public FhirJsonOutputFormatter(
FhirJsonSerializer fhirJsonSerializer,
ResourceDeserializer deserializer,
ILogger <FhirJsonOutputFormatter> logger,
ArrayPool <char> charPool,
BundleSerializer bundleSerializer)
{
EnsureArg.IsNotNull(fhirJsonSerializer, nameof(fhirJsonSerializer));
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
EnsureArg.IsNotNull(logger, nameof(logger));
EnsureArg.IsNotNull(charPool, nameof(charPool));
EnsureArg.IsNotNull(bundleSerializer, nameof(bundleSerializer));
_fhirJsonSerializer = fhirJsonSerializer;
_deserializer = deserializer;
_logger = logger;
_charPool = new JsonArrayPool(charPool);
_bundleSerializer = bundleSerializer;
SupportedEncodings.Add(Encoding.UTF8);
SupportedEncodings.Add(Encoding.Unicode);
SupportedMediaTypes.Add(KnownContentTypes.JsonContentType);
SupportedMediaTypes.Add(KnownMediaTypeHeaderValues.ApplicationJson);
SupportedMediaTypes.Add(KnownMediaTypeHeaderValues.TextJson);
SupportedMediaTypes.Add(KnownMediaTypeHeaderValues.ApplicationAnyJsonSyntax);
}
public void GivenARawResourceOfUnknownType_WhenDeserializing_ThenANotSupportedExceptionIsThrown()
{
var raw = new RawResource("{}", ResourceFormat.Unknown);
var wrapper = new ResourceWrapper("id1", "version1", "Observation", raw, new ResourceRequest("http://fhir", HttpMethod.Post), Clock.UtcNow, false, null, null);
Assert.Throws <NotSupportedException>(() => ResourceDeserializer.Deserialize(wrapper));
}
public void DeserializesHasManyRelationship()
{
var target = new ResourceDeserializer(_singleJson, typeof(Person));
var result = target.Deserialize() as Person;
var expectedFriend = _person.Friends.Single();
var actualFriend = result?.Friends.Single();
Assert.Equal(expectedFriend.Identifier, actualFriend?.Identifier);
Assert.Null(actualFriend?.FirstName);
Assert.Null(actualFriend?.LastName);
Assert.Equal(default(int?), actualFriend?.Age);
Assert.Null(actualFriend?.Job);
Assert.Null(actualFriend?.Friends);
var expectedFamilyMembers = _person.FamilyMembers.ToArray();
var actualFamilyMembers = result?.FamilyMembers?.ToArray();
Assert.NotNull(actualFamilyMembers);
Assert.Equal(expectedFamilyMembers.Length, actualFamilyMembers.Length);
expectedFamilyMembers.Zip(actualFamilyMembers, (expected, actual) =>
{
Assert.Equal(expected.Identifier, actual.Identifier);
return(true);
});
}
public void ValidatesTopLevelMemberExclusivity()
{
var content = FileAsJson("invalid-top-level.json");
var target = new ResourceDeserializer(content, typeof(Person));
Assert.Throws <JsonApiException>(() => target.Deserialize());
}
public void ValidatesRootIsObject()
{
var content = FileAsJson("no-object-root.json");
var target = new ResourceDeserializer(content, typeof(Person));
Assert.Throws <JsonApiException>(() => target.Deserialize());
}
public void ValidatesMutuallyExclusiveTopLevelMembers()
{
var content = FileAsJson("errors-and-data.json");
var target = new ResourceDeserializer(content, typeof(Person));
Assert.Throws <JsonApiException>(() => target.Deserialize());
}
public void ValidatesNoIncludedWithoutData()
{
var content = FileAsJson("included-no-data.json");
var target = new ResourceDeserializer(content, typeof(Person));
Assert.Throws <JsonApiException>(() => target.Deserialize());
}
public void ValidatesRequiredTopLevelMembers()
{
var content = FileAsJson("no-data-errors-meta.json");
var target = new ResourceDeserializer(content, typeof(Person));
Assert.Throws <JsonApiException>(() => target.Deserialize());
}
public static Resource ToPoco(this RawResourceElement resource, ResourceDeserializer deserializer)
