public void CommittingNewCohortFile_CallPipeline()
{
var listener = new ThrowImmediatelyDataLoadEventListener();
var proj = new Project(DataExportRepository, projName);
proj.ProjectNumber = 999;
proj.SaveToDatabase();
CohortCreationRequest request = new CohortCreationRequest(proj, new CohortDefinition(null, "CommittingNewCohorts", 1, 999, _externalCohortTable), (DataExportRepository)DataExportRepository, "fish");
request.Check(new ThrowImmediatelyCheckNotifier());
DelimitedFlatFileDataFlowSource source = new DelimitedFlatFileDataFlowSource();
BasicCohortDestination destination = new BasicCohortDestination();
source.Separator = ",";
source.StronglyTypeInput = true;
DataFlowPipelineEngine <DataTable> pipeline = new DataFlowPipelineEngine <DataTable>((DataFlowPipelineContext <DataTable>)request.GetContext(), source, destination, listener);
pipeline.Initialize(new FlatFileToLoad(new FileInfo(filename)), request);
pipeline.ExecutePipeline(new GracefulCancellationToken());
//there should be a new ExtractableCohort now
Assert.NotNull(request.NewCohortDefinition.ID);
var ec = DataExportRepository.GetAllObjects <ExtractableCohort>().Single(c => c.OriginID == request.NewCohortDefinition.ID);
//with the data in it from the test file
Assert.AreEqual(ec.Count, 3);
}
public void CommitCohortExampleTest(DatabaseType dbType, string privateDataType)
{
RunBlitzDatabases(RepositoryLocator);
//find the test server (where we will create the store schema)
var db = GetCleanedServer(dbType);
//create the cohort store table
var wizard = new CreateNewCohortDatabaseWizard(db, CatalogueRepository, DataExportRepository, false);
var privateColumn = new PrivateIdentifierPrototype("chi", privateDataType);
var externalCohortTable = wizard.CreateDatabase(privateColumn, new ThrowImmediatelyCheckNotifier());
Assert.AreEqual(dbType, externalCohortTable.DatabaseType);
//create a project into which we want to import a cohort
var project = new Project(DataExportRepository, "MyProject");
project.ProjectNumber = 500;
project.SaveToDatabase();
//create a description of the cohort we are importing
var definition = new CohortDefinition(null, "MyCohort", 1, 500, externalCohortTable);
//create our cohort (normally this would be read from a file or be the results of cohort identification query)
var dt = new DataTable();
dt.Columns.Add("chi");
dt.Rows.Add("0101010101");
dt.Rows.Add("0202020202");
//Create a pipeline (we only need the destination)
var pipelineDestination = new BasicCohortDestination();
//choose how to allocate the anonymous release identifiers
pipelineDestination.ReleaseIdentifierAllocator = typeof(ProjectConsistentGuidReleaseIdentifierAllocator);
//initialize the destination
pipelineDestination.PreInitialize(
new CohortCreationRequest(project, definition, DataExportRepository, "A cohort created in an example unit test"),
new ThrowImmediatelyDataLoadEventListener());
//process the cohort data table
pipelineDestination.ProcessPipelineData(dt, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
//there should be no cohorts yet
Assert.IsEmpty(DataExportRepository.GetAllObjects <ExtractableCohort>());
//dispose of the pipeline
pipelineDestination.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
//now there should be one
ExtractableCohort cohort = DataExportRepository.GetAllObjects <ExtractableCohort>().Single();
//make sure we are all on the same page about what the DBMS type is (nothing cached etc)
Assert.AreEqual(dbType, cohort.ExternalCohortTable.DatabaseType);
Assert.AreEqual(dbType, cohort.GetQuerySyntaxHelper().DatabaseType);
Assert.AreEqual(500, cohort.ExternalProjectNumber);
Assert.AreEqual(2, cohort.CountDistinct);
var tbl = externalCohortTable.DiscoverCohortTable();
Assert.AreEqual(2, tbl.GetRowCount());
var dtInDatabase = tbl.GetDataTable();
//guid will be something like "6fb23de5-e8eb-46eb-84b5-dd368da21073"
Assert.AreEqual(36, dtInDatabase.Rows[0]["ReleaseId"].ToString().Length);
Assert.AreEqual("0101010101", dtInDatabase.Rows[0]["chi"]);
}
public void TestActuallyCreatingIt(DatabaseType type)
{
var db = GetCleanedServer(type);
//drop it
db.Drop();
CreateNewCohortDatabaseWizard wizard = new CreateNewCohortDatabaseWizard(db, CatalogueRepository, DataExportRepository, false);
_extractionInfo2.IsExtractionIdentifier = true;
_extractionInfo2.SaveToDatabase();
var candidate = wizard.GetPrivateIdentifierCandidates().Single(c => c.RuntimeName.Equals("PrivateIdentifierB"));
var ect = wizard.CreateDatabase(
candidate,
new ThrowImmediatelyCheckNotifier());
//database should exist
DiscoveredServerICanCreateRandomDatabasesAndTablesOn.ExpectDatabase(cohortDatabaseName);
Assert.IsTrue(db.Exists());
//did it create the correct type?
