public void HandleCStoreRequest(DicomCStoreRequest request, string calledAeTitle, uint associationId)
{
Guard.Against.Null(request, nameof(request));
if (!_aeTitleManagers.ContainsKey(calledAeTitle))
{
throw new ArgumentException($"Called AE Title '{calledAeTitle}' is not configured");
}
if (!_storageInfoProvider.HasSpaceAvailableToStore)
{
throw new InsufficientStorageAvailableException($"Insufficient storage available. Available storage space: {_storageInfoProvider.AvailableFreeSpace:D}");
}
_logger.Log(LogLevel.Information, $"Preparing to save instance received for {calledAeTitle} in {_aeTitleManagers[calledAeTitle].Value.AeStorageRootFullPath}.");
var instanceStorage = InstanceStorageInfo.CreateInstanceStorageInfo(request, _aeTitleManagers[calledAeTitle].Value.AeStorageRootFullPath, calledAeTitle, associationId);
using (_logger.BeginScope("SOPInstanceUID={0}", instanceStorage.SopInstanceUid))
{
_logger.Log(LogLevel.Information, "Patient ID: {PatientId}", instanceStorage.PatientId);
_logger.Log(LogLevel.Information, "Study Instance UID: {StudyInstanceUid}", instanceStorage.StudyInstanceUid);
_logger.Log(LogLevel.Information, "Series Instance UID: {SeriesInstanceUid}", instanceStorage.SeriesInstanceUid);
_logger.Log(LogLevel.Information, "Storage File Path: {InstanceStorageFullPath}", instanceStorage.InstanceStorageFullPath);
_aeTitleManagers[calledAeTitle].Value.Save(request, instanceStorage);
_logger.Log(LogLevel.Debug, $"Instance saved with handler {instanceStorage.InstanceStorageFullPath}");
}
}
public void CreateWithValidData()
{
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(
_request,
_storageRoot,
"MyAeTitle",
_fileSystem);
var expectedAaeStoragePath = Path.Combine(_storageRoot, "MyAeTitle");
var expectedPatientStoragePath = Path.Combine(expectedAaeStoragePath, "PID");
var expectedSeriesStoragePath = Path.Combine(expectedPatientStoragePath, Path.Combine(_studyInstanceUid, _seriesInstanceUid));
var expectedInstanceStoragePath = Path.Combine(expectedSeriesStoragePath, $"{_sopInstanceUid}.dcm");
Assert.Equal("1.2.3", instance.SopClassUid);
Assert.Equal("PID", instance.PatientId);
Assert.Equal(_studyInstanceUid, instance.StudyInstanceUid);
Assert.Equal(_seriesInstanceUid, instance.SeriesInstanceUid);
Assert.Equal(_sopInstanceUid, instance.SopInstanceUid);
Assert.Equal("MyAeTitle", instance.CalledAeTitle);
Assert.Equal(_storageRoot, instance.StorageRootPath);
Assert.Equal(expectedAaeStoragePath, instance.AeStoragePath);
Assert.Equal(expectedPatientStoragePath, instance.PatientStoragePath);
Assert.Equal(expectedInstanceStoragePath, instance.InstanceStorageFullPath);
Assert.True(_fileSystem.Directory.Exists(expectedSeriesStoragePath));
var logger = new Mock <ILogger>();
logger.Setup(p => p.Information("", ""));
}
private async Task RetrieveInstances(IDicomWebClient dicomWebClient, string studyInstanceUid, RequestedSeries series, string storagePath, Dictionary <string, InstanceStorageInfo> retrievedInstance)
{
Guard.Against.NullOrWhiteSpace(studyInstanceUid, nameof(studyInstanceUid));
Guard.Against.Null(series, nameof(series));
Guard.Against.Null(storagePath, nameof(storagePath));
Guard.Against.Null(retrievedInstance, nameof(retrievedInstance));
foreach (var instance in series.Instances)
{
if (instance.IsRetrieved)
{
continue;
}
foreach (var sopInstanceUid in instance.SopInstanceUid)
{
_logger.Log(LogLevel.Information, $"Retrieving instance {sopInstanceUid}");
