py: fix profile extension serialisation and field-format handling

examples/python-us-core/fhir_types/hl7_fhir_us_core/profiles/patient_uscore_patient_profile.py

@@ -113,7 +113,7 @@ def set_race(self, value: "UscoreRaceExtension | Extension | dict") -> "UscorePa
                 sub_extensions.append({"url": "detailed", "value_coding": item})
             if value.get("text") is not None:
                 sub_extensions.append({"url": "text", "value_string": value["text"]})
-            push_extension(self._resource, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", "extension": sub_extensions})
+            push_extension(self._resource, Extension(url="http://hl7.org/fhir/us/core/StructureDefinition/us-core-race", extension=sub_extensions))
         return self
 
     @overload
@@ -150,7 +150,7 @@ def set_ethnicity(self, value: "UscoreEthnicityExtension | Extension | dict") ->
                 sub_extensions.append({"url": "detailed", "value_coding": item})
             if value.get("text") is not None:
                 sub_extensions.append({"url": "text", "value_string": value["text"]})
-            push_extension(self._resource, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", "extension": sub_extensions})
+            push_extension(self._resource, Extension(url="http://hl7.org/fhir/us/core/StructureDefinition/us-core-ethnicity", extension=sub_extensions))
         return self
 
     @overload
@@ -185,7 +185,7 @@ def set_tribal_affiliation(self, value: "UscoreTribalAffiliationExtension | Exte
                 sub_extensions.append({"url": "tribalAffiliation", "value_codeable_concept": value["tribalAffiliation"]})
             if value.get("isEnrolled") is not None:
                 sub_extensions.append({"url": "isEnrolled", "value_boolean": value["isEnrolled"]})
-            push_extension(self._resource, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-tribal-affiliation", "extension": sub_extensions})
+            push_extension(self._resource, Extension(url="http://hl7.org/fhir/us/core/StructureDefinition/us-core-tribal-affiliation", extension=sub_extensions))
         return self
 
     @overload
@@ -214,7 +214,7 @@ def set_sex(self, value: "UscoreIndividualSexExtension | Extension | Any") -> "U
                 raise ValueError(f"Expected extension url 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-individual-sex', got {_get_key(value, 'url')!r}")
             push_extension(self._resource, value)
         else:
-            push_extension(self._resource, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-individual-sex", "value_coding": value})
+            push_extension(self._resource, Extension(url="http://hl7.org/fhir/us/core/StructureDefinition/us-core-individual-sex", value_coding=value))
         return self
 
     @overload
@@ -243,7 +243,7 @@ def set_interpreter_required(self, value: "UscoreInterpreterNeededExtension | Ex
                 raise ValueError(f"Expected extension url 'http://hl7.org/fhir/us/core/StructureDefinition/us-core-interpreter-needed', got {_get_key(value, 'url')!r}")
             push_extension(self._resource, value)
         else:
-            push_extension(self._resource, {"url": "http://hl7.org/fhir/us/core/StructureDefinition/us-core-interpreter-needed", "value_coding": value})
+            push_extension(self._resource, Extension(url="http://hl7.org/fhir/us/core/StructureDefinition/us-core-interpreter-needed", value_coding=value))
         return self
 
     def validate(self) -> dict[str, list[str]]:

examples/python-us-core/test_profile_patient.py

@@ -267,7 +267,7 @@ def test_set_race_get_race_round_trip_with_detailed_categories():
     )
 
     race = profile.get_race()
-    assert race["ombCategory"]["code"] == "2106-3"
+    assert race["ombCategory"].code == "2106-3"
     assert race["text"] == "White European"
 
 
@@ -350,7 +350,7 @@ def test_fluent_chaining_across_extensions():
     assert profile.get_race()["text"] == "White"
     assert profile.get_ethnicity()["text"] == "Not Hispanic or Latino"
     assert profile.get_sex().code == "male"
-    assert profile.get_tribal_affiliation()["tribalAffiliation"]["text"] == "Navajo"
+    assert profile.get_tribal_affiliation()["tribalAffiliation"].text == "Navajo"
     assert profile.get_interpreter_required().code == "no"
 
