/// <summary>
/// Creates new databases on the given server for RDMP platform databases
/// </summary>
/// <param name="options"></param>
public void CreatePlatformDatabases(PlatformDatabaseCreationOptions options)
{
DiscoveredServerHelper.CreateDatabaseTimeoutInSeconds = options.CreateDatabaseTimeout;
Create(DefaultCatalogueDatabaseName, new CataloguePatcher(), options);
Create(DefaultDataExportDatabaseName, new DataExportPatcher(), options);
var dqe = Create(DefaultDQEDatabaseName, new DataQualityEnginePatcher(), options);
var logging = Create(DefaultLoggingDatabaseName, new LoggingDatabasePatcher(), options);
CatalogueRepository.SuppressHelpLoading = true;
var repo = new PlatformDatabaseCreationRepositoryFinder(options);
if (!options.SkipPipelines)
{
var creator = new CataloguePipelinesAndReferencesCreation(repo, logging, dqe);
creator.Create();
}
if (options.ExampleDatasets)
{
var examples = new ExampleDatasetsCreation(new ThrowImmediatelyActivator(repo, null), repo);
var server = new DiscoveredServer(options.GetBuilder("ExampleData"));
examples.Create(server.GetCurrentDatabase(), new ThrowImmediatelyCheckNotifier()
{
WriteToConsole = true
}, options);
}
}
public PlatformDatabaseCreationRepositoryFinder(PlatformDatabaseCreationOptions options)
{
var cata = options.GetBuilder(PlatformDatabaseCreation.DefaultCatalogueDatabaseName);
var export = options.GetBuilder(PlatformDatabaseCreation.DefaultDataExportDatabaseName);
_linkedRepositoryProvider = new LinkedRepositoryProvider(cata.ConnectionString, export.ConnectionString);
}
internal void Create(DiscoveredDatabase db, ICheckNotifier notifier, PlatformDatabaseCreationOptions options)
{
if (db.Exists())
{
if (options.DropDatabases)
{
db.Drop();
}
else
{
throw new Exception("Database " + db.GetRuntimeName() + " already exists and allowDrop option was not specified");
}
}
notifier.OnCheckPerformed(new CheckEventArgs("About to create " + db.GetRuntimeName(), CheckResult.Success));
//create a new database for the datasets
db.Create();
notifier.OnCheckPerformed(new CheckEventArgs("Succesfully created " + db.GetRuntimeName(), CheckResult.Success));
//fixed seed so everyone gets the same datasets
var r = new Random(options.Seed);
notifier.OnCheckPerformed(new CheckEventArgs("Generating people", CheckResult.Success));
//people
var people = new PersonCollection();
people.GeneratePeople(options.NumberOfPeople, r);
//datasets
var biochem = ImportCatalogue(Create <Biochemistry>(db, people, r, notifier, options.NumberOfRowsPerDataset, "chi", "Healthboard", "SampleDate", "TestCode"));
var demography = ImportCatalogue(Create <Demography>(db, people, r, notifier, options.NumberOfRowsPerDataset, "chi", "dtCreated", "hb_extract"));
var prescribing = ImportCatalogue(Create <Prescribing>(db, people, r, notifier, options.NumberOfRowsPerDataset, "chi", "PrescribedDate", "Name")); //<- this is slooo!
var admissions = ImportCatalogue(Create <HospitalAdmissions>(db, people, r, notifier, options.NumberOfRowsPerDataset, "chi", "AdmissionDate"));
var carotid = Create <CarotidArteryScan>(db, people, r, notifier, options.NumberOfRowsPerDataset, "RECORD_NUMBER");
//the following should not be extractable
ForExtractionInformations(demography,
e => e.DeleteInDatabase(),
"chi_num_of_curr_record",
"surname",
"forename",
"current_address_L1",
"current_address_L2",
"current_address_L3",
"current_address_L4",
"birth_surname",
"previous_surname",
"midname",
"alt_forename",
"other_initials",
"previous_address_L1",
"previous_address_L2",
"previous_address_L3",
"previous_address_L4",
"previous_postcode",
"date_address_changed",
"adr",
"previous_gp_accept_date",
"hic_dataLoadRunID");
//the following should be special approval only
ForExtractionInformations(demography,
e => {
e.ExtractionCategory = ExtractionCategory.SpecialApprovalRequired;
e.SaveToDatabase();
},
"current_postcode",
"current_gp",
"previous_gp",
"date_of_birth");
CreateAdmissionsViews(db);
var vConditions = ImportCatalogue(db.ExpectTable("vConditions"));
var vOperations = ImportCatalogue(db.ExpectTable("vOperations"));
CreateGraph(biochem, "Test Codes", "TestCode", false, null);
CreateGraph(biochem, "Test Codes By Date", "SampleDate", true, "TestCode");
CreateFilter(biochem, "Creatinine", "TestCode", "TestCode like '%CRE%'", @"Serum creatinine is a blood measurement. It is an indicator of renal health.");
