public override void Execute() { base.Execute(); if (_aggregateConfiguration == null) { _aggregateConfiguration = SelectOne <AggregateConfiguration>(BasicActivator.RepositoryLocator.CatalogueRepository); } if (_aggregateConfiguration == null) { return; } if (_aggregateConfiguration.IsJoinablePatientIndexTable()) { if (!BasicActivator.YesNo("Would you like to constrain the records to only those in a committed cohort?", "Cohort Records Only", out bool chosen)) { return; } if (chosen) { _cohort = SelectOne <ExtractableCohort>(BasicActivator.RepositoryLocator.DataExportRepository); if (_cohort == null) { return; } } if (_cohort != null) { var externalData = _cohort.GetExternalData(); if (externalData != null) { var projNumber = externalData.ExternalProjectNumber; var projs = BasicActivator.RepositoryLocator.DataExportRepository.GetAllObjects <Project>().Where(p => p.ProjectNumber == projNumber).ToArray(); if (projs.Length == 1) { ProjectSpecific = projs[0]; } } } } _table = SelectTable(true, "Choose destination table name"); if (_table == null) { return; } var useCase = new CreateTableFromAggregateUseCase(_aggregateConfiguration, _cohort, _table); var runner = BasicActivator.GetPipelineRunner(useCase, null /*TODO inject Pipeline in CLI constructor*/); runner.PipelineExecutionFinishedsuccessfully += ui_PipelineExecutionFinishedsuccessfully; runner.Run(BasicActivator.RepositoryLocator, null, null, null); }
public DataExportChildProvider(IRDMPPlatformRepositoryServiceLocator repositoryLocator, IChildProvider[] pluginChildProviders, ICheckNotifier errorsCheckNotifier, DataExportChildProvider previousStateIfKnown) : base(repositoryLocator.CatalogueRepository, pluginChildProviders, errorsCheckNotifier, previousStateIfKnown) { BlackListedSources = previousStateIfKnown?.BlackListedSources ?? new List <ExternalCohortTable>(); _errorsCheckNotifier = errorsCheckNotifier; dataExportRepository = repositoryLocator.DataExportRepository; AllProjectAssociatedCics = GetAllObjects <ProjectCohortIdentificationConfigurationAssociation>(dataExportRepository); _cicAssociations = new HashSet <int>(AllProjectAssociatedCics.Select(a => a.CohortIdentificationConfiguration_ID)); CohortSources = GetAllObjects <ExternalCohortTable>(dataExportRepository); ExtractableDataSets = GetAllObjects <ExtractableDataSet>(dataExportRepository); AddToDictionaries(new HashSet <object>(AllCohortIdentificationConfigurations.Where(cic => _cicAssociations.Contains(cic.ID))), new DescendancyList(AllProjectCohortIdentificationConfigurationsNode)); AddToDictionaries(new HashSet <object>(AllCohortIdentificationConfigurations.Where(cic => !_cicAssociations.Contains(cic.ID))), new DescendancyList(AllFreeCohortIdentificationConfigurationsNode)); _selectedDataSetsWithNoIsExtractionIdentifier = new HashSet <ISelectedDataSets>(dataExportRepository.GetSelectedDatasetsWithNoExtractionIdentifiers()); SelectedDataSets = GetAllObjects <SelectedDataSets>(dataExportRepository); ReportProgress("Fetching data export objects"); var dsDictionary = ExtractableDataSets.ToDictionary(ds => ds.ID, d => d); foreach (SelectedDataSets s in SelectedDataSets) { s.InjectKnown(dsDictionary[s.ExtractableDataSet_ID]); } ReportProgress("Injecting SelectedDataSets"); //This means that the ToString method in ExtractableDataSet doesn't need to go lookup catalogue info var catalogueIdDict = AllCatalogues.ToDictionary(c => c.ID, c2 => c2); foreach (ExtractableDataSet ds in ExtractableDataSets) { if (catalogueIdDict.TryGetValue(ds.Catalogue_ID, out Catalogue cata)) { ds.InjectKnown(cata); } } ReportProgress("Injecting ExtractableDataSet"); AllPackages = GetAllObjects <ExtractableDataSetPackage>(dataExportRepository); Projects = GetAllObjects <Project>(dataExportRepository); ExtractionConfigurations = GetAllObjects <ExtractionConfiguration>(dataExportRepository); ReportProgress("Get Projects and Configurations"); ExtractionConfigurationsByProject = ExtractionConfigurations.GroupBy(k => k.Project_ID).ToDictionary(gdc => gdc.Key, gdc => gdc.ToList()); ReportProgress("Grouping Extractions by Project"); AllGlobalExtractionFilterParameters = GetAllObjects <GlobalExtractionFilterParameter>(dataExportRepository); AllContainers = GetAllObjects <FilterContainer>(dataExportRepository).ToDictionary(o => o.ID, o => o); AllDeployedExtractionFilters = GetAllObjects <DeployedExtractionFilter>(dataExportRepository); _allParameters = GetAllObjects <DeployedExtractionFilterParameter>(dataExportRepository); ReportProgress("Getting Filters"); //if we are using a database repository then we can make use of the caching class DataExportFilterManagerFromChildProvider to speed up //filter contents var dbRepo = dataExportRepository as DataExportRepository; _dataExportFilterManager = dbRepo == null ? dataExportRepository.FilterManager : new DataExportFilterManagerFromChildProvider(dbRepo, this); ReportProgress("Building FilterManager"); Cohorts = GetAllObjects <ExtractableCohort>(dataExportRepository); _cohortsByOriginId = new Dictionary <int, HashSet <ExtractableCohort> >(); foreach (ExtractableCohort c in Cohorts) { if (!