public void ShouldDeserializeResourceInJson()
{
var json = "{ \"Name\":\"John Doe\", \"Amount\":123.45 }";
var resource = deserializer.Deserialize(json, typeof(SomeResource)) as SomeResource;
Assert.AreEqual("John Doe", resource.Name);
Assert.AreEqual(123.45, resource.Amount);
}
private async Task ProcessSearchResultsAsync(IEnumerable <SearchResultEntry> searchResults, string partId, IAnonymizer anonymizer, CancellationToken cancellationToken)
{
foreach (SearchResultEntry result in searchResults)
{
ResourceWrapper resourceWrapper = result.Resource;
ResourceElement element = _resourceDeserializer.Deserialize(resourceWrapper);
if (anonymizer != null)
{
try
{
element = anonymizer.Anonymize(element);
}
catch (Exception ex)
{
throw new FailedToAnonymizeResourceException(ex.Message, ex);
}
}
// Serialize into NDJson and write to the file.
byte[] bytesToWrite = _resourceToByteArraySerializer.Serialize(element);
await _fileManager.WriteToFile(resourceWrapper.ResourceTypeName, partId, bytesToWrite, cancellationToken);
}
}
private ResourceElement CreatePatientWithIdentity(ResourceElement patient, SearchResult results)
{
var searchMatchOnly = results.Results.Where(x => x.SearchEntryMode == ValueSets.SearchEntryMode.Match).ToList();
if (searchMatchOnly.Count > 1)
{
throw new MemberMatchMatchingException(Core.Resources.MemberMatchMultipleMatchesFound);
}
if (searchMatchOnly.Count == 0)
{
throw new MemberMatchMatchingException(Core.Resources.MemberMatchNoMatchFound);
}
var match = searchMatchOnly[0];
var element = _resourceDeserializer.Deserialize(match.Resource);
var foundPatient = element.ToPoco <Patient>();
var id = foundPatient.Identifier.Where(x => x.Type != null && x.Type.Coding != null && x.Type.Coding.Exists(x => x.Code == "MB")).FirstOrDefault();
if (id == null)
{
throw new MemberMatchMatchingException(Core.Resources.MemberMatchNoMatchFound);
}
var resultPatient = patient.ToPoco <Patient>();
var resultId = new Identifier(id.System, id.Value);
resultId.Type = new CodeableConcept("http://terminology.hl7.org/CodeSystem/v2-0203", "UMB", "Member Match");
resultPatient.Identifier.Add(resultId);
var result = resultPatient.ToResourceElement();
return(result);
}
private async Task ProcessSearchResultsAsync(IEnumerable <SearchResultEntry> searchResults, string partId, IAnonymizer anonymizer, CancellationToken cancellationToken)
{
foreach (SearchResultEntry result in searchResults)
{
ResourceWrapper resourceWrapper = result.Resource;
string resourceType = resourceWrapper.ResourceTypeName;
// Check whether we already have an existing file for the current resource type.
if (!_resourceTypeToFileInfoMapping.TryGetValue(resourceType, out ExportFileInfo exportFileInfo))
{
// Check whether we have seen this file previously (in situations where we are resuming an export)
if (_exportJobRecord.Output.TryGetValue(resourceType, out exportFileInfo))
{
// A file already exists for this resource type. Let us open the file on the client.
await _exportDestinationClient.OpenFileAsync(exportFileInfo.FileUri, cancellationToken);
}
else
{
// File does not exist. Create it.
string fileName;
if (_exportJobRecord.StorageAccountContainerName.Equals(_exportJobRecord.Id, StringComparison.OrdinalIgnoreCase))
{
fileName = $"{resourceType}.ndjson";
}
else
{
string dateTime = _exportJobRecord.QueuedTime.UtcDateTime.ToString("s")
.Replace("-", string.Empty, StringComparison.OrdinalIgnoreCase)
.Replace(":", string.Empty, StringComparison.OrdinalIgnoreCase);
fileName = $"{dateTime}-{_exportJobRecord.Id}/{resourceType}.ndjson";
}
Uri fileUri = await _exportDestinationClient.CreateFileAsync(fileName, cancellationToken);
exportFileInfo = new ExportFileInfo(resourceType, fileUri, sequence: 0);
// Since we created a new file the JobRecord Output also needs to know about it.
_exportJobRecord.Output.TryAdd(resourceType, exportFileInfo);
}
_resourceTypeToFileInfoMapping.Add(resourceType, exportFileInfo);
}
ResourceElement element = _resourceDeserializer.Deserialize(resourceWrapper);
if (anonymizer != null)
{
element = anonymizer.Anonymize(element);
}
// Serialize into NDJson and write to the file.
byte[] bytesToWrite = _resourceToByteArraySerializer.Serialize(element);
await _exportDestinationClient.WriteFilePartAsync(exportFileInfo.FileUri, partId, bytesToWrite, cancellationToken);
// Increment the file information.
exportFileInfo.IncrementCount(bytesToWrite.Length);
}
}
/// <inheritdoc />
public void Update(ResourceWrapper resourceWrapper)
{
var resourceElement = _resourceDeserializer.Deserialize(resourceWrapper);
var newIndices = _searchIndexer.Extract(resourceElement);
ExtractMinAndMaxValues(newIndices);
resourceWrapper.UpdateSearchIndices(newIndices);
}
public object Build(string xml, Type objectType)
{
try
{
return(string.IsNullOrEmpty(xml) ? null : deserializer.Deserialize(xml, objectType));
} catch (Exception e)
{
throw new UnmarshallingException(e.Message);
}
}
public async Task <ReindexSingleResourceResponse> Handle(ReindexSingleResourceRequest request, CancellationToken cancellationToken)
{
EnsureArg.IsNotNull(request, nameof(request));
if (await _authorizationService.CheckAccess(DataActions.Reindex) != DataActions.Reindex)
{
throw new UnauthorizedFhirActionException();
}
var key = new ResourceKey(request.ResourceType, request.ResourceId);
ResourceWrapper storedResource = await _fhirDataStore.GetAsync(key, cancellationToken);
if (storedResource == null)
{
throw new ResourceNotFoundException(string.Format(Core.Resources.ResourceNotFoundById, request.ResourceType, request.ResourceId));
}
// We need to extract the "new" search indices since the assumption is that
// a new search parameter has been added to the fhir server.
ResourceElement resourceElement = _resourceDeserializer.Deserialize(storedResource);
IReadOnlyCollection <SearchIndexEntry> newIndices = _searchIndexer.Extract(resourceElement);
// Create a new parameter resource and include the new search indices and the corresponding values.
var parametersResource = new Parameters
{
Id = Guid.NewGuid().ToString(),
VersionId = "1",
Parameter = new List <Parameters.ParameterComponent>(),
};
parametersResource.Parameter.Add(new Parameters.ParameterComponent()
{
Name = "originalResourceId", Value = new FhirString(request.ResourceId)
});
parametersResource.Parameter.Add(new Parameters.ParameterComponent()
{
Name = "originalResourceType", Value = new FhirString(request.ResourceType)
});
foreach (SearchIndexEntry searchIndex in newIndices)
{
parametersResource.Parameter.Add(new Parameters.ParameterComponent()
{
Name = searchIndex.SearchParameter.Name.ToString(), Value = new FhirString(searchIndex.Value.ToString())
});
}
return(new ReindexSingleResourceResponse(parametersResource.ToResourceElement()));
}
