public void Test_DodgyTagNames()
{
_helper.TruncateTablesIfExists();
DirectoryInfo d = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(Test_DodgyTagNames)));
d.Create();
var fi = TestData.Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile.dcm")));
var fi2 = TestData.Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile2.dcm")));
DicomFile dcm;
using (var stream = File.OpenRead(fi.FullName))
{
dcm = DicomFile.Open(stream);
dcm.Dataset.AddOrUpdate(DicomTag.PrintRETIRED, "FISH");
dcm.Dataset.AddOrUpdate(DicomTag.Date, new DateTime(2001, 01, 01));
dcm.Save(fi2.FullName);
}
var adder = new TagColumnAdder(DicomTypeTranslaterReader.GetColumnNameForTag(DicomTag.Date, false), "datetime2", _helper.ImageTableInfo, new AcceptAllCheckNotifier());
adder.Execute();
adder = new TagColumnAdder(DicomTypeTranslaterReader.GetColumnNameForTag(DicomTag.PrintRETIRED, false), "datetime2", _helper.ImageTableInfo, new AcceptAllCheckNotifier());
adder.Execute();
fi.Delete();
File.Move(fi2.FullName, fi.FullName);
//creates the queues, exchanges and bindings
var tester = new MicroserviceTester(_globals.RabbitOptions, _globals.DicomRelationalMapperOptions);
tester.CreateExchange(_globals.RabbitOptions.FatalLoggingExchange, null);
using (var host = new DicomRelationalMapperHost(_globals))
{
host.Start();
using (var timeline = new TestTimeline(tester))
{
timeline.SendMessage(_globals.DicomRelationalMapperOptions, _helper.GetDicomFileMessage(_globals.FileSystemOptions.FileSystemRoot, fi));
//start the timeline
timeline.StartTimeline();
Thread.Sleep(TimeSpan.FromSeconds(10));
new TestTimelineAwaiter().Await(() => host.Consumer.AckCount >= 1, null, 30000, () => host.Consumer.DleErrors);
Assert.AreEqual(1, _helper.SeriesTable.GetRowCount(), "SeriesTable did not have the expected number of rows in LIVE");
Assert.AreEqual(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 SetUpSuite()
{
SetUpDefaults();
// Create the test Series/Image exchanges
Options.RabbitOptions.RabbitMqControlExchangeName = "TEST.ControlExchange";
var tester = new MicroserviceTester(Options.RabbitOptions);
tester.CreateExchange(Options.DicomTagReaderOptions.ImageProducerOptions.ExchangeName, TestImageQueueName);
tester.CreateExchange(Options.DicomTagReaderOptions.SeriesProducerOptions.ExchangeName, TestSeriesQueueName);
tester.CreateExchange(Options.RabbitOptions.FatalLoggingExchange, null);
tester.CreateExchange(Options.RabbitOptions.RabbitMqControlExchangeName, null);
tester.Shutdown();
_testConnection = new ConnectionFactory
{
HostName = Options.RabbitOptions.RabbitMqHostName,
Port = Options.RabbitOptions.RabbitMqHostPort,
VirtualHost = Options.RabbitOptions.RabbitMqVirtualHost,
UserName = Options.RabbitOptions.RabbitMqUserName,
Password = Options.RabbitOptions.RabbitMqPassword
}.CreateConnection("TestConnection");
_testModel = _testConnection.CreateModel();
MockHost = Mock.Of <IMicroserviceHost>();
}
public void TestLoadingOneImage_SingleFileMessage(int numberOfMessagesToSend, bool mixInATextFile)
{
_helper.TruncateTablesIfExists();
DirectoryInfo d = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestLoadingOneImage_SingleFileMessage)));
d.Create();
var fi = TestData.Create(new FileInfo(Path.Combine(d.FullName, "MyTestFile.dcm")));
if (mixInATextFile)
{
var randomText = new FileInfo(Path.Combine(d.FullName, "RandomTextFile.dcm"));
File.WriteAllLines(randomText.FullName, new[] { "I love dancing", "all around the world", "boy the world is a big place eh?" });
}
//creates the queues, exchanges and bindings
var tester = new MicroserviceTester(_globals.RabbitOptions, _globals.DicomRelationalMapperOptions);
tester.CreateExchange(_globals.RabbitOptions.FatalLoggingExchange, null);
using (var host = new DicomRelationalMapperHost(_globals))
{
host.Start();
using (var timeline = new TestTimeline(tester))
{
//send the message 10 times over a 10 second period
for (int i = 0; i < numberOfMessagesToSend; i++)
{
timeline
