/// <inheritdoc />
public RawResource Create(ResourceElement resource, bool keepMeta)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco <Resource>();
poco.Meta = poco.Meta ?? new Meta();
var versionId = poco.Meta.VersionId;
try
{
// Clear meta version if keepMeta is false since this is set based on generated values when saving the resource
if (!keepMeta)
{
poco.Meta.VersionId = null;
}
else
{
// Assume it's 1, though it may get changed by the database.
poco.Meta.VersionId = "1";
}
return(new RawResource(_fhirJsonSerializer.SerializeToString(poco), FhirResourceFormat.Json, keepMeta));
}
finally
{
if (!keepMeta)
{
poco.Meta.VersionId = versionId;
}
}
}
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);
}
/// <inheritdoc />
public IReadOnlyCollection <SearchIndexEntry> Extract(ResourceElement resource)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco();
var entries = new List <SearchIndexEntry>();
var context = new FhirEvaluationContext(poco);
IEnumerable <SearchParameterInfo> searchParameters = _searchParameterDefinitionManager.GetSearchParameters(resource.InstanceType);
foreach (SearchParameterInfo searchParameter in searchParameters)
{
if (searchParameter.Name == SearchParameterNames.ResourceType)
{
// We don't index the resource type value. We just use the property on the root document.
continue;
}
if (searchParameter.Type == SearchParamType.Composite)
{
entries.AddRange(ProcessCompositeSearchParameter(searchParameter, poco, context));
}
else
{
entries.AddRange(ProcessNonCompositeSearchParameter(searchParameter, poco, context));
}
}
return(entries);
}
/// <inheritdoc />
public RawResource Create(ResourceElement resource)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco <Resource>();
var versionId = poco.Meta?.VersionId;
var lastUpdated = poco.Meta?.LastUpdated;
try
{
// Clear meta version and lastUpdated since these are set based on generated values when saving the resource
if (poco.Meta != null)
{
poco.Meta.VersionId = null;
poco.Meta.LastUpdated = null;
}
return(new RawResource(_fhirJsonSerializer.SerializeToString(poco), FhirResourceFormat.Json));
}
finally
{
if (poco.Meta != null)
{
poco.Meta.VersionId = versionId;
poco.Meta.LastUpdated = lastUpdated;
}
}
}
public static ResourceElement UpdateLastUpdated(this ResourceElement resource, DateTimeOffset lastUpdated)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco();
poco.Meta.LastUpdated = lastUpdated;
return(poco.ToResourceElement());
}
public static ResourceElement UpdateId(this ResourceElement resource, string newId)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco();
poco.Id = newId;
return(poco.ToResourceElement());
}
public static ResourceElement UpdateVersion(this ResourceElement resource, string newVersion)
{
EnsureArg.IsNotNull(resource, nameof(resource));
var poco = resource.ToPoco();
poco.VersionId = newVersion;
return(poco.ToResourceElement());
}
public void GivenASearchResult_WhenCreateSearchBundle_ThenCorrectBundleShouldBeReturned()
{
_urlResolver.ResolveResourceWrapperUrl(Arg.Any <ResourceWrapper>()).Returns(x => new Uri(string.Format(_resourceUrlFormat, x.ArgAt <ResourceWrapper>(0).ResourceId)));
_urlResolver.ResolveRouteUrl(_unsupportedSearchParameters).Returns(_selfUrl);
ResourceElement observation1 = Samples.GetDefaultObservation().UpdateId("123");
ResourceElement observation2 = Samples.GetDefaultObservation().UpdateId("abc");
var resourceWrappers = new SearchResultEntry[]
{
new SearchResultEntry(CreateResourceWrapper(observation1, HttpMethod.Post)),
new SearchResultEntry(CreateResourceWrapper(observation2, HttpMethod.Post)),
};
var searchResult = new SearchResult(resourceWrappers, continuationToken: null, sortOrder: null, unsupportedSearchParameters: _unsupportedSearchParameters);
ResourceElement actual = null;
using (Mock.Property(() => ClockResolver.UtcNowFunc, () => _dateTime))
{
actual = _bundleFactory.CreateSearchBundle(searchResult);
}
// Since there is no continuation token, there should not be next link.
