Update Microsoft fhir-codegen with Firely SDK6 codegen

.run/firely-all.run.xml

@@ -0,0 +1,11 @@
+<component name="ProjectRunConfigurationManager">
+  <configuration default="false" name="firely-all" type="CompoundRunConfigurationType">
+    <toRun name="fhir-codegen: Firely 5.x Base" type="LaunchSettings" />
+    <toRun name="fhir-codegen: Firely 5.x Conformance" type="LaunchSettings" />
+    <toRun name="fhir-codegen: Firely 5.x R4" type="LaunchSettings" />
+    <toRun name="fhir-codegen: Firely 5.x R4B" type="LaunchSettings" />
+    <toRun name="fhir-codegen: Firely 5.x R5" type="LaunchSettings" />
+    <toRun name="fhir-codegen: Firely 5.x STU3" type="LaunchSettings" />
+    <method v="2" />
+  </configuration>
+</component>

src/Microsoft.Health.Fhir.CodeGen/FhirExtensions/ElementDefinitionExtensions.cs

@@ -78,7 +78,7 @@ public static int cgComponentFieldOrder(this ElementDefinition ed)
     public static string cgBasePath(this ElementDefinition ed) => ed.Base?.Path ?? string.Empty;
 
     /// <summary>Gets the explicit name of this element if set, or returns an empty string.</summary>
-    public static string cgExplicitName(this ElementDefinition ed) => ed.GetExtensionValue<FhirString>(CommonDefinitions.ExtUrlExplicitTypeName)?.ToString() ?? string.Empty;
+    public static string? cgExplicitName(this ElementDefinition ed) => ed.GetExtensionValue<FhirString>(CommonDefinitions.ExtUrlExplicitTypeName)?.ToString();
 
     /// <summary>Gets the short name of this element, or explicit name if there is one.</summary>
     /// <param name="ed">                The ed to act on.</param>
@@ -89,12 +89,10 @@ public static string cgName(this ElementDefinition ed, bool allowExplicitName =
     {
         if (allowExplicitName)
         {
-            string en = ed.cgExplicitName();
+            string? en = ed.cgExplicitName();
 
-            if (!string.IsNullOrEmpty(en))
-            {
+            if (en is not null)
                 return en;
-            }
         }
 
         if (removeChoiceMarker && ed.Path.EndsWith("[x]", StringComparison.Ordinal))

src/Microsoft.Health.Fhir.CodeGen/Language/Firely/CSharpFirelyCommon.cs

@@ -4,8 +4,12 @@
 // </copyright>
 
 using System.ComponentModel;
+using System.Text;
 using Hl7.Fhir.Model;
 using Microsoft.Health.Fhir.CodeGen.FhirExtensions;
+using Microsoft.Health.Fhir.CodeGenCommon.Extensions;
+using Microsoft.Health.Fhir.CodeGenCommon.Packaging;
+using Microsoft.Health.Fhir.CodeGenCommon.Utils;
 
 #if NETSTANDARD2_0
 using Microsoft.Health.Fhir.CodeGenCommon.Polyfill;
@@ -17,7 +21,7 @@ public static class CSharpFirelyCommon
 {
 
     /// <summary>Dictionary mapping FHIR primitive types to language equivalents (see Template-Model.tt#1252).</summary>
-    public static readonly Dictionary<string, string> PrimitiveTypeMap = new Dictionary<string, string>()
+    public static readonly Dictionary<string, string> PrimitiveTypeMap = new()
     {
         { "base64Binary", "byte[]" },
         { "boolean", "bool?" },
@@ -61,22 +65,6 @@ public static class CSharpFirelyCommon
         { "Resource", "DomainResource" },
     };
 