{
EnsureArg.IsNotNull(resource, nameof(resource));
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
return(resource.ToPoco <Resource>(deserializer));
}
public ValidateController(IMediator mediator, ResourceDeserializer resourceDeserializer)
{
EnsureArg.IsNotNull(mediator, nameof(mediator));
_mediator = mediator;
_resourceDeserializer = resourceDeserializer;
}
private T GetResourceDefinition <T>(TagResourceReference resourceReference)
{
var tagResource = GetPageableResource(resourceReference).Resource;
T result;
byte[] resourceDefinitionData = tagResource.DefinitionData;
ApplyResourceDefinitionFixups(tagResource, resourceDefinitionData);
byte[] resourceRawData = GetResourceData(resourceReference);
if (resourceRawData == null)
{
resourceRawData = new byte[0];
}
// deserialize the resource definition again
using (var definitionDataStream = new MemoryStream(resourceDefinitionData))
using (var definitionDataReader = new EndianReader(definitionDataStream, EndianFormat.LittleEndian))
using (var dataStream = new MemoryStream(resourceRawData))
using (var dataReader = new EndianReader(dataStream, EndianFormat.LittleEndian))
{
var context = new ResourceDefinitionSerializationContext(dataReader, definitionDataReader, tagResource.DefinitionAddress.Type);
var deserializer = new ResourceDeserializer(Cache.Version);
// deserialize without access to the data
definitionDataReader.SeekTo(tagResource.DefinitionAddress.Offset);
result = deserializer.Deserialize <T>(context);
}
return(result);
}
public ResourceHandlerTests()
{
_fhirDataStore = Substitute.For <IFhirDataStore>();
_conformanceProvider = Substitute.For <ConformanceProviderBase>();
_searchService = Substitute.For <ISearchService>();
// TODO: FhirRepository instantiate ResourceDeserializer class directly
// which will try to deserialize the raw resource. We should mock it as well.
_rawResourceFactory = Substitute.For <RawResourceFactory>(new FhirJsonSerializer());
_resourceWrapperFactory = Substitute.For <IResourceWrapperFactory>();
_resourceWrapperFactory
.Create(Arg.Any <ResourceElement>(), Arg.Any <bool>(), Arg.Any <bool>())
.Returns(x => CreateResourceWrapper(x.ArgAt <ResourceElement>(0), x.ArgAt <bool>(1)));
_conformanceStatement = CapabilityStatementMock.GetMockedCapabilityStatement();
CapabilityStatementMock.SetupMockResource(_conformanceStatement, ResourceType.Observation, null);
var observationResource = _conformanceStatement.Rest.First().Resource.Find(x => x.Type == ResourceType.Observation);
observationResource.ReadHistory = false;
observationResource.UpdateCreate = true;
observationResource.ConditionalCreate = true;
observationResource.ConditionalUpdate = true;
observationResource.Versioning = CapabilityStatement.ResourceVersionPolicy.Versioned;
CapabilityStatementMock.SetupMockResource(_conformanceStatement, ResourceType.Patient, null);
var patientResource = _conformanceStatement.Rest.First().Resource.Find(x => x.Type == ResourceType.Patient);
patientResource.ReadHistory = true;
patientResource.UpdateCreate = true;
patientResource.ConditionalCreate = true;
patientResource.ConditionalUpdate = true;
patientResource.Versioning = CapabilityStatement.ResourceVersionPolicy.VersionedUpdate;
_conformanceProvider.GetCapabilityStatementOnStartup().Returns(_conformanceStatement.ToTypedElement().ToResourceElement());
var lazyConformanceProvider = new Lazy <IConformanceProvider>(() => _conformanceProvider);
var collection = new ServiceCollection();
// an auth service that allows all.
