@atomic-ehr/codegen 0.0.16 → 0.0.17-canary.20260727063227.c50c42b

package/LICENSE

@@ -1,6 +1,6 @@
 MIT License
 
-Copyright (c) 2025 Atomic EHR Team
+Copyright (c) 2025-2026 Atomic EHR Team
 
 Permission is hereby granted, free of charge, to any person obtaining a copy
 of this software and associated documentation files (the "Software"), to deal

package/README.md

@@ -16,6 +16,7 @@
   - [Quick Start](#quick-start)
     - [Usage Examples](#usage-examples)
   - [Architecture](#architecture)
+    - [Generator Options](#generator-options)
     - [Input - FHIR packages & resolves canonicals](#input---fhir-packages--resolves-canonicals)
       - [Load Local StructureDefinitions & TGZ Archives](#load-local-structuredefinitions--tgz-archives)
     - [Intermediate - Type Schema](#intermediate---type-schema)
@@ -188,6 +189,44 @@ const builder = new APIBuilder()
 
 Each method returns the builder instance, allowing method chaining. The `generate()` method executes the pipeline and returns a report with success status and generated file details.
 
+### Generator Options
+
+Each language generator accepts its own option object. All options are optional; the tables below list the defaults.
+
+**TypeScript** — `.typescript({ ... })`
+
+| Option | Type | Default | Description |
+|--------|------|---------|-------------|
+| `generateProfile` | `boolean` | `true` | Generate profile wrapper classes (factories, typed slice/extension accessors, `validate()`). |
+| `primitiveTypeExtension` | `boolean` | `true` | Emit sibling `_field` properties for [primitive element extensions](https://www.hl7.org/fhir/element.html#json). |
+| `openResourceTypeSet` | `boolean` | `false` | For resource families (`Resource`, `DomainResource`), keep the `resourceType` union open by adding a `string` fallback instead of a closed literal union. |
+| `extensionGetterDefault` | `"flat" \| "profile" \| "raw"` | `"flat"` | Default return shape for generated extension getters. |
+| `sliceGetterDefault` | `"flat" \| "raw"` | `"flat"` | Default return shape for generated slice getters (`flat` strips discriminators, `raw` returns the full FHIR element). |
+| `lineWidth` | `number` | `120` | Maximum line width before wrapping. |
+| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |
+
+**Python** — `.python({ ... })`
+
+| Option | Type | Default | Description |
+|--------|------|---------|-------------|
+| `client` | `"fhirpy" \| "none"` | `"fhirpy"` | Client integration baked into the models: `"fhirpy"` makes models extend `FhirpyBaseModel` for the fhirpy async client; `"none"` emits plain Pydantic models. |
+| `fieldFormat` | `"camelCase" \| "snake_case" \| "PascalCase"` | `"camelCase"` | Naming convention for generated model fields. |
+| `generateProfile` | `boolean` | `false` | Generate profile wrapper classes (`create()`, typed accessors, `validate()`) around the Pydantic models. |
+| `primitiveTypeExtension` | `boolean` | `false` | Emit primitive element extension fields. |
+| `allowExtraFields` | `boolean` | `false` | Allow fields not present in the schema on generated models (Pydantic `extra`). |
+| `rootPackageName` | `string` | `"fhir_types"` | Root Python package name for the generated module tree. |
+| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |
+
+> `fhirpyClient?: boolean` is **deprecated** — use `client` instead (`true` → `"fhirpy"`, `false` → `"none"`).
+
+**C#** — `.csharp({ ... })`
+
+| Option | Type | Default | Description |
+|--------|------|---------|-------------|
+| `rootNamespace` | `string` | `"Fhir.Types"` | Root namespace for generated classes. |
+| `staticSourceDir` | `string` | — | Directory of static `.cs` source files copied verbatim into the output. |
+| `withDebugComment` | `boolean` | `false` | Emit comments tracing each generated type back to its source schema. |
+
 ### Input - FHIR packages & resolves canonicals
 
 The input stage leverages [Canonical Manager](https://github.com/atomic-ehr/canonical-manager) to handle FHIR package management and dependency resolution. It processes FHIR packages from multiple sources (registry, local files, TGZ archives) and resolves all canonical URLs to their concrete definitions, ensuring all references between resources are properly linked before transformation.