var file = await dicomWebClient.Wado.Retrieve(studyInstanceUid, series.SeriesInstanceUid, sopInstanceUid);
var instanceStorageInfo = InstanceStorageInfo.CreateInstanceStorageInfo(file, storagePath, _fileSystem);
if (retrievedInstance.ContainsKey(instanceStorageInfo.SopInstanceUid))
{
_logger.Log(LogLevel.Warning, $"Instance '{instanceStorageInfo.SopInstanceUid}' already retrieved/stored.");
continue;
}
SaveFile(file, instanceStorageInfo);
retrievedInstance.Add(instanceStorageInfo.SopInstanceUid, instanceStorageInfo);
}
instance.IsRetrieved = true;
}
}
public void ShallSaveAndNotify()
{
_dicomToolkit.Setup(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()));
_notificationService.Setup(p => p.NewInstanceStored(It.IsAny <InstanceStorageInfo>()));
var config = new ClaraApplicationEntity();
config.AeTitle = "my-aet";
config.Processor = "Nvidia.Clara.DicomAdapter.Test.Unit.MockJobProcessor, Nvidia.Clara.Dicom.Test.Unit";
var handler = new ApplicationEntityHandler(_serviceProvider, config, _rootStoragePath, _cancellationTokenSource.Token, _fileSystem);
var request = GenerateRequest();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _rootStoragePath, config.AeTitle, _fileSystem);
handler.Save(request, instance);
_fileSystem.File.Create(instance.InstanceStorageFullPath);
handler.Save(request, instance);
_logger.VerifyLogging(LogLevel.Error, Times.Never());
_logger.VerifyLogging("Instance already exists, skipping.", LogLevel.Information, Times.Once());
_logger.VerifyLogging("Instance saved successfully.", LogLevel.Debug, Times.Once());
_logger.VerifyLogging("Instance stored and notified successfully.", LogLevel.Information, Times.Once());
_dicomToolkit.Verify(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()), Times.Exactly(1));
_notificationService.Verify(p => p.NewInstanceStored(instance), Times.Once());
}
private async Task SaveFiles(IAsyncEnumerable <DicomFile> files, string storagePath, Dictionary <string, InstanceStorageInfo> retrievedInstance)
{
Guard.Against.Null(files, nameof(files));
Guard.Against.Null(storagePath, nameof(storagePath));
Guard.Against.Null(retrievedInstance, nameof(retrievedInstance));
var total = 0;
var saved = 0;
await foreach (var file in files)
{
total++;
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(file, storagePath, _fileSystem);
if (retrievedInstance.ContainsKey(instance.SopInstanceUid))
{
_logger.Log(LogLevel.Warning, $"Instance '{instance.SopInstanceUid}' already retrieved/stored.");
continue;
}
SaveFile(file, instance);
retrievedInstance.Add(instance.SopInstanceUid, instance);
saved++;
}
_logger.Log(LogLevel.Information, $"Saved {saved} out of {total} instances retrieved");
}
private void RestoreExistingInstances(InferenceRequest inferenceRequest, Dictionary <string, InstanceStorageInfo> retrievedInstances)
{
Guard.Against.Null(inferenceRequest, nameof(inferenceRequest));
Guard.Against.Null(retrievedInstances, nameof(retrievedInstances));
_logger.Log(LogLevel.Debug, $"Restoring previously retrieved DICOM instances from {inferenceRequest.StoragePath}");
foreach (var file in _fileSystem.Directory.EnumerateFiles(inferenceRequest.StoragePath, "*.dcm", System.IO.SearchOption.AllDirectories))
{
if (_dicomToolkit.HasValidHeader(file))
{
var dicomFile = _dicomToolkit.Open(file);
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(dicomFile, inferenceRequest.StoragePath, _fileSystem);
