3049 Use poco based parsers

src/Hl7.Fhir.Base/ElementModel/ElementNodeComparator.cs

@@ -23,11 +23,16 @@ public static TreeComparisonResult IsEqualTo(this ITypedElement expected, ITyped
         {
             if (expected.Name != actual.Name)
                 return TreeComparisonResult.Fail(actual.Location, $"name: was '{actual.Name}', expected '{expected.Name}'");
-            if (!Object.Equals(expected.Value, actual.Value))
-                return TreeComparisonResult.Fail(actual.Location, $"value: was '{actual.Value}', expected '{expected.Value}'");
+
+            var cleanedValueL = expected.Value is string el ? el.Replace("\r", "") : expected.Value;
+            var cleanedValueR = actual.Value is string er ? er.Replace("\r", "") : actual.Value;
+
+            if (!Equals(cleanedValueL, cleanedValueR))
+                return TreeComparisonResult.Fail(actual.Location, $"value: was '{cleanedValueL}', expected '{cleanedValueR}'");
             if (expected.InstanceType != actual.InstanceType && actual.InstanceType != null) 
                 return TreeComparisonResult.Fail(actual.Location, $"type: was '{actual.InstanceType}', expected '{expected.InstanceType}'");
-            if (expected.Location != actual.Location) TreeComparisonResult.Fail(actual.Location, $"Path: was '{actual.Location}', expected '{expected.Location}'");
+            if (expected.Location != actual.Location)
+                TreeComparisonResult.Fail(actual.Location, $"Path: was '{actual.Location}', expected '{expected.Location}'");
 
             // Ignore ordering (only relevant to xml)
             var childrenExp = expected.Children().OrderBy(e => e.Name);
@@ -51,4 +56,4 @@ public static TreeComparisonResult IsEqualTo(this ITypedElement expected, ITyped
             return TreeComparisonResult.OK;
         }
     }
-}
+}

src/Hl7.Fhir.Base/ElementModel/PocoBuilderSettings.cs

@@ -67,6 +67,17 @@ public void CopyTo(PocoBuilderSettings other)
         other.ExceptionHandler = ExceptionHandler;
     }
 
+    /// <summary>
+    /// Initializes the current instance from the specified <see cref="PocoBuilderSettings"/> instance.
+    /// </summary>
+    public void CopyFrom(ParserSettings settings)
+    {
+        if (settings == null) throw Error.ArgumentNull(nameof(settings));
+
+        AllowUnrecognizedEnums = settings.AllowUnrecognizedEnums;
+        IgnoreUnknownMembers = settings.AcceptUnknownMembers;
+    }
+
     /// <summary>Creates a new <see cref="PocoBuilderSettings"/> object that is a copy of the current instance.</summary>
     public PocoBuilderSettings Clone() => new(this);
 

src/Hl7.Fhir.Base/Rest/BaseFhirClient.cs

@@ -787,7 +787,7 @@ public async Task DeleteHistoryVersionAsync(string location, CancellationToken?
 
     public Task<TResource?> executeAsync<TResource>(Model.Bundle tx, HttpStatusCode expect, CancellationToken? ct) where TResource : Model.Resource
     {
-        return executeAsync<TResource>(tx, new[] { expect }, ct);
+        return executeAsync<TResource>(tx, [expect], ct);
     }
 
     private async Task<TResource?> executeAsync<TResource>(Bundle tx, IEnumerable<HttpStatusCode> expect, CancellationToken? ct) where TResource : Resource
@@ -974,7 +974,9 @@ private static bool isPostOrPutOrPatch(HttpMethod method) =>
 
     private IFhirSerializationEngine getSerializationEngine()
     {
-        return Settings.SerializationEngine ?? FhirSerializationEngineFactory.Legacy.FromParserSettings(Inspector, Settings.ParserSettings ?? new());
+#pragma warning disable CS0618 // Type or member is obsolete
+        return Settings.SerializationEngine ?? FhirSerializationEngineFactory.Legacy.FromParserSettings(Inspector, Settings.ParserSettings);
+#pragma warning restore CS0618 // Type or member is obsolete
     }
 