_cohortsByOriginId.ContainsKey(c.OriginID)) { _cohortsByOriginId.Add(c.OriginID, new HashSet <ExtractableCohort>()); } _cohortsByOriginId[c.OriginID].Add(c); } _configurationToDatasetMapping = new Dictionary <ExtractionConfiguration, List <SelectedDataSets> >(); ReportProgress("Fetching Cohorts"); GetCohortAvailability(); ReportProgress("GetCohortAvailability"); var configToSds = SelectedDataSets.GroupBy(k => k.ExtractionConfiguration_ID).ToDictionary(gdc => gdc.Key, gdc => gdc.ToList()); foreach (ExtractionConfiguration configuration in ExtractionConfigurations) { if (configToSds.TryGetValue(configuration.ID, out List <SelectedDataSets> result)) { _configurationToDatasetMapping.Add(configuration, result); } } ReportProgress("Mapping configurations to datasets"); RootCohortsNode = new AllCohortsNode(); AddChildren(RootCohortsNode, new DescendancyList(RootCohortsNode)); foreach (ExtractableDataSetPackage package in AllPackages) { AddChildren(package, new DescendancyList(package)); } ReportProgress("Packages and Cohorts"); foreach (Project p in Projects) { AddChildren(p, new DescendancyList(p)); } ReportProgress("Projects"); //work out all the Catalogues that are extractable (Catalogues are extractable if there is an ExtractableDataSet with the Catalogue_ID that matches them) var cataToEds = new Dictionary <int, ExtractableDataSet>(ExtractableDataSets.ToDictionary(k => k.Catalogue_ID)); //inject extractability into Catalogues foreach (Catalogue catalogue in AllCatalogues) { if (cataToEds.TryGetValue(catalogue.ID, out ExtractableDataSet result)) { catalogue.InjectKnown(result.GetCatalogueExtractabilityStatus()); } else { catalogue.InjectKnown(new CatalogueExtractabilityStatus(false, false)); } } ReportProgress("Catalogue extractability injection"); try { AddPipelineUseCases(new Dictionary <string, PipelineUseCase> { { "File Import", UploadFileUseCase.DesignTime() }, { "Extraction", ExtractionPipelineUseCase.DesignTime() }, { "Release", ReleaseUseCase.DesignTime() }, { "Cohort Creation", CohortCreationRequest.DesignTime() }, { "Caching", CachingPipelineUseCase.DesignTime() }, { "Aggregate Committing", CreateTableFromAggregateUseCase.DesignTime(repositoryLocator.CatalogueRepository) } }); } catch (Exception ex) { _errorsCheckNotifier.OnCheckPerformed(new CheckEventArgs("Failed to build DesignTime PipelineUseCases", CheckResult.Fail, ex)); } ReportProgress("Pipeline adding"); }
public override void Execute() { base.Execute(); if (_aggregateConfiguration == null) { _aggregateConfiguration = SelectOne <AggregateConfiguration>(Activator.RepositoryLocator.CatalogueRepository); } if (_aggregateConfiguration == null) { return; } if (_aggregateConfiguration.IsJoinablePatientIndexTable()) { var dr = MessageBox.Show("Would you like to constrain the records to only those in a committed cohort?", "Cohort Records Only", MessageBoxButtons.YesNoCancel); if (dr == DialogResult.Cancel) { return; } if (dr == DialogResult.Yes) { _cohort = SelectOne <ExtractableCohort>(Activator.RepositoryLocator.DataExportRepository); if (_cohort == null) { return; } } if (_cohort != null) { var externalData = _cohort.GetExternalData(); if (externalData != null) { var projNumber = externalData.ExternalProjectNumber; var projs = Activator.RepositoryLocator.DataExportRepository.GetAllObjects <Project>().Where(p => p.ProjectNumber == projNumber).ToArray(); if (projs.Length == 1) { _projectSpecific = projs[0]; } } } } _table = SelectTable(true, "Choose destination table name"); if (_table == null) { return; } var useCase = new CreateTableFromAggregateUseCase(_aggregateConfiguration, _cohort, _table); var ui = new ConfigureAndExecutePipelineUI(useCase, Activator); ui.PipelineExecutionFinishedsuccessfully += ui_PipelineExecutionFinishedsuccessfully; Activator.ShowWindow(ui, true); }