if (retrievedInstances.ContainsKey(instance.SopInstanceUid))
{
continue;
}
retrievedInstances.Add(instance.SopInstanceUid, instance);
_logger.Log(LogLevel.Debug, $"Restored previously retrieved instance {instance.SopInstanceUid}");
}
else
{
_logger.Log(LogLevel.Warning, $"Unable to restore previously retrieved instance from {file}; file does not contain valid DICOM header.");
}
}
}
public void CreateWithValidData()
{
var expectedAeStoragePath = Path.Combine(_storageRoot, "MyAeTitle");
var expectedAeAssocationStoragePath = Path.Combine(expectedAeStoragePath, "1", "dcm");
var expectedPatientStoragePath = Path.Combine(expectedAeAssocationStoragePath, "PID");
var expectedSeriesStoragePath = Path.Combine(expectedPatientStoragePath, Path.Combine(_studyInstanceUid, _seriesInstanceUid));
var expectedInstanceStoragePath = Path.Combine(expectedSeriesStoragePath, $"{_sopInstanceUid}.dcm");
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(
_request,
expectedAeStoragePath,
"MyAeTitle",
1,
_fileSystem);
Assert.Equal("1.2.3", instance.SopClassUid);
Assert.Equal("PID", instance.PatientId);
Assert.Equal(_studyInstanceUid, instance.StudyInstanceUid);
Assert.Equal(_seriesInstanceUid, instance.SeriesInstanceUid);
Assert.Equal(_sopInstanceUid, instance.SopInstanceUid);
Assert.Equal("MyAeTitle", instance.CalledAeTitle);
Assert.Equal(expectedAeAssocationStoragePath, instance.AeStoragePath);
Assert.Equal(expectedPatientStoragePath, instance.PatientStoragePath);
Assert.Equal(expectedInstanceStoragePath, instance.InstanceStorageFullPath);
Assert.True(_fileSystem.Directory.Exists(expectedSeriesStoragePath));
}
public void CreateWithNullDicomCStoreRequestShallThrow()
{
Assert.Throws <ArgumentNullException>(() =>
{
InstanceStorageInfo.CreateInstanceStorageInfo(
null,
_storageRoot,
"AETITLE");
});
}
public void CreateWithoutSourceAeTitleShallThrow()
{
Assert.Throws <ArgumentException>(() =>
{
InstanceStorageInfo.CreateInstanceStorageInfo(
_request,
_storageRoot,
" ");
});
}
public void CreateWithoutStorageRootFullPathShallThrow()
{
Assert.Throws <ArgumentException>(() =>
{
InstanceStorageInfo.CreateInstanceStorageInfo(
_request,
string.Empty,
"AETITLE");
});
}
public static InstanceStorageInfo GenerateInstance(
string storageRootFullPath,
string calledAeTitle,
uint associationId = 1,
IFileSystem fileSystem = null)
{
fileSystem = fileSystem ?? new MockFileSystem();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(
GenerateDicomCStoreRequest(),
storageRootFullPath,
calledAeTitle,
associationId,
fileSystem ?? new MockFileSystem());
fileSystem.File.Create(instance.InstanceStorageFullPath).Close();
return(instance);
}
public async Task ShallDeleteFiles()
{
var files = new List <InstanceStorageInfo>()
{
InstanceStorageInfo.CreateInstanceStorageInfo(GenerateRequest(), "/test", "AET", _fileSystem),
InstanceStorageInfo.CreateInstanceStorageInfo(GenerateRequest(), "/test", "AET", _fileSystem),
InstanceStorageInfo.CreateInstanceStorageInfo(GenerateRequest(), "/test", "AET", _fileSystem)
};
foreach (var file in files)
{
_fileSystem.File.Create(file.InstanceStorageFullPath);
}
var cancellationTokenSource = new CancellationTokenSource();
var stack = new Stack <InstanceStorageInfo>(files);
_queue.Setup(p => p.Dequeue(It.IsAny <CancellationToken>()))
.Returns(() =>
{
if (stack.TryPop(out InstanceStorageInfo result))
{
return(result);
}