Assert.AreEqual(type, ect.DatabaseType);
//the ExternalCohortTable should pass tests
ect.Check(new ThrowImmediatelyCheckNotifier());
//now try putting someone in it
//the project it will go under
var project = new Project(DataExportRepository, "MyProject");
project.ProjectNumber = 10;
project.SaveToDatabase();
//the request to put it under there
var request = new CohortCreationRequest(project, new CohortDefinition(null, "My cohort", 1, 10, ect), DataExportRepository, "Blah");
//the actual cohort data
DataTable dt = new DataTable();
dt.Columns.Add(_extractionInfo2.GetRuntimeName());
dt.Rows.Add(101243); //_extractionInfo2 is of type int
//the destination component that will put it there
var dest = new BasicCohortDestination();
dest.PreInitialize(request, new ThrowImmediatelyDataLoadEventListener());
//tell it to use the guid allocator
dest.ReleaseIdentifierAllocator = typeof(GuidReleaseIdentifierAllocator);
dest.ProcessPipelineData(dt, new ThrowImmediatelyDataLoadEventListener(), new GracefulCancellationToken());
dest.Dispose(new ThrowImmediatelyDataLoadEventListener(), null);
var cohort = request.CohortCreatedIfAny;
Assert.IsNotNull(cohort);
var externalData = cohort.GetExternalData();
Assert.AreEqual(10, externalData.ExternalProjectNumber);
Assert.IsFalse(string.IsNullOrEmpty(externalData.ExternalDescription));
Assert.AreEqual(DateTime.Now.Year, externalData.ExternalCohortCreationDate.Value.Year);
Assert.AreEqual(DateTime.Now.Month, externalData.ExternalCohortCreationDate.Value.Month);
Assert.AreEqual(DateTime.Now.Day, externalData.ExternalCohortCreationDate.Value.Day);
Assert.AreEqual(DateTime.Now.Hour, externalData.ExternalCohortCreationDate.Value.Hour);
cohort.AppendToAuditLog("Test");
Assert.IsTrue(cohort.AuditLog.Contains("Test"));
Assert.AreEqual(1, cohort.Count);
Assert.AreEqual(1, cohort.CountDistinct);
var cohortTable = cohort.FetchEntireCohort();
Assert.AreEqual(1, cohortTable.Rows.Count);
var helper = ect.GetQuerySyntaxHelper();
Assert.AreEqual(101243, cohortTable.Rows[0][helper.GetRuntimeName(ect.PrivateIdentifierField)]);
var aguid = cohortTable.Rows[0][helper.GetRuntimeName(ect.ReleaseIdentifierField)].ToString();
Assert.IsFalse(string.IsNullOrWhiteSpace(aguid)); //should be a guid
//test reversing the anonymisation of something
var dtAno = new DataTable();
dtAno.Columns.Add(cohort.GetReleaseIdentifier(true));
dtAno.Columns.Add("Age");
dtAno.Rows.Add(aguid, 23);
dtAno.Rows.Add(aguid, 99);
cohort.ReverseAnonymiseDataTable(dtAno, new ThrowImmediatelyDataLoadEventListener(), true);
Assert.AreEqual(2, dtAno.Columns.Count);
Assert.IsTrue(dtAno.Columns.Contains(cohort.GetPrivateIdentifier(true)));
Assert.AreEqual("101243", dtAno.Rows[0][cohort.GetPrivateIdentifier(true)]);
Assert.AreEqual("101243", dtAno.Rows[1][cohort.GetPrivateIdentifier(true)]);
}
