public async Task InsufficientStorageSpace()
{
var cancellationTokenSource = new CancellationTokenSource();
cancellationTokenSource.CancelAfter(1000);
_storageInfoProvider.Setup(p => p.HasSpaceAvailableToRetrieve).Returns(false);
_storageInfoProvider.Setup(p => p.AvailableFreeSpace).Returns(100);
var store = new DataRetrievalService(
_loggerFactory.Object,
_httpClientFactory.Object,
_logger.Object,
_fileSystem,
_dicomToolkit.Object,
_serviceScopeFactory.Object,
_cleanupQueue.Object,
_storageInfoProvider.Object);
await store.StartAsync(cancellationTokenSource.Token);
Thread.Sleep(250);
await store.StopAsync(cancellationTokenSource.Token);
_logger.VerifyLogging($"Data Retriever Hosted Service is running.", LogLevel.Information, Times.Once());
_logger.VerifyLogging($"Data Retriever Hosted Service is stopping.", LogLevel.Information, Times.Once());
_storageInfoProvider.Verify(p => p.HasSpaceAvailableToRetrieve, Times.AtLeastOnce());
_storageInfoProvider.Verify(p => p.AvailableFreeSpace, Times.AtLeastOnce());
}
public void CancellationTokenShallCancelTheService()
{
var cancellationTokenSource = new CancellationTokenSource();
cancellationTokenSource.Cancel();
var store = new DataRetrievalService(
_dicomWebClient.Object,
_logger.Object,
_inferenceRequestStore.Object,
_fileSystem,
_dicomToolkit.Object,
_jobStore.Object);
store.StartAsync(cancellationTokenSource.Token);
store.StopAsync(cancellationTokenSource.Token);
_logger.VerifyLogging($"Data Retriever Hosted Service is running.", LogLevel.Information, Times.Once());
_logger.VerifyLogging($"Data Retriever Hosted Service is stopping.", LogLevel.Information, Times.Once());
}
public async Task ProcessorRequest_ShallRetrieveFhirResources()
{
var cancellationTokenSource = new CancellationTokenSource();
var storagePath = "/store";
_fileSystem.Directory.CreateDirectory(storagePath);
#region Test Data
var url = "http://uri.test/";
var request = new InferenceRequest
{
PayloadId = Guid.NewGuid().ToString(),
JobId = Guid.NewGuid().ToString(),
TransactionId = Guid.NewGuid().ToString(),
};
request.InputMetadata = new InferenceRequestMetadata
{
Details = new InferenceRequestDetails
{
Type = InferenceRequestType.FhireResource,
Resources = new List <FhirResource>()
{
new FhirResource
{
Id = "1",
Type = "Patient"
}
}
},
Inputs = new List <InferenceRequestDetails>()
{
new InferenceRequestDetails
{
Type = InferenceRequestType.FhireResource,
Resources = new List <FhirResource>()
{
new FhirResource
{
Id = "2",
Type = "Observation"
}
}
}
}
};
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Algorithm,
ConnectionDetails = new InputConnectionDetails()
});
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Fhir,
ConnectionDetails = new InputConnectionDetails
{
AuthId = "token",
AuthType = ConnectionAuthType.Bearer,
Uri = url
}
});
Assert.True(request.IsValid(out string _));
#endregion Test Data
request.ConfigureTemporaryStorageLocation(storagePath);
_inferenceRequestStore.SetupSequence(p => p.Take(It.IsAny <CancellationToken>()))
.Returns(Task.FromResult(request))
.Returns(() =>
{
cancellationTokenSource.Cancel();
throw new OperationCanceledException("canceled");
});
_jobStore.Setup(p => p.Add(It.IsAny <InferenceJob>(), It.IsAny <bool>()));
_handlerMock = new Mock <HttpMessageHandler>();
_handlerMock.Protected()
.Setup <Task <HttpResponseMessage> >(
"SendAsync",
ItExpr.IsAny <HttpRequestMessage>(),
ItExpr.IsAny <CancellationToken>())
.ReturnsAsync(() => new HttpResponseMessage(System.Net.HttpStatusCode.OK)
{
Content = new StringContent("{}")
});
_httpClientFactory.Setup(p => p.CreateClient(It.IsAny <string>()))