 

package.json

@@ -51,16 +51,16 @@
     "@atomic-ehr/fhirschema": "0.0.11",
     "mustache": "^4.2.0",
     "picocolors": "^1.1.1",
-    "yaml": "^2.8.3",
+    "yaml": "^2.9.0",
     "yargs": "^18.0.0"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.4",
-    "@types/bun": "^1.3.9",
+    "@biomejs/biome": "^2.5.0",
+    "@types/bun": "^1.3.14",
     "@types/mustache": "^4.2.6",
-    "@types/node": "^22.19.11",
+    "@types/node": "^25.9.3",
     "@types/yargs": "^17.0.35",
-    "knip": "^5.88.1",
+    "knip": "^6.17.1",
     "tsup": "^8.5.1",
     "typescript": "^5.9.3"
   },
@@ -69,6 +69,7 @@
     "rollup": ">=4.59.0",
     "smol-toml": ">=1.6.1",
     "brace-expansion": ">=5.0.6",
-    "picomatch": ">=4.0.4"
+    "picomatch": ">=4.0.4",
+    "esbuild": ">=0.28.1"
   }
 }

src/api/writer-generator/python/profile-extensions.ts

@@ -71,7 +71,7 @@ export const generateExtensionMethods = (
             generateComplexExtensionSetter(w, ext, className, baseName, targetPath, extProfileInfo);
         } else if (ext.valueFieldTypes?.length === 1 && ext.valueFieldTypes[0]) {
             const valueType = ext.valueFieldTypes[0];
-            const valueField = pyValueFieldName(valueType);
+            const valueField = pyValueFieldName(valueType, w.nameFormatFunction);
             const pyType = pyTypeFromIdentifier(valueType);
             generateSingleValueExtensionGetter(w, ext, baseName, targetPath, valueField, pyType, extProfileInfo);
             generateSingleValueExtensionSetter(w, ext, className, baseName, targetPath, valueField, extProfileInfo);
@@ -224,7 +224,9 @@ const generateComplexExtensionGetter = (
 ): void => {
     generateExtensionGetter(w, ext, baseName, "dict", targetPath, extProfileInfo, () => {
         const configItems = (ext.subExtensions ?? []).map((sub) => {
-            const valueField = sub.valueFieldType ? pyValueFieldName(sub.valueFieldType) : "value";
+            const valueField = sub.valueFieldType
+                ? pyValueFieldName(sub.valueFieldType, w.nameFormatFunction)
+                : "value";
             const isArray = sub.max === "*";
             return `{"name": ${JSON.stringify(sub.url)}, "valueField": ${JSON.stringify(valueField)}, "isArray": ${isArray ? "True" : "False"}}`;
         });
@@ -269,7 +271,9 @@ const generateComplexExtensionSetter = (
     generateExtensionSetter(w, ext, className, baseName, "dict", targetPath, extProfileInfo, () => {
         w.line("sub_extensions = []");
         for (const sub of ext.subExtensions ?? []) {
-            const valueField = sub.valueFieldType ? pyValueFieldName(sub.valueFieldType) : "value";
+            const valueField = sub.valueFieldType
+                ? pyValueFieldName(sub.valueFieldType, w.nameFormatFunction)
+                : "value";
             if (sub.max === "*") {
                 w.line(`for item in value.get(${JSON.stringify(sub.url)}, []):`);
                 w.indentBlock(() => {
@@ -286,7 +290,9 @@ const generateComplexExtensionSetter = (
                 });
             }
         }
-        const extObj = `{"url": ${JSON.stringify(ext.url)}, "extension": sub_extensions}`;
+        // Wrap in an Extension model so Pydantic coerces the sub-extension dicts and
+        // serializes their value fields with FHIR aliases (valueCoding, not value_coding).
+        const extObj = `Extension(url=${JSON.stringify(ext.url)}, extension=sub_extensions)`;
         emitExtPush(w, targetPath, extObj);
     });
 };
@@ -319,7 +325,8 @@ const generateSingleValueExtensionSetter = (
     extProfileInfo: ExtensionProfileInfo | undefined,
 ): void => {
     generateExtensionSetter(w, ext, className, baseName, "Any", targetPath, extProfileInfo, () => {
-        emitExtPush(w, targetPath, `{"url": ${JSON.stringify(ext.url)}, ${JSON.stringify(valueField)}: value}`);
+        // Wrap in an Extension model so the value field serializes with its FHIR alias.
+        emitExtPush(w, targetPath, `Extension(url=${JSON.stringify(ext.url)}, ${valueField}=value)`);
     });
 };
 