@@ -240,7 +279,7 @@ Tree shaking optimizes the generated output by including only the resources you
 })
 ```
 
-This feature automatically resolves and includes all dependencies (referenced types, base resources, nested types, and extension definitions used by profiles) while excluding unused resources, significantly reducing the size of generated code and improving compilation times.
+This feature automatically resolves and includes all dependencies (field types, base resources, nested types, and extension definitions used by profiles) while excluding unused resources, significantly reducing the size of generated code and improving compilation times. Reference targets are not dependencies: a field typed `Reference<"Patient">` does not pull the `Patient` type into the output, since the reference is rendered as a string literal.
 
 ##### Field-Level Tree Shaking
 
@@ -272,6 +311,33 @@ Beyond resource-level filtering, tree shaking supports fine-grained field select
 
 FHIR choice types (like `multipleBirth[x]` which can be boolean or integer) are handled intelligently. Selecting/ignoring the base field affects all variants, while targeting specific variants only affects those types.
 
+##### Following Reference Targets
+
+To also generate types for a schema's reference targets — both the base resources (`reference.resource`) and the target profiles (`reference.profiles`) — enable `followReferences` on the rule (default: `false`):
+
+```typescript
+.typeSchema({
+    treeShake: {
+        "kbv.basis": {
+            "https://fhir.kbv.de/StructureDefinition/KBV_PR_Base_Condition_Diagnosis": {
+                followReferences: true
+            }
+        }
+    }
+})
+```
+
+With this rule, `Condition.subject` targeting `KBV_PR_Base_Patient` pulls the Patient profile (and the `Patient`/`Group` resources) into the generated output, including their regular dependencies. Following is **non-transitive**: the pulled-in types keep their own reference targets as plain string literals, so a single flag cannot drag in the whole package. If a followed target is also listed as a tree-shake root, the root's rule wins.
+
+To enable it for every tree-shake root at once, use `treeShakeDefaults` (a rule's own `followReferences` still wins over the default):
+
+```typescript
+.typeSchema({
+    treeShake: { ... },
+    treeShakeDefaults: { followReferences: true }
+})
+```
+
 #### Logical Model Promotion
 
 Some implementation guides expose logical models (logical-kind StructureDefinitions) that are intended to be used like resources in generated SDKs. The code generator supports promoting selected logical models to behave as resources during generation.

package/assets/api/writer-generator/python/fhirpy_base_model.py

@@ -1,5 +1,6 @@
 from typing import Any, Union, Optional, Iterator, Tuple, Dict
 from pydantic import BaseModel, Field
+from pydantic_core import PydanticUndefined
 from typing import Protocol
 
 
@@ -22,7 +23,10 @@ class FhirpyBaseModel(BaseModel):
     def __pydantic_init_subclass__(cls, **kwargs: Any) -> None:
         super().__pydantic_init_subclass__(**kwargs)
         field = cls.model_fields.get("resource_type") or cls.model_fields.get("resourceType")
-        if field is not None and field.default is not None:
+        # Only concrete resources carry a default resourceType. Abstract/family base types
+        # (Resource, DomainResource) leave it unset, so we skip them to avoid registering a
+        # class attribute that concrete subclasses would shadow.
+        if field is not None and field.default is not None and field.default is not PydanticUndefined:
             type.__setattr__(cls, "resourceType", str(field.default))
 
     def __iter__(self) -> Iterator[Tuple[str, Any]]:  # type: ignore[override]

package/assets/api/writer-generator/python/fhirpy_base_model_camel_case.py

@@ -1,5 +1,6 @@
 from typing import Any, Union, Optional, Iterator, Tuple, Dict
 from pydantic import BaseModel, Field
+from pydantic_core import PydanticUndefined
 from typing import Protocol
 
 
@@ -21,7 +22,10 @@ class FhirpyBaseModel(BaseModel):
     def __pydantic_init_subclass__(cls, **kwargs: Any) -> None:
         super().__pydantic_init_subclass__(**kwargs)
         field = cls.model_fields.get("resource_type") or cls.model_fields.get("resourceType")
-        if field is not None and field.default is not None:
+        # Only concrete resources carry a default resourceType. Abstract/family base types
+        # (Resource, DomainResource) leave it unset, so we skip them to avoid registering a
+        # class attribute that concrete subclasses would shadow.