cancellationTokenSource.Cancel();
return(null);
});
await _service.StartAsync(cancellationTokenSource.Token);
while (!cancellationTokenSource.IsCancellationRequested)
{
Thread.Sleep(100);
}
_queue.Verify(p => p.Dequeue(It.IsAny <CancellationToken>()), Times.AtLeast(3));
foreach (var file in files)
{
Assert.False(_fileSystem.File.Exists(file.InstanceStorageFullPath));
}
_logger.VerifyLogging("Cancellation requested.", LogLevel.Information, Times.Once());
}
public void ShallRespectRetryPolicyOnFailures()
{
_dicomToolkit.Setup(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>())).Throws <Exception>();
var config = new ClaraApplicationEntity();
config.AeTitle = "my-aet";
config.Processor = "Nvidia.Clara.DicomAdapter.Test.Unit.MockJobProcessor, Nvidia.Clara.Dicom.Test.Unit";
var handler = new ApplicationEntityHandler(_serviceProvider, config, _rootStoragePath, _cancellationTokenSource.Token, _fileSystem);
var request = GenerateRequest();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _rootStoragePath, config.AeTitle, _fileSystem);
var exception = Assert.Throws <Exception>(() =>
{
handler.Save(request, instance);
});
_logger.VerifyLogging(LogLevel.Error, Times.Exactly(3));
_dicomToolkit.Verify(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()), Times.Exactly(4));
}
public void WorkflowTest()
{
var service = new InstanceStoredNotificationService(_logger.Object, _cleanupQueue.Object);
var observer = new Mock <IObserver <InstanceStorageInfo> >();
observer.Setup(p => p.OnNext(It.IsAny <InstanceStorageInfo>()));
var cancel = service.Subscribe(observer.Object);
var request = GenerateRequest();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, "/storage", "AET", new MockFileSystem());
service.NewInstanceStored(instance);
service.NewInstanceStored(instance);
service.NewInstanceStored(instance);
observer.Verify(p => p.OnNext(It.IsAny <InstanceStorageInfo>()), Times.Exactly(3));
cancel.Dispose();
observer.Reset();
service.NewInstanceStored(instance);
observer.Verify(p => p.OnNext(It.IsAny <InstanceStorageInfo>()), Times.Never());
}
public void ShallQueueAndDequeueItems()
{
for (var i = 0; i < 10; i++)
{
_queue.QueueInstance(InstanceStorageInfo.CreateInstanceStorageInfo(
GenerateRequest(),
"/test",
"AET",
new MockFileSystem()
));
}
_cancellationTokenSource.CancelAfter(500);
var items = new List <InstanceStorageInfo>();
for (var i = 0; i < 10; i++)
{
items.Add(_queue.Dequeue(_cancellationTokenSource.Token));
}
Assert.Equal(10, items.Count);
}
public void ShallIngoreInstancesWithConfiguredSopClassUids()
{
_dicomToolkit.Setup(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()));
var config = new ClaraApplicationEntity();
config.AeTitle = "my-aet";
config.IgnoredSopClasses = new List <string>()
{
DicomUID.SecondaryCaptureImageStorage.UID
};
config.Processor = "Nvidia.Clara.DicomAdapter.Test.Unit.MockJobProcessor, Nvidia.Clara.Dicom.Test.Unit";
var handler = new ApplicationEntityHandler(_serviceProvider, config, _rootStoragePath, _cancellationTokenSource.Token, _fileSystem);
var request = GenerateRequest();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _rootStoragePath, config.AeTitle, _fileSystem);
handler.Save(request, instance);
_logger.VerifyLogging($"Instance with SOP Class {DicomUID.SecondaryCaptureImageStorage.UID} ignored based on configured AET {config.AeTitle}", LogLevel.Warning, Times.Once());