_authorizationService = Substitute.For <IAuthorizationService <DataActions> >();
_authorizationService.CheckAccess(Arg.Any <DataActions>(), Arg.Any <CancellationToken>()).Returns(ci => ci.Arg <DataActions>());
var referenceResolver = new ResourceReferenceResolver(_searchService, new TestQueryStringParser());
_resourceIdProvider = new ResourceIdProvider();
collection.Add(x => _mediator).Singleton().AsSelf();
collection.Add(x => new CreateResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _resourceIdProvider, referenceResolver, _authorizationService)).Singleton().AsSelf().AsImplementedInterfaces();
collection.Add(x => new UpsertResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _resourceIdProvider, _authorizationService, ModelInfoProvider.Instance)).Singleton().AsSelf().AsImplementedInterfaces();
collection.Add(x => new ConditionalCreateResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _searchService, x.GetService <IMediator>(), _resourceIdProvider, _authorizationService)).Singleton().AsSelf().AsImplementedInterfaces();
collection.Add(x => new ConditionalUpsertResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _searchService, x.GetService <IMediator>(), _resourceIdProvider, _authorizationService)).Singleton().AsSelf().AsImplementedInterfaces();
collection.Add(x => new GetResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _resourceIdProvider, _authorizationService)).Singleton().AsSelf().AsImplementedInterfaces();
collection.Add(x => new DeleteResourceHandler(_fhirDataStore, lazyConformanceProvider, _resourceWrapperFactory, _resourceIdProvider, _authorizationService)).Singleton().AsSelf().AsImplementedInterfaces();
ServiceProvider provider = collection.BuildServiceProvider();
_mediator = new Mediator(type => provider.GetService(type));
_deserializer = new ResourceDeserializer(
(FhirResourceFormat.Json, new Func <string, string, DateTimeOffset, ResourceElement>((str, version, lastUpdated) => _fhirJsonParser.Parse(str).ToResourceElement())));
}
public ResourceToNdjsonBytesSerializer(ResourceDeserializer resourceDeserializer, FhirJsonSerializer fhirJsonSerializer)
{
EnsureArg.IsNotNull(resourceDeserializer, nameof(resourceDeserializer));
EnsureArg.IsNotNull(fhirJsonSerializer, nameof(fhirJsonSerializer));
_resourceDeserializer = resourceDeserializer;
_fhirJsonSerializer = fhirJsonSerializer;
}
public FhirStorageTests(FhirStorageTestsFixture fixture)
{
_fixture = fixture;
_searchService = Substitute.For <ISearchService>();
_dataStore = fixture.DataStore;
_conformance = CapabilityStatementMock.GetMockedCapabilityStatement();
CapabilityStatementMock.SetupMockResource(_conformance, ResourceType.Observation, null);
var observationResource = _conformance.Rest[0].Resource.Find(r => r.Type == ResourceType.Observation);
observationResource.UpdateCreate = true;
observationResource.Versioning = CapabilityStatement.ResourceVersionPolicy.Versioned;
CapabilityStatementMock.SetupMockResource(_conformance, ResourceType.Organization, null);
var organizationResource = _conformance.Rest[0].Resource.Find(r => r.Type == ResourceType.Organization);
organizationResource.UpdateCreate = true;
organizationResource.Versioning = CapabilityStatement.ResourceVersionPolicy.NoVersion;
var provider = Substitute.For <ConformanceProviderBase>();
provider.GetCapabilityStatementAsync().Returns(_conformance.ToTypedElement().ToResourceElement());
// TODO: FhirRepository instantiate ResourceDeserializer class directly
// which will try to deserialize the raw resource. We should mock it as well.