+        if field is not None and field.default is not None and field.default is not PydanticUndefined:
             type.__setattr__(cls, "resourceType", str(field.default))
 
     def __iter__(self) -> Iterator[Tuple[str, Any]]:  # type: ignore[override]

package/assets/api/writer-generator/python/profile_helpers.py

@@ -26,6 +26,8 @@ from __future__ import annotations
 import copy
 from typing import Any, Iterable, Mapping, MutableMapping, MutableSequence, Sequence, TypeVar
 
+from typing_extensions import TypeGuard
+
 T = TypeVar("T")
 
 # ---------------------------------------------------------------------------
@@ -33,9 +35,9 @@ T = TypeVar("T")
 # ---------------------------------------------------------------------------
 
 
-def is_record(value: Any) -> bool:
+def is_record(value: object) -> TypeGuard[MutableMapping[str, Any]]:
     """True when ``value`` is a non-None mapping (dict-like, not a list)."""
-    return isinstance(value, Mapping)
+    return isinstance(value, MutableMapping)
 
 
 def ensure_path(root: MutableMapping[str, Any], path: Sequence[str]) -> MutableMapping[str, Any]:
@@ -85,14 +87,14 @@ def apply_slice_match(input_obj: Mapping[str, Any], match: Mapping[str, Any]) ->
     return result
 
 
-def _get_key(obj: Any, key: str) -> Any:
+def _get_key(obj: object, key: str) -> Any:
     """Retrieve ``key`` from a dict-like or Pydantic-model-like object."""
     if is_record(obj):
         return obj.get(key)
     return getattr(obj, key, None)
 
 
-def _model_get(value: Any, key: str) -> Any:
+def _model_get(value: object, key: str) -> Any:
     """Get an attribute from a Pydantic model by Python name or field alias.
 
     Pydantic stores fields as snake_case attributes but slice match dicts use
@@ -110,7 +112,7 @@ def _model_get(value: Any, key: str) -> Any:
     return None
 
 
-def matches_value(value: Any, match: Any) -> bool:
+def matches_value(value: object, match: object) -> bool:
     """Recursively test whether ``value`` structurally contains everything in
     ``match``. Lists use "every match item has a corresponding value item"
     semantics; mappings are matched key-by-key; primitives use ``==``.
@@ -149,7 +151,7 @@ def matches_value(value: Any, match: Any) -> bool:
     return bool(value == match)
 
 
-def is_extension(value: Any, url: str | None = None) -> bool:
+def is_extension(value: object, url: str | None = None) -> bool:
     """True when ``value`` looks like a raw FHIR Extension (has a ``url``).
     When ``url`` is given, also checks the URL matches.
     Works with both plain dicts and Pydantic model instances."""
@@ -159,7 +161,7 @@ def is_extension(value: Any, url: str | None = None) -> bool:
     return url is None or bool(ext_url == url)
 
 
-def get_extension_value(ext: Any | None, field: str) -> Any:
+def get_extension_value(ext: object | None, field: str) -> Any:
     """Read a single typed value field from an Extension dict or Pydantic model,
     returning ``None`` when the extension itself is absent or the field is not set."""
     if ext is None:
@@ -192,7 +194,7 @@ def push_extension(target: Any, ext: Any) -> None:
 
 
 def extract_complex_extension(
-    extension: Any | None,
+    extension: object | None,
     config: Sequence[Mapping[str, Any]],
 ) -> dict[str, Any] | None:
     """Read a complex (nested) FHIR extension into a plain key/value dict.
