public void TestBasicOperation()
{
_helper.Options.FileSystemOptions.FileSystemRoot = _helper.TestDir.FullName;
_helper.TestAccessionDirectoryMessage.DirectoryPath = _helper.TestDir.FullName;
var tester = new MicroserviceTester(_helper.Options.RabbitOptions, _helper.AccessionConsumerOptions);
var host = new DicomTagReaderHost(_helper.Options);
host.Start();
tester.SendMessage(_helper.AccessionConsumerOptions, new MessageHeader(), _helper.TestAccessionDirectoryMessage);
var timeout = 30000;
const int stepSize = 500;
while (!_helper.CheckQueues(1, 1) && timeout > 0)
{
timeout -= 500;
Thread.Sleep(stepSize);
}
host.Stop("Test end");
tester.Dispose();
if (timeout <= 0)
{
Assert.Fail("Failed to process expected number of messages within the timeout");
}
}
private static int OnParse(GlobalOptions globals, DicomTagReaderCliOptions opts)
{
if (opts.File != null)
{
try
{
var host = new DicomTagReaderHost(globals);
host.AccessionDirectoryMessageConsumer.RunSingleFile(opts.File);
return(0);
}
catch (Exception ex)
{
LogManager.GetCurrentClassLogger().Error(ex);
return(1);
}
}
var bootstrapper = new MicroserviceHostBootstrapper(() => new DicomTagReaderHost(globals));
int ret = bootstrapper.Main();
return(ret);
}
public void TestTagReader_SingleFileMode()
{
var dirRoot = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.WorkDirectory, "TestTagReader_SingleFileMode"));
if (dirRoot.Exists)
{
dirRoot.Delete(true);
}
dirRoot.Create();
var julyFolder = dirRoot.CreateSubdirectory("July");
_helper.Options.FileSystemOptions.FileSystemRoot = dirRoot.FullName;
new MicroserviceTester(_helper.Options.RabbitOptions, _helper.AccessionConsumerOptions);
var host = new DicomTagReaderHost(_helper.Options);
var r = new Random(5);
var generator = new DicomDataGenerator(r, julyFolder, "CT");
var files = generator.GenerateImageFiles(10, r).ToArray();
host.AccessionDirectoryMessageConsumer.RunSingleFile(files[2]);
Assert.AreEqual(1, _helper.ImageCount);
Assert.AreEqual(1, _helper.SeriesCount);
var julyZip = Path.Combine(dirRoot.FullName, "july.zip");
ZipFile.CreateFromDirectory(julyFolder.FullName, julyZip);
host.AccessionDirectoryMessageConsumer.RunSingleFile(new FileInfo(julyZip));
Assert.AreEqual(11, _helper.ImageCount);
Assert.GreaterOrEqual(_helper.SeriesCount, 1);
}
private void RunTest(DirectoryInfo dir, int numberOfExpectedRows, Action <FileSystemOptions> adjustFileSystemOptions)
{
TestLogger.Setup();
var logger = LogManager.GetLogger("MicroservicesIntegrationTest");
_globals.FileSystemOptions.FileSystemRoot = TestContext.CurrentContext.TestDirectory;
var readFromFatalErrors = new ConsumerOptions
{
QueueName = "TEST.FatalLoggingQueue"
};
///////////////////////////////////// Directory //////////////////////////
var processDirectoryOptions = new DicomDirectoryProcessorCliOptions();
processDirectoryOptions.ToProcessDir = dir;
processDirectoryOptions.DirectoryFormat = "Default";
adjustFileSystemOptions?.Invoke(_globals.FileSystemOptions);
//////////////////////////////////////////////// Mongo Db Populator ////////////////////////
// Make this a GUID or something, should be unique per test
var currentSeriesCollectionName = "Integration_HappyPath_Series" + DateTime.Now.Ticks;
var currentImageCollectionName = "Integration_HappyPath_Image" + DateTime.Now.Ticks;
_globals.MongoDbPopulatorOptions.SeriesCollection = currentSeriesCollectionName;
_globals.MongoDbPopulatorOptions.ImageCollection = currentImageCollectionName;