var rawResourceFactory = Substitute.For <RawResourceFactory>(new FhirJsonSerializer());
var resourceWrapperFactory = Substitute.For <IResourceWrapperFactory>();
resourceWrapperFactory
.Create(Arg.Any <ResourceElement>(), Arg.Any <bool>(), Arg.Any <bool>())
.Returns(x =>
{
ResourceElement resource = x.ArgAt <ResourceElement>(0);
return(new ResourceWrapper(resource, rawResourceFactory.Create(resource, keepMeta: true), new ResourceRequest(HttpMethod.Post, "http://fhir"), x.ArgAt <bool>(1), null, null, null));
});
var collection = new ServiceCollection();
var resourceIdProvider = new ResourceIdProvider();
_searchParameterUtilities = Substitute.For <ISearchParameterUtilities>();
collection.AddSingleton(typeof(IRequestHandler <CreateResourceRequest, UpsertResourceResponse>), new CreateResourceHandler(_dataStore, new Lazy <IConformanceProvider>(() => provider), resourceWrapperFactory, resourceIdProvider, new ResourceReferenceResolver(_searchService, new TestQueryStringParser()), DisabledFhirAuthorizationService.Instance, _searchParameterUtilities));
collection.AddSingleton(typeof(IRequestHandler <UpsertResourceRequest, UpsertResourceResponse>), new UpsertResourceHandler(_dataStore, new Lazy <IConformanceProvider>(() => provider), resourceWrapperFactory, resourceIdProvider, DisabledFhirAuthorizationService.Instance, ModelInfoProvider.Instance));
collection.AddSingleton(typeof(IRequestHandler <GetResourceRequest, GetResourceResponse>), new GetResourceHandler(_dataStore, new Lazy <IConformanceProvider>(() => provider), resourceWrapperFactory, resourceIdProvider, DisabledFhirAuthorizationService.Instance));
collection.AddSingleton(typeof(IRequestHandler <DeleteResourceRequest, DeleteResourceResponse>), new DeleteResourceHandler(_dataStore, new Lazy <IConformanceProvider>(() => provider), resourceWrapperFactory, resourceIdProvider, DisabledFhirAuthorizationService.Instance));
ServiceProvider services = collection.BuildServiceProvider();
Mediator = new Mediator(type => services.GetService(type));
_deserializer = new ResourceDeserializer(
(FhirResourceFormat.Json, new Func <string, string, DateTimeOffset, ResourceElement>((str, version, lastUpdated) => _fhirJsonParser.Parse(str).ToResourceElement())));
}
public FhirStorageTests(FhirStorageTestsFixture fixture)
{
_fixture = fixture;
_capabilityStatement = fixture.CapabilityStatement;
_deserializer = fixture.Deserializer;
_dataStore = fixture.DataStore;
_fhirJsonParser = fixture.JsonParser;
_conformanceProvider = fixture.ConformanceProvider;
Mediator = fixture.Mediator;
}
public void DeserializesBelongsToRelationships()
{
var target = new ResourceDeserializer(_singleJson, typeof(Person));
var result = target.Deserialize() as Person;
var job = result?.Job;
Assert.Equal(_person.Job.Id, job?.Id);
Assert.Null(job?.Name);
Assert.Equal(0, job?.NumberOfEmployees);
}
public static T ToPoco <T>(this RawResourceElement resource, ResourceDeserializer deserializer)
where T : Resource
{
EnsureArg.IsNotNull(resource, nameof(resource));
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
var deserialized = deserializer.DeserializeRawResourceElement(resource);
return(deserialized.ToPoco <T>());
}
public BundleFactory(IUrlResolver urlResolver, IFhirRequestContextAccessor fhirRequestContextAccessor, ResourceDeserializer deserializer)
{
EnsureArg.IsNotNull(urlResolver, nameof(urlResolver));
EnsureArg.IsNotNull(fhirRequestContextAccessor, nameof(fhirRequestContextAccessor));
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
_urlResolver = urlResolver;
