private CohortIdentificationConfiguration CreateCohortIdentificationConfiguration(ExtractionFilter inclusionFilter1)
{
//Create the top level configuration object
var cic = new CohortIdentificationConfiguration(_repos.CatalogueRepository, "Tayside Lung Cancer Cohort");
//create a UNION container for Inclusion Criteria
var container = new CohortAggregateContainer(_repos.CatalogueRepository, SetOperation.UNION);
container.Name = "Inclusion Criteria";
container.SaveToDatabase();
cic.RootCohortAggregateContainer_ID = container.ID;
cic.SaveToDatabase();
//Create a new cohort set to the 'Inclusion Criteria' based on the filters Catalogue
var cata = inclusionFilter1.ExtractionInformation.CatalogueItem.Catalogue;
var ac = cic.CreateNewEmptyConfigurationForCatalogue(cata, (a, b) => { throw new Exception("Problem encountered with chi column(s)"); }, false);
container.AddChild(ac, 0);
//Add the filter to the WHERE logic of the cohort set
var whereContainer = new AggregateFilterContainer(_repos.CatalogueRepository, FilterContainerOperation.OR);
ac.Name = "People with " + inclusionFilter1.Name;
ac.RootFilterContainer_ID = whereContainer.ID;
cic.EnsureNamingConvention(ac); //this will put cicx at the front and cause implicit SaveToDatabase
FilterImporter filterImporter = new FilterImporter(new AggregateFilterFactory(_repos.CatalogueRepository), null);
var cloneFilter = filterImporter.ImportFilter(inclusionFilter1, null);
whereContainer.AddChild(cloneFilter);
return(cic);
}
public AggregateConfigurationCombineable GenerateAggregateConfigurationFor(IBasicActivateItems activator,
CohortIdentificationConfiguration cic, bool importMandatoryFilters = true,
[CallerMemberName] string caller = null)
{
var newAggregate = cic.CreateNewEmptyConfigurationForCatalogue(Catalogue,
ResolveMultipleExtractionIdentifiers ??
((a,b)=> CohortCombineToCreateCommandHelper.PickOneExtractionIdentifier(activator,a, b)),
importMandatoryFilters);
return new AggregateConfigurationCombineable(newAggregate);
}
private void PopulateCohortDatabaseWithRecordsFromNonTvfCatalogue()
{
//create a cohort identification configuration (identifies people from datasets using set operations - see CohortManager)
_cic = new CohortIdentificationConfiguration(CatalogueRepository, "TbvfCIC");
_cic.CreateRootContainerIfNotExists();
//turn the catalogue _nonTvfCatalogue into a cohort set and add it to the root container
var newAggregate = _cic.CreateNewEmptyConfigurationForCatalogue(_nonTvfCatalogue, (s, e) => { throw new Exception("Did not expect there to be more than 1!"); });
var root = _cic.RootCohortAggregateContainer;
root.AddChild(newAggregate, 0);
//create a pipeline for executing this CIC and turning it into a cohort
_pipe = new Pipeline(CatalogueRepository, "CREATE COHORT:By Executing CIC");
var source = new PipelineComponent(CatalogueRepository, _pipe, typeof(CohortIdentificationConfigurationSource), 0, "CIC Source");
_project = new Project(DataExportRepository, "TvfProject");
_project.ProjectNumber = 12;
_project.ExtractionDirectory = TestContext.CurrentContext.TestDirectory;
_project.SaveToDatabase();
var destination = new PipelineComponent(CatalogueRepository, _pipe, typeof(BasicCohortDestination), 1, "Destination");
_pipe.SourcePipelineComponent_ID = source.ID;
_pipe.DestinationPipelineComponent_ID = destination.ID;
_pipe.SaveToDatabase();
//create pipeline arguments
source.CreateArgumentsForClassIfNotExists <CohortIdentificationConfigurationSource>();
destination.CreateArgumentsForClassIfNotExists <BasicCohortDestination>();
//create pipeline initialization objects
var request = new CohortCreationRequest(_project, new CohortDefinition(null, "MyFirstCohortForTvfTest", 1, 12, _externalCohortTable), (DataExportRepository)DataExportRepository, "Here goes nothing");
request.CohortIdentificationConfiguration = _cic;
var engine = request.GetEngine(_pipe, new ThrowImmediatelyDataLoadEventListener());
engine.ExecutePipeline(new GracefulCancellationToken());
}
public void RefreshCohort_WithCaching()
{
ExtractionPipelineUseCase useCase;
IExecuteDatasetExtractionDestination results;
var pipe = new Pipeline(CatalogueRepository, "RefreshPipeWithCaching");
var source = new PipelineComponent(CatalogueRepository, pipe, typeof(CohortIdentificationConfigurationSource), 0);