.SendMessage(_globals.DicomRelationalMapperOptions, _helper.GetDicomFileMessage(_globals.FileSystemOptions.FileSystemRoot, fi))
.Wait(1000);
}
//start the timeline
timeline.StartTimeline();
Thread.Sleep(TimeSpan.FromSeconds(10));
new TestTimelineAwaiter().Await(() => host.Consumer.AckCount >= numberOfMessagesToSend, null, 30000, () => host.Consumer.DleErrors);
Assert.AreEqual(1, _helper.SeriesTable.GetRowCount(), "SeriesTable did not have the expected number of rows in LIVE");
Assert.AreEqual(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 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 TestPopulatorBasic(int nMessages)
{
// Arrange
string currentCollectionName = MongoDbPopulatorTestHelper.GetCollectionNameForTest(string.Format("TestPopulatorBasic({0})", nMessages));
_helper.Globals.MongoDbPopulatorOptions.SeriesCollection = currentCollectionName;
var tester = new MicroserviceTester(_helper.Globals.RabbitOptions, _helper.Globals.MongoDbPopulatorOptions.SeriesQueueConsumerOptions, _helper.Globals.MongoDbPopulatorOptions.ImageQueueConsumerOptions);
var host = new MongoDbPopulatorHost(_helper.Globals);
host.Start();
using (var timeline = new TestTimeline(tester))
{
var ds = new DicomDataset
{
new DicomUniqueIdentifier(DicomTag.SOPInstanceUID, "1.2.3.4")
};
var message = new SeriesMessage
{
NationalPACSAccessionNumber = "NationalPACSAccessionNumber-test",
DirectoryPath = "DirectoryPath-test",
StudyInstanceUID = "StudyInstanceUID-test",
SeriesInstanceUID = "SeriesInstanceUID-test",
ImagesInSeries = 123,
DicomDataset = DicomTypeTranslater.SerializeDatasetToJson(ds)
};
// Act
for (var i = 0; i < nMessages; i++)
{
timeline.SendMessage(_helper.Globals.MongoDbPopulatorOptions.SeriesQueueConsumerOptions, message);
}
timeline.StartTimeline();
var timeout = 30000;
const int stepSize = 500;
if (Debugger.IsAttached)
{
timeout = int.MaxValue;
}
var nWritten = 0L;
while (nWritten < nMessages && timeout > 0)
{
nWritten = _helper.TestDatabase.GetCollection <BsonDocument>(currentCollectionName).CountDocuments(new BsonDocument());
Thread.Sleep(stepSize);
timeout -= stepSize;
}
// Assert
if (timeout <= 0)
{
Assert.Fail("Failed to process expected number of messages within the timeout");
}
host.Stop("Test end");
tester.Shutdown();
}
}
public void TestLoadingOneImage_MileWideTest()
{
_helper.TruncateTablesIfExists();
DirectoryInfo d = new DirectoryInfo(Path.Combine(TestContext.CurrentContext.TestDirectory, nameof(TestLoadingOneImage_MileWideTest)));
d.Create();
var r = new Random(5000);
FileInfo[] files;
using (var g = new DicomDataGenerator(r, d, "CT"))
files = g.GenerateImageFiles(1, r).ToArray();
Assert.AreEqual(1, files.Length);
var existingColumns = _helper.ImageTable.DiscoverColumns();
//Add 200 random tags
foreach (string tag in TagColumnAdder.GetAvailableTags().OrderBy(a => r.Next()).Take(200))
{
string dataType;
try
{
dataType = TagColumnAdder.GetDataTypeForTag(tag, new MicrosoftSQLTypeTranslater());
}
catch (Exception)
{
continue;
}
if (existingColumns.Any(c => c.GetRuntimeName().Equals(tag)))
{
continue;
}
var adder = new TagColumnAdder(tag, dataType, _helper.ImageTableInfo, new AcceptAllCheckNotifier());
adder.SkipChecksAndSynchronization = true;
adder.Execute();
}
new TableInfoSynchronizer(_helper.ImageTableInfo).Synchronize(new AcceptAllCheckNotifier());
//creates the queues, exchanges and bindings
var tester = new MicroserviceTester(_globals.RabbitOptions, _globals.DicomRelationalMapperOptions);
tester.CreateExchange(_globals.RabbitOptions.FatalLoggingExchange, null);
using (var host = new DicomRelationalMapperHost(_globals))
{
host.Start();
using (var timeline = new TestTimeline(tester))
{
foreach (var f in files)
{
timeline.SendMessage(_globals.DicomRelationalMapperOptions,
_helper.GetDicomFileMessage(_globals.FileSystemOptions.FileSystemRoot, f));
}
//start the timeline
timeline.StartTimeline();
new TestTimelineAwaiter().Await(() => host.Consumer.MessagesProcessed == 1, 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();
}
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
}