private async Task startJsonSimulationRun(JsonRunOptions runOptions)
{
var inputFolder = runOptions.InputFolder;
var outputFolder = runOptions.OutputFolder;
var exportMode = runOptions.ExportMode;
clear();
var inputDirectory = new DirectoryInfo(inputFolder);
if (!inputDirectory.Exists)
{
throw new OSPSuiteException($"Input folder '{inputFolder}' does not exist");
}
var allSnapshsotFiles = inputDirectory.GetFiles(Constants.Filter.JSON_FILTER);
if (allSnapshsotFiles.Length == 0)
{
throw new OSPSuiteException($"No snapshot file found in '{inputFolder}'");
}
var outputDirectory = new DirectoryInfo(outputFolder);
if (!outputDirectory.Exists)
{
_logger.AddDebug($"Creating folder '{outputFolder}'");
outputDirectory.Create();
}
var allExistingFiles = outputDirectory.GetFiles("*.csv");
allExistingFiles.Each(outputFile =>
{
FileHelper.DeleteFile(outputFile.FullName);
_logger.AddDebug($"Deleting file '{outputFile.FullName}'");
});
var begin = DateTime.UtcNow;
_logger.AddInfo($"Found {allSnapshsotFiles.Length} files in '{inputFolder}'");
foreach (var snapshotFile in allSnapshsotFiles)
{
await runAndExportSimulationsInSnapshotFile(snapshotFile, outputFolder, exportMode)
.ConfigureAwait(false);
}
var end = DateTime.UtcNow;
var timeSpent = end - begin;
_logger.AddInfo($"{_allSimulationNames.Count} simulations calculated and exported in '{timeSpent.ToDisplay()}'");
createSummaryFilesIn(outputDirectory, exportMode);
}
public override async Task <ModelSimulation> MapToModel(SnapshotSimulation snapshot, PKSimProject project)
{
_logger.AddDebug(PKSimConstants.Information.LoadingSimulation(snapshot.Name), project.Name);
var simulation = await createSimulationFrom(snapshot, project);
simulation.Solver = await _solverSettingsMapper.MapToModel(snapshot.Solver);
simulation.OutputSchema = await _outputSchemaMapper.MapToModel(snapshot.OutputSchema);
simulation.OutputSelections = await _outputSelectionsMapper.MapToModel(snapshot.OutputSelections, simulation);
await updateParameters(simulation, snapshot.Parameters);
await updateAdvancedParameters(simulation, snapshot.AdvancedParameters);
updateUsedObservedData(simulation, snapshot.ObservedData, project);
await runSimulation(snapshot, simulation);
simulation.AddAnalyses(await individualAnalysesFrom(simulation, snapshot.IndividualAnalyses, project));
simulation.AddAnalyses(await populationAnalysesFrom(simulation, snapshot.PopulationAnalyses, project));
_simulationParameterOriginIdUpdater.UpdateSimulationId(simulation);
return(simulation);
}
private async Task exportProject(ExportRunOptions runOptions)
{
var projectFile = runOptions.ProjectFile;
if (!FileHelper.FileExists(projectFile))
{
throw new OSPSuiteException($"Project file '{projectFile}' does not exist.");
}
DirectoryHelper.CreateDirectory(runOptions.OutputFolder);
_logger.AddInfo($"Starting project export for '{projectFile}'");
_workspacePersistor.LoadSession(_workspace, projectFile);
_logger.AddDebug($"Project loaded successfully from '{projectFile}'");
await ExportSimulationsIn(_workspace.Project, runOptions);
_logger.AddInfo($"Project export for '{projectFile}' terminated");
}
public async Task RunAndExport(Simulation simulation, string outputFolder, SimulationRunOptions simulationRunOptions, SimulationExportMode simulationExportMode, string projectName = null)
{
_logger.AddDebug($"Running simulation '{simulation.Name}'");
await _simulationRunner.RunSimulation(simulation, simulationRunOptions);
await Export(simulation, outputFolder, simulationExportMode, projectName);
}
public async Task RunAsync(QualificationPlan qualificationPlan)
{
_logger.AddDebug(PKSimConstants.Information.StartingQualificationPlan(qualificationPlan.Name));
//this needs to be run in order. Await EACH run
foreach (var qualificationStep in qualificationPlan.Steps)
{
using (var runner = _qualificationStepRunnerFactory.CreateFor(qualificationStep))
{
await runner.RunAsync(qualificationStep);
}
}
}
