public void AnnotationsFromParsingTest()
{
var _sdsProvider = new PocoStructureDefinitionSummaryProvider();
var patientJson = "{\"resourceType\":\"Patient\", \"active\":\"true\"}";
var patient = FhirJsonNode.Parse(patientJson);
var typedPatient = patient.ToTypedElement(_sdsProvider, "Patient");
var sourceNode = typedPatient.ToSourceNode();
var result = patient.Annotation <ISourceNode>();
Assert.IsNotNull(result);
Assert.AreEqual(typeof(FhirJsonNode), result.GetType(), "ISourceNode is provided by FhirJsonNode");
Assert.AreSame(patient, result);
var result2 = sourceNode.Annotation <ISourceNode>();
Assert.IsNotNull(result2);
Assert.AreEqual(typeof(TypedElementToSourceNodeAdapter), result2.GetType(), "Now ISourceNode is provided by TypedElementToSourceNodeAdapter");
Assert.AreSame(sourceNode, result2);
var result3 = sourceNode.Annotation <IResourceTypeSupplier>();
Assert.IsNotNull(result3);
Assert.AreEqual(typeof(TypedElementToSourceNodeAdapter), result3.GetType());
}
private static Bundle ParseJSON(string content, bool permissive)
{
Bundle bundle = null;
// Grab all errors found by visiting all nodes and report if not permissive
if (!permissive)
{
List <string> entries = new List <string>();
ISourceNode node = FhirJsonNode.Parse(content, "Bundle", new FhirJsonParsingSettings {
PermissiveParsing = permissive
});
foreach (Hl7.Fhir.Utility.ExceptionNotification problem in node.VisitAndCatch())
{
entries.Add(problem.Message);
}
if (entries.Count > 0)
{
throw new System.ArgumentException(String.Join("; ", entries).TrimEnd());
}
}
// Try Parse
try
{
FhirJsonParser parser = new FhirJsonParser(GetParserSettings(permissive));
bundle = parser.Parse <Bundle>(content);
}
catch (Exception e)
{
throw new System.ArgumentException(e.Message);
}
return(bundle);
}
public void CompareToOtherElementNavigator()
{
var json = TestDataHelper.ReadTestData("TestPatient.json");
var xml = TestDataHelper.ReadTestData("TestPatient.xml");
var pocoP = (new FhirJsonParser()).Parse <Patient>(json).ToTypedElement();
var jsonP = FhirJsonNode.Parse(json, settings: new FhirJsonParsingSettings {
AllowJsonComments = true
})
.ToTypedElement(new PocoStructureDefinitionSummaryProvider());
var xmlP = FhirXmlNode.Parse(xml).ToTypedElement(new PocoStructureDefinitionSummaryProvider());
doCompare(pocoP, jsonP, "poco<->json");
doCompare(pocoP, xmlP, "poco<->xml");
void doCompare(ITypedElement one, ITypedElement two, string what)
{
var compare = one.IsEqualTo(two);
if (compare.Success == false)
{
Debug.WriteLine($"{what}: Difference in {compare.Details} at {compare.FailureLocation}");
Assert.Fail();
}
}
}
internal override ResourceElement GetPatchedResourceElement(ResourceWrapper resourceToPatch)
{
var resourceJsonNode = (FhirJsonNode)FhirJsonNode.Parse(resourceToPatch.RawResource.Data);
try
{
PatchDocument.ApplyTo(resourceJsonNode.JsonObject);
}
catch (JsonPatchException e)
{
throw new RequestNotValidException(e.Message, OperationOutcomeConstants.IssueType.Processing);
}
catch (ArgumentNullException e)
{
throw new RequestNotValidException(e.Message, OperationOutcomeConstants.IssueType.Processing);
}
Resource resourcePoco;
try
{
resourcePoco = resourceJsonNode
.ToTypedElement(ModelInfoProvider.StructureDefinitionSummaryProvider)
.ToPoco <Resource>();
}
catch (Exception e)
{
throw new RequestNotValidException(string.Format(Core.Resources.PatchResourceError, e.Message));
}
return(resourcePoco.ToResourceElement());
}
private ITypedElement ParseJsonToTypedElement(string json)
{
try
{
return(FhirJsonNode.Parse(json).ToTypedElement(_provider));
}
catch (Exception ex)
{
throw new InvalidInputException($"The input FHIR resource JSON is invalid.", ex);
}
}
public ResourceElement Patch(ResourceWrapper resourceToPatch, JsonPatchDocument patchDocument, WeakETag weakETag)
{
EnsureArg.IsNotNull(resourceToPatch, nameof(resourceToPatch));
Validate(resourceToPatch, weakETag, patchDocument);
var node = (FhirJsonNode)FhirJsonNode.Parse(resourceToPatch.RawResource.Data);
// Capture the state of properties that are immutable
ITypedElement resource = node.ToTypedElement(_modelInfoProvider.StructureDefinitionSummaryProvider);
(string path, object result)[] preState = _immutableProperties.Select(x => (path: x, result: resource.Scalar(x))).ToArray();
public void TryInvalidUntypedSource()
{
var jsonNav = FhirJsonNode.Parse("{ 'resourceType': 'Patient', 'active':true }");
