExportMode);
}
else if (simulation.HasResults)
{
await _simulationExporter.Export(simulation, outputFolder, exportRunOptions.ExportMode);
}
else
{
_logger.AddWarning($"Simulation '{simulation.Name}' does not have any results and will not be exported");
}
}
public override void GlobalContext()
{
base.GlobalContext();
_compoundProcessRepository = IoC.Resolve <ICompoundProcessRepository>();
_cloneManager = IoC.Resolve <ICloneManager>();
_enzymeFactory = IoC.Resolve <IIndividualEnzymeFactory>();
_transporterFactory = IoC.Resolve <IIndividualTransporterFactory>();
_modelPropertiesTask = IoC.Resolve <IModelPropertiesTask>();
_modelConfigurationRepository = IoC.Resolve <IModelConfigurationRepository>();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_enzyme = _enzymeFactory.CreateFor(_individual).DowncastTo <IndividualEnzyme>().WithName("CYP");
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.Plasma).Value = _relExpNormPls;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.BloodCells).Value = _relExpNormBloodCells;
_enzyme.GetRelativeExpressionNormParameterFor(CoreConstants.Compartment.VascularEndothelium).Value = _relExpVascEndo;
_individual.AddMolecule(_enzyme);
_hct = _individual.Organism.Parameter(CoreConstants.Parameters.HCT).Value;
_metabolizationProcess = _cloneManager.Clone(_compoundProcessRepository.ProcessByName(CoreConstantsForSpecs.Process.METABOLIZATION_SPECIFIC_FIRST_ORDER).DowncastTo <PartialProcess>());
_metabolizationProcess.Name = "My Partial Process";
_metabolizationProcess.Parameter(ConverterConstants.Parameter.CLspec).Value = 15;
_compound.AddProcess(_metabolizationProcess);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public async Task RunAndExport(Simulation simulation, string outputFolder, SimulationRunOptions simulationRunOptions, SimulationExportMode simulationExportMode, string projectName = null)
{
_logger.AddDebug($"Running simulation '{simulation.Name}'");
await _simulationRunner.RunSimulation(simulation, simulationRunOptions);
await Export(simulation, outputFolder, simulationExportMode, projectName);
}
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));
}
}));
}
protected override async Task Context()
{
await base.Context();
_simulationRunOptions = new SimulationRunOptions();
_simulation = A.Fake <IndividualSimulation>();
A.CallTo(() => _entityTask.Validate(_simulation)).Returns(true);
}
public override void GlobalContext()
{
base.GlobalContext();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_globalPKAnalysisTask = IoC.Resolve <IGlobalPKAnalysisTask>();
_simulationRunOptions = new SimulationRunOptions();
}
public async Task <SimulationExport> ExportSimulation(Simulation simulation, ExportRunOptions exportRunOptions, PKSimProject project)
{
var projectName = project.Name;
var simulationName = simulation.Name;
var simulationFolder = Path.Combine(exportRunOptions.OutputFolder, FileHelper.RemoveIllegalCharactersFrom(simulationName));
DirectoryHelper.CreateDirectory(simulationFolder);
var simulationExport = new SimulationExport
{
Project = projectName,
SimulationFolder = simulationFolder,
Simulation = simulationName
};
var simulationRunOptions = new SimulationRunOptions();
_lazyLoadTask.Load(simulation);
_lazyLoadTask.LoadResults(simulation);
var simulationExportOptions = new SimulationExportOptions
{
OutputFolder = simulationFolder,
ExportMode = exportRunOptions.ExportMode,
ProjectName = projectName,
};
if (!simulation.OutputSelections.HasSelection)
{
_logger.AddWarning($"Simulation '{simulationName}' does not have any selected output and will not be exported", projectName);
return(simulationExport);
}
if (exportRunOptions.RunSimulation)
{
await _simulationExporter.RunAndExport(simulation, simulationRunOptions, simulationExportOptions);
}
else if (simulation.HasResults)
{
await _simulationExporter.Export(simulation, simulationExportOptions);
}
else