public override async Task <ModelProject> MapToModel(SnapshotProject snapshot)
{
_logger.AddDebug($"Loading project '{snapshot.Name}' from snapshot...", snapshot.Name);
var project = new ModelProject
{
Name = snapshot.Name,
Description = snapshot.Description,
Creation = _creationMetaDataFactory.Create()
};
project.Creation.InternalVersion = snapshot.Version;
project.Creation.Version = ProjectVersions.FindBy(snapshot.Version)?.VersionDisplay;
var buildingBlocks = await allBuidingBlocksFrom(snapshot);
buildingBlocks?.Each(project.AddBuildingBlock);
var observedData = await observedDataFrom(snapshot.ObservedData);
observedData?.Each(repository => addObservedDataToProject(project, repository));
var allSimulations = await allSimulationsFrom(snapshot.Simulations, project);
allSimulations?.Each(simulation => addSimulationToProject(project, simulation));
var allSimulationComparisons = await allSimulationComparisonsFrom(snapshot.SimulationComparisons, project);
allSimulationComparisons?.Each(comparison => addComparisonToProject(project, comparison));
var allParameterIdentifications = await allParameterIdentificationsFrom(snapshot.ParameterIdentifications, project);
allParameterIdentifications?.Each(parameterIdentification => addParameterIdentificationToProject(project, parameterIdentification));
var allQualificationPlans = await allQualificationPlansFrom(snapshot.QualificationPlans, project);
allQualificationPlans?.Each(qualificationPlan => addQualificationPlanToProject(project, qualificationPlan));
//Map all classifications once project is loaded
await updateProjectClassifications(snapshot, project);
return(project);
}
public override async Task <ModelSimulation> MapToModel(SnapshotSimulation snapshot, PKSimProject project)
{
_logger.AddDebug(PKSimConstants.Information.LoadingSimulation(snapshot.Name), project.Name);
//Local cache of ids' that will be used to retrieve original building block parameters as the project is only registered
//in global context once the whole snapshot mapping process is completed
var withIdRepository = new WithIdRepository();
var registrationVisitor = new RegisterObjectVisitor(withIdRepository);
var simulation = await createSimulationFrom(snapshot, project);
simulation.Solver = await _solverSettingsMapper.MapToModel(snapshot.Solver);
simulation.OutputSchema = await _outputSchemaMapper.MapToModel(snapshot.OutputSchema);
simulation.OutputSelections = await _outputSelectionsMapper.MapToModel(snapshot.OutputSelections, simulation);
registrationVisitor.Register(simulation);
await updateParameters(simulation, snapshot.Parameters, withIdRepository);
await updateAdvancedParameters(simulation, snapshot.AdvancedParameters);
updateUsedObservedData(simulation, snapshot.ObservedData, project);
updateAlteredBuildingBlock(simulation, snapshot.AlteredBuildingBlocks);
await runSimulation(snapshot, simulation);
simulation.AddAnalyses(await individualAnalysesFrom(simulation, snapshot.IndividualAnalyses, project));
simulation.AddAnalyses(await populationAnalysesFrom(simulation, snapshot.PopulationAnalyses, project));
_simulationParameterOriginIdUpdater.UpdateSimulationId(simulation);
return(simulation);
}
public async Task RunBatchAsync(QualificationRunOptions runOptions)
{
_runOptions = runOptions;
if (!FileHelper.FileExists(runOptions.ConfigurationFile))
{
throw new QualificationRunException(ConfigurationFileNotFound(runOptions.ConfigurationFile));
}
setupOutputFolder();
dynamic qualificationPlan = await _jsonSerializer.Deserialize <dynamic>(runOptions.ConfigurationFile);
IReadOnlyList <Project> projects = GetListFrom <Project>(qualificationPlan.Projects);
if (projects == null)
{
throw new QualificationRunException(ProjectsNotDefinedInQualificationFile);
}
IReadOnlyList <SimulationPlot> allPlots = retrieveProjectPlots(qualificationPlan);
IReadOnlyList <Input> allInputs = retrieveInputs(qualificationPlan);
var begin = DateTime.UtcNow;
await updateProjectsFullPath(projects);
//Configurations only need to be created once!