-    /// <summary>Primitive types that have a specific validation attribute on their Value property.</summary>
-    public static readonly Dictionary<string, string> PrimitiveValidationPatterns = new()
-    {
-        ["uri"] = "UriPattern",
-        ["uuid"] = "UuidPattern",
-        ["id"] = "IdPattern",
-        ["date"] = "DatePattern",
-        ["dateTime"] = "DateTimePattern",
-        ["oid"] = "OidPattern",
-        ["code"] = "CodePattern",
-        ["time"] = "TimePattern",
-        ["string"] = "StringPattern",
-        ["markdown"] = "StringPattern",
-        ["xhtml"] = "NarrativeXhtmlPattern"
-    };
-
     /// <summary>
     /// Determines the subset of code to generate.
     /// </summary>
@@ -251,4 +239,27 @@ public static int GetOrder(int relativeOrder)
     {
         return (relativeOrder * 10) + 10;
     }
+
+    public static string BuildOpenAllowedTypesAttribute() => "[AllowedTypes(OpenChoice = true)]";
+
+    public static string BuildAllowedTypesAttribute(IEnumerable<TypeReference> types, FhirReleases.FhirSequenceCodes? since)
+    {
+        StringBuilder sb = new();
+        sb.Append("[AllowedTypes(");
+
+        string typesList = string.Join(",",
+            types.Select(t => $"typeof({t.PropertyTypeString})"));
+
+        sb.Append(typesList);
+        if (since is not null)
+            sb.Append($", Since = FhirRelease.{since}");
+        sb.Append(")]");
+        return sb.ToString();
+    }
+}
+
+
+public static class StringHelpers
+{
+    public static string EnsurePeriod(this string s) => s.EndsWith('.') ? s : s + ".";
 }

src/Microsoft.Health.Fhir.CodeGen/Language/Firely/FirelyNetIG.cs

@@ -724,7 +724,7 @@ private void ProcessAndWriteValueSets()
         foreach ((string unversionedUrl, string[] versions) in _info.ValueSetVersions.OrderBy(kvp => kvp.Key))
         {
             // check for exclusions
-            if (CSharpFirely2._exclusionSet.Contains(unversionedUrl))
+            if (CSharpFirely2.ExclusionSet.Contains(unversionedUrl))
             {
                 continue;
             }
@@ -808,7 +808,7 @@ private void ProcessAndWriteValueSet(
 
         // Enums and their containing classes cannot have the same name,
         // so we have to correct these here
-        if (CSharpFirely2._enumNamesOverride.TryGetValue(vs.Url, out var replacementName))
+        if (CSharpFirely2.EnumNamesOverride.TryGetValue(vs.Url, out var replacementName))
         {
             nameSanitized = replacementName;
         }
@@ -2159,9 +2159,9 @@ private void WriteProfile(StructureDefinition sd)
                                 break;
                                 //throw new Exception($"Found multiple discriminators for {id}");
                             }
- 
+
                             if (discriminators.Length == 1)
-                            { 
+                            {
                                 discriminator = discriminators[0];
 
                                 bool isExtensionSlice = _findExtensionPathRegex.IsMatch(discriminator.Path);
@@ -3361,7 +3361,7 @@ private ExtensionData GetExtensionData(
             remarks = (remarks == null ? string.Empty : remarks + "\n") +
                 $"Structure Definition Name: {cd.Structure.Name}";
         }
-  
+
         string directive;
         if (_info.TryGetPackageSource(cd.Structure, out string packageId, out string packageVersion))
         {
@@ -3567,7 +3567,7 @@ private ExtensionData GetExtensionData(
                         Expression = "DataType",
                     },
                     ContextTarget = null,
-                    ContextElementInfo = new("", "", "", new ChoiceTypeReference(), null),
+                    ContextElementInfo = new("", "", "", ComplexTypeReference.DataTypeReference, null),
                     //ContextElementInfo = new CSharpFirely2.WrittenElementInfo()
                     //{
                     //    ElementType = "Hl7.Fhir.Model.DataType",