.Returns(new HttpClient(_handlerMock.Object));
_storageInfoProvider.Setup(p => p.HasSpaceAvailableToRetrieve).Returns(true);
_storageInfoProvider.Setup(p => p.AvailableFreeSpace).Returns(100);
var store = new DataRetrievalService(
_loggerFactory.Object,
_httpClientFactory.Object,
_logger.Object,
_fileSystem,
_dicomToolkit.Object,
_serviceScopeFactory.Object,
_cleanupQueue.Object,
_storageInfoProvider.Object);
await store.StartAsync(cancellationTokenSource.Token);
BlockUntilCancelled(cancellationTokenSource.Token);
_handlerMock.Protected().Verify(
"SendAsync",
Times.Once(),
ItExpr.Is <HttpRequestMessage>(req =>
req.Method == HttpMethod.Get &&
req.RequestUri.PathAndQuery.Contains("Patient/1")),
ItExpr.IsAny <CancellationToken>());
_handlerMock.Protected().Verify(
"SendAsync",
Times.Once(),
ItExpr.Is <HttpRequestMessage>(req =>
req.Method == HttpMethod.Get &&
req.RequestUri.PathAndQuery.Contains("Observation/2")),
ItExpr.IsAny <CancellationToken>());
_jobStore.Verify(p => p.Add(It.IsAny <InferenceJob>(), false), Times.Once());
_storageInfoProvider.Verify(p => p.HasSpaceAvailableToRetrieve, Times.AtLeastOnce());
_storageInfoProvider.Verify(p => p.AvailableFreeSpace, Times.Never());
_cleanupQueue.Verify(p => p.QueueInstance(It.IsAny <string>()), Times.Exactly(2));
}
public async Task ProcessorRequest_ShallQueryByAccessionNumberAndRetrieve()
{
var cancellationTokenSource = new CancellationTokenSource();
var storagePath = "/store";
_fileSystem.Directory.CreateDirectory(storagePath);
#region Test Data
var url = "http://uri.test/";
var request = new InferenceRequest
{
PayloadId = Guid.NewGuid().ToString(),
JobId = Guid.NewGuid().ToString(),
TransactionId = Guid.NewGuid().ToString(),
};
request.InputMetadata = new InferenceRequestMetadata
{
Details = new InferenceRequestDetails
{
Type = InferenceRequestType.AccessionNumber,
AccessionNumber = new List <string>()
{
"ABC"
}
}
};
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Algorithm,
ConnectionDetails = new InputConnectionDetails()
});
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.DicomWeb,
ConnectionDetails = new InputConnectionDetails
{
AuthId = "token",
AuthType = ConnectionAuthType.Basic,
Uri = url
}
});
Assert.True(request.IsValid(out string _));
#endregion Test Data
request.ConfigureTemporaryStorageLocation(storagePath);
_dicomToolkit.Setup(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()));
_inferenceRequestStore.SetupSequence(p => p.Take(It.IsAny <CancellationToken>()))
.Returns(Task.FromResult(request))
.Returns(() =>
{
cancellationTokenSource.Cancel();
throw new OperationCanceledException("canceled");
});
_jobStore.Setup(p => p.Add(It.IsAny <InferenceJob>(), It.IsAny <bool>()));
var studyInstanceUids = new List <string>()
{
DicomUIDGenerator.GenerateDerivedFromUUID().UID,
DicomUIDGenerator.GenerateDerivedFromUUID().UID
};
_handlerMock = new Mock <HttpMessageHandler>();
_handlerMock.Protected()
.Setup <Task <HttpResponseMessage> >(
"SendAsync",
ItExpr.Is <HttpRequestMessage>(p => p.RequestUri.Query.Contains("ABC")),
ItExpr.IsAny <CancellationToken>())
.ReturnsAsync(() =>
{
return(GenerateQueryResult(DicomTag.AccessionNumber, "ABC", studyInstanceUids));
});
_handlerMock.Protected()
.Setup <Task <HttpResponseMessage> >(
"SendAsync",
ItExpr.Is <HttpRequestMessage>(p => !p.RequestUri.Query.Contains("ABC")),
ItExpr.IsAny <CancellationToken>())
.ReturnsAsync(() =>
{
return(GenerateMultipartResponse());
});
_httpClientFactory.Setup(p => p.CreateClient(It.IsAny <string>()))
.Returns(new HttpClient(_handlerMock.Object));
_storageInfoProvider.Setup(p => p.HasSpaceAvailableToRetrieve).Returns(true);