@@ -325,7 +327,7 @@ def ensure_profile(resource: Any, canonical_url: str) -> None:
         profiles.append(canonical_url)
 
 
-def set_array_slice(lst: MutableSequence[Any], match: Mapping[str, Any], value: Any) -> None:
+def set_array_slice(lst: MutableSequence[Any], match: Mapping[str, Any], value: object) -> None:
     """Find or insert a slice element. If an element matching ``match``
     already exists it is replaced in place; otherwise ``value`` is appended."""
     for i, item in enumerate(lst):
@@ -355,7 +357,7 @@ def get_array_slices(lst: Sequence[Any] | None, match: Mapping[str, Any]) -> lis
 def set_array_slices(
     lst: MutableSequence[Any],
     match: Mapping[str, Any],
-    values: Sequence[Any],
+    values: Sequence[object],
 ) -> None:
     """Remove all elements matching ``match``, then append ``values``."""
     indices = [i for i, item in enumerate(lst) if matches_value(item, match)]
@@ -372,13 +374,13 @@ def set_array_slices(
 # ---------------------------------------------------------------------------
 
 
-def _get_field(res: Any, field: str) -> Any:
+def _get_field(res: object, field: str) -> Any:
     if isinstance(res, Mapping):
         return res.get(field)
     return getattr(res, field, None)
 
 
-def validate_required(res: Any, profile_name: str, field: str) -> list[str]:
+def validate_required(res: object, profile_name: str, field: str) -> list[str]:
     """Checks that ``field`` is present (not ``None``)."""
     return (
         [f"{profile_name}: required field '{field}' is missing"]
@@ -387,7 +389,7 @@ def validate_required(res: Any, profile_name: str, field: str) -> list[str]:
     )
 
 
-def validate_must_support(res: Any, profile_name: str, field: str) -> list[str]:
+def validate_must_support(res: object, profile_name: str, field: str) -> list[str]:
     """Checks that a must-support field is populated (warning, not error)."""
     return (
         [f"{profile_name}: must-support field '{field}' is not populated"]
@@ -396,7 +398,7 @@ def validate_must_support(res: Any, profile_name: str, field: str) -> list[str]:
     )
 
 
-def validate_excluded(res: Any, profile_name: str, field: str) -> list[str]:
+def validate_excluded(res: object, profile_name: str, field: str) -> list[str]:
     """Checks that ``field`` is absent."""
     return (
         [f"{profile_name}: field '{field}' must not be present"]
@@ -405,7 +407,7 @@ def validate_excluded(res: Any, profile_name: str, field: str) -> list[str]:
     )
 
 
-def validate_fixed_value(res: Any, profile_name: str, field: str, expected: Any) -> list[str]:
+def validate_fixed_value(res: object, profile_name: str, field: str, expected: object) -> list[str]:
     """Checks that ``field`` structurally contains the expected fixed value."""
     actual = _get_field(res, field)
     return (
@@ -416,7 +418,7 @@ def validate_fixed_value(res: Any, profile_name: str, field: str, expected: Any)
 
 
 def validate_slice_cardinality(
-    res: Any,
+    res: object,
     profile_name: str,
     field: str,
     match: Mapping[str, Any],
@@ -442,14 +444,48 @@ def validate_slice_cardinality(
     return errors
 
 
-def validate_choice_required(res: Any, profile_name: str, choices: Sequence[str]) -> list[str]:
+def validate_slice_fields(
+    res: object,
+    profile_name: str,
+    field: str,
+    match: Mapping[str, Any],
+    slice_name: str,
+    required_fields: Sequence[str],
+) -> list[str]:
+    """Validates required fields within matched slice elements. For each array
+    item matching the discriminator, checks that the listed fields are present."""
+    items = _get_field(res, field) or []
+    if not isinstance(items, Iterable):
+        items = []
+    errors: list[str] = []
+    for item in items:
+        if not matches_value(item, match):
+            continue
+        for rf in required_fields:
+            if _get_field(item, rf) is None:
+                errors.append(f"{profile_name}.{field}[{slice_name}].{rf} is required")
+    return errors
+
+
+def validate_choice_required(res: object, profile_name: str, choices: Sequence[str]) -> list[str]:
     """Checks that at least one of the listed choice-type variants is present."""
     if any(_get_field(res, c) is not None for c in choices):
         return []
     return [f"{profile_name}: at least one of {', '.join(choices)} is required"]
 
 
-def validate_enum(res: Any, profile_name: str, field: str, allowed: Sequence[str]) -> list[str]:
+def validate_choice_prohibited(res: object, profile_name: str, prohibited: Sequence[str]) -> list[str]:
+    """Checks that none of the listed prohibited choice-type variants is present.