//use the test catalogue not the one in the combined app.config
_globals.RDMPOptions.CatalogueConnectionString = ((TableRepository)RepositoryLocator.CatalogueRepository).DiscoveredServer.Builder.ConnectionString;
_globals.RDMPOptions.DataExportConnectionString = ((TableRepository)RepositoryLocator.DataExportRepository).DiscoveredServer.Builder.ConnectionString;
_globals.DicomRelationalMapperOptions.RunChecks = true;
if (_globals.DicomRelationalMapperOptions.MinimumBatchSize < 1)
{
_globals.DicomRelationalMapperOptions.MinimumBatchSize = 1;
}
using (var tester = new MicroserviceTester(_globals.RabbitOptions, _globals.CohortExtractorOptions))
{
tester.CreateExchange(_globals.ProcessDirectoryOptions.AccessionDirectoryProducerOptions.ExchangeName, _globals.DicomTagReaderOptions.QueueName);
tester.CreateExchange(_globals.DicomTagReaderOptions.SeriesProducerOptions.ExchangeName, _globals.MongoDbPopulatorOptions.SeriesQueueConsumerOptions.QueueName);
tester.CreateExchange(_globals.DicomTagReaderOptions.ImageProducerOptions.ExchangeName, _globals.IdentifierMapperOptions.QueueName);
tester.CreateExchange(_globals.DicomTagReaderOptions.ImageProducerOptions.ExchangeName, _globals.MongoDbPopulatorOptions.ImageQueueConsumerOptions.QueueName, true);
tester.CreateExchange(_globals.IdentifierMapperOptions.AnonImagesProducerOptions.ExchangeName, _globals.DicomRelationalMapperOptions.QueueName);
tester.CreateExchange(_globals.RabbitOptions.FatalLoggingExchange, readFromFatalErrors.QueueName);
tester.CreateExchange(_globals.CohortExtractorOptions.ExtractFilesProducerOptions.ExchangeName, null, false, _globals.CohortExtractorOptions.ExtractIdentRoutingKey);
tester.CreateExchange(_globals.CohortExtractorOptions.ExtractFilesProducerOptions.ExchangeName, null, true, _globals.CohortExtractorOptions.ExtractAnonRoutingKey);
tester.CreateExchange(_globals.CohortExtractorOptions.ExtractFilesInfoProducerOptions.ExchangeName, null);
#region Running Microservices
var processDirectory = new DicomDirectoryProcessorHost(_globals, processDirectoryOptions);
processDirectory.Start();
tester.StopOnDispose.Add(processDirectory);
var dicomTagReaderHost = new DicomTagReaderHost(_globals);
dicomTagReaderHost.Start();
tester.StopOnDispose.Add(dicomTagReaderHost);
var mongoDbPopulatorHost = new MongoDbPopulatorHost(_globals);
mongoDbPopulatorHost.Start();
tester.StopOnDispose.Add(mongoDbPopulatorHost);
var identifierMapperHost = new IdentifierMapperHost(_globals, new SwapForFixedValueTester("FISHFISH"));
identifierMapperHost.Start();
tester.StopOnDispose.Add(identifierMapperHost);
new TestTimelineAwaiter().Await(() => dicomTagReaderHost.AccessionDirectoryMessageConsumer.AckCount >= 1);
logger.Info("\n### DicomTagReader has processed its messages ###\n");
// FIXME: This isn't exactly how the pipeline runs
new TestTimelineAwaiter().Await(() => identifierMapperHost.Consumer.AckCount >= 1);
logger.Info("\n### IdentifierMapper has processed its messages ###\n");
using (var relationalMapperHost = new DicomRelationalMapperHost(_globals))
{
var start = DateTime.Now;
relationalMapperHost.Start();
tester.StopOnDispose.Add(relationalMapperHost);
Assert.True(mongoDbPopulatorHost.Consumers.Count == 2);
new TestTimelineAwaiter().Await(() => mongoDbPopulatorHost.Consumers[0].Processor.AckCount >= 1);
new TestTimelineAwaiter().Await(() => mongoDbPopulatorHost.Consumers[1].Processor.AckCount >= 1);
logger.Info("\n### MongoDbPopulator has processed its messages ###\n");
