private IExtractionRequestFulfiller CreateRequestFulfiller(CohortExtractorOptions opts)
{
var c = WhenIHaveA <ExtractionInformation>().CatalogueItem.Catalogue;
var t = c.GetTableInfoList(false).Single();
var repo = Repository.CatalogueRepository;
foreach (string requiredColumn in new string[]
{
QueryToExecuteColumnSet.DefaultImagePathColumnName,
QueryToExecuteColumnSet.DefaultStudyIdColumnName,
QueryToExecuteColumnSet.DefaultSeriesIdColumnName,
QueryToExecuteColumnSet.DefaultInstanceIdColumnName,
})
{
var ei = new ExtractionInformation(repo, new CatalogueItem(repo, c, "a"), new ColumnInfo(repo, requiredColumn, "varchar(10)", (TableInfo)t), requiredColumn);
ei.ExtractionCategory = ExtractionCategory.Core;
ei.SaveToDatabase();
}
c.ClearAllInjections();
Assert.AreEqual(5, c.GetAllExtractionInformation(ExtractionCategory.Any).Length);
var f = new MicroserviceObjectFactory();
var fulfiller = f.CreateInstance <IExtractionRequestFulfiller>(opts.RequestFulfillerType,
typeof(IExtractionRequestFulfiller).Assembly,
new object[] { new[] { c } });
if (fulfiller != null)
{
fulfiller.Rejectors.Add(f.CreateInstance <IRejector>(opts.RejectorType, typeof(TestRejector).Assembly) ?? new RejectNone());
}
return(fulfiller);
}
public IsIdentifiableHost(
[NotNull] GlobalOptions globals,
[NotNull] IsIdentifiableServiceOptions serviceOpts
)
: base(globals)
{
_consumerOptions = globals.IsIdentifiableOptions;
string classifierTypename = globals.IsIdentifiableOptions.ClassifierType;
string dataDirectory = globals.IsIdentifiableOptions.DataDirectory;
if (string.IsNullOrWhiteSpace(classifierTypename))
{
throw new ArgumentException("No IClassifier has been set in options. Enter a value for ClassifierType", nameof(globals));
}
if (string.IsNullOrWhiteSpace(dataDirectory))
{
throw new ArgumentException("A DataDirectory must be set", nameof(globals));
}
var objectFactory = new MicroserviceObjectFactory();
var classifier = objectFactory.CreateInstance <IClassifier>(classifierTypename, typeof(IClassifier).Assembly, new DirectoryInfo(dataDirectory), serviceOpts);
if (classifier == null)
{
throw new TypeLoadException($"Could not find IClassifier Type { classifierTypename }");
}
_producerModel = RabbitMqAdapter.SetupProducer(globals.IsIdentifiableOptions.IsIdentifiableProducerOptions, isBatch: false);
Consumer = new IsIdentifiableQueueConsumer(_producerModel, globals.FileSystemOptions.FileSystemRoot, globals.FileSystemOptions.ExtractRoot, classifier);
}
/// <summary>
/// Loads logging, sets up fatal behaviour, subscribes rabbit etc.
/// </summary>
/// <param name="globals">Settings for the microservice (location of rabbit, queue names etc)</param>
/// <param name="rabbitMqAdapter"></param>
/// <param name="threaded"></param>
protected MicroserviceHost(
[NotNull] GlobalOptions globals,
IRabbitMqAdapter rabbitMqAdapter = null,
bool threaded = false)
{
if (globals == null || globals.FileSystemOptions == null || globals.RabbitOptions == null || globals.LoggingOptions == null)
{
throw new ArgumentException("All or part of the global options are null");
}
HostProcessName = SmiCliInit.HostProcessName;
Logger = LogManager.GetLogger(GetType().Name);
Logger.Info("Host logger created");
HostProcessID = Process.GetCurrentProcess().Id;
Logger.Info($"Starting {HostProcessName} (Host={Environment.MachineName} PID={HostProcessID} User={Environment.UserName})");
// log centrally
Globals = globals;
Logger.Debug("Loaded global options:\n" + globals);
// should also be centralized for non-host uses
// Ensure this is false in case the default changes
DicomTypeTranslater.SerializeBinaryData = false;
_fatalLoggingProducerOptions = new ProducerOptions
{
ExchangeName = Globals.RabbitOptions.FatalLoggingExchange
};
//TODO This won't pass for testing with mocked filesystems
//if(!Directory.Exists(options.FileSystemRoot))
// throw new ArgumentException("Could not locate the FileSystemRoot \"" + options.FileSystemRoot + "\"");
OnFatal += (sender, args) => Fatal(args.Message, args.Exception);
RabbitMqAdapter = rabbitMqAdapter;
if (RabbitMqAdapter == null)
{
ConnectionFactory connectionFactory = globals.RabbitOptions.CreateConnectionFactory();
RabbitMqAdapter = new RabbitMqAdapter(connectionFactory, HostProcessName + HostProcessID, OnFatal, threaded);
_controlMessageConsumer = new ControlMessageConsumer(connectionFactory, HostProcessName, HostProcessID, globals.RabbitOptions.RabbitMqControlExchangeName, this.Stop);
}
ObjectFactory = new MicroserviceObjectFactory();
ObjectFactory.FatalHandler = (s, e) => Fatal(e.Message, e.Exception);
}
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");
}
}
private IAuditExtractions CreateAuditor(CohortExtractorOptions opts)
{
var f = new MicroserviceObjectFactory();
return(f.CreateInstance <IAuditExtractions>(opts.AuditorType, typeof(IAuditExtractions).Assembly));
}
public void TestCreatingByReflection()
{
var instance = new MicroserviceObjectFactory().CreateInstance <IProjectPathResolver>("Microservices.CohortExtractor.Execution.ProjectPathResolvers.NoSuffixProjectPathResolver", typeof(IProjectPathResolver).Assembly, RepositoryLocator);
Assert.IsInstanceOf <NoSuffixProjectPathResolver>(instance);
}