Assert.Null(actual.Scalar <string>("Bundle.link.where(relation='next').url"));
Assert.Collection(
actual.ToPoco <Bundle>().Entry,
async e => await ValidateEntry(observation1.ToPoco <Observation>(), e),
async e => await ValidateEntry(observation2.ToPoco <Observation>(), e));
async Task ValidateEntry(Observation expected, Bundle.EntryComponent actualEntry)
{
Assert.NotNull(actualEntry);
var raw = actualEntry as RawBundleEntryComponent;
using (var ms = new MemoryStream())
using (var sr = new StreamReader(ms))
{
await raw?.ResourceElement?.SerializeToStreamAsUtf8Json(ms);
ms.Seek(0, SeekOrigin.Begin);
var resourceData = await sr.ReadToEndAsync();
Assert.NotNull(resourceData);
Resource resource;
resource = new FhirJsonParser().Parse(resourceData) as Resource;
Assert.Equal(expected.Id, resource.Id);
Assert.Equal(string.Format(_resourceUrlFormat, expected.Id), raw.FullUrl);
Assert.NotNull(raw.Search);
Assert.Equal(Bundle.SearchEntryMode.Match, raw.Search.Mode);
}
}
}
/// <inheritdoc />
public byte[] Serialize(ResourceElement resourceElement)
{
EnsureArg.IsNotNull(resourceElement, nameof(resourceElement));
string resourceData = _fhirJsonSerializer.SerializeToString(resourceElement.ToPoco <Resource>());
byte[] bytesToWrite = Encoding.UTF8.GetBytes($"{resourceData}\n");
return(bytesToWrite);
}
private ResourceWrapper CreateResourceWrapper(ResourceElement resourceElement, HttpMethod httpMethod)
{
return(new ResourceWrapper(
resourceElement,
new RawResource(_fhirJsonSerializer.SerializeToString(resourceElement.ToPoco <Observation>()), FhirResourceFormat.Json, isMetaSet: false),
new ResourceRequest(httpMethod, url: "http://test/Resource/resourceId"),
false,
null,
null,
null));
}
/// <inheritdoc />
public byte[] Serialize(ResourceWrapper resourceWrapper)
{
EnsureArg.IsNotNull(resourceWrapper, nameof(resourceWrapper));
ResourceElement resource = _resourceDeserializer.DeserializeRaw(resourceWrapper.RawResource, resourceWrapper.Version, resourceWrapper.LastModified);
string resourceData = _fhirJsonSerializer.SerializeToString(resource.ToPoco <Resource>());
byte[] bytesToWrite = Encoding.UTF8.GetBytes($"{resourceData}\n");
return(bytesToWrite);
}
/// <summary>
/// Executes a FHIRPath Patch Delete operation. Delete operations will
/// remove the element at the specified operation.Path.
///
/// Deletion at a non-existing path is not supposed to result in an error.
///
/// Fhir package has a built-in "Remove" operation which accomplishes
/// this easily.
/// </summary>
/// <returns>Patched FHIR Resource as POCO.</returns>
internal override Resource Execute()
{
try
{
Target.Parent.Remove(Target);
return(ResourceElement.ToPoco <Resource>());
}
catch (InvalidOperationException)
{
return(ResourceElement.ToPoco <Resource>());
}
}
public void GivenASearchResult_WhenCreateSearchBundle_ThenCorrectBundleShouldBeReturned()
{
_urlResolver.ResolveResourceUrl(Arg.Any <ResourceElement>()).Returns(x => new Uri(string.Format(_resourceUrlFormat, x.ArgAt <ResourceElement>(0).Id)));
_urlResolver.ResolveRouteUrl(_unsupportedSearchParameters).Returns(_selfUrl);
ResourceElement observation1 = Samples.GetDefaultObservation().UpdateId("123");
ResourceElement observation2 = Samples.GetDefaultObservation().UpdateId("abc");
var resourceWrappers = new ResourceWrapper[]
{
CreateResourceWrapper(observation1),
CreateResourceWrapper(observation2),
};
var searchResult = new SearchResult(resourceWrappers, _unsupportedSearchParameters, continuationToken: null);
ResourceElement actual = null;
using (Mock.Property(() => Clock.UtcNowFunc, () => _dateTime))
{
actual = _bundleFactory.CreateSearchBundle(searchResult);
}
// Since there is no continuation token, there should not be next link.