     private async Task verifyServerVersion(CancellationToken ct)
@@ -985,12 +987,12 @@ private async Task verifyServerVersion(CancellationToken ct)
         _versionChecked = true;      // So we can now start calling Conformance() without getting into a loop
 
         string? serverVersion;
-        var settings = Settings;
+        var originalEngine = Settings.SerializationEngine;
 
         try
         {
-            Settings = Settings.Clone();
-            Settings.ParserSettings = new() { AllowUnrecognizedEnums = true };
+            // Temporarily set the engine to ignore most errors.
+            Settings.SerializationEngine = FhirSerializationEngineFactory.Ostrich(Inspector);
             serverVersion = await getFhirVersionOfServer(ct).ConfigureAwait(false);
         }
         catch (FormatException fe)
@@ -1000,8 +1002,8 @@ private async Task verifyServerVersion(CancellationToken ct)
         }
         finally
         {
-            // put back the original settings
-            Settings = settings;
+            // put back the original engine
+            Settings.SerializationEngine = originalEngine;
         }
 
         if (serverVersion == null)
@@ -1059,6 +1061,4 @@ public void Dispose()
         GC.SuppressFinalize(this);
     }
     #endregion
-}
-
-#nullable restore
+}

src/Hl7.Fhir.Base/Rest/FhirClientSerializationEngineExtensions.cs

@@ -23,7 +23,10 @@ public static class FhirClientSerializationEngineExtensions
         public static BaseFhirClient WithLegacySerializer(this BaseFhirClient client)
         {
             client.Settings.SerializationEngine =
-                FhirSerializationEngineFactory.Legacy.FromParserSettings(client.Inspector, client.Settings.ParserSettings ?? new());
+                FhirSerializationEngineFactory.Legacy.FromParserSettings(client.Inspector,
+#pragma warning disable CS0618 // Type or member is obsolete
+                    client.Settings.ParserSettings);
+#pragma warning restore CS0618 // Type or member is obsolete
             return client;
         }
 
@@ -96,8 +99,8 @@ public static BaseFhirClient WithOstrichModeSerializer(this BaseFhirClient clien
 
         public static BaseFhirClient WithCustomIgnoreListSerializer(this BaseFhirClient client, string[] ignoreList)
         {
-            var xmlSettings = new FhirXmlPocoDeserializerSettings().Ignoring(ignoreList);
-            var jsonSettings = new FhirJsonConverterOptions().Ignoring(ignoreList);
+            var xmlSettings = new ParserSettings().Ignoring(ignoreList);
+            var jsonSettings = (FhirJsonConverterOptions)new FhirJsonConverterOptions().Ignoring(ignoreList);
 
             client.Settings.SerializationEngine = FhirSerializationEngineFactory.Custom(client.Inspector, jsonSettings, xmlSettings);
 

src/Hl7.Fhir.Base/Rest/FhirClientSettings.cs

@@ -93,7 +93,9 @@ public class FhirClientSettings
         /// <summary>
         /// ParserSettings for the pre-5.0 SDK parsers. Are only used when <see cref="SerializationEngine"/> is not set.
         /// </summary>
-        public ParserSettings? ParserSettings = ParserSettings.CreateDefault();
+        [Obsolete(
+            "Use the SerializationEngine setting instead, chosing one of the options on FhirSerializationEngineFactory.")]
+        public ParserSettings ParserSettings = new ParserSettings().UsingMode(DeserializationMode.Recoverable);
 
         /// <summary>
         /// How to transfer binary data when sending data to a Binary endpoint.
@@ -104,7 +106,6 @@ public class FhirClientSettings
         /// Whether we ask the server to return us binary data or a Binary resource.
         /// </summary>
         public BinaryTransferBehaviour BinaryReceivePreference = BinaryTransferBehaviour.UseData;
-
 
         public FhirClientSettings() { }
 
@@ -123,7 +124,9 @@ public void CopyTo(FhirClientSettings other)
         {
             if (other == null) throw Error.ArgumentNull(nameof(other));
 