+    E.g. a profile narrowing ``value[x]`` to ``value_quantity`` prohibits every
+    other variant."""
+    return [
+        f"{profile_name}: field '{c}' must not be present"
+        for c in prohibited
+        if _get_field(res, c) is not None
+    ]
+
+
+def validate_enum(res: object, profile_name: str, field: str, allowed: Sequence[str]) -> list[str]:
     """Checks that the value of ``field`` has a code within ``allowed``.
     Handles plain strings, Coding, and CodeableConcept."""
     value = _get_field(res, field)
@@ -481,7 +517,7 @@ def validate_enum(res: Any, profile_name: str, field: str, allowed: Sequence[str
     return []
 
 
-def validate_reference(res: Any, profile_name: str, field: str, allowed: Sequence[str]) -> list[str]:
+def validate_reference(res: object, profile_name: str, field: str, allowed: Sequence[str]) -> list[str]:
     """Checks that a Reference field points to one of the ``allowed`` resource
     types. Extracts the type from the ``reference`` string (the part before
     the first ``/``)."""

package/assets/api/writer-generator/typescript/profile-helpers.ts

@@ -437,6 +437,17 @@ export const validateChoiceRequired = (res: object, profileName: string, choices
         : [`${profileName}: at least one of ${choices.join(", ")} is required`];
 };
 
+/**
+ * Checks that none of the listed prohibited choice-type variants is present.
+ * E.g. a profile narrowing `value[x]` to `valueAddress` prohibits every other variant.
+ */
+export const validateChoiceProhibited = (res: object, profileName: string, prohibited: string[]): string[] => {
+    const rec = res as Record<string, unknown>;
+    return prohibited
+        .filter((c) => rec[c] !== undefined)
+        .map((c) => `${profileName}: field '${c}' must not be present`);
+};
+
 /**
  * Checks that the value of `field` has a code within `allowed`.
  * Handles plain strings, Coding objects, and CodeableConcept objects.

package/dist/cli/index.js

@@ -1,15 +1,15 @@
 #!/usr/bin/env node
-import T from'picocolors';import Dn from'yargs';import {hideBin}from'yargs/helpers';import {mkdir,writeFile}from'fs/promises';import {dirname}from'path';import Pe from'assert';import {createHash}from'crypto';import {CanonicalManager}from'@atomic-ehr/fhir-canonical-manager';import*as he from'@atomic-ehr/fhirschema';import {isStructureDefinition}from'@atomic-ehr/fhirschema';var ie=e=>{console.log(),console.log(T.cyan(T.bold(`\u2501\u2501\u2501 ${e} \u2501\u2501\u2501`)));},re=(e,n,i)=>{let t=e;if(n&&(t+=` ${T.gray(`(${n}ms)`)}`),console.log(`${T.green("")} ${t}`),i)for(let[r,o]of Object.entries(i))console.log(T.gray(`  ${r}: ${o}`));},F=(e,n="\u2022")=>{for(let i of e)console.log(T.gray(`  ${n} ${i}`));};var oe={DEBUG:0,INFO:1,WARN:2,ERROR:3,SILENT:4};function k(e={}){let n=e.prefix??"",i=new Set(e.suppressTags??[]),t={},r=[],o=new Set,a=e.level??"INFO",s=p=>oe[p]>=oe[a],c={DEBUG:p=>p,INFO:p=>p,WARN:T.yellow,ERROR:T.red,SILENT:p=>p},l=(p,m,f,y)=>{let h=n?`${n}: `:"",S=y?` ${T.dim(`(${y})`)}`:"";return c[p](`${m} ${h}${f}`)+S},d=(p,m,f,y=false)=>{r.push({level:p,tag:f,message:m,suppressed:y,prefix:n,timestamp:Date.now()});},u=(p,m,f,y=false)=>(...h)=>{let S=h.length===2?h[0]:void 0,x=h.length===2?h[1]:h[0];S&&(t[S]=(t[S]??0)+1);let C=S!==void 0&&i.has(S);if(d(p,x,S,C),!C&&s(p)){if(y){let N=`${p}::${S??""