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");
}
}
public void TestClassifierName_ValidClassifier()
{
var options = new GlobalOptionsFactory().Load();
var testDcm = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm")); Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm");
TestData.Create(testDcm);
using (var tester = new MicroserviceTester(options.RabbitOptions, options.IsIdentifiableOptions))
{
tester.CreateExchange(options.IsIdentifiableOptions.IsIdentifiableProducerOptions.ExchangeName, null);
options.IsIdentifiableOptions.ClassifierType = typeof(RejectAllClassifier).FullName;
options.IsIdentifiableOptions.DataDirectory = TestContext.CurrentContext.TestDirectory;
var host = new IsIdentifiableHost(options, new IsIdentifiableServiceOptions());
Assert.IsNotNull(host);
host.Start();
tester.SendMessage(options.IsIdentifiableOptions, new ExtractedFileStatusMessage()
{
DicomFilePath = "yay.dcm",
OutputFilePath = testDcm.FullName,
ProjectNumber = "100",
ExtractionDirectory = "./fish",
StatusMessage = "yay!",
Status = ExtractedFileStatus.Anonymised
});
var awaiter = new TestTimelineAwaiter();
awaiter.Await(() => host.Consumer.AckCount == 1);
}
}
public void Test_FileCopierHost_HappyPath()
{
GlobalOptions globals = new GlobalOptionsFactory().Load();
globals.FileSystemOptions.FileSystemRoot = "root";
globals.FileSystemOptions.ExtractRoot = "exroot";
using var tester = new MicroserviceTester(globals.RabbitOptions, globals.FileCopierOptions);
string outputQueueName = globals.FileCopierOptions.CopyStatusProducerOptions.ExchangeName.Replace("Exchange", "Queue");
tester.CreateExchange(
globals.FileCopierOptions.CopyStatusProducerOptions.ExchangeName,
outputQueueName,
false,
globals.FileCopierOptions.NoVerifyRoutingKey);
var mockFileSystem = new MockFileSystem();
mockFileSystem.AddDirectory(globals.FileSystemOptions.FileSystemRoot);
mockFileSystem.AddDirectory(globals.FileSystemOptions.ExtractRoot);
mockFileSystem.AddFile(mockFileSystem.Path.Combine(globals.FileSystemOptions.FileSystemRoot, "file.dcm"), MockFileData.NullObject);
var host = new FileCopierHost(globals, mockFileSystem);
tester.StopOnDispose.Add(host);
host.Start();
var message = new ExtractFileMessage
{
ExtractionJobIdentifier = Guid.NewGuid(),
JobSubmittedAt = DateTime.UtcNow,
ProjectNumber = "1234",
ExtractionDirectory = "1234/foo",
DicomFilePath = "file.dcm",
IsIdentifiableExtraction = true,
OutputPath = "output.dcm",
};
tester.SendMessage(globals.FileCopierOptions, message);
using IConnection conn = tester.Factory.CreateConnection();
using IModel model = conn.CreateModel();
var consumer = new EventingBasicConsumer(model);
ExtractedFileStatusMessage statusMessage = null;
consumer.Received += (_, ea) => statusMessage = JsonConvert.DeserializeObject <ExtractedFileStatusMessage>(Encoding.UTF8.GetString(ea.Body.ToArray()));
model.BasicConsume(outputQueueName, true, "", consumer);
new TestTimelineAwaiter().Await(() => statusMessage != null);
Assert.AreEqual(ExtractedFileStatus.Copied, statusMessage.Status);
}
public void IdenticalDatasetsTest()
{
_helper.TruncateTablesIfExists();
var ds = new DicomDataset();
ds.AddOrUpdate(DicomTag.SeriesInstanceUID, "123");
ds.AddOrUpdate(DicomTag.SOPInstanceUID, "123");
ds.AddOrUpdate(DicomTag.StudyInstanceUID, "123");
ds.AddOrUpdate(DicomTag.PatientID, "123");
var msg1 = _helper.GetDicomFileMessage(ds, _globals.FileSystemOptions.FileSystemRoot, Path.Combine(_globals.FileSystemOptions.FileSystemRoot, "mydicom.dcm"));
var msg2 = _helper.GetDicomFileMessage(ds, _globals.FileSystemOptions.FileSystemRoot, Path.Combine(_globals.FileSystemOptions.FileSystemRoot, "mydicom.dcm"));
//creates the queues, exchanges and bindings
using (var tester = new MicroserviceTester(_globals.RabbitOptions, _globals.DicomRelationalMapperOptions))
{
tester.CreateExchange(_globals.RabbitOptions.FatalLoggingExchange, null);
tester.SendMessage(_globals.DicomRelationalMapperOptions, msg1);
tester.SendMessage(_globals.DicomRelationalMapperOptions, msg2);
_globals.DicomRelationalMapperOptions.RunChecks = true;
using (var host = new DicomRelationalMapperHost(_globals))
{
host.Start();
new TestTimelineAwaiter().Await(() => host.Consumer.MessagesProcessed == 2, null, 30000, () => host.Consumer.DleErrors);
Assert.GreaterOrEqual(1, _helper.SeriesTable.GetRowCount(), "SeriesTable did not have the expected number of rows in LIVE");