_storageInfoProvider.Setup(p => p.AvailableFreeSpace).Returns(100);
var store = new DataRetrievalService(
_loggerFactory.Object,
_httpClientFactory.Object,
_logger.Object,
_fileSystem,
_dicomToolkit.Object,
_serviceScopeFactory.Object,
_cleanupQueue.Object,
_storageInfoProvider.Object);
await store.StartAsync(cancellationTokenSource.Token);
BlockUntilCancelled(cancellationTokenSource.Token);
_handlerMock.Protected().Verify(
"SendAsync",
Times.Once(),
ItExpr.Is <HttpRequestMessage>(req =>
req.Method == HttpMethod.Get &&
req.RequestUri.Query.Contains("00080050=ABC")),
ItExpr.IsAny <CancellationToken>());
foreach (var studyInstanceUid in studyInstanceUids)
{
_handlerMock.Protected().Verify(
"SendAsync",
Times.Once(),
ItExpr.Is <HttpRequestMessage>(req =>
req.Method == HttpMethod.Get &&
req.RequestUri.ToString().StartsWith($"{url}studies/{studyInstanceUid}")),
ItExpr.IsAny <CancellationToken>());
}
_jobStore.Verify(p => p.Add(It.IsAny <InferenceJob>(), false), Times.Once());
_dicomToolkit.Verify(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()), Times.Exactly(studyInstanceUids.Count));
_storageInfoProvider.Verify(p => p.HasSpaceAvailableToRetrieve, Times.AtLeastOnce());
_storageInfoProvider.Verify(p => p.AvailableFreeSpace, Times.Never());
_cleanupQueue.Verify(p => p.QueueInstance(It.IsAny <string>()), Times.Exactly(2));
}
public async Task ProcessorRequest_ShallRestorePreviouslyRetrievedFiles()
{
var cancellationTokenSource = new CancellationTokenSource();
var storagePath = "/store";
_fileSystem.Directory.CreateDirectory(storagePath);
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file1.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file2.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file3.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "corrupted.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "text.txt"));
var request = new InferenceRequest
{
PayloadId = Guid.NewGuid().ToString(),
JobId = Guid.NewGuid().ToString(),
TransactionId = Guid.NewGuid().ToString(),
InputMetadata = new InferenceRequestMetadata()
};
request.InputMetadata.Details = new InferenceRequestDetails()
{
Type = InferenceRequestType.DicomPatientId,
PatientId = "123"
};
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Algorithm,
ConnectionDetails = new InputConnectionDetails()
});
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.DicomWeb,
ConnectionDetails = new InputConnectionDetails()
{
Uri = "http://valid.uri/api",
AuthType = ConnectionAuthType.None
}
});
request.ConfigureTemporaryStorageLocation(storagePath);
Assert.True(request.IsValid(out string _));
_dicomToolkit.Setup(p => p.HasValidHeader(It.IsAny <string>()))
.Returns((string filename) =>
{
if (filename.EndsWith("text.txt"))
{
return(false);
}
else if (filename.EndsWith("corrupted.dcm"))
{
return(false);
}
return(true);
});
_dicomToolkit.Setup(p => p.Open(It.IsAny <string>()))
.Returns(() => InstanceGenerator.GenerateDicomFile());
_inferenceRequestStore.SetupSequence(p => p.Take(It.IsAny <CancellationToken>()))
.Returns(Task.FromResult(request))
.Returns(() =>
{
cancellationTokenSource.Cancel();
throw new OperationCanceledException("canceled");
});
_jobStore.Setup(p => p.Add(It.IsAny <InferenceJob>(), It.IsAny <bool>()));
_handlerMock = new Mock <HttpMessageHandler>();
_handlerMock
.Protected()
.Setup <Task <HttpResponseMessage> >(
"SendAsync",
ItExpr.IsAny <HttpRequestMessage>(),
ItExpr.IsAny <CancellationToken>())
.ReturnsAsync(() =>
{
return(new HttpResponseMessage(System.Net.HttpStatusCode.OK)
{
Content = new StringContent("[]")
});
});