Assert.Null(actual.Scalar <string>("Bundle.link.where(relation='next').url"));
Assert.Collection(
actual.ToPoco <Bundle>().Entry,
e => ValidateEntry(observation1.ToPoco <Observation>(), e),
e => ValidateEntry(observation2.ToPoco <Observation>(), e));
ResourceWrapper CreateResourceWrapper(ResourceElement resourceElement)
{
return(new ResourceWrapper(
resourceElement,
new RawResource(_fhirJsonSerializer.SerializeToString(resourceElement.ToPoco <Observation>()), FhirResourceFormat.Json),
null,
false,
null,
null,
null));
}
void ValidateEntry(Observation expected, Bundle.EntryComponent actualEntry)
{
Assert.NotNull(actualEntry);
Assert.NotNull(actualEntry.Resource);
Assert.Equal(expected.Id, actualEntry.Resource.Id);
Assert.Equal(string.Format(_resourceUrlFormat, expected.Id), actualEntry.FullUrl);
Assert.NotNull(actualEntry.Search);
Assert.Equal(Bundle.SearchEntryMode.Match, actualEntry.Search.Mode);
}
}
/// <summary>
/// Executes a FHIRPath Patch Move operation. Move operations will
/// move an existing element inside a list at the specified
/// operation.Path from the index of operation.Source to the index of
/// operation.Destination.
///
/// Fhir package does NOT have a built-in operation which accomplishes
/// this. So we must inspect the existing list and recreate it with the
/// correct elements in order.
/// </summary>
/// <returns>Patched FHIR Resource as POCO.</returns>
internal override Resource Execute()
{
// Setup
var targetParent = Target.Parent;
var name = Target.Name;
// Check indexes
var targetLen = targetParent.Children(name).Count();
if (Operation.Source < 0 || Operation.Source >= targetLen)
{
throw new InvalidOperationException("Move source index out of bounds of target list");
}
if (Operation.Destination < 0 || Operation.Destination >= targetLen)
{
throw new InvalidOperationException("Move destination index out of bounds of target list");
}
// Remove specified element from the list
var elementToMove = targetParent.AtIndex(name, Operation.Source ?? -1);
if (!targetParent.Remove(elementToMove))
{
throw new InvalidOperationException();
}
// There is no easy "move" operation in the FHIR library, so we must
// iterate over the list to reconstruct it.
foreach (var child in targetParent.Children(name).ToList()
.Select(x => x.ToElementNode())
.Select((value, index) => (value, index)))
{
// Add the new item at the correct index
if (Operation.Destination == child.index)
{
targetParent.Add(Provider, elementToMove, name);
}
// Remove the old element from the list so the new order is used
if (!targetParent.Remove(child.value))
{
throw new InvalidOperationException();
}
// Add the old element back to the list
targetParent.Add(Provider, child.value, name);
}
return(ResourceElement.ToPoco <Resource>());
}
private void SetupDataStoreToReturnDummyResourceWrapper()
{
ResourceElement patientResourceElement = Samples.GetDefaultPatient();
Patient patientResource = patientResourceElement.ToPoco <Patient>();
RawResource rawResource = new RawResource(new FhirJsonSerializer().SerializeToString(patientResource), FhirResourceFormat.Json, isMetaSet: false);
ResourceWrapper dummyResourceWrapper = new ResourceWrapper(
patientResourceElement,
rawResource,
request: null,
deleted: false,
searchIndices: null,
compartmentIndices: null,
lastModifiedClaims: null);
_fhirDataStore.GetAsync(Arg.Any <ResourceKey>(), _cancellationToken).Returns(Task.FromResult(dummyResourceWrapper));
}
public ResourceElement CreateSearchBundle(SearchResult result)
{
return(CreateBundle(result, Bundle.BundleType.Searchset, r =>
{
ResourceElement resource = _deserializer.Deserialize(r.Resource);
return new Bundle.EntryComponent
{
FullUrlElement = new FhirUri(_urlResolver.ResolveResourceUrl(resource)),
Resource = resource.ToPoco <Resource>(),
Search = new Bundle.SearchComponent
{
Mode = r.SearchEntryMode == SearchEntryMode.Match ? Bundle.SearchEntryMode.Match : Bundle.SearchEntryMode.Include,
},
};
}));
}
public async Task GivenAResourceTypeWithNoVersionVersioningPolicy_WhenSearchingHistory_ThenOnlyLatestVersionIsReturned()
{
// The FHIR storage fixture configures organization resources to have the "no-version" versioning policy
RawResourceElement organizationResource = await Mediator.CreateResourceAsync(Samples.GetDefaultOrganization());
ResourceElement newResourceValues = Samples.GetDefaultOrganization().UpdateId(organizationResource.Id);
SaveOutcome updateResult = await Mediator.UpsertResourceAsync(newResourceValues, WeakETag.FromVersionId(organizationResource.VersionId));
ResourceElement historyResults = await Mediator.SearchResourceHistoryAsync(KnownResourceTypes.Organization, updateResult.RawResourceElement.Id);
// The history bundle only has one entry because resource history is not kept
Bundle bundle = historyResults.ToPoco <Bundle>();
Assert.Single(bundle.Entry);
Assert.Equal(WeakETag.FromVersionId(updateResult.RawResourceElement.VersionId).ToString(), bundle.Entry[0].Response.Etag);
}
public async Task <SearchResourceResponse> Handle(SearchResourceRequest request, CancellationToken cancellationToken, RequestHandlerDelegate <SearchResourceResponse> next)
{
EnsureArg.IsNotNull(request, nameof(request));
Tuple <string, string> listParameter = request.Queries
.FirstOrDefault(x => string.Equals(x.Item1, KnownQueryParameterNames.List, StringComparison.OrdinalIgnoreCase));
// if _list was not requested, or _list was requested with invalid value, continue...