}::${x}`;if(o.has(N))return;o.add(N);}f(l(p,m,x,S));}},g={warn:u("WARN","!",console.warn),dryWarn:u("WARN","!",console.warn,true),info:u("INFO","i",console.log),error:u("ERROR","X",console.error),debug:u("DEBUG","D",console.log),fork(p,m){let f=n?`${n}/${p}`:p,y=[...i,...m?.suppressTags??[]];return k({prefix:f,suppressTags:y,level:m?.level??a})},as(){return g},tagCounts(){return t},printTagSummary(){let p=Object.entries(t);if(p.length===0)return;let m=n?`${n}: `:"",f=p.filter(([h])=>!i.has(h)),y=p.filter(([h])=>i.has(h));if(f.length>0){let h=f.reduce((x,[,C])=>x+C,0),S=f.map(([x,C])=>`${x}: ${C}`).join(", ");console.warn(T.yellow(`! ${m}${h} warnings (${S})`));}if(y.length>0){let h=y.reduce((x,[,C])=>x+C,0),S=y.map(([x,C])=>`${x}: ${C}`).join(", ");console.log(T.dim(`i ${m}${h} suppressed (${S})`));}},buffer(){return r},bufferClear(){r.length=0;}};return g}var b="Use CodeableReference which is not provided by FHIR R4.",Oe="Use Availability which is not provided by FHIR R4.",A={"hl7.fhir.uv.extensions.r4":{"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-manipulation":b,"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-processing":b,"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":Oe,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":b,"http://hl7.org/fhir/StructureDefinition/specimen-additive":b,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":b,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":b,"http://hl7.org/fhir/StructureDefinition/workflow-reason":b},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. 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m=p&&p.length>0,f=u?e.resolveFs(n.package_meta,u):void 0,y=f?I(f):void 0,h=[...c,"extension"].join(".");t.push({name:l,path:h,url:u,profile:y,min:d.min,max:d.max!==void 0?String(d.max):void 0,mustSupport:d.mustSupport,valueFieldTypes:g,subExtensions:p,isComplex:m,nameCandidates:fe({name:l,path:h})});},o=(c,l)=>{if(l.extensions)for(let[d,u]of Object.entries(l.extensions))r(c,d,u);if(l.elements)for(let[d,u]of Object.entries(l.elements))o([...c,d],u);};o([],n);let a=new Set,s=t.filter(c=>{let l=`${c.url}:${c.path}`;return a.has(l)?false:(a.add(l),true)});return s.length===0?void 0:s};function bn(e,n,i,t,r){if(!t)return;let o={};for(let a of e.getAllElementKeys(t)){let s=[...i,a],c=e.resolveElementSnapshot(n,s),l=c.type?e.ensureSpecializationCanonicalUrl(c.type):void 0;if(l&&v(n.package_meta,l).shouldSkip){r?.warn("#skipCanonical",`Skipping field ${s} for ${l} due to skip hack ${v(n.package_meta,l).reason}`);continue}Q(e,n,s,c,t[a])?o[a]=M(e,n,s,c):o[a]=B(e,n,s,c,r,t[a]);}return o}function Tn(e){let n=[];for(let i of Object.values(e))"type"in i&&i.type&&n.push(i.type),"binding"in i&&i.binding&&n.push(i.binding);return n}async function De(e,n,i){if(!n.url)throw new Error("ValueSet URL is required");let t=L(e,n.package_meta,n.url),r=q(e,n.package_meta,n.url);return {identifier:t,description:n.description,concept:r,compose:r?void 0:n.compose}}var Le=(e,n,i)=>{let t=[];return e&&t.push(e),n&&t.push(...Tn(n)),i&&t.push(...Ie(i)),t},Ne=(e,n,i,t)=>{let o=Le(n,i,t).filter(a=>!(a.url===e.url||G(a)));return E(o)},Fn=(e,n,i,t)=>{let o=Le(n,i,t).filter(a=>a.url!