_httpClientFactory.Setup(p => p.CreateClient(It.IsAny <string>()))
.Returns(new HttpClient(_handlerMock.Object));
_storageInfoProvider.Setup(p => p.HasSpaceAvailableToRetrieve).Returns(true);
_storageInfoProvider.Setup(p => p.AvailableFreeSpace).Returns(100);
_cleanupQueue.Setup(p => p.QueueInstance(It.IsAny <string>()));
var store = new DataRetrievalService(
_loggerFactory.Object,
_httpClientFactory.Object,
_logger.Object,
_fileSystem,
_dicomToolkit.Object,
_serviceScopeFactory.Object,
_cleanupQueue.Object,
_storageInfoProvider.Object);
await store.StartAsync(cancellationTokenSource.Token);
BlockUntilCancelled(cancellationTokenSource.Token);
_logger.VerifyLoggingMessageBeginsWith($"Restored previously retrieved instance", LogLevel.Debug, Times.Exactly(3));
_logger.VerifyLoggingMessageBeginsWith($"Restored previously retrieved instance", LogLevel.Debug, Times.Exactly(3));
_logger.VerifyLoggingMessageBeginsWith($"Unable to restore previously retrieved instance from", LogLevel.Warning, Times.Once());
_jobStore.Verify(p => p.Add(It.IsAny <InferenceJob>(), false), Times.Once());
_storageInfoProvider.Verify(p => p.HasSpaceAvailableToRetrieve, Times.AtLeastOnce());
_storageInfoProvider.Verify(p => p.AvailableFreeSpace, Times.Never());
}
public async Task ProcessorRequest_ShallRetrieveViaDicomWebWithDicomUid()
{
var cancellationTokenSource = new CancellationTokenSource();
var storagePath = "/store";
_fileSystem.Directory.CreateDirectory(storagePath);
#region Test Data
var request = new InferenceRequest
{
PayloadId = Guid.NewGuid().ToString(),
JobId = Guid.NewGuid().ToString(),
TransactionId = Guid.NewGuid().ToString()
};
request.InputMetadata = new InferenceRequestMetadata
{
Details = new InferenceRequestDetails
{
Type = InferenceRequestType.DicomUid,
Studies = new List <RequestedStudy>
{
new RequestedStudy
{
StudyInstanceUid = "1",
Series = new List <RequestedSeries>
{
new RequestedSeries
{
SeriesInstanceUid = "1.1",
Instances = new List <RequestedInstance>
{
new RequestedInstance
{
SopInstanceUid = new List <string>
{
"1.1.2",
"1.1.3"
}
}
}
}
}
},
new RequestedStudy
{
StudyInstanceUid = "2",
Series = new List <RequestedSeries>
{
new RequestedSeries
{
SeriesInstanceUid = "2.1"
}
}
},
new RequestedStudy
{
StudyInstanceUid = "3"
},
}
}
};
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Algorithm,
ConnectionDetails = new InputConnectionDetails()
});
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.DicomWeb,
ConnectionDetails = new InputConnectionDetails
{
AuthId = "token",
AuthType = ConnectionAuthType.Basic,
Uri = "http://uri.test/"
}
});
#endregion Test Data
request.ConfigureTemporaryStorageLocation(storagePath);
_dicomToolkit.Setup(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()));
_inferenceRequestStore.SetupSequence(p => p.Take(It.IsAny <CancellationToken>()))
.Returns(Task.FromResult(request))
.Returns(() =>
{
cancellationTokenSource.Cancel();
throw new OperationCanceledException("canceled");
});
_jobStore.Setup(p => p.Add(It.IsAny <Job>(), It.IsAny <string>(), It.IsAny <IList <InstanceStorageInfo> >()));
_wadoService.Setup(p => p.Retrieve(It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()))
.Returns((string studyInstanceUid, DicomTransferSyntax[] dicomTransferSyntaxes) => GenerateInstance(studyInstanceUid));
_wadoService.Setup(p => p.Retrieve(It.IsAny <string>(), It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()))
.Returns((string studyInstanceUid, string seriesInstanceUid, DicomTransferSyntax[] dicomTransferSyntaxes) => GenerateInstance(studyInstanceUid, seriesInstanceUid));