src/Microsoft.Health.Fhir.CodeGen/Language/Firely/TypeReference.cs

@@ -1,12 +1,23 @@
-#nullable enable
-
 using Microsoft.Health.Fhir.CodeGenCommon.Extensions;
 using Microsoft.Health.Fhir.CodeGenCommon.Utils;
 
 namespace Microsoft.Health.Fhir.CodeGen.Language.Firely;
 
 public abstract record TypeReference(string Name)
 {
+    public static TypeReference BuildFromFhirTypeName(string name, string? vsName=null, string? vsClass=null)
+    {
+        // Elements of type Code or Code<T> have their own naming/types, so handle those separately.
+        if (name == "code" && vsName is not null)
+            return new CodedTypeReference(vsName, vsClass);
+
+        if (PrimitiveTypeReference.IsFhirPrimitiveType(name))
+            return PrimitiveTypeReference.GetTypeReference(name);
+
+        // Otherwise, this is a "normal" name for a complex type.
+        return new ComplexTypeReference(name, MapTypeName(name));
+    }
+
     public abstract string PropertyTypeString { get; }
 
     internal static string MapTypeName(string name)
@@ -43,27 +54,42 @@ public record PrimitiveTypeReference(string Name, string PocoTypeName, Type Conv
     public static PrimitiveTypeReference ForTypeName(string name, Type propertyType) =>
         new(name, MapTypeName(name), propertyType);
 
+    public static readonly PrimitiveTypeReference PrimitiveType = ForTypeName("PrimitiveType", typeof(object));
+    public static readonly PrimitiveTypeReference Boolean = ForTypeName("boolean", typeof(bool));
+    public static readonly PrimitiveTypeReference Base64Binary = ForTypeName("base64Binary", typeof(byte[]));
+    public static readonly PrimitiveTypeReference Canonical = ForTypeName("canonical", typeof(string));
+    public static readonly PrimitiveTypeReference Code = ForTypeName("code", typeof(string));
+    public static readonly PrimitiveTypeReference Date = ForTypeName("date", typeof(string));
+    public static readonly PrimitiveTypeReference DateTime = ForTypeName("dateTime", typeof(string));
+    public static readonly PrimitiveTypeReference Decimal = ForTypeName("decimal", typeof(decimal));
+    public static readonly PrimitiveTypeReference Id = ForTypeName("id", typeof(string));
+    public static readonly PrimitiveTypeReference Instant = ForTypeName("instant", typeof(DateTimeOffset));
+    public static readonly PrimitiveTypeReference Integer = ForTypeName("integer", typeof(int));
+    public static readonly PrimitiveTypeReference Integer64 = ForTypeName("integer64", typeof(long));
+    public static readonly PrimitiveTypeReference Oid = ForTypeName("oid", typeof(string));
+    public static readonly PrimitiveTypeReference PositiveInt = ForTypeName("positiveInt", typeof(int));
+    public static readonly PrimitiveTypeReference String = ForTypeName("string", typeof(string));
+    public static readonly PrimitiveTypeReference Time = ForTypeName("time", typeof(string));
+    public static readonly PrimitiveTypeReference UnsignedInt = ForTypeName("unsignedInt", typeof(int));
+    public static readonly PrimitiveTypeReference Uri = ForTypeName("uri", typeof(string));
+    public static readonly PrimitiveTypeReference Url = ForTypeName("url", typeof(string));
+    public static readonly PrimitiveTypeReference Xhtml = ForTypeName("xhtml", typeof(string));
+    public static readonly PrimitiveTypeReference Markdown = ForTypeName("markdown", typeof(string));
+
     public static readonly IReadOnlyCollection<PrimitiveTypeReference> PrimitiveList =
     [
-        ForTypeName("base64Binary", typeof(byte[])), ForTypeName("boolean", typeof(bool)),
-        ForTypeName("canonical", typeof(string)), ForTypeName("code", typeof(string)),
-        ForTypeName("date", typeof(string)), ForTypeName("dateTime", typeof(string)),
-        ForTypeName("decimal", typeof(decimal)), ForTypeName("id", typeof(string)),
-        ForTypeName("instant", typeof(DateTimeOffset)), ForTypeName("integer", typeof(int)),
-        ForTypeName("integer64", typeof(long)), ForTypeName("oid", typeof(string)),
-        ForTypeName("positiveInt", typeof(int)), ForTypeName("string", typeof(string)),
-        ForTypeName("time", typeof(string)), ForTypeName("unsignedInt", typeof(int)),
-        ForTypeName("uri", typeof(string)), ForTypeName("url", typeof(string)),
-        ForTypeName("xhtml", typeof(string)), ForTypeName("markdown", typeof(string))
+        Boolean, Base64Binary, Canonical, Code, Date, DateTime, Decimal, Id,
+        Instant, Integer, Integer64, Oid, PositiveInt, String, Time, UnsignedInt,
+        Uri, Url, Xhtml, Markdown
     ];
 
