private async Task RetrieveViaDicomWeb(InferenceRequest inferenceRequest, RequestInputDataResource source, Dictionary <string, InstanceStorageInfo> retrievedInstance)
{
Guard.Against.Null(inferenceRequest, nameof(inferenceRequest));
Guard.Against.Null(retrievedInstance, nameof(retrievedInstance));
var authenticationHeaderValue = GenerateAuthenticationHeader(source.ConnectionDetails.AuthType, source.ConnectionDetails.AuthId);
var dicomWebClient = _dicomWebClientFactory.CreateDicomWebClient(
new Uri(source.ConnectionDetails.Uri),
authenticationHeaderValue,
null,
null,
null,
null);
switch (inferenceRequest.InputMetadata.Details.Type)
{
case InferenceRequestType.DicomUid:
await RetrieveStudies(inferenceRequest.InputMetadata.Details.Studies, inferenceRequest.StoragePath, dicomWebClient, retrievedInstance);
break;
default:
throw new InferenceRequestException($"The 'inputMetadata' type '{inferenceRequest.InputMetadata.Details.Type}' specified is not supported.");
}
}
private async Task RetrieveViaFhir(InferenceRequest inferenceRequest, RequestInputDataResource source, Dictionary <string, string> retrievedResources)
{
Guard.Against.Null(inferenceRequest, nameof(inferenceRequest));
Guard.Against.Null(retrievedResources, nameof(retrievedResources));
foreach (var input in inferenceRequest.InputMetadata.Inputs)
{
if (input.Resources.IsNullOrEmpty())
{
continue;
}
await RetrieveFhirResources(input, source, retrievedResources, _fileSystem.Path.GetFhirStoragePath(inferenceRequest.StoragePath));
}
}
private async Task RetrieveViaDicomWeb(InferenceRequest inferenceRequest, RequestInputDataResource source, Dictionary <string, InstanceStorageInfo> retrievedInstance)
{
Guard.Against.Null(inferenceRequest, nameof(inferenceRequest));
Guard.Against.Null(retrievedInstance, nameof(retrievedInstance));
var authenticationHeaderValue = AuthenticationHeaderValueExtensions.ConvertFrom(source.ConnectionDetails.AuthType, source.ConnectionDetails.AuthId);
var dicomWebClient = new DicomWebClient(_httpClientFactory.CreateClient("dicomweb"), _loggerFactory.CreateLogger <DicomWebClient>());
dicomWebClient.ConfigureServiceUris(new Uri(source.ConnectionDetails.Uri, UriKind.Absolute));
if (!(authenticationHeaderValue is null))
{
dicomWebClient.ConfigureAuthentication(authenticationHeaderValue);
}
foreach (var input in inferenceRequest.InputMetadata.Inputs)
{
switch (input.Type)
{
case InferenceRequestType.DicomUid:
await RetrieveStudies(dicomWebClient, input.Studies, _fileSystem.Path.GetDicomStoragePath(inferenceRequest.StoragePath), retrievedInstance);
break;
case InferenceRequestType.DicomPatientId:
await QueryStudies(dicomWebClient, inferenceRequest, retrievedInstance, $"{DicomTag.PatientID.Group:X4}{DicomTag.PatientID.Element:X4}", input.PatientId);
break;
case InferenceRequestType.AccessionNumber:
foreach (var accessionNumber in input.AccessionNumber)
{
await QueryStudies(dicomWebClient, inferenceRequest, retrievedInstance, $"{DicomTag.AccessionNumber.Group:X4}{DicomTag.AccessionNumber.Element:X4}", accessionNumber);
}
break;
case InferenceRequestType.FhireResource:
continue;
default:
throw new InferenceRequestException($"The 'inputMetadata' type '{input.Type}' specified is not supported.");
}
}
}
private async Task <bool> RetrieveFhirResource(HttpClient httpClient, FhirResource resource, RequestInputDataResource source, Dictionary <string, string> retrievedResources, string storagePath, FhirStorageFormat fhirFormat, string acceptHeader)
{
Guard.Against.Null(httpClient, nameof(httpClient));
Guard.Against.Null(resource, nameof(resource));
Guard.Against.Null(source, nameof(source));
Guard.Against.Null(retrievedResources, nameof(retrievedResources));
Guard.Against.NullOrWhiteSpace(storagePath, nameof(storagePath));
Guard.Against.NullOrWhiteSpace(acceptHeader, nameof(acceptHeader));
_logger.Log(LogLevel.Debug, $"Retriving FHIR resource {resource.Type}/{resource.Id} with media format {acceptHeader} and file format {fhirFormat}.");
var request = new HttpRequestMessage(HttpMethod.Get, $"{source.ConnectionDetails.Uri}{resource.Type}/{resource.Id}");
request.Headers.Accept.Add(MediaTypeWithQualityHeaderValue.Parse(acceptHeader));
var response = await Policy
.HandleResult <HttpResponseMessage>(p => !p.IsSuccessStatusCode)
.WaitAndRetryAsync(3,
(retryAttempt) =>
{
return(retryAttempt == 1 ? TimeSpan.FromMilliseconds(250) : TimeSpan.FromMilliseconds(500));
},
(result, timeSpan, retryCount, context) =>
{
_logger.Log(LogLevel.Error, result.Exception, $"Failed to retrieve resource {resource.Type}/{resource.Id} with status code {result.Result.StatusCode}, retry count={retryCount}.");
})
.ExecuteAsync(async() => await httpClient.SendAsync(request));
if (response.IsSuccessStatusCode)
{
var json = await response.Content.ReadAsStringAsync();
var filename = _fileSystem.Path.Combine(storagePath, $"{resource.Type}-{resource.Id}.{fhirFormat}".ToLowerInvariant());
await _fileSystem.File.WriteAllTextAsync(filename, json);
retrievedResources.Add(_fileSystem.Path.GetFileName(filename), filename);
return(true);
}
else
{
_logger.Log(LogLevel.Error, $"Error retriving FHIR resource {resource.Type}/{resource.Id}. Recevied HTTP status code {response.StatusCode}.");
return(false);
}
}
private async Task RetrieveFhirResources(InferenceRequestDetails requestDetails, RequestInputDataResource source, Dictionary <string, string> retrievedResources, string storagePath)
{
Guard.Against.Null(requestDetails, nameof(requestDetails));
Guard.Against.Null(source, nameof(source));
Guard.Against.Null(retrievedResources, nameof(retrievedResources));
Guard.Against.NullOrWhiteSpace(storagePath, nameof(storagePath));
var pendingResources = new Queue <FhirResource>(requestDetails.Resources.Where(p => !p.IsRetrieved));
if (pendingResources.Count == 0)
{
return;
}
var authenticationHeaderValue = AuthenticationHeaderValueExtensions.ConvertFrom(source.ConnectionDetails.AuthType, source.ConnectionDetails.AuthId);
var httpClient = _httpClientFactory.CreateClient("fhir");
httpClient.DefaultRequestHeaders.Clear();
httpClient.DefaultRequestHeaders.Authorization = authenticationHeaderValue;
_fileSystem.Directory.CreateDirectory(storagePath);
FhirResource resource = null;
try
{
while (pendingResources.Count > 0)
{
resource = pendingResources.Dequeue();
resource.IsRetrieved = await RetrieveFhirResource(
httpClient,
resource,
source,
retrievedResources,
storagePath,
requestDetails.FhirFormat,
requestDetails.FhirAcceptHeader);
}
}
catch (System.Exception ex)
{
_logger.Log(LogLevel.Error, ex, $"Error retrieving FHIR resource {resource?.Type}/{resource?.Id}");
}
}