if ((listParameter == null) || string.IsNullOrWhiteSpace(listParameter.Item2))
{
return(await next());
}
ResourceWrapper listWrapper =
await _dataStore.Value.GetAsync(new ResourceKey <Hl7.Fhir.Model.List>(listParameter.Item2), cancellationToken);
// wanted list was not found
if (listWrapper == null)
{
return(CreateEmptySearchResponse(request));
}
ResourceElement list = _deserializer.Deserialize(listWrapper);
IEnumerable <ReferenceSearchValue> references = list.ToPoco <Hl7.Fhir.Model.List>()
.Entry
.Where(x => x.Deleted != true)
.Select(x => _referenceSearchValueParser.Parse(x.Item.Reference))
.Where(x => string.IsNullOrWhiteSpace(request.ResourceType) ||
string.Equals(request.ResourceType, x.ResourceType, StringComparison.Ordinal))
.ToArray();
// the requested resource was not found in the list
if (!references.Any())
{
return(CreateEmptySearchResponse(request));
}
// Remove the 'list' params from the queries, to be later replaced with specific ids of resources
IEnumerable <Tuple <string, string> > query = request.Queries.Except(new[] { listParameter });
query = query.Concat(new[] { Tuple.Create(KnownQueryParameterNames.Id, string.Join(",", references.Select(x => x.ResourceId))) });
request.Queries = query.ToArray();
return(await next());
}
public async Task GivenAResourceTypeWithVersionedUpdateVersioningPolicy_WhenSearchingHistory_ThenAllVersionsAreReturned()
{
// The FHIR storage fixture configures medication resources to have the "versioned-update" versioning policy
RawResourceElement medicationResource = await Mediator.CreateResourceAsync(Samples.GetDefaultMedication());
ResourceElement newResourceValues = Samples.GetDefaultMedication().UpdateId(medicationResource.Id);
SaveOutcome updateResult = await Mediator.UpsertResourceAsync(newResourceValues, WeakETag.FromVersionId(medicationResource.VersionId));
ResourceElement historyResults = await Mediator.SearchResourceHistoryAsync(KnownResourceTypes.Medication, updateResult.RawResourceElement.Id);
// The history bundle has both versions because history is kept
Bundle bundle = historyResults.ToPoco <Bundle>();
Assert.Equal(2, bundle.Entry.Count);
Assert.Equal(WeakETag.FromVersionId(updateResult.RawResourceElement.VersionId).ToString(), bundle.Entry.Max(entry => entry.Response.Etag));
Assert.Equal(WeakETag.FromVersionId(medicationResource.VersionId).ToString(), bundle.Entry.Min(entry => entry.Response.Etag));
}
/// <summary>
/// Executes a FHIRPath Patch Insert operation. Insert operations will
/// add a new element to a list at the specified operation.Path with the
/// index operation.index.
///
/// Fhir package does NOT have a built-in operation which accomplishes
/// this. So we must inspect the existing list and recreate it with the
/// correct elements in order.
/// </summary>
/// <returns>Patched FHIR Resource as POCO.</returns>
internal override Resource Execute()
{
// Setup;
var targetParent = Target.Parent;
var name = Target.Name;
var listElements = targetParent.Children(name).ToList()
.Select(x => x as ElementNode)
.Select((value, index) => (value, index))
.ToList();
// Ensure index is in bounds
if (Operation.Index < 0 || Operation.Index > listElements.Count)
{
throw new InvalidOperationException("Insert index out of bounds of target list");
}
// There is no easy "insert" operation in the FHIR library, so we must
// iterate over the list and recreate it.