-    private static readonly Dictionary<string, PrimitiveTypeReference> s_primitiveDictionary =
+    private static readonly Dictionary<string, PrimitiveTypeReference> _primitiveDictionary =
         PrimitiveList.ToDictionary(ptr => ptr.Name);
 
-    public static bool IsFhirPrimitiveType(string name) => s_primitiveDictionary.ContainsKey(name);
+    public static bool IsFhirPrimitiveType(string name) => _primitiveDictionary.ContainsKey(name);
 
     public static PrimitiveTypeReference GetTypeReference(string name) =>
-        s_primitiveDictionary.TryGetValue(name, out var tr)
+        _primitiveDictionary.TryGetValue(name, out var tr)
             ? tr
             : throw new InvalidOperationException($"Unknown FHIR primitive {name}");
 
@@ -83,10 +109,12 @@ public record CqlTypeReference(string Name, Type PropertyType) : TypeReference(N
 
 public record ComplexTypeReference(string Name, string PocoTypeName) : TypeReference(Name)
 {
+    public ComplexTypeReference(string name) : this(name, name) { }
+
     public override string PropertyTypeString => $"Hl7.Fhir.Model.{PocoTypeName}";
-}
 
-public record ChoiceTypeReference() : ComplexTypeReference("DataType", "DataType");
+    public static readonly ComplexTypeReference DataTypeReference = new("DataType");
+}
 
 public record CodedTypeReference(string EnumName, string? EnumClassName)
     : PrimitiveTypeReference("code", EnumName, typeof(Enum))

src/Microsoft.Health.Fhir.CodeGen/Loader/PackageLoader.cs

@@ -126,7 +126,7 @@ public PackageLoader(ConfigRoot? config = null, LoaderOptions? opts = null)
 
         _defaultFhirVersion = FhirReleases.FhirVersionToSequence(_rootConfiguration.FhirVersion);
 
-        _jsonOptions = opts.FhirJsonOptions;
+        _jsonOptions = opts.FhirJsonOptions.UsingMode(DeserializerModes.Ostrich);
         _jsonParser = new(opts.FhirJsonSettings);
 
 #if !DISABLE_XML

src/Microsoft.Health.Fhir.CodeGen/Microsoft.Health.Fhir.CodeGen.csproj

@@ -33,7 +33,7 @@
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="System.Text.Json" Version="8.0.4" />
+    <PackageReference Include="System.Text.Json" Version="8.0.5" />
   </ItemGroup>
 
   <ItemGroup>
@@ -51,5 +51,5 @@
   <ItemGroup>
     <Folder Include="Polyfill\" />
   </ItemGroup>
-  
+
 </Project>

src/Microsoft.Health.Fhir.CodeGen/Models/ComponentDefinition.cs

@@ -60,7 +60,7 @@ public ComponentDefinition(StructureDefinition sd)
 
     /// <summary>Cg explicit name.</summary>
     /// <returns>A string.</returns>
-    public string cgExplicitName() => Element?.cgExplicitName() ?? string.Empty;
+    public string? cgExplicitName() => Element.cgExplicitName();
 