new TestTimelineAwaiter().Await(() => identifierMapperHost.Consumer.AckCount >= 1);//number of series
logger.Info("\n### IdentifierMapper has processed its messages ###\n");
Assert.AreEqual(0, dicomTagReaderHost.AccessionDirectoryMessageConsumer.NackCount);
Assert.AreEqual(0, identifierMapperHost.Consumer.NackCount);
Assert.AreEqual(0, ((Consumer <SeriesMessage>)mongoDbPopulatorHost.Consumers[0]).NackCount);
Assert.AreEqual(0, ((Consumer <DicomFileMessage>)mongoDbPopulatorHost.Consumers[1]).NackCount);
try
{
Thread.Sleep(TimeSpan.FromSeconds(10));
new TestTimelineAwaiter().Await(() => relationalMapperHost.Consumer.AckCount >= numberOfExpectedRows, null, 30000, () => relationalMapperHost.Consumer.DleErrors); //number of image files
logger.Info("\n### DicomRelationalMapper has processed its messages ###\n");
}
finally
{
//find out what happens from the logging database
var rdmpLogging = new Rdmp.Core.Logging.LogManager(_helper.LoadMetadata.GetDistinctLoggingDatabase());
//if error was reported during the dicom relational mapper run
foreach (var dli in rdmpLogging.GetArchivalDataLoadInfos(_helper.LoadMetadata.GetDistinctLoggingTask(), null, null))
{
if (dli.StartTime > start)
{
foreach (ArchivalFatalError e in dli.Errors)
{
logger.Error(e.Date.TimeOfDay + ":" + e.Source + ":" + e.Description);
}
}
}
}
Assert.AreEqual(numberOfExpectedRows, _helper.ImageTable.GetRowCount(), "All images should appear in the image table");
Assert.LessOrEqual(_helper.SeriesTable.GetRowCount(), numberOfExpectedRows, "Only unique series data should appear in series table, there should be less unique series than images (or equal)");
Assert.LessOrEqual(_helper.StudyTable.GetRowCount(), numberOfExpectedRows, "Only unique study data should appear in study table, there should be less unique studies than images (or equal)");
Assert.LessOrEqual(_helper.StudyTable.GetRowCount(), _helper.SeriesTable.GetRowCount(), "There should be less studies than series (or equal)");
//make sure that the substitution identifier (that replaces old the PatientId) is the correct substitution (FISHFISH)/
Assert.AreEqual("FISHFISH", _helper.StudyTable.GetDataTable().Rows.OfType <DataRow>().First()["PatientId"]);
//The file size in the final table should be more than 0
Assert.Greater((long)_helper.ImageTable.GetDataTable().Rows.OfType <DataRow>().First()["DicomFileSize"], 0);
dicomTagReaderHost.Stop("TestIsFinished");
mongoDbPopulatorHost.Stop("TestIsFinished");
DropMongoTestDb(_globals.MongoDatabases.DicomStoreOptions.HostName, _globals.MongoDatabases.DicomStoreOptions.Port);
identifierMapperHost.Stop("TestIsFinished");
relationalMapperHost.Stop("Test end");
}
//Now do extraction
var extractorHost = new CohortExtractorHost(_globals, null, null);
extractorHost.Start();
var extract = new ExtractionRequestMessage
{
ExtractionJobIdentifier = Guid.NewGuid(),
ProjectNumber = "1234-5678",
ExtractionDirectory = "1234-5678_P1",
KeyTag = "SeriesInstanceUID",
};
foreach (DataRow row in _helper.ImageTable.GetDataTable().Rows)
{
var ser = (string)row["SeriesInstanceUID"];
if (!extract.ExtractionIdentifiers.Contains(ser))
{
extract.ExtractionIdentifiers.Add(ser);
}
}
tester.SendMessage(_globals.CohortExtractorOptions, extract);
//wait till extractor picked up the messages and dispatched the responses
new TestTimelineAwaiter().Await(() => extractorHost.Consumer.AckCount == 1);
extractorHost.Stop("TestIsFinished");
tester.Shutdown();
}
#endregion
}