_wadoService.Setup(p => p.Retrieve(It.IsAny <string>(), It.IsAny <string>(), It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()))
.Returns((string studyInstanceUid, string seriesInstanceUid, string sopInstanceUid, DicomTransferSyntax[] dicomTransferSyntaxes) =>
{
return(Task.FromResult(InstanceGenerator.GenerateDicomFile(studyInstanceUid, seriesInstanceUid, sopInstanceUid, _fileSystem)));
});
var store = new DataRetrievalService(
_dicomWebClient.Object,
_logger.Object,
_inferenceRequestStore.Object,
_fileSystem,
_dicomToolkit.Object,
_jobStore.Object);
await store.StartAsync(cancellationTokenSource.Token);
BlockUntilCancelled(cancellationTokenSource.Token);
_jobStore.Verify(p => p.Add(It.IsAny <Job>(), It.IsAny <string>(), It.IsAny <IList <InstanceStorageInfo> >()), Times.Once());
_wadoService.Verify(p => p.Retrieve(It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()), Times.Once());
_wadoService.Verify(p => p.Retrieve(It.IsAny <string>(), It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()), Times.Once());
_wadoService.Verify(p => p.Retrieve(It.IsAny <string>(), It.IsAny <string>(), It.IsAny <string>(), It.IsAny <DicomTransferSyntax[]>()), Times.Exactly(2));
_dicomToolkit.Verify(p => p.Save(It.IsAny <DicomFile>(), It.IsAny <string>()), Times.Exactly(4));
}
public async Task ProcessorRequest_ShallRestorePreviouslyRetrievedFiles()
{
var cancellationTokenSource = new CancellationTokenSource();
var storagePath = "/store";
_fileSystem.Directory.CreateDirectory(storagePath);
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file1.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file2.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "file3.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "corrupted.dcm"));
_fileSystem.File.Create(_fileSystem.Path.Combine(storagePath, "text.txt"));
var request = new InferenceRequest
{
PayloadId = Guid.NewGuid().ToString(),
JobId = Guid.NewGuid().ToString(),
TransactionId = Guid.NewGuid().ToString()
};
request.InputResources.Add(
new RequestInputDataResource
{
Interface = InputInterfaceType.Algorithm,
ConnectionDetails = new InputConnectionDetails()
});
request.ConfigureTemporaryStorageLocation(storagePath);
_dicomToolkit.Setup(p => p.HasValidHeader(It.IsAny <string>()))
.Returns((string filename) =>
{
if (filename.EndsWith("text.txt"))
{
return(false);
}
else if (filename.EndsWith("corrupted.dcm"))
{
return(false);
}
return(true);
});
_dicomToolkit.Setup(p => p.Open(It.IsAny <string>()))
.Returns(() => InstanceGenerator.GenerateDicomFile());
_inferenceRequestStore.SetupSequence(p => p.Take(It.IsAny <CancellationToken>()))
.Returns(Task.FromResult(request))
.Returns(() =>
{
cancellationTokenSource.Cancel();
throw new OperationCanceledException("canceled");
});
_jobStore.Setup(p => p.Add(It.IsAny <Job>(), It.IsAny <string>(), It.IsAny <IList <InstanceStorageInfo> >()));
var store = new DataRetrievalService(
_dicomWebClient.Object,
_logger.Object,
_inferenceRequestStore.Object,
_fileSystem,
_dicomToolkit.Object,
_jobStore.Object);
await store.StartAsync(cancellationTokenSource.Token);
BlockUntilCancelled(cancellationTokenSource.Token);
_logger.VerifyLoggingMessageBeginsWith($"Restored previously retrieved instance", LogLevel.Debug, Times.Exactly(3));
_logger.VerifyLoggingMessageBeginsWith($"Restored previously retrieved instance", LogLevel.Debug, Times.Exactly(3));
_logger.VerifyLoggingMessageBeginsWith($"Unable to restore previously retrieved instance from", LogLevel.Warning, Times.Once());
_jobStore.Verify(p => p.Add(It.IsAny <Job>(), It.IsAny <string>(), It.IsAny <IList <InstanceStorageInfo> >()), Times.Once());
}