{
_logger.AddWarning($"Simulation '{simulationName}' does not have any results and will not be exported", projectName);
return(simulationExport);
}
_logger.AddDebug($"Simulation '{simulationName}' exported to '{simulationFolder}'", projectName);
return(simulationExport);
}
protected override async Task Context()
{
await base.Context();
_populationSimulation = A.Fake <PopulationSimulation>();
_modelSimulation = A.Fake <IModelCoreSimulation>();
_populationData = A.Fake <DataTable>();
_runResults = new PopulationRunResults();
_simulationRunOptions = new SimulationRunOptions();
A.CallTo(() => _popExportTask.CreatePopulationDataFor(_populationSimulation, A <bool> ._)).Returns(_populationData);
A.CallTo(() => _simMapper.MapFrom(_populationSimulation, false)).Returns(_modelSimulation);
A.CallTo(() => _populationRunner.RunPopulationAsync(_modelSimulation, _populationData, A <DataTable> ._, A <DataTable> ._)).Returns(_runResults);
}
public JsonSimulationRunner(
ISimulationExporter simulationExporter,
IOSPSuiteLogger logger,
ISnapshotTask snapshotTask
)
{
_simulationExporter = simulationExporter;
_logger = logger;
_snapshotTask = snapshotTask;
_simulationRunOptions = new SimulationRunOptions
{
Validate = false,
CheckForNegativeValues = false,
};
}
public InteractiveSimulationRunner(ISimulationSettingsRetriever simulationSettingsRetriever, ISimulationRunner simulationRunner, ICloner cloner, ISimulationAnalysisCreator simulationAnalysisCreator)
{
_simulationSettingsRetriever = simulationSettingsRetriever;
_simulationRunner = simulationRunner;
_cloner = cloner;
_simulationAnalysisCreator = simulationAnalysisCreator;
_simulationRunOptions = new SimulationRunOptions
{
CheckForNegativeValues = true,
RaiseEvents = true,
RunForAllOutputs = false,
SimModelExportMode = SimModelExportMode.Optimized
};
}
protected override Task Context()
{
_simulationEngine = A.Fake <IIndividualSimulationEngine>();
_popSimulationEngine = A.Fake <IPopulationSimulationEngine>();
_simulationEngineFactory = A.Fake <ISimulationEngineFactory>();
_simulationPersistableUpdater = A.Fake <ISimulationPersistableUpdater>();
_lazyLoadTask = A.Fake <ILazyLoadTask>();
_entityTask = A.Fake <IEntityValidationTask>();
A.CallTo(() => _simulationEngineFactory.Create <PopulationSimulation, PopulationRunResults>()).Returns(_popSimulationEngine);
A.CallTo(() => _simulationEngineFactory.Create <IndividualSimulation, SimulationRunResults>()).Returns(_simulationEngine);
sut = new SimulationRunner(_simulationEngineFactory, _lazyLoadTask, _entityTask, _simulationPersistableUpdater);
_simulationRunOptions = new SimulationRunOptions();
return(_completed);
}
protected override Task Context()
{
_simModelManager = A.Fake <ISimModelManager>();
_progressUpdater = A.Fake <IProgressUpdater>();
_progressManager = A.Fake <IProgressManager>();
_eventPublisher = A.Fake <IEventPublisher>();
_simulationResultsSynchronizer = A.Fake <ISimulationResultsSynchronizer>();
_modelCoreSimulationMapper = A.Fake <ISimulationToModelCoreSimulationMapper>();
sut = new IndividualSimulationEngine(_simModelManager, _progressManager, _simulationResultsSynchronizer,
_eventPublisher, _modelCoreSimulationMapper);
A.CallTo(() => _progressManager.Create()).Returns(_progressUpdater);
_simulationRunOption = new SimulationRunOptions {
RaiseEvents = true
};
return(_completed);
}
public override void GlobalContext()
{
base.GlobalContext();
_compound = DomainFactoryForSpecs.CreateStandardCompound().WithName("Parent");
_metabolite = DomainFactoryForSpecs.CreateStandardCompound().WithName("Metabolite");
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
_cyp3A4 = AddEnzymeTo(_individual, "CYP3A4");
_parentMetabolizationCYP3A4 = AddEnzymaticProcess(_compound, _cyp3A4);
_cyp2D6 = AddEnzymeTo(_individual, "CYP2D6");
_parentMetabolizationCYP2D6 = AddEnzymaticProcess(_compound, _cyp2D6);