_fhirRequestContextAccessor = fhirRequestContextAccessor;
_deserializer = deserializer;
}
/// <summary>
/// Converts json into an object of a specified type
/// </summary>
/// <param name="object">Json to convert</param>
/// <param name="type">Type to convert to</param>
/// <param name="config">The configuration to be used for deserialization</param>
/// <returns>Json converted into the specified type of object</returns>
public object Deserialize(JToken @object, Type type, JsonApiConfiguration config = null)
{
if (config == null)
{
config = new JsonApiConfiguration();
}
var target = new ResourceDeserializer(@object, type, config.PropertyNameConverter);
return target.Deserialize();
}
public void DeserializesBelongsToRelationshipsWithNullData()
{
var person = JToken.Parse("{'data': {'relationships': {'job': {data: null}}}}");
var target = new ResourceDeserializer(person, typeof(Person));
var result = target.Deserialize() as Person;
var job = result?.Job;
Assert.Null(job);
}
public void DeserializesAttributes()
{
var target = new ResourceDeserializer(_singleJson, typeof(Person));
var result = target.Deserialize() as Person;
Assert.Equal(_person.Identifier, result?.Identifier);
Assert.Equal(_person.FirstName, result?.FirstName);
Assert.Equal(_person.LastName, result?.LastName);
Assert.Equal(_person.Age, result?.Age);
}
public GetResourceHandler(
IFhirDataStore fhirDataStore,
Lazy <IConformanceProvider> conformanceProvider,
IResourceWrapperFactory resourceWrapperFactory,
ResourceDeserializer deserializer)
: base(fhirDataStore, conformanceProvider, resourceWrapperFactory)
{
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
_deserializer = deserializer;
}
public void DeserializesEnumerables()
{
var target = new ResourceDeserializer(_collectionJson, typeof(Person[]));
var result = target.Deserialize() as Person[];
Assert.Equal(_people.Length, result?.Length);
for (var i = 0; i < _people.Length; i++)
{
Assert.Equal(_people[i].Identifier, result?[i].Identifier);
}
}
public void DeserializesWithoutId()
{
(_singleJson["data"] as JObject)?.Property("id").Remove();
var target = new ResourceDeserializer(_singleJson, typeof(Person));
var result = target.Deserialize() as Person;
Assert.Equal(null, result?.Identifier);
Assert.Equal(_person.FirstName, result?.FirstName);
Assert.Equal(_person.LastName, result?.LastName);
Assert.Equal(_person.Age, result?.Age);
}
public Bundle CreateHistoryBundle(IEnumerable <Tuple <string, string> > unsupportedSearchParams, SearchResult result)
{
// Create the bundle from the result.
var bundle = new Bundle();
if (result != null)
{
IEnumerable <Bundle.EntryComponent> entries = result.Results.Select(r =>
{
Resource resource = ResourceDeserializer.Deserialize(r);
var hasVerb = Enum.TryParse(r.Request?.Method, true, out Bundle.HTTPVerb httpVerb);
return(new Bundle.EntryComponent
{
FullUrlElement = new FhirUri(_urlResolver.ResolveResourceUrl(resource, true)),
Resource = resource,
Request = new Bundle.RequestComponent
{
Method = hasVerb ? (Bundle.HTTPVerb?)httpVerb: null,
Url = r.Request?.Url?.ToString(),
},
Response = new Bundle.ResponseComponent
{
LastModified = r.LastModified,
Etag = WeakETag.FromVersionId(r.Version).ToString(),
},
});
});
bundle.Entry.AddRange(entries);
if (result.ContinuationToken != null)
{
bundle.NextLink = _urlResolver.ResolveRouteUrl(
_fhirRequestContextAccessor.FhirRequestContext.RouteName,
unsupportedSearchParams,
result.ContinuationToken);
}
}
// Add the self link to indicate which search parameters were used.
