/// <summary>
/// For refreshing the current extraction configuration CohortIdentificationConfiguration ONLY. The ExtractionConfiguration must have a cic and a refresh pipeline configured on it.
/// </summary>
/// <param name="configuration"></param>
public CohortCreationRequest(ExtractionConfiguration configuration)
{
_repository = (DataExportRepository)configuration.Repository;
if (configuration.CohortIdentificationConfiguration_ID == null)
{
throw new NotSupportedException("Configuration '" + configuration + "' does not have an associated CohortIdentificationConfiguration for cohort refreshing");
}
var origCohort = configuration.Cohort;
var origCohortData = origCohort.GetExternalData();
CohortIdentificationConfiguration = configuration.CohortIdentificationConfiguration;
Project = configuration.Project;
if (Project.ProjectNumber == null)
{
throw new ProjectNumberException("Project '" + Project + "' does not have a ProjectNumber");
}
var definition = new CohortDefinition(null, origCohortData.ExternalDescription, origCohortData.ExternalVersion + 1, (int)Project.ProjectNumber, origCohort.ExternalCohortTable);
definition.CohortReplacedIfAny = origCohort;
NewCohortDefinition = definition;
DescriptionForAuditLog = "Cohort Refresh";
AddInitializationObject(Project);
AddInitializationObject(CohortIdentificationConfiguration);
AddInitializationObject(FileToLoad);
AddInitializationObject(ExtractionIdentifierColumn);
AddInitializationObject(this);
GenerateContext();
}
public CohortCreationRequest(Project project, CohortDefinition newCohortDefinition, IDataExportRepository repository, string descriptionForAuditLog)
{
_repository = repository;
Project = project;
NewCohortDefinition = newCohortDefinition;
DescriptionForAuditLog = descriptionForAuditLog;
AddInitializationObject(Project);
AddInitializationObject(this);
GenerateContext();
}
public void DeprecateOldCohort(bool deprecate)
{
var proj = new Project(DataExportRepository, projName);
proj.ProjectNumber = 999;
proj.SaveToDatabase();
// we are replacing this imaginary cohort
var definition998 = new CohortDefinition(null, "CommittingNewCohorts", 1, 999, _externalCohortTable);
// with this one (v2)
var definition999 = new CohortDefinition(null, "CommittingNewCohorts", 2, 999, _externalCohortTable);
// Create a basic cohort first
CohortCreationRequest request1 = new CohortCreationRequest(proj, definition998, (DataExportRepository)DataExportRepository, "fish");
request1.Check(new ThrowImmediatelyCheckNotifier());
using var con = _cohortDatabase.Server.GetManagedConnection();
request1.PushToServer(con);
request1.ImportAsExtractableCohort(deprecate, false);
// the definition was imported and should now be a saved ExtractableCohort
var cohort998 = request1.CohortCreatedIfAny;
Assert.IsNotNull(cohort998);
Assert.IsFalse(cohort998.IsDeprecated);
// define that the new definition attempts to replace the old one
definition999.CohortReplacedIfAny = cohort998;
CohortCreationRequest request2 = new CohortCreationRequest(proj, definition999, (DataExportRepository)DataExportRepository, "fish");
request2.Check(new ThrowImmediatelyCheckNotifier());
request2.PushToServer(con);
request2.ImportAsExtractableCohort(deprecate, false);
// after committing the new cohort the old one should be deprecated?
cohort998.RevertToDatabaseState();
Assert.AreEqual(deprecate, cohort998.IsDeprecated);
}
private void btnExecute_Click(object sender, EventArgs e)
{
Cursor = Cursors.WaitCursor;
string problem = AllRequiredDataPresent();
try
{
if (problem != null)
{
MessageBox.Show(problem);
return;
}
ragExecute.Reset();
//create the project
if (_project == null)
{
_project = new Project(Activator.RepositoryLocator.DataExportRepository, tbProjectName.Text);
}
_project.ProjectNumber = int.Parse(tbProjectNumber.Text);
_project.ExtractionDirectory = tbExtractionDirectory.Text;
if (!Directory.Exists(_project.ExtractionDirectory))
{
Directory.CreateDirectory(_project.ExtractionDirectory);
}
_project.SaveToDatabase();
if (_configuration == null)
{
_configuration = new ExtractionConfiguration(Activator.RepositoryLocator.DataExportRepository,
_project);
_configuration.Name = "Cases";
_configuration.SaveToDatabase();
}
foreach (ExtractableDataSet ds in _selectedDatasets)
{
_configuration.AddDatasetToConfiguration(ds);
}
ICommandExecution cmdAssociateCicWithProject = null;
if (_cohortCreated == null && cbDefineCohort.Checked)
{
var cohortDefinition = new CohortDefinition(null, tbCohortName.Text, 1, _project.ProjectNumber.Value,
(ExternalCohortTable)ddCohortSources.SelectedItem);
//execute the cohort creation bit
var cohortRequest = new CohortCreationRequest(_project, cohortDefinition,
(DataExportRepository)Activator.RepositoryLocator.DataExportRepository, tbCohortName.Text);
ComboBox dd;
if (_cohortFile != null)
{
//execute cohort creation from file.