==e.url);return E(o)};function He(e,n,i){let t;if(n.base){let l=e.resolveFs(n.package_meta,e.ensureSpecializationCanonicalUrl(n.base));if(!l)throw new Error(`Base resource not found '${n.base}' for <${n.url}> from ${R(n.package_meta)}`);let d=I(l);Pe(!G(d),`Unexpected nested base for ${n.url}`),t=d;}let r=bn(e,n,[],n.elements,i),o=ke(e,n,i),a=me(e,n,i);if(n.derivation==="constraint"){let l=I(n);if(!t)throw new Error(`Profile 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versions`),r.push(c.typeSchema);o[d]??={},o[d][l]=s.flatMap(g=>g.sources.map(p=>({typeSchema:g.typeSchema,sourcePackage:p.sourcePackage,sourceCanonical:p.sourceCanonical})));}else r.push(c.typeSchema);}return {schemas:r,collisions:o}},we=async(e,n,i)=>{let t=[];for(let r of e.allFs()){let o=R(r.package_meta),a=v(r.package_meta,r.url);if(a.shouldSkip){i?.dryWarn("#skipCanonical",`Skip ${r.url} from ${o}. Reason: ${a.reason}`);continue}for(let s of He(e,r,i))t.push({schema:s,sourcePackage:o,sourceCanonical:r.url});}for(let r of e.allVs())t.push({schema:await De(e,r),sourcePackage:R(r.package_meta),sourceCanonical:r.url});return vn(t,n,i)};var Ue={command:"generate <packages..>",describe:"Generate TypeSchema files from FHIR packages",builder:{packages:{type:"string",array:true,demandOption:true,describe:"FHIR packages to process (e.g., hl7.fhir.r4.core@4.0.1)"},output:{alias:"o",type:"string",describe:"Output file or directory",default:"./schemas.ndjson"},format:{alias:"f",type:"string",choices:["ndjson","json"],default:"ndjson",describe:"Output format for TypeSchema files"},treeshake:{alias:"t",type:"string",array:true,describe:"Only generate TypeSchemas for specific ResourceTypes (treeshaking)"},singleFile:{alias:"s",type:"boolean",default:false,describe:"Generate single TypeSchema file instead of multiple files (NDJSON format)"},verbose:{alias:"v",type:"boolean",default:false,describe:"Enable verbose output"},registry:{alias:"r",type:"string",describe:"Custom FHIR package registry URL (default: https://fs.get-ig.org/pkgs/)"}},handler:async e=>{let n=k({prefix:"TypeSchema"});try{n.info("Generating TypeSchema from FHIR packages"),n.info(`Packages: ${e.packages.join(", ")}`),n.info(`Output: ${e.output}`);let i=e.singleFile?"ndjson":e.format;n.debug(`Format: ${i}${e.singleFile&&e.format==="json"?" (forced from json due to singleFile)":""}`),e.treeshake&&e.treeshake.length>0&&n.info(`Treeshaking enabled for ResourceTypes: ${e.treeshake.join(", ")}`),e.singleFile&&n.info("Single file output enabled (NDJSON format)"),e.registry&&n.info(`Using custom registry: ${e.registry}`);let t=Date.now(),r=e.packages.map(d=>{if(d.includes("@")){let u=d.lastIndexOf("@");return {name:d.slice(0,u),version:d.slice(u+1)||"latest"}}return {name:d,version:"latest"}});n.info(`Processing packages: ${r.map(d=>`${d.name}@${d.version}`).join(", ")}`);let o=await xe(r,{logger:n,registry:e.registry,focusedPackages:r}),{schemas:a}=await we(o,void 0,n);if(a.length===0)throw new Error("No schemas were generated from the specified packages");let s=e.output;if(!s)throw new Error("Output format not specified");await mkdir(dirname(s),{recursive:!0});let c;i==="json"?c=JSON.stringify(a,null,2):c=a.map(d=>JSON.stringify(d)).join(`