bundle.SelfLink = _urlResolver.ResolveRouteUrl(_fhirRequestContextAccessor.FhirRequestContext.RouteName, unsupportedSearchParams);
bundle.Id = _fhirRequestContextAccessor.FhirRequestContext.CorrelationId;
bundle.Type = Bundle.BundleType.History;
bundle.Total = result?.TotalCount;
bundle.Meta = new Meta
{
LastUpdated = Clock.UtcNow,
};
return(bundle);
}
public void GivenARawResource_WhenDeserializingFromJson_ThenTheObjectIsReturned()
{
var observation = Samples.GetDefaultObservation();
observation.Id = "id1";
var wrapper = new ResourceWrapper(observation, _rawResourceFactory.Create(observation), new ResourceRequest("http://fhir", HttpMethod.Post), false, null, null);
var newObject = ResourceDeserializer.Deserialize(wrapper);
Assert.Equal(observation.Id, newObject.Id);
Assert.Equal(observation.VersionId, newObject.VersionId);
}
public ReindexUtilities(
Func <IScoped <IFhirDataStore> > fhirDataStoreFactory,
ISearchIndexer searchIndexer,
ResourceDeserializer deserializer)
{
EnsureArg.IsNotNull(fhirDataStoreFactory, nameof(fhirDataStoreFactory));
EnsureArg.IsNotNull(searchIndexer, nameof(searchIndexer));
EnsureArg.IsNotNull(deserializer, nameof(deserializer));
_fhirDataStoreFactory = fhirDataStoreFactory;
_searchIndexer = searchIndexer;
_deserializer = deserializer;
}
public GroupMemberExtractor(
IScoped <IFhirDataStore> fhirDataStore,
ResourceDeserializer resourceDeserializer,
IReferenceToElementResolver referenceToElementResolver)
{
EnsureArg.IsNotNull(fhirDataStore, nameof(fhirDataStore));
EnsureArg.IsNotNull(resourceDeserializer, nameof(resourceDeserializer));
EnsureArg.IsNotNull(referenceToElementResolver, nameof(referenceToElementResolver));
_fhirDataStore = fhirDataStore;
_resourceDeserializer = resourceDeserializer;
_referenceToElementResolver = referenceToElementResolver;
}
public void TestStringListProps()
{
ResourceSerializer serializer = new ResourceSerializer();
IResource origin = _storage.NewResource("Email");
origin.SetProp(_propSize, 100);
origin.SetProp(_propReceived, DateTime.Now);
IStringList strLst = origin.GetStringListProp(_propValueList);
using ( strLst )
{
strLst.Add("One");
strLst.Add("Two");
strLst.Add("Three");
}
origin.SetProp(_propUnread, true);
origin.SetProp(_propSimilarity, 1.0);
ResourceNode resNode = serializer.AddResource(origin);
foreach (IResourceProperty prop in origin.Properties)
{
resNode.AddProperty(prop);
}
serializer.GenerateXML("SerializationResult.xml");
origin.Delete();
StreamReader sr = new StreamReader("SerializationResult.xml", Encoding.Default);
string str = Utils.StreamReaderReadToEnd(sr);
Console.WriteLine(str);
sr.Close();
ResourceDeserializer deserializer = new ResourceDeserializer("SerializationResult.xml");
ArrayList list = deserializer.GetSelectedResources();
Assert.AreEqual(1, list.Count, "List must contain only one resource. Current count is [" + list.Count + "]");
ResourceUnpack ru = (ResourceUnpack)list[0];
origin = ru.Resource;
Assert.IsTrue(origin.HasProp(_propValueList),
"Resource must contain StringList property");
IStringList stringsList = origin.GetStringListProp(_propValueList);
Assert.AreEqual(3, stringsList.Count, "StringList must contain three elements. Current count is [" + stringsList.Count + "]");
Assert.AreEqual("One", stringsList [0], "StringList[ 0 ] must be equal to [One]. Current value is [" + stringsList[0] + "]");
Assert.AreEqual("Two", stringsList [1], "StringList[ 1 ] must be equal to [Two]. Current value is [" + stringsList[1] + "]");
Assert.AreEqual("Three", stringsList [2], "StringList[ 2 ] must be equal to [Three]. Current value is [" + stringsList[2] + "]");
}
private void PopulateTreeView()
{
ResourceDeserializer resSer = new ResourceDeserializer(_fileName);
foreach (ResourceUnpack resourceNode in resSer.GetSelectedResources())
{
int iconIndex = GetIcon(resourceNode.Resource);
TreeNode node = new TreeNode(GetTypeDisplayName(resourceNode.Resource.Type) + ": " + resourceNode.Resource.DisplayName, iconIndex, iconIndex);
node.Tag = resourceNode;
_resourceTreeView.Nodes.Add(node);
AddLinks(node, resourceNode);
_resourceTreeView.SetNodeCheckState(node, NodeCheckState.Checked);
node.Expand();
}
}