_dicomToolkit.Verify(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()), Times.Never());
}
private void GenerateInstances()
{
var request = GenerateRequest(_patient1, _study1, _series1);
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _fileSystem.Path.DirectorySeparatorChar.ToString(), _aeTitle, 1, _fileSystem);
_instances.Add(instance);
_fileSystem.File.CreateText(instance.InstanceStorageFullPath);
request = GenerateRequest(_patient1, _study1, _series2);
instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _fileSystem.Path.DirectorySeparatorChar.ToString(), _aeTitle, 1, _fileSystem);
_instances.Add(instance);
_fileSystem.File.CreateText(instance.InstanceStorageFullPath);
request = GenerateRequest(_patient1, _study2, _series3);
instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _fileSystem.Path.DirectorySeparatorChar.ToString(), _aeTitle, 1, _fileSystem);
_instances.Add(instance);
_fileSystem.File.CreateText(instance.InstanceStorageFullPath);
request = GenerateRequest(_patient2, _study3, _series4);
instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, _fileSystem.Path.DirectorySeparatorChar.ToString(), _aeTitle, 1, _fileSystem);
_instances.Add(instance);
_fileSystem.File.CreateText(instance.InstanceStorageFullPath);
}
public void HandleCStoreRequest(DicomCStoreRequest request, string calledAeTitle, uint associationId)
{
Guard.Against.Null(request, nameof(request));
if (!_aeTitleManagers.ContainsKey(calledAeTitle))
{
throw new ArgumentException($"Called AE Title '{calledAeTitle}' is not configured");
}
_logger.Log(LogLevel.Information, "Preparing to save instance from {callingAeTitle}.", calledAeTitle);
var instanceStorage = InstanceStorageInfo.CreateInstanceStorageInfo(request, Configuration.Value.Storage.Temporary, calledAeTitle, associationId);
using (_logger.BeginScope("SOPInstanceUID={0}", instanceStorage.SopInstanceUid))
{
_logger.Log(LogLevel.Information, "Patient ID: {PatientId}", instanceStorage.PatientId);
_logger.Log(LogLevel.Information, "Study Instance UID: {StudyInstanceUid}", instanceStorage.StudyInstanceUid);
_logger.Log(LogLevel.Information, "Series Instance UID: {SeriesInstanceUid}", instanceStorage.SeriesInstanceUid);
_logger.Log(LogLevel.Information, "Storage File Path: {InstanceStorageFullPath}", instanceStorage.InstanceStorageFullPath);
_aeTitleManagers[calledAeTitle].Value.Save(request, instanceStorage);
_logger.Log(LogLevel.Debug, "Instance saved with handler", instanceStorage.InstanceStorageFullPath);
}
}
public void NewInstanceStored_NoSupportedObservers()
{
var request = GenerateRequest();
var instance = InstanceStorageInfo.CreateInstanceStorageInfo(request, "/storage", "AET", new MockFileSystem());
_cleanupQueue.Setup(p => p.QueueInstance(It.IsAny <InstanceStorageInfo>()));
var service = new InstanceStoredNotificationService(_logger.Object, _cleanupQueue.Object);
var observer = new Mock <IObserver <InstanceStorageInfo> >();
observer.Setup(p => p.OnNext(It.IsAny <InstanceStorageInfo>())).Throws(new InstanceNotSupportedException(instance));
var cancel = service.Subscribe(observer.Object);
service.NewInstanceStored(instance);
observer.Verify(p => p.OnNext(It.IsAny <InstanceStorageInfo>()), Times.Once());
_cleanupQueue.Verify(p => p.QueueInstance(instance), Times.Once());
cancel.Dispose();
observer.Reset();
service.NewInstanceStored(instance);
observer.Verify(p => p.OnNext(It.IsAny <InstanceStorageInfo>()), Times.Never());
}