src/api/writer-generator/python/profile-factory.ts

@@ -179,27 +179,27 @@ export const collectProfileFactoryInfo = (
 // ---------------------------------------------------------------------------
 
 /** Build `*, param1: Type1, param2: Type2` keyword-only signature. */
-export const buildParamSignature = (factoryInfo: ProfileFactoryInfo): string => {
+export const buildParamSignature = (factoryInfo: ProfileFactoryInfo, formatName: (s: string) => string): string => {
     const parts: string[] = [];
     for (const f of factoryInfo.sliceAutoFields) {
-        parts.push(`${pyFieldName(f.name)}: ${f.pyType} | None = None`);
+        parts.push(`${pyFieldName(f.name, formatName)}: ${f.pyType} | None = None`);
     }
     for (const p of factoryInfo.params) {
-        parts.push(`${pyFieldName(p.name)}: ${p.pyType}`);
+        parts.push(`${pyFieldName(p.name, formatName)}: ${p.pyType}`);
     }
     if (parts.length === 0) return "";
     return `*, ${parts.join(", ")}`;
 };
 
 /** Build call-site args matching the param signature. */
-export const buildCallArgs = (factoryInfo: ProfileFactoryInfo): string => {
+export const buildCallArgs = (factoryInfo: ProfileFactoryInfo, formatName: (s: string) => string): string => {
     const parts: string[] = [];
     for (const f of factoryInfo.sliceAutoFields) {
-        const name = pyFieldName(f.name);
+        const name = pyFieldName(f.name, formatName);
         parts.push(`${name}=${name}`);
     }
     for (const p of factoryInfo.params) {
-        const name = pyFieldName(p.name);
+        const name = pyFieldName(p.name, formatName);
         parts.push(`${name}=${name}`);
     }
     return parts.join(", ");
@@ -217,15 +217,16 @@ export const generateCreateResource = (
     hasParams: boolean,
     factoryInfo: ProfileFactoryInfo,
 ): void => {
+    const fmt = w.nameFormatFunction;
     w.line("@classmethod");
     if (hasParams) {
-        w.line(`def create_resource(cls, ${buildParamSignature(factoryInfo)}) -> ${annotatedBaseTypeName}:`);
+        w.line(`def create_resource(cls, ${buildParamSignature(factoryInfo, fmt)}) -> ${annotatedBaseTypeName}:`);
     } else {
         w.line(`def create_resource(cls) -> ${annotatedBaseTypeName}:`);
     }
     w.indentBlock(() => {
         for (const f of factoryInfo.sliceAutoFields) {
-            const fieldName = pyFieldName(f.name);
+            const fieldName = pyFieldName(f.name, fmt);
             const matchRefs = f.sliceNames.map((s) => `cls.${pySliceStaticName(s)}`);
             if (matchRefs.length === 1) {
                 w.line(`${fieldName}_with_defaults = ensure_slice_defaults(list(${fieldName} or []), ${matchRefs[0]})`);
@@ -242,13 +243,13 @@ export const generateCreateResource = (
 
