private static int OnParse(GlobalOptions globals, object opts)
{
var parsedOptions = SmiCliInit.Verify <TriggerUpdatesCliOptions>(opts);
ITriggerUpdatesSource source = parsedOptions switch
{
TriggerUpdatesFromMapperOptions o => new MapperSource(globals, o),
TriggerUpdatesFromMongoOptions o => new MongoSource(globals, o),
_ => throw new NotImplementedException($"No case for '{parsedOptions.GetType()}'")
};
var bootstrapper = new MicroserviceHostBootstrapper(() => new TriggerUpdatesHost(globals, source));
int ret = bootstrapper.Main();
return(ret);
}
}
public MapperSource([NotNull] GlobalOptions globalOptions, TriggerUpdatesFromMapperOptions cliOptions)
{
_cliOptions = cliOptions;
_globalOptions = globalOptions;
FansiImplementations.Load();
try
{
var objectFactory = new MicroserviceObjectFactory();
_swapper = objectFactory.CreateInstance <ISwapIdentifiers>(globalOptions.IdentifierMapperOptions.SwapperType, typeof(ISwapIdentifiers).Assembly);
}
catch (System.Exception ex)
{
throw new System.Exception($"Could not create IdentifierMapper Swapper with SwapperType:{globalOptions.IdentifierMapperOptions?.SwapperType ?? "Null"}", ex);
}
if (_swapper == null)
{
throw new ArgumentException("No SwapperType has been specified in GlobalOptions.IdentifierMapperOptions");
}
}
public void MapperSource_IntegrationTest(DatabaseType dbType)
{
var db = GetCleanedServer(dbType);
DataTable dt = new DataTable();
dt.Columns.Add("PatientID", typeof(string));
dt.Columns.Add("StudyDescription", typeof(string));
dt.SetDoNotReType(true);
// We have a live table with anonymised data. There is one person with a known ECHI 0101010101=0A0A0A0A0A
dt.Rows.Add("0A0A0A0A0A", "CT Head");
//There are 2 people for whome we have added temporary identifiers
dt.Rows.Add("bbb-bbb-bbb", "CT Tail");
dt.Rows.Add("ccc-ccc-ccc", "CT Wings");
var liveTable = db.CreateTable("MyLiveTable", dt);
DiscoveredTable map;
using (var dtMap = new DataTable())
{
dtMap.Columns.Add("CHI");
dtMap.Columns.Add("ECHI");
dtMap.PrimaryKey = new [] { dtMap.Columns["CHI"] };
dtMap.Rows.Add("0101010101", "0A0A0A0A0A");
map = db.CreateTable("Map", dtMap);
}
// Import into RDMP the live table so we have a TableInfo pointer to it floating around
Import(liveTable);
var mapperOptions = new IdentifierMapperOptions()
{
MappingTableName = map.GetFullyQualifiedName(),
MappingConnectionString = db.Server.Builder.ConnectionString,
SwapColumnName = "CHI",
ReplacementColumnName = "ECHI",
MappingDatabaseType = db.Server.DatabaseType,
SwapperType = typeof(TableLookupWithGuidFallbackSwapper).FullName
};
var swapper = new TableLookupWithGuidFallbackSwapper();
swapper.Setup(mapperOptions);
var guidTable = swapper.GetGuidTableIfAny(mapperOptions);
Assert.AreEqual(0, guidTable.GetRowCount(), "No temporary guids should exist yet");
Assert.AreEqual(1, map.GetRowCount(), "We should have a mapping table with 1 entry");
guidTable.Insert(new Dictionary <string, object>()
{
{ "CHI", "0202020202" },
{ TableLookupWithGuidFallbackSwapper.GuidColumnName, "bbb-bbb-bbb" }
});
guidTable.Insert(new Dictionary <string, object>()
{
{ "CHI", "0303030303" },
{ TableLookupWithGuidFallbackSwapper.GuidColumnName, "ccc-ccc-ccc" }
});
Assert.AreEqual(1, map.GetRowCount(), "We should have a mapping table with 1 entry");
Assert.AreEqual(2, guidTable.GetRowCount(), "We should have a temporary guid for 0202020202");
// make a fake data load into this table (create trigger and insert/update)
var triggerImplementer = new TriggerImplementerFactory(dbType).Create(map);
triggerImplementer.CreateTrigger(new ThrowImmediatelyCheckNotifier());
//create a brand new mapping
map.Insert(new Dictionary <string, object>()
{
{ "CHI", "0303030303" },
{ "ECHI", "0C0C0C0C0C" },
{ SpecialFieldNames.ValidFrom, DateTime.Now },
{ SpecialFieldNames.DataLoadRunID, 55 },
});
var globals = new GlobalOptionsFactory().Load();
var cliOptions = new TriggerUpdatesFromMapperOptions()
{
DateOfLastUpdate = new DateTime(2020, 01, 01),
LiveDatabaseFieldName = "PatientID",
Qualifier = '\'',
};
globals.UseTestValues(
RequiresRabbit.GetConnectionFactory(),
RequiresMongoDb.GetMongoClientSettings(),
RequiresRelationalDb.GetRelationalDatabaseConnectionStrings(),
((TableRepository)RepositoryLocator.CatalogueRepository).ConnectionStringBuilder,
((TableRepository)RepositoryLocator.DataExportRepository).ConnectionStringBuilder);
//make sure the identifier mapper goes to the right table
globals.IdentifierMapperOptions.MappingConnectionString = db.Server.Builder.ConnectionString;
globals.IdentifierMapperOptions.MappingDatabaseType = dbType;
globals.IdentifierMapperOptions.MappingTableName = map.GetFullyQualifiedName();
globals.IdentifierMapperOptions.SwapperType = typeof(TableLookupWithGuidFallbackSwapper).FullName;
using (var tester = new MicroserviceTester(globals.RabbitOptions, globals.CohortExtractorOptions))
{
tester.CreateExchange(globals.TriggerUpdatesOptions.ExchangeName, globals.UpdateValuesOptions.QueueName);
var sourceHost = new TriggerUpdatesHost(globals, new MapperSource(globals, cliOptions));
var destHost = new UpdateValuesHost(globals);
sourceHost.Start();
tester.StopOnDispose.Add(sourceHost);
destHost.Start();
tester.StopOnDispose.Add(destHost);
//wait till updater is done updating the live table
new TestTimelineAwaiter().Await(() => destHost.Consumer.AckCount == 1);
}
var liveDtAfter = liveTable.GetDataTable();
Assert.AreEqual(1, liveDtAfter.Rows.Cast <DataRow>().Count(r => (string)r["PatientID"] == "0A0A0A0A0A"), "Expected original data to still be intact");
Assert.AreEqual(1, liveDtAfter.Rows.Cast <DataRow>().Count(r => (string)r["PatientID"] == "bbb-bbb-bbb"), "Expected unknown CHI with guid bbb to still be unknown");
Assert.AreEqual(1, liveDtAfter.Rows.Cast <DataRow>().Count(r => (string)r["PatientID"] == "0C0C0C0C0C"), "Expected the unknown CHI ccc to be now known as 0C0C0C0C0C");
}