try
{
var output = jsonNav.ToXml();
Assert.Fail();
}
catch (NotSupportedException)
{
}
}
public ITypedElement DeserializeToElement(
string resourceContent,
FhirJsonParsingSettings settings = null)
{
if (_fhirVersion == FhirVersion.Stu3)
{
return(FhirJsonNode.Parse(resourceContent, settings: settings).ToTypedElement(_stu3Provider));
}
else
{
return(FhirJsonNode.Parse(resourceContent).ToTypedElement(_r4Provider));
}
}
public void PreservesParsingExceptionDetails()
{
try
{
var nav = FhirJsonNode.Parse("<bla", "test");
var dummy = nav.Text;
Assert.Fail();
}
catch (FormatException fe)
{
Assert.IsInstanceOfType(fe.InnerException, typeof(JsonException));
}
}
internal static ITypedElement ParseToTypedElement(string json, IStructureDefinitionSummaryProvider provider, string rootName = null,
FhirJsonParsingSettings settings = null, TypedElementSettings tnSettings = null)
{
if (json == null)
{
throw Error.ArgumentNull(nameof(json));
}
if (provider == null)
{
throw Error.ArgumentNull(nameof(provider));
}
return(FhirJsonNode.Parse(json, rootName, settings).ToTypedElement(provider, null, tnSettings));
}
public void CatchNullErrors()
{
var nav = FhirJsonNode.Parse("{ 'a': null }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ '_a': null }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': null, '_a' : null }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': [null] }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': [null], '_a': [null] }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
}
public void SourceNodeFromElementNodeReturnsResourceTypeSupplier()
{
var _sdsProvider = new PocoStructureDefinitionSummaryProvider();
var patientJson = "{\"resourceType\":\"Patient\", \"active\":\"true\"}";
var patientNode = FhirJsonNode.Parse(patientJson);
var typedPatient = patientNode.ToTypedElement(_sdsProvider, "Patient");
var elementNode = ElementNode.FromElement(typedPatient);
var adapter = elementNode.ToSourceNode();
Assert.AreEqual(typeof(TypedElementToSourceNodeAdapter), adapter.GetType(), "ISourceNode is provided by TypedElementToSourceNodeAdapter");
var result = adapter.Annotation <IResourceTypeSupplier>();
Assert.IsNotNull(result);
Assert.AreEqual(typeof(TypedElementToSourceNodeAdapter), result.GetType());
Assert.AreEqual("Patient", adapter.GetResourceTypeIndicator());
Assert.AreSame(adapter, result);
}
public void CannotUseAbstractType()
{
var bundleJson = "{\"resourceType\":\"Bundle\", \"entry\":[{\"fullUrl\":\"http://example.org/Patient/1\"}]}";
var bundle = FhirJsonNode.Parse(bundleJson);
var typedBundle = bundle.ToTypedElement(provider, "Bundle");
//Type of entry is BackboneElement, but you can't set that, see below.
Assert.Equal("BackboneElement", typedBundle.Select("$this.entry[0]").First().InstanceType);
var entry = SourceNode.Node("entry", SourceNode.Valued("fullUrl", "http://example.org/Patient/1"));
try
{
var typedEntry =
entry.ToTypedElement(provider, "Element");
Microsoft.VisualStudio.TestTools.UnitTesting.Assert.Fail("Should have thrown on invalid Div format");
}
catch (ArgumentException)
{
}
}
public void CatchesArrayMismatch()
{
var nav = FhirJsonNode.Parse("{ 'a': [2,3,4], '_a' : [2,4] }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': 2, '_a' : [2] }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': [2,3,4], '_a' : {} }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ '_a': [4,5,6] }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': [2,3,4] }", "test");
Assert.IsTrue(nav.Children().Any());
nav = FhirJsonNode.Parse("{ 'a': [null,2], '_a' : [{'active':true},null] }", "test");
Assert.IsTrue(nav.Children().Any());
}
public ITypedElement Build()
{
// To build a CapabilityStatement we use a custom JsonConverter that serializes
// the ListedCapabilityStatement into a CapabilityStatement poco
var json = JsonConvert.SerializeObject(_statement, new JsonSerializerSettings
{
ContractResolver = new CamelCasePropertyNamesContractResolver(),
Converters = new List <JsonConverter>
{
new DefaultOptionHashSetJsonConverter(),
new EnumLiteralJsonConverter(),
},
NullValueHandling = NullValueHandling.Ignore,
});
ISourceNode jsonStatement = FhirJsonNode.Parse(json);
// Using a version specific StructureDefinitionSummaryProvider ensures the metadata to be
// compatible with the current FhirSerializer/output formatter.