         const buildArgs: string[] = [];
         for (const f of factoryInfo.autoFields) {
-            buildArgs.push(`${pyFieldName(f.name)}=${f.value}`);
+            buildArgs.push(`${pyFieldName(f.name, fmt)}=${f.value}`);
         }
         for (const f of factoryInfo.sliceAutoFields) {
-            buildArgs.push(`${pyFieldName(f.name)}=${pyFieldName(f.name)}_with_defaults`);
+            buildArgs.push(`${pyFieldName(f.name, fmt)}=${pyFieldName(f.name, fmt)}_with_defaults`);
         }
         for (const p of factoryInfo.params) {
-            buildArgs.push(`${pyFieldName(p.name)}=${pyFieldName(p.name)}`);
+            buildArgs.push(`${pyFieldName(p.name, fmt)}=${pyFieldName(p.name, fmt)}`);
         }
         if (isResourceBase) {
             buildArgs.push(`meta={"profile": [cls.canonical_url]}`);
@@ -275,8 +276,9 @@ export const generateFieldAccessors = (
     factoryInfo: ProfileFactoryInfo,
     extSliceMethodBaseNames: Set<string>,
 ): void => {
+    const fmt = w.nameFormatFunction;
     for (const p of factoryInfo.params) {
-        const fieldName = pyFieldName(p.name);
+        const fieldName = pyFieldName(p.name, fmt);
         const methodSuffix = pySnakeName(p.name);
         w.line(`def get_${methodSuffix}(self) -> ${p.pyType} | None:`);
         w.indentBlock(() => {
@@ -294,7 +296,7 @@ export const generateFieldAccessors = (
     for (const a of factoryInfo.accessors) {
         const methodSuffix = pySnakeName(a.name);
         if (extSliceMethodBaseNames.has(methodSuffix)) continue;
-        const fieldName = pyFieldName(a.name);
+        const fieldName = pyFieldName(a.name, fmt);
         w.line(`def get_${methodSuffix}(self) -> ${a.pyType} | None:`);
         w.indentBlock(() => {
             w.line(`return getattr(self._resource, ${JSON.stringify(fieldName)}, None)`);
@@ -304,7 +306,7 @@ export const generateFieldAccessors = (
         w.indentBlock(() => {
             if (a.choiceSiblings?.length) {
                 for (const sibling of a.choiceSiblings) {
-                    w.line(`setattr(self._resource, ${JSON.stringify(pyFieldName(sibling))}, None)`);
+                    w.line(`setattr(self._resource, ${JSON.stringify(pyFieldName(sibling, fmt))}, None)`);
                 }
             }
             w.line(`setattr(self._resource, ${JSON.stringify(fieldName)}, value)`);

src/api/writer-generator/python/profile-naming.ts

@@ -38,9 +38,12 @@ export const pySnakeName = (name: string): string => {
     return snakeCase(cleaned);
 };
 
-/** Snake-case a field name, escaping Python keywords. */
-export const pyFieldName = (n: string): string => {
-    const out = pySnakeName(n);
+/** Format a field name per the active field-naming mode (defaults to snake_case),
+ *  escaping Python keywords. The result must match the model's field name, so the
+ *  same `formatName` used to generate the models is threaded through. */
+export const pyFieldName = (n: string, formatName: (s: string) => string = snakeCase): string => {
+    const cleaned = n.replace(/\[x\]/g, "").replace(/[:./]/g, "_");
+    const out = formatName(cleaned);
     return PYTHON_KEYWORDS.has(out) ? `${out}_` : out;
 };
 
@@ -83,8 +86,10 @@ export const pySliceStaticName = (name: string): string => {
     return `_${snakeCase(cleaned)}_slice_match`;
 };
 