+#pragma warning disable CS0618 // Type or member is obsolete
             other.ParserSettings = ParserSettings;
+#pragma warning restore CS0618 // Type or member is obsolete
             other.PreferCompressedResponses = PreferCompressedResponses;
             other.PreferredFormat = PreferredFormat;
             other.ReturnPreference = ReturnPreference;

src/Hl7.Fhir.Base/Serialization/BaseFhirJsonPocoDeserializer.cs

@@ -23,19 +23,16 @@
 
 namespace Hl7.Fhir.Serialization;
 
-/// <summary>
-/// Deserializes a byte stream into FHIR POCO objects.
-/// </summary>
-/// <remarks>The serializer uses the format documented in https://www.hl7.org/fhir/json.html. </remarks>
-public class BaseFhirJsonPocoDeserializer
+public class BaseFhirJsonPocoDeserializer : BaseFhirJsonParser
 {
     /// <summary>
     /// Initializes an instance of the deserializer.
     /// </summary>
     /// <param name="assembly">Assembly containing the POCO classes to be used for deserialization.</param>
     [Obsolete("Use the constructor that takes a ModelInspector instead. " +
               "You can find the right ModelInspector for an assembly by calling ModelInspector.ForAssembly(assembly).")]
-    public BaseFhirJsonPocoDeserializer(Assembly assembly) : this(ModelInspector.ForAssembly(assembly), new FhirJsonConverterOptions())
+    public BaseFhirJsonPocoDeserializer(Assembly assembly) : this(ModelInspector.ForAssembly(assembly),
+        new FhirJsonConverterOptions())
     {
         // Nothing
     }
@@ -55,15 +52,43 @@ public class BaseFhirJsonPocoDeserializer
     /// <param name="inspector">The <see cref="ModelInspector"/> containing the POCO classes to be used for deserialization.</param>
     /// <param name="settings">A settings object to be used by this instance.</param>
     public BaseFhirJsonPocoDeserializer(ModelInspector inspector, FhirJsonConverterOptions settings)
+        : base(inspector, settings)
+    {
+        // nothing
+    }
+}
+
+
+/// <summary>
+/// Deserializes Json into FHIR POCO objects.
+/// </summary>
+/// <remarks>The serializer uses the format documented in https://www.hl7.org/fhir/json.html. </remarks>
+public class BaseFhirJsonParser
+{
+    /// <summary>
+    /// Initializes an instance of the deserializer.
+    /// </summary>
+    /// <param name="inspector">The <see cref="ModelInspector"/> containing the POCO classes to be used for deserialization.</param>
+    public BaseFhirJsonParser(ModelInspector inspector) : this(inspector, new ParserSettings())
+    {
+        // nothing
+    }
+
+    /// <summary>
+    /// Initializes an instance of the deserializer.
+    /// </summary>
+    /// <param name="inspector">The <see cref="ModelInspector"/> containing the POCO classes to be used for deserialization.</param>
+    /// <param name="settings">A settings object to be used by this instance.</param>
+    public BaseFhirJsonParser(ModelInspector inspector, ParserSettings? settings)
     {
-        Settings = settings;
+        Settings = settings ?? new ParserSettings();
         _inspector = inspector;
     }
 