CreateFilter(biochem, "Test Code", "TestCode", "TestCode like @code", "Filters any test code set");
CreateExtractionInformation(demography, "Age", "date_of_birth", "FLOOR(DATEDIFF(DAY, date_of_birth, GETDATE()) / 365.25) As Age");
var fAge = CreateFilter(demography, "Older at least x years", "Age", "FLOOR(DATEDIFF(DAY, date_of_birth, GETDATE()) / 365.25) >= @age", "Patients age is greater than or equal to the provided @age");
SetParameter(fAge, "@age", "int", "16");
CreateGraph(demography, "Patient Ages", "Age", false, null);
CreateGraph(prescribing, "Approved Name", "ApprovedName", false, null);
CreateGraph(prescribing, "Approved Name Over Time", "PrescribedDate", true, "ApprovedName");
CreateGraph(prescribing, "Bnf", "FormattedBnfCode", false, null);
CreateGraph(prescribing, "Bnf Over Time", "PrescribedDate", true, "FormattedBnfCode");
CreateFilter(
CreateGraph(vConditions, "Conditions frequency", "Field", false, "Condition"),
"Common Conditions Only",
@"(Condition in
(select top 40 Condition from vConditions c
WHERE Condition <> 'NULL' AND Condition <> 'Nul'
group by Condition order by count(*) desc))");
CreateFilter(
CreateGraph(vOperations, "Operation frequency", "Field", false, "Operation"),
"Common Operation Only",
@"(Operation in
(select top 40 Operation from vOperations c
WHERE Operation <> 'NULL' AND Operation <> 'Nul'
group by Operation order by count(*) desc))");
//group these all into the same folder
admissions.Folder = new CatalogueFolder(admissions, @"\admissions");
admissions.SaveToDatabase();
vConditions.Folder = new CatalogueFolder(vConditions, @"\admissions");
vConditions.SaveToDatabase();
vOperations.Folder = new CatalogueFolder(vOperations, @"\admissions");
vOperations.SaveToDatabase();
//Create cohort store database
var wizard = new CreateNewCohortDatabaseWizard(db, _repos.CatalogueRepository, _repos.DataExportRepository, false);
var externalCohortTable = wizard.CreateDatabase(new PrivateIdentifierPrototype("chi", "varchar(10)"), new ThrowImmediatelyCheckNotifier());
//Find the pipeline for committing cohorts
var cohortCreationPipeline = _repos.CatalogueRepository.GetAllObjects <Pipeline>().FirstOrDefault(p => p?.Source?.Class == typeof(CohortIdentificationConfigurationSource).FullName);
if (cohortCreationPipeline == null)
{
throw new Exception("Could not find a cohort committing pipeline");
}
//A cohort creation query
var f = CreateFilter(vConditions, "Lung Cancer Condition", "Condition", "Condition like 'C349'", "ICD-10-CM Diagnosis Code C34.9 Malignant neoplasm of unspecified part of bronchus or lung");
var cic = CreateCohortIdentificationConfiguration((ExtractionFilter)f);
var cohort = CommitCohortToNewProject(cic, externalCohortTable, cohortCreationPipeline, "Lung Cancer Project", "P1 Lung Cancer Patients", 123, out Project project);
var cohortTable = cohort.ExternalCohortTable.DiscoverCohortTable();
using (var con = cohortTable.Database.Server.GetConnection())
{
con.Open();
//delete half the records (so we can simulate cohort refresh)
var cmd = cohortTable.Database.Server.GetCommand(string.Format("DELETE TOP (10) PERCENT from {0}", cohortTable.GetFullyQualifiedName()), con);
cmd.ExecuteNonQuery();
}
var ec1 = CreateExtractionConfiguration(project, cohort, "First Extraction (2016 - project 123)", true, notifier, biochem, prescribing, demography);
var ec2 = CreateExtractionConfiguration(project, cohort, "Project 123 - 2017 Refresh", true, notifier, biochem, prescribing, demography, admissions);
var ec3 = CreateExtractionConfiguration(project, cohort, "Project 123 - 2018 Refresh", true, notifier, biochem, prescribing, demography, admissions);
ReleaseAllConfigurations(notifier, ec1, ec2, ec3);
}
private SqlConnectionStringBuilder Create(string databaseName, IPatcher patcher, PlatformDatabaseCreationOptions options)
{
SqlConnection.ClearAllPools();
var builder = options.GetBuilder(databaseName);
DiscoveredDatabase db = new DiscoveredServer(builder).ExpectDatabase(builder.InitialCatalog);
if (options.DropDatabases && db.Exists())
{
Console.WriteLine("Dropping Database:" + builder.InitialCatalog);
db.Drop();
}
MasterDatabaseScriptExecutor executor = new MasterDatabaseScriptExecutor(db);
executor.BinaryCollation = options.BinaryCollation;
executor.CreateAndPatchDatabase(patcher, new AcceptAllCheckNotifier());
Console.WriteLine("Created " + builder.InitialCatalog + " on server " + builder.DataSource);
return(builder);
}