_simulationRunOptions = new SimulationRunOptions {
RaiseEvents = false
};
}
public async Task <SimulationMapping> ExportSimulation(Simulation simulation, ExportRunOptions exportRunOptions, PKSimProject project)
{
var projectName = project.Name;
var simulationName = simulation.Name;
var simulationFile = FileHelper.RemoveIllegalCharactersFrom(simulationName);
var simulationFolder = Path.Combine(exportRunOptions.OutputFolder, simulationFile);
DirectoryHelper.CreateDirectory(simulationFolder);
var simulationExport = new SimulationMapping
{
Project = projectName,
Path = simulationFolder,
Simulation = simulationName,
SimulationFile = simulationFile
};
var simulationRunOptions = new SimulationRunOptions();
_lazyLoadTask.Load(simulation);
_lazyLoadTask.LoadResults(simulation);
var simulationExportOptions = new SimulationExportOptions
{
OutputFolder = simulationFolder,
ExportMode = exportRunOptions.ExportMode,
ProjectName = projectName,
};
if (exportRunOptions.RunSimulation)
{
await _simulationExporter.RunAndExport(simulation, simulationRunOptions, simulationExportOptions);
}
else
{
await _simulationExporter.Export(simulation, simulationExportOptions);
}
_logger.AddDebug($"Simulation '{simulationName}' exported to '{simulationFolder}'", projectName);
return(simulationExport);
}
public override void GlobalContext()
{
base.GlobalContext();
_compound = DomainFactoryForSpecs.CreateStandardCompound();
_individual = DomainFactoryForSpecs.CreateStandardIndividual();
_protocol = DomainFactoryForSpecs.CreateStandardIVBolusProtocol();
var cmRepo = IoC.Resolve <ICalculationMethodRepository>();
var intestinalPermGroup = _compound.ParameterAlternativeGroup(CoreConstants.Groups.COMPOUND_INTESTINAL_PERMEABILITY);
var paramAlternativeFactory = IoC.Resolve <IParameterAlternativeFactory>();
var alternative = paramAlternativeFactory.CreateAlternativeFor(intestinalPermGroup).WithName(_intestinalPermAlternativeName);
intestinalPermGroup.AddAlternative(alternative);
_intestinalPermeabilityCalcMethods = cmRepo.Where(cm => cm.Category.Equals(CoreConstants.Category.IntestinalPermeability)).ToList();
_alternativeIntestinalPermParam = alternative.Parameter(CoreConstants.Parameters.SPECIFIC_INTESTINAL_PERMEABILITY);
_simulationEngine = IoC.Resolve <IIndividualSimulationEngine>();
_simulationRunOptions = new SimulationRunOptions();
}
public Task RunSimulation(Simulation simulation, SimulationRunOptions simulationRunOptions = null)
{
_simulationRunOptions = simulationRunOptions ?? new SimulationRunOptions();
_lazyLoadTask.Load(simulation);
if (_simulationRunOptions.Validate && !_entityValidationTask.Validate(simulation))
{
return(_simulationDidNotRun);
}
switch (simulation)
{
case IndividualSimulation individualSimulation:
return(runSimulation(individualSimulation, _simulationPersistableUpdater.UpdatePersistableFromSettings));
case PopulationSimulation populationSimulation:
return(runSimulation(populationSimulation, _simulationPersistableUpdater.UpdatePersistableFromSettings));
}
return(_simulationDidNotRun);
}
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 RunAsync(PopulationSimulation populationSimulation, SimulationRunOptions simulationRunOptions)
{
_progressUpdater = _progressManager.Create();
_progressUpdater.Initialize(populationSimulation.NumberOfItems, PKSimConstants.UI.Calculating);
_populationRunner.NumberOfCoresToUse = _userSettings.MaximumNumberOfCoresToUse;
var begin = SystemTime.UtcNow();
try
{
var populationData = _populationExporter.CreatePopulationDataFor(populationSimulation);
var modelCoreSimulation = _modelCoreSimulationMapper.MapFrom(populationSimulation, shouldCloneModel: false);
_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)
{
simulationTerminated();
throw;
}
finally
{
var end = SystemTime.UtcNow();
var timeSpent = end - begin;
_eventPublisher.PublishEvent(new SimulationRunFinishedEvent(populationSimulation, timeSpent));
}
}