-/** snake_case the FHIR `value[x]` field for a TypeIdentifier. */
-export const pyValueFieldName = (id: TypeIdentifier): string => `value_${snakeCase(normalizePyName(id.name))}`;
+/** The FHIR `value[x]` field name for a TypeIdentifier, formatted per the active
+ *  field-naming mode (e.g. `value_coding` for snake_case, `valueCoding` for camelCase). */
+export const pyValueFieldName = (id: TypeIdentifier, formatName: (s: string) => string = snakeCase): string =>
+    formatName(`value${pascalCase(normalizePyName(id.name))}`);
 
 export type ResolvedProfileMethods = {
     extensions: Record<string, string>;

src/api/writer-generator/python/profile-slices.ts

@@ -165,7 +165,7 @@ export const generateSliceGetters = (
         const baseName =
             sliceBaseNames[`${sliceDef.fieldName}:${sliceDef.sliceName}`] ?? sliceDef.nameCandidates.recommended;
         const staticName = pySliceStaticName(sliceDef.sliceName);
-        const fieldName = pyFieldName(sliceDef.fieldName);
+        const fieldName = pyFieldName(sliceDef.fieldName, w.nameFormatFunction);
         const matchKeys = JSON.stringify(Object.keys(sliceDef.match));
 
         if (sliceDef.isTypeDiscriminated) {
@@ -236,7 +236,7 @@ export const generateSliceSetters = (
         const baseName =
             sliceBaseNames[`${sliceDef.fieldName}:${sliceDef.sliceName}`] ?? sliceDef.nameCandidates.recommended;
         const staticName = pySliceStaticName(sliceDef.sliceName);
-        const fieldName = pyFieldName(sliceDef.fieldName);
+        const fieldName = pyFieldName(sliceDef.fieldName, w.nameFormatFunction);
         if (sliceDef.isTypeDiscriminated) {
             const retType = sliceElementRetType(sliceDef);
             const isUnbounded = sliceDef.array && sliceDef.max === 0;

src/api/writer-generator/python/profile-validation.ts

@@ -21,19 +21,20 @@ export const collectValidateBody = (
     resolveRef: TypeSchemaIndex["findLastSpecializationByIdentifier"],
     errorLines: string[],
     warningLines: string[],
+    formatName: (s: string) => string,
 ): Set<string> => {
     const helpers = new Set<string>();
     const fields = flatProfile.fields;
     for (const [name, field] of Object.entries(fields)) {
-        const pyName = pyFieldName(name);
+        const pyName = pyFieldName(name, formatName);
         if (isChoiceInstanceField(field)) {
             collectProhibitedChoiceValidation(fields, name, pyName, helpers, errorLines);
             continue;
         }
         if (isChoiceDeclarationField(field)) {
             if (field.required) {
                 helpers.add("validate_choice_required");
-                const pyChoices = field.choices.map(pyFieldName);
+                const pyChoices = field.choices.map((c) => pyFieldName(c, formatName));
                 errorLines.push(
                     `errors.extend(validate_choice_required(self._resource, profile_name, ${JSON.stringify(pyChoices)}))`,
                 );

src/api/writer-generator/python/profile.ts

@@ -292,8 +292,10 @@ const generateCreateMethod = (
 ): void => {
     w.line("@classmethod");
     if (hasParams) {
-        w.line(`def create(cls, ${buildParamSignature(factoryInfo)}) -> "${className}":`);
-        w.indentBlock(() => w.line(`return cls.apply(cls.create_resource(${buildCallArgs(factoryInfo)}))`));
+        w.line(`def create(cls, ${buildParamSignature(factoryInfo, w.nameFormatFunction)}) -> "${className}":`);
+        w.indentBlock(() =>
+            w.line(`return cls.apply(cls.create_resource(${buildCallArgs(factoryInfo, w.nameFormatFunction)}))`),
+        );
     } else {
         w.line(`def create(cls) -> "${className}":`);
         w.indentBlock(() => w.line("return cls.apply(cls.create_resource())"));
@@ -387,6 +389,7 @@ const generateProfileModule = (w: Python, tsIndex: TypeSchemaIndex, flatProfile:
         tsIndex.findLastSpecializationByIdentifier,
         errorLines,
         warningLines,
+        w.nameFormatFunction,
     );
 
     const helperImports = collectHelperImports(isResourceBase, factoryInfo, sliceDefs, extensions, validationHelpers);