     /// <summary>Gets the code generation name.</summary>
     /// <remarks>Note: Firely generation uses this version.</remarks>

src/Microsoft.Health.Fhir.CodeGen/Models/DefinitionCollection.cs

@@ -854,8 +854,14 @@ private void ProcessParameters(OperationDefinition op)
                 fo = outFieldOrder.Count + 1;
                 outFieldOrder.Add(pc.Name, fo);
             }
-            else 
+            else
             {
+                if (inFieldOrder.ContainsKey(pc.Name))
+                {
+                    Console.WriteLine($"Operation: {op.Id} ({op.Url}) defines the parameter {pc.Name} more than once!!!");
+                    continue;
+                }
+
                 fo = inFieldOrder.Count + 1;
                 inFieldOrder.Add(pc.Name, fo);
             }

src/Microsoft.Health.Fhir.CodeGenCommon/Extensions/FhirNameConventionExtensions.cs

@@ -95,7 +95,7 @@ public static string ToPascalCase(
             return string.Join(joinDelimiter, word.Split(delimitersToRemove, _wordSplitOptions).Select(w => w.ToPascalCase(false)));
         }
 
-        return string.Concat(word.Substring(0, 1).ToUpperInvariant(), word.Substring(1));
+        return string.Concat(word[..1].ToUpperInvariant(), word[1..]);
     }
 
     /// <summary>An extension method that converts an array of words each to PascalCase.</summary>
@@ -163,10 +163,10 @@ public static string ToCamelCase(
         {
             // converting to pascal and changing the initial letter is faster than accumulating here
             string pc = word.ToPascalCase(removeDelimiters, joinDelimiter, delimitersToRemove);
-            return string.Concat(pc.Substring(0, 1).ToLowerInvariant(), pc.Substring(1));
+            return string.Concat(pc[..1].ToLowerInvariant(), pc[1..]);
         }
 
-        return string.Concat(word.Substring(0, 1).ToLowerInvariant(), word.Substring(1));
+        return string.Concat(word[..1].ToLowerInvariant(), word[1..]);
     }
 
     /// <summary>An extension method that converts an array of words each to camelCase.</summary>

src/Microsoft.Health.Fhir.CodeGenCommon/Microsoft.Health.Fhir.CodeGenCommon.csproj

@@ -10,7 +10,7 @@
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="System.Text.Json" Version="8.0.4" />
+    <PackageReference Include="System.Text.Json" Version="8.0.5" />
   </ItemGroup>
 
 </Project>

src/Microsoft.Health.Fhir.CodeGenCommon/Packaging/FhirReleases.cs

@@ -37,7 +37,7 @@ public enum FhirSequenceCodes : int
         /// <summary>FHIR R5.</summary>
         R5 = 5,
 
-        /// <summary>FHIR R5.</summary>
+        /// <summary>FHIR R6.</summary>
         R6 = 6,
     }
 

src/Microsoft.Health.Fhir.CrossVersion/Microsoft.Health.Fhir.CrossVersion.csproj

@@ -19,7 +19,7 @@
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="System.Text.Json" Version="8.0.4" />
+    <PackageReference Include="System.Text.Json" Version="8.0.5" />
   </ItemGroup>
 
   <ItemGroup>

src/Microsoft.Health.Fhir.MappingLanguage/Microsoft.Health.Fhir.MappingLanguage.csproj

@@ -16,7 +16,7 @@
       <PrivateAssets>all</PrivateAssets>
       <IncludeAssets>runtime; build; native; contentfiles; analyzers; buildtransitive</IncludeAssets>
     </PackageReference>
-    <PackageReference Include="System.Text.Json" Version="8.0.4" />
+    <PackageReference Include="System.Text.Json" Version="8.0.5" />
   </ItemGroup>
 
   <ItemGroup>