var args = source.CreateArgumentsForClassIfNotExists <CohortIdentificationConfigurationSource>();
var freezeArg = args.Single(a => a.Name.Equals("FreezeAfterSuccessfulImport"));
freezeArg.SetValue(false);
freezeArg.SaveToDatabase();
var dest = new PipelineComponent(CatalogueRepository, pipe, typeof(BasicCohortDestination), 0);
var argsDest = dest.CreateArgumentsForClassIfNotExists <BasicCohortDestination>();
var allocatorArg = argsDest.Single(a => a.Name.Equals("ReleaseIdentifierAllocator"));
allocatorArg.SetValue(null);
allocatorArg.SaveToDatabase();
pipe.SourcePipelineComponent_ID = source.ID;
pipe.DestinationPipelineComponent_ID = dest.ID;
pipe.SaveToDatabase();
Execute(out useCase, out results);
var oldcohort = _configuration.Cohort;
//Create a query cache
var p = new QueryCachingPatcher();
ExternalDatabaseServer queryCacheServer = new ExternalDatabaseServer(CatalogueRepository, "TestCohortRefreshing_CacheTest", p);
DiscoveredDatabase cachedb = DiscoveredServerICanCreateRandomDatabasesAndTablesOn.ExpectDatabase("TestCohortRefreshing_CacheTest");
if (cachedb.Exists())
{
cachedb.Drop();
}
new MasterDatabaseScriptExecutor(cachedb).CreateAndPatchDatabase(p, new ThrowImmediatelyCheckNotifier());
queryCacheServer.SetProperties(cachedb);
//Create a Cohort Identification configuration (query) that will identify the cohort
CohortIdentificationConfiguration cic = new CohortIdentificationConfiguration(RepositoryLocator.CatalogueRepository, "RefreshCohort.cs");;
try
{
//make it use the cache
cic.QueryCachingServer_ID = queryCacheServer.ID;
cic.SaveToDatabase();
//give it a single table query to fetch distinct chi from test data
var agg = cic.CreateNewEmptyConfigurationForCatalogue(_catalogue, null);
//add the sub query as the only entry in the cic (in the root container)
cic.CreateRootContainerIfNotExists();
cic.RootCohortAggregateContainer.AddChild(agg, 1);
//make the ExtractionConfiguration refresh cohort query be the cic
_configuration.CohortIdentificationConfiguration_ID = cic.ID;
_configuration.CohortRefreshPipeline_ID = pipe.ID;
_configuration.SaveToDatabase();
//get a refreshing engine
var engine = new CohortRefreshEngine(new ThrowImmediatelyDataLoadEventListener(), _configuration);
engine.Execute();
Assert.NotNull(engine.Request.NewCohortDefinition);
var oldData = oldcohort.GetExternalData();
Assert.AreEqual(oldData.ExternalDescription, engine.Request.NewCohortDefinition.Description);
Assert.AreEqual(oldData.ExternalVersion + 1, engine.Request.NewCohortDefinition.Version);
Assert.AreNotEqual(oldcohort.CountDistinct, engine.Request.CohortCreatedIfAny.CountDistinct);
//now nuke all data in the catalogue so the cic returns nobody (except that the identifiers are cached eh?)
DataAccessPortal.GetInstance().ExpectDatabase(_tableInfo, DataAccessContext.InternalDataProcessing).ExpectTable(_tableInfo.GetRuntimeName()).Truncate();
var toMem = new ToMemoryDataLoadEventListener(false);
//get a new engine
engine = new CohortRefreshEngine(toMem, _configuration);
//execute it
var ex = Assert.Throws <Exception>(() => engine.Execute());
Assert.IsTrue(ex.InnerException.InnerException.Message.Contains("CohortIdentificationCriteria execution resulted in an empty dataset"));
//expected this message to happen
//that it did clear the cache
Assert.AreEqual(1, toMem.EventsReceivedBySender.SelectMany(kvp => kvp.Value).Count(msg => msg.Message.Equals("Clearing Cohort Identifier Cache")));
}
finally
{
//make the ExtractionConfiguration not use the cic query
_configuration.CohortRefreshPipeline_ID = null;
_configuration.CohortIdentificationConfiguration_ID = null;
_configuration.SaveToDatabase();
//delete the cic query
cic.QueryCachingServer_ID = null;
cic.SaveToDatabase();
cic.DeleteInDatabase();
//delete the caching database
queryCacheServer.DeleteInDatabase();
cachedb.Drop();
}
}
public AggregateConfigurationCommand GenerateAggregateConfigurationFor(CohortIdentificationConfiguration cic, bool importMandatoryFilters = true, [CallerMemberName] string caller = null)
{
var newAggregate = cic.CreateNewEmptyConfigurationForCatalogue(Catalogue, ResolveMultipleExtractionIdentifiers ?? CohortCommandHelper.PickOneExtractionIdentifier, importMandatoryFilters);
return(new AggregateConfigurationCommand(newAggregate));
}