return(jsonStatement.ToTypedElement(_modelInfoProvider.StructureDefinitionSummaryProvider));
}
private static ITypedElement parseResource(string bodyText, string contentType, IStructureDefinitionSummaryProvider provider, bool throwOnFormatException)
{
if (bodyText == null)
{
throw Error.ArgumentNull(nameof(bodyText));
}
if (provider == null)
{
throw Error.ArgumentNull(nameof(provider));
}
var fhirType = ContentType.GetResourceFormatFromContentType(contentType);
if (fhirType == ResourceFormat.Unknown)
{
throw new UnsupportedBodyTypeException(
"Endpoint returned a body with contentType '{0}', while a valid FHIR xml/json body type was expected. Is this a FHIR endpoint?"
.FormatWith(contentType), contentType, bodyText);
}
if (!SerializationUtil.ProbeIsJson(bodyText) && !SerializationUtil.ProbeIsXml(bodyText))
{
throw new UnsupportedBodyTypeException(
"Endpoint said it returned '{0}', but the body is not recognized as either xml or json.".FormatWith(contentType), contentType, bodyText);
}
try
{
return((fhirType == ResourceFormat.Json)
? FhirJsonNode.Parse(bodyText).ToTypedElement(provider)
: FhirXmlNode.Parse(bodyText).ToTypedElement(provider));
}
catch (FormatException) when(!throwOnFormatException)
{
return(null);
}
}
public void CanUseBackboneTypeForEntry()
{
var _sdsProvider = new PocoStructureDefinitionSummaryProvider();
var bundleJson = "{\"resourceType\":\"Bundle\", \"entry\":[{\"fullUrl\":\"http://example.org/Patient/1\"}]}";
var bundle = FhirJsonNode.Parse(bundleJson);
var typedBundle = bundle.ToTypedElement(_sdsProvider, "Bundle");
//Type of entry is BackboneElement, but you can't set that, see below.
Assert.Equal("BackboneElement", typedBundle.Select("$this.entry[0]").First().InstanceType);
var entry = SourceNode.Node("entry", SourceNode.Valued("fullUrl", "http://example.org/Patient/1"));
//What DOES work:
var typedEntry = entry.ToTypedElement(_sdsProvider, "Element"); //But you can't use BackboneElement here, see below.
Assert.Equal("Element", typedEntry.InstanceType);
//But this leads to a System.ArgumentException:
//Type BackboneElement is not a mappable Fhir datatype or resource
//Parameter name: type
typedEntry = entry.ToTypedElement(_sdsProvider, "BackboneElement");
Assert.Equal("BackboneElement", typedEntry.InstanceType);
// Expected to be able to use BackboneElement as type for the entry SourceNode;
}
public void CatchesUnsupportedFeatures()
{
var nav = FhirJsonNode.Parse("{ 'a': ' ' }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': {}, '_a' : {} }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': {'active':true}, '_a': {'dummy':4} }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ '_a' : {} }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': 3, '_a' : 4 }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ 'a': new DateTime() }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
nav = FhirJsonNode.Parse("{ '_a': new DateTime() }", "test");
Assert.ThrowsException <FormatException>(() => nav.VisitAll());
}
ISourceNode FhirJsonNodeParse(string json, string rootName) =>
FhirJsonNode.Parse(json, rootName, new FhirJsonParsingSettings()
{
PermissiveParsing = false
});
public ISourceNode getJsonNodeU(string json, FhirJsonParsingSettings settings = null) => FhirJsonNode.Parse(json, settings: settings);
/// <inheritdoc />
public void Load(IServiceCollection services)
{
EnsureArg.IsNotNull(services, nameof(services));
var jsonParser = new FhirJsonParser(DefaultParserSettings.Settings);
var jsonSerializer = new FhirJsonSerializer();
var xmlParser = new FhirXmlParser();
var xmlSerializer = new FhirXmlSerializer();
services.AddSingleton(jsonParser);
services.AddSingleton(jsonSerializer);
services.AddSingleton(xmlParser);
services.AddSingleton(xmlSerializer);
services.AddSingleton <BundleSerializer>();
FhirPathCompiler.DefaultSymbolTable.AddFhirExtensions();