cohortRequest.FileToLoad = new FlatFileToLoad(_cohortFile);
dd = ddFilePipeline;
}
else
{
//execute cohort creation from cic
cohortRequest.CohortIdentificationConfiguration =
(CohortIdentificationConfiguration)cbxCohort.SelectedItem;
dd = ddCicPipeline;
//since we are about to execute a cic and store the results we should associate it with the Project (if successful)
cmdAssociateCicWithProject = new ExecuteCommandAssociateCohortIdentificationConfigurationWithProject(Activator).SetTarget(
_project).SetTarget(cohortRequest.CohortIdentificationConfiguration);
}
var engine = cohortRequest.GetEngine((Pipeline)dd.SelectedItem, new ThrowImmediatelyDataLoadEventListener());
engine.ExecutePipeline(new GracefulCancellationToken());
_cohortCreated = cohortRequest.CohortCreatedIfAny;
}
if (cbDefineCohort.Checked)
{
//associate the configuration with the cohort
_configuration.Cohort_ID = _cohortCreated.ID;
//set the pipeline to use
var pipeline = (Pipeline)ddExtractionPipeline.SelectedItem;
if (pipeline != null)
{
_configuration.DefaultPipeline_ID = pipeline.ID;
}
_configuration.SaveToDatabase();
//User defined cohort if it came from cic then associate the cic with the project
if (cmdAssociateCicWithProject != null && !cmdAssociateCicWithProject.IsImpossible)
{
cmdAssociateCicWithProject.Execute();
}
}
Cursor = Cursors.Default;
ExtractionConfigurationCreatedIfAny = _configuration;
DialogResult = DialogResult.OK;
MessageBox.Show("Project Created Successfully");
Close();
}
catch (Exception exception)
{
ragExecute.Fatal(exception);
}
finally
{
Cursor = Cursors.Default;
}
}
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 MigrateUsages(bool migrate)
{
var proj = new Project(DataExportRepository, projName);
proj.ProjectNumber = 999;
proj.SaveToDatabase();
// we are replacing this imaginary cohort
var definition998 = new CohortDefinition(null, "CommittingNewCohorts", 1, 999, _externalCohortTable);
// with this one (v2)
var definition999 = new CohortDefinition(null, "CommittingNewCohorts", 2, 999, _externalCohortTable);
// Create a basic cohort first
CohortCreationRequest request1 = new CohortCreationRequest(proj, definition998, (DataExportRepository)DataExportRepository, "fish");
request1.Check(new ThrowImmediatelyCheckNotifier());
using var con = _cohortDatabase.Server.GetManagedConnection();
request1.PushToServer(con);
request1.ImportAsExtractableCohort(true, migrate);
// the definition was imported and should now be a saved ExtractableCohort
var cohort998 = request1.CohortCreatedIfAny;
Assert.IsNotNull(cohort998);
Assert.IsFalse(cohort998.IsDeprecated);
// legit user 1
var ec1 = new ExtractionConfiguration(DataExportRepository, proj)
{
IsReleased = false,
Cohort_ID = cohort998.ID
};
ec1.SaveToDatabase();
// legit user 2
var ec2 = new ExtractionConfiguration(DataExportRepository, proj)
{
IsReleased = false,
Cohort_ID = cohort998.ID
};
ec2.SaveToDatabase();
// has no cohort yet defined so should not be migrated
var ec3 = new ExtractionConfiguration(DataExportRepository, proj);
// is frozen so should not be migrated
var ec4 = new ExtractionConfiguration(DataExportRepository, proj)
{
IsReleased = true,
Cohort_ID = cohort998.ID
};
ec4.SaveToDatabase();
// define that the new definition attempts to replace the old one
definition999.CohortReplacedIfAny = cohort998;
CohortCreationRequest request2 = new CohortCreationRequest(proj, definition999, (DataExportRepository)DataExportRepository, "fish");
request2.Check(new ThrowImmediatelyCheckNotifier());
request2.PushToServer(con);
request2.ImportAsExtractableCohort(true, migrate);
// the definition was imported and should now be a saved ExtractableCohort
var cohort999 = request2.CohortCreatedIfAny;
Assert.IsNotNull(cohort999);
// after committing the new cohort who should be migrated?
ec1.RevertToDatabaseState();
ec2.RevertToDatabaseState();
ec3.RevertToDatabaseState();
ec4.RevertToDatabaseState();
// should have been updated to use the new cohort
Assert.AreEqual(ec1.Cohort_ID, migrate ? cohort999.ID : cohort998.ID);
Assert.AreEqual(ec2.Cohort_ID, migrate ? cohort999.ID: cohort998.ID);
// should not have magically gotten a cohort
Assert.IsNull(ec3.Cohort_ID);
// is frozen so should not have been changed to the new cohort (and therefore still use cohort998)
Assert.AreEqual(ec4.Cohort_ID, cohort998.ID);
}