     /// <summary>
     /// The settings that were passed to the constructor.
     /// </summary>
-    public FhirJsonConverterOptions Settings { get; }
+    public ParserSettings Settings { get; set; }
 
     private const string INSTANCE_VALIDATION_KEY_SUFFIX = ":instance";
     private const string PROPERTY_VALIDATION_KEY_SUFFIX = ":property";
@@ -76,7 +101,7 @@ public BaseFhirJsonPocoDeserializer(ModelInspector inspector, FhirJsonConverterO
     /// <param name="instance">The result of deserialization. May be incomplete when there are issues.</param>
     /// <param name="issues">Issues encountered while deserializing. Will be empty when the function returns true.</param>
     /// <returns><c>false</c> if there are issues, <c>true</c> otherwise.</returns>
-    /// <remarks>The <see cref="FhirXmlPocoDeserializerSettings.ExceptionFilter"/> influences which issues are returned.</remarks>
+    /// <remarks>The <see cref="ParserSettings.ExceptionFilter"/> influences which issues are returned.</remarks>
     public bool TryDeserializeResource(ref Utf8JsonReader reader, [NotNullWhen(true)] out Resource? instance, out IEnumerable<CodedException> issues)
     {
         if (reader.CurrentState.Options.CommentHandling is not JsonCommentHandling.Skip and not JsonCommentHandling.Disallow)
@@ -103,7 +128,7 @@ public bool TryDeserializeResource(ref Utf8JsonReader reader, [NotNullWhen(true)
     /// <param name="instance">The result of deserialization. May be incomplete when there are issues.</param>
     /// <param name="issues">Issues encountered while deserializing. Will be empty when the function returns true.</param>
     /// <returns><c>false</c> if there are issues, <c>true</c> otherwise.</returns>
-    /// <remarks>The <see cref="FhirXmlPocoDeserializerSettings.ExceptionFilter"/> influences which issues are returned.</remarks>
+    /// <remarks>The <see cref="ParserSettings.ExceptionFilter"/> influences which issues are returned.</remarks>
     public bool TryDeserializeObject(Type targetType, ref Utf8JsonReader reader, [NotNullWhen(true)] out Base? instance, out IEnumerable<CodedException> issues)
     {
         if (reader.CurrentState.Options.CommentHandling is not JsonCommentHandling.Skip and not JsonCommentHandling.Disallow)
@@ -496,7 +521,6 @@ public void ScheduleDelayedValidation(string key, Action validation)
             _validations[key] = validation;
         }
 
-        //public CodedValidationException[] Run() => _validations.Values.SelectMany(delayed => delayed()).ToArray();
         public void RunDelayedValidation()
         {
             foreach (var validation in _validations.Values) validation();
@@ -713,7 +737,7 @@ FhirJsonPocoDeserializerState state
         (object? partial, ERR? error) result = reader.TokenType switch
         {
             JsonTokenType.Null => (null, ERR.EXPECTED_PRIMITIVE_NOT_NULL(ref reader, pathStack.GetInstancePath())),
-            JsonTokenType.String when string.IsNullOrEmpty(reader.GetString()) => (reader.GetString(), ERR.PROPERTY_MAY_NOT_BE_EMPTY(ref reader, pathStack.GetInstancePath())),
+            JsonTokenType.String when string.IsNullOrWhiteSpace(reader.GetString()) => (reader.GetString(), ERR.PROPERTY_MAY_NOT_BE_EMPTY(ref reader, pathStack.GetInstancePath())),
             JsonTokenType.String => (reader.GetString(), null),
             JsonTokenType.Number => (tryGetMatchingNumber(ref reader, valuePropertyType), null),
             JsonTokenType.True or JsonTokenType.False => (reader.GetBoolean(), null),
@@ -737,7 +761,7 @@ JsonTokenType.String when string.IsNullOrEmpty(reader.GetString()) => (reader.Ge
     /// This function tries to map from the json-format "generic" number to the kind of numeric type defined in the POCO.
     /// </summary>
     /// <remarks>Reader must be positioned on a number token. This function will not move the reader to the next token.</remarks>
-    private static object? tryGetMatchingNumber(ref Utf8JsonReader reader, Type implementingType)
+    private static object tryGetMatchingNumber(ref Utf8JsonReader reader, Type implementingType)
     {
         if (reader.TokenType != JsonTokenType.Number)
             throw new InvalidOperationException($"Cannot read a numeric when reader is on a {reader.TokenType}. " +