ResourceElement SetMetadata(Resource resource, string versionId, DateTimeOffset lastModified)
{
resource.VersionId = versionId;
resource.Meta.LastUpdated = lastModified;
return(resource.ToResourceElement());
}
services.AddSingleton <IReadOnlyDictionary <FhirResourceFormat, Func <string, string, DateTimeOffset, ResourceElement> > >(_ =>
{
return(new Dictionary <FhirResourceFormat, Func <string, string, DateTimeOffset, ResourceElement> >
{
{
FhirResourceFormat.Json, (str, version, lastModified) =>
{
Resource resource = null;
var parsed = false;
var i = 0;
do
{
try
{
resource = jsonParser.Parse <Resource>(str);
parsed = true;
}
catch (StructuralTypeException ex)
{
var match = MessageChecker.Match(ex.Message);
if (match.Success && match.Groups.Count == 4 && match.Groups["type"].Value == "date")
{
i++;
if (i > 100)
{
throw;
}
var valueToReplace = match.Groups["value"].Value;
var location = match.Groups["location"].Value;
var replace = valueToReplace.Substring(0, 10);
var root = FhirJsonNode.Parse(str, KnownResourceTypes.Resource);
var currentNode = root;
while (currentNode != null)
{
foreach (var child in currentNode.Children())
{
if (location.StartsWith(child.Location, StringComparison.OrdinalIgnoreCase))
{
currentNode = child;
break;
}
}
if (currentNode.Location == location)
{
break;
}
}
(currentNode as FhirJsonNode).JsonValue.Value = replace;
str = root.ToJson();
}
else
{
throw;
}
}
}while (!parsed);
return SetMetadata(resource, version, lastModified);
}
},
{
FhirResourceFormat.Xml, (str, version, lastModified) =>
{
var resource = xmlParser.Parse <Resource>(str);
return SetMetadata(resource, version, lastModified);
}
},
});
});
services.Add <ResourceDeserializer>()
.Singleton()
.AsSelf()
.AsService <IResourceDeserializer>();
services.Add <FormatterConfiguration>()
.Singleton()
.AsSelf()
.AsService <IPostConfigureOptions <MvcOptions> >();
services.AddSingleton <IFormatParametersValidator, FormatParametersValidator>();
services.AddSingleton <OperationOutcomeExceptionFilterAttribute>();
services.AddSingleton <ValidateFormatParametersAttribute>();
services.AddSingleton <ValidateExportRequestFilterAttribute>();
services.AddSingleton <ValidateReindexRequestFilterAttribute>();
// Support for resolve()
FhirPathCompiler.DefaultSymbolTable.AddFhirExtensions();
services.Add <FhirJsonInputFormatter>()
.Singleton()
.AsSelf()
.AsService <TextInputFormatter>();
services.Add <FhirJsonOutputFormatter>()
.Singleton()
.AsSelf()
.AsService <TextOutputFormatter>();
services.Add <FhirRequestContextAccessor>()
.Singleton()
.AsSelf()
.AsService <RequestContextAccessor <IFhirRequestContext> >();
services.AddSingleton <CorrelationIdProvider>(_ => () => Guid.NewGuid().ToString());
// Add conformance provider for implementation metadata.
services.Add <SystemConformanceProvider>()
.Singleton()
.AsSelf()
.AsImplementedInterfaces();
services.TypesInSameAssembly(KnownAssemblies.All)
.AssignableTo <IProvideCapability>()
.Transient()
.AsService <IProvideCapability>();
services.AddSingleton <IClaimsExtractor, PrincipalClaimsExtractor>();
ModelExtensions.SetModelInfoProvider();
services.Add(_ => ModelInfoProvider.Instance).Singleton().AsSelf().AsImplementedInterfaces();
// Register a factory to resolve a scope that returns all components that provide capabilities
services.AddFactory <IScoped <IEnumerable <IProvideCapability> > >();
// Register pipeline behavior to intercept create/update requests and check presence of provenace header.
services.Add <ProvenanceHeaderBehavior>().Scoped().AsSelf().AsImplementedInterfaces();
services.Add <ProvenanceHeaderState>().Scoped().AsSelf().AsImplementedInterfaces();
// Register pipeline behavior to check service permission for CUD actions on StructuredDefinition,ValueSet,CodeSystem, ConceptMap.
services.Add <ProfileResourcesBehaviour>().Singleton().AsSelf().AsImplementedInterfaces();
services.AddLazy();
services.AddScoped();
}