foreach (var child in listElements)
{
// Add the new item at the correct index
if (Operation.Index == child.index)
{
targetParent.Add(Provider, ValueElementNode);
}
// Remove the old element from the list so the new order is used
if (!targetParent.Remove(child.value))
{
throw new InvalidOperationException();
}
// Add the old element back to the list
targetParent.Add(Provider, child.value, name);
}
return(ResourceElement.ToPoco <Resource>());
}
/// <inheritdoc />
public byte[] Serialize(ResourceWrapper resourceWrapper)
{
EnsureArg.IsNotNull(resourceWrapper, nameof(resourceWrapper));
string resourceData = null;
if (resourceWrapper.RawResource.Format == Core.Models.FhirResourceFormat.Json)
{
// This is JSON already, we can write as is.
resourceData = resourceWrapper.RawResource.Data;
}
else
{
// This is not JSON, so deserialize it and serialize it to JSON.
ResourceElement resource = _resourceDeserializer.DeserializeRaw(resourceWrapper.RawResource, resourceWrapper.Version, resourceWrapper.LastModified);
resourceData = _fhirJsonSerializer.SerializeToString(resource.ToPoco <Resource>());
}
byte[] bytesToWrite = Encoding.UTF8.GetBytes($"{resourceData}\n");
return(bytesToWrite);
}
/// <inheritdoc />
public IReadOnlyCollection <SearchIndexEntry> Extract(ResourceElement resource)
{
EnsureArg.IsNotNull(resource, nameof(resource));
Resource poco = resource.ToPoco();
var entries = new List <SearchIndexEntry>();
var context = new FhirEvaluationContext(poco)
{
// Allows the indexer to parse the 'resolve' function i.e. CarePlan.subject.where(resolve() is Patient)
ElementResolver = _referenceToElementResolver.Resolve,
};
IEnumerable <SearchParameterInfo> searchParameters = _searchParameterDefinitionManager.GetSearchParameters(resource.InstanceType);
foreach (SearchParameterInfo searchParameter in searchParameters)
{
if (searchParameter.Code == SearchParameterNames.ResourceType)
{
// We don't index the resource type value. We just use the property on the root document.
continue;
}
if (searchParameter.Type == SearchParamType.Composite)
{
entries.AddRange(ProcessCompositeSearchParameter(searchParameter, poco, context));
}
else
{
entries.AddRange(ProcessNonCompositeSearchParameter(searchParameter, poco, context));
}
}
return(entries);
}
public async Task GivenAResourceTypeWithVersionedVersioningPolicy_WhenSearchingHistory_ThenAllVersionsAreReturned()
{
// The FHIR storage fixture configures observation resources to have the "versioned" versioning policy
RawResourceElement observationResource = await Mediator.CreateResourceAsync(Samples.GetDefaultObservation());
ResourceElement newResourceValues = Samples.GetDefaultObservation().UpdateId(observationResource.Id);
newResourceValues.ToPoco <Observation>().Text = new Narrative
{
Status = Narrative.NarrativeStatus.Generated,
Div = $"<div>{ContentUpdated}</div>",
};
SaveOutcome updateResult = await Mediator.UpsertResourceAsync(newResourceValues, WeakETag.FromVersionId(observationResource.VersionId));
ResourceElement historyResults = await Mediator.SearchResourceHistoryAsync(KnownResourceTypes.Observation, updateResult.RawResourceElement.Id);
// The history bundle has both versions because history is kept
Bundle bundle = historyResults.ToPoco <Bundle>();
Assert.Equal(2, bundle.Entry.Count);
Assert.Equal(WeakETag.FromVersionId(updateResult.RawResourceElement.VersionId).ToString(), bundle.Entry.Max(entry => entry.Response.Etag));
Assert.Equal(WeakETag.FromVersionId(observationResource.VersionId).ToString(), bundle.Entry.Min(entry => entry.Response.Etag));
}
/// <summary>
/// Executes a FHIRPath Patch Add operation. Add operations will add a new
/// element of the specified opearation.Name at the specified operation.Path.
///
/// Adding of a non-existent element will create the new element. Add on
/// a list will append the list.
///
/// Fhir package has a built-in "Add" operation which accomplishes this
/// easily.
/// </summary>
/// <returns>Patched FHIR Resource as POCO.</returns>
internal override Resource Execute()
{
Target.Add(Provider, ValueElementNode);
return(ResourceElement.ToPoco <Resource>());
}
public bool TryValidate(ResourceElement value, ICollection <ValidationResult> validationResults = null, bool recurse = false)
{
return(DotNetAttributeValidation.TryValidate(value.ToPoco(), validationResults, recurse));
}