Assert.GreaterOrEqual(1, _helper.StudyTable.GetRowCount(), "StudyTable did not have the expected number of rows in LIVE");
Assert.AreEqual(1, _helper.ImageTable.GetRowCount(), "ImageTable did not have the expected number of rows in LIVE");
host.Stop("Test end");
}
tester.Shutdown();
}
}
public void TestIsIdentifiable_TesseractStanfordDicomFileClassifier()
{
var options = new GlobalOptionsFactory().Load();
// Create a test data directory containing IsIdentifiableRules with 0 rules, and tessdata with the eng.traineddata classifier
// TODO(rkm 2020-04-14) This is a stop-gap solution until the tests are properly refactored
var testRulesDir = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, "data", "IsIdentifiableRules"));
testRulesDir.Create();
options.IsIdentifiableOptions.DataDirectory = testRulesDir.Parent.FullName;
var tessDir = new DirectoryInfo(Path.Combine(testRulesDir.Parent.FullName, "tessdata"));
tessDir.Create();
var dest = Path.Combine(tessDir.FullName, "eng.traineddata");
if (!File.Exists(dest))
{
File.Copy(Path.Combine(DataDirectory, "tessdata", "eng.traineddata"), dest);
}
var testDcm = new FileInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestIsIdentifiable_TesseractStanfordDicomFileClassifier), "f1.dcm"));
Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestClassifierName_ValidClassifier), "f1.dcm");
TestData.Create(testDcm);
using (var tester = new MicroserviceTester(options.RabbitOptions, options.IsIdentifiableOptions))
{
options.IsIdentifiableOptions.ClassifierType = typeof(TesseractStanfordDicomFileClassifier).FullName;
var host = new IsIdentifiableHost(options, new IsIdentifiableServiceOptions());
host.Start();
tester.SendMessage(options.IsIdentifiableOptions, new ExtractedFileStatusMessage
{
DicomFilePath = "yay.dcm",
OutputFilePath = testDcm.FullName,
ProjectNumber = "100",
ExtractionDirectory = "./fish",
StatusMessage = "yay!",
Status = ExtractedFileStatus.Anonymised
});
var awaiter = new TestTimelineAwaiter();
awaiter.Await(() => host.Consumer.AckCount == 1 || host.Consumer.NackCount == 1);
Assert.AreEqual(1, host.Consumer.AckCount, "Tesseract not acking");
}
}
private void VerifyReports(GlobalOptions globals, PathFixtures pf, ReportFormat reportFormat, IEnumerable <Tuple <ConsumerOptions, IMessage> > toSend)
{
globals.FileSystemOptions.ExtractRoot = pf.ExtractRootAbsolute;
globals.CohortPackagerOptions.JobWatcherTimeoutInSeconds = 5;
globals.CohortPackagerOptions.ReporterType = "FileReporter";
globals.CohortPackagerOptions.ReportFormat = reportFormat.ToString();
MongoClient client = MongoClientHelpers.GetMongoClient(globals.MongoDatabases.ExtractionStoreOptions, "test", true);
globals.MongoDatabases.ExtractionStoreOptions.DatabaseName += "-" + Guid.NewGuid().ToString().Split('-')[0];
client.DropDatabase(globals.MongoDatabases.ExtractionStoreOptions.DatabaseName);
using (var tester = new MicroserviceTester(
globals.RabbitOptions,
globals.CohortPackagerOptions.ExtractRequestInfoOptions,
globals.CohortPackagerOptions.FileCollectionInfoOptions,
globals.CohortPackagerOptions.NoVerifyStatusOptions,
globals.CohortPackagerOptions.VerificationStatusOptions))
{
foreach ((ConsumerOptions consumerOptions, IMessage message) in toSend)
{
tester.SendMessage(consumerOptions, new MessageHeader(), message);
}
var host = new CohortPackagerHost(globals);
host.Start();
var timeoutSecs = 10;
while (!HaveFiles(pf) && timeoutSecs > 0)
{
--timeoutSecs;
Thread.Sleep(TimeSpan.FromSeconds(1));
}
host.Stop("Test end");
}
var firstLine = $"# SMI extraction validation report for testProj1/{pf.ExtractName}";
switch (reportFormat)
{
case ReportFormat.Combined:
{
string reportContent = File.ReadAllText(Path.Combine(pf.ProjReportsDirAbsolute, $"{pf.ExtractName}_report.txt"));
Assert.True(reportContent.StartsWith(firstLine));
break;
}
case ReportFormat.Split:
{
string extractReportsDirAbsolute = Path.Combine(pf.ProjReportsDirAbsolute, pf.ExtractName);
Assert.AreEqual(6, Directory.GetFiles(extractReportsDirAbsolute).Length);
string reportContent = File.ReadAllText(Path.Combine(extractReportsDirAbsolute, "README.md"));
Assert.True(reportContent.StartsWith(firstLine));
break;
}
default:
Assert.Fail($"No case for ReportFormat {reportFormat}");
break;
}
}
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
}