var projectConfigurations = await Task.WhenAll(projects.Select(p => createQualifcationConfigurationFor(p, projects, allPlots, allInputs)));
_logger.AddDebug("Copying static files");
StaticFiles staticFiles = await copyStaticFiles(qualificationPlan);
_logger.AddInfo("Starting validation runs...");
var validations = await Task.WhenAll(projectConfigurations.Select(validateProject));
var invalidConfigurations = validations.Where(x => !x.Success).ToList();
if (invalidConfigurations.Any())
{
throw new QualificationRunException(errorMessageFrom(invalidConfigurations));
}
//Run all qualification projects
_logger.AddInfo("Starting qualification runs...");
var runResults = await Task.WhenAll(projectConfigurations.Select(runQualification));
var invalidRunResults = runResults.Where(x => !x.Success).ToList();
if (invalidRunResults.Any())
{
throw new QualificationRunException(errorMessageFrom(invalidRunResults));
}
await createReportConfigurationPlan(runResults, staticFiles, qualificationPlan);
var end = DateTime.UtcNow;
var timeSpent = end - begin;
_logger.AddInfo($"Qualification scenario finished in {timeSpent.ToDisplay()}");
}
public async Task RunBatchAsync(QualificationRunOptions runOptions)
{
_snapshotProjectCache.Clear();
_logger.AddInfo(runOptions.Validate ? "Starting validation run..." : "Starting qualification run...");
var config = await readConfigurationFrom(runOptions);
if (config == null)
{
throw new QualificationRunException(UnableToLoadQualificationConfigurationFromFile(runOptions.ConfigurationFile));
}
var errorMessage = config.Validate().Message;
if (!string.IsNullOrEmpty(errorMessage))
{
throw new QualificationRunException(errorMessage);
}
_logger.AddDebug($"Loading project from snapshot file '{config.SnapshotFile}'...");
var snapshot = await snapshotProjectFromFile(config.SnapshotFile);
//Ensures that the name of the snapshot is also the name of the project as defined in the configuration
snapshot.Name = config.Project;
_logger.AddDebug($"Project {snapshot.Name} loaded from snapshot file '{config.SnapshotFile}'.");
await performBuildingBlockSwap(snapshot, config.BuildingBlocks);
await performSimulationParameterSwap(snapshot, config.SimulationParameters);
//Retrieve charts and validate inputs before exiting validation to ensure that we can throw error messages if an element is not available
var plots = retrievePlotDefinitionsFrom(snapshot, config);
validateInputs(snapshot, config);
if (runOptions.Validate)
{
_logger.AddInfo($"Validation run terminated for {snapshot.Name}");
return;
}
var begin = DateTime.UtcNow;
var project = await _snapshotTask.LoadProjectFromSnapshot(snapshot);
_workspace.Project = project;
var projectOutputFolder = createProjectOutputFolder(config.OutputFolder, project.Name);
_logger.AddDebug($"Exporting project {project.Name} to '{projectOutputFolder}'", project.Name);
var exportRunOptions = new ExportRunOptions
{
OutputFolder = projectOutputFolder,
ExportMode = SimulationExportMode.Xml | SimulationExportMode.Csv
};
var simulationExports = await _exportSimulationRunner.ExportSimulationsIn(project, exportRunOptions);
var simulationMappings = simulationExports.Select(x => simulationMappingFrom(x, config)).ToArray();
var observedDataMappings = await exportAllObservedData(project, config);
var inputMappings = exportInputs(project, config);
var mapping = new QualificationMapping
{
SimulationMappings = simulationMappings,
ObservedDataMappings = observedDataMappings,
Plots = plots,
Inputs = inputMappings
};
await _jsonSerializer.Serialize(mapping, config.MappingFile);
_logger.AddDebug($"Project mapping for '{project.Name}' exported to '{config.MappingFile}'", project.Name);
var projectFile = Path.Combine(config.TempFolder, $"{project.Name}{CoreConstants.Filter.PROJECT_EXTENSION}");
_workspacePersistor.SaveSession(_workspace, projectFile);
_logger.AddDebug($"Project saved to '{projectFile}'", project.Name);
var snapshotFile = Path.Combine(config.TempFolder, $"{project.Name}{Constants.Filter.JSON_EXTENSION}");
await _snapshotTask.ExportModelToSnapshot(project, snapshotFile);
_logger.AddDebug($"Project snapshot saved to '{snapshotFile}'", project.Name);
var end = DateTime.UtcNow;
var timeSpent = end - begin;
_logger.AddInfo($"Project '{project.Name}' exported for qualification in {timeSpent.ToDisplay()}", project.Name);
}
public async Task RunAsync(IQualificationStep qualificationStep)
{
_logger.AddDebug(PKSimConstants.Information.StartingQualificationStep(qualificationStep.Display));
await RunAsync(qualificationStep.DowncastTo <T>());
}