-`),await writeFile(s,c,"utf-8");let l=Date.now()-t;if(re(`Generated ${a.length} TypeSchema definitions`,l,{schemas:a.length}),n.info(`Output: ${s}`),e.verbose){n.debug("Generated schemas:");let d=a.map(u=>`${u.identifier?.name||"Unknown"} (${u.identifier?.kind||"unknown"})`);F(d);}}catch(i){n.error(`Failed to generate TypeSchema: ${i instanceof Error?i.message:String(i)}`),process.exit(1);}}};var ee=k({prefix:"typeschema"}),$e={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:e=>e.command(Ue).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:e=>{if(!e.subcommand&&e._.length===1){ee.info("Available typeschema subcommands:"),F(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
+  type:    ${t.type}${l}`)}return k(s)}t.choices||n.derivation!=="constraint"&&r?.dryWarn("#fieldTypeNotFound",`Can't recognize element type: <${n.url}>.${i.join(".")} (pkg: '${R(n.package_meta)}'): missing type info`);}var j=(e,n,i,t,r,o)=>{let s,a;t.binding&&(s=w(n,i,t),J.has(t.type??"")&&(a=Z(e,n,t,r)));let c=P(e,n,i,t,r);c||r?.dryWarn("#fieldTypeNotFound",`Field type not found for '${n.url}#${i.join(".")}' (${n.derivation})`);let l;t.pattern?l={kind:"pattern",type:t.pattern.type,value:t.pattern.value}:t.fixed&&(l={kind:"fixed",type:t.fixed.type,value:t.fixed.value});let p=o??t;if(!l&&p.elements?.coding?.slicing?.slices){let m=p.elements.coding.slicing.slices,g=Object.values(m);g.length>0&&g.every(u=>u.min!==void 0&&u.min>=1&&u.match&&typeof u.match=="object"&&Object.keys(u.match).length>0)&&(l={kind:"fixed",type:"CodeableConcept",value:{coding:g.flatMap(f=>f.match?[f.match]:[])}});}return {type:c,required:Ne(e,n,i),excluded:De(e,n,i),reference:Rn(e,n,t),array:t.array||false,min:t.min,max:t.max,choices:t.choices,choiceOf:t.choiceOf,binding:s,enum:a,valueConstraint:l,mustSupport:t.mustSupport}};function _(e,n,i,t){return {type:B(e,n,i),array:t.array||false,required:Ne(e,n,i),excluded:De(e,n,i)}}var Fn=(e,n,i,t)=>{let r=e.resolveFs(n.package_meta,i);if(!r?.elements)return;let o=[];for(let[s,a]of Object.entries(r.elements)){if(a.choiceOf!=="value"&&!s.startsWith("value"))continue;let c=P(e,r,[s],a,t);c&&o.push(c);}return E(o)},Tn=(e,n,i)=>{let t=[];if(!n.elements)return t;for(let[r,o]of Object.entries(n.elements)){if(!r.startsWith("extension:"))continue;let s=r.split(":")[1];if(!s)continue;let a;for(let[c,l]of Object.entries(o.elements??{}))if(!(l.choiceOf!=="value"&&!c.startsWith("value"))&&(a=P(e,n,[r,c],l,i),a))break;t.push({name:s,url:o.url??s,valueFieldType:a,min:o.min,max:o.max!==void 0?String(o.max):void 0});}return t},vn=(e,n,i)=>{let t=[],o=n.elements?.extension?.slicing?.slices;if(!o||typeof o!="object")return t;for(let[s,a]of Object.entries(o)){let c=a,l=c.schema;if(!l)continue;let p;for(let[m,g]of Object.entries(l.elements??{})){let d=g;if(!(d.choiceOf!=="value"&&!m.startsWith("value"))&&(p=P(e,n,[m],d,i),p))break}t.push({name:s,url:c.match?.url??s,valueFieldType:p,min:l._required?1:l.min??0,max:l.max!==void 0?String(l.max):l.array?"*":"1"});}return t},En=(e,n,i,t)=>{let r=e.resolveFs(n.package_meta,i);if(!r?.elements)return;let o=Tn(e,r,t),s=vn(e,r,t),a=[...o,...s];return a.length>0?a:void 0},He=(e,n,i)=>{let t=[],r=(c,l,p)=>{let m=p.url,g=m?Fn(e,n,m,i):void 0,d=m?En(e,n,m,i):void 0;if(!m){let S=n.elements?.extension?.slicing?.slices?.[l]?.schema;if(S){m=S.elements?.url?.fixed?.value??l;for(let[x,C]of Object.entries(S.elements??{})){let N=C;if(N.choiceOf==="value"||x.startsWith("value")){let oe=P(e,n,[x],N,i);if(oe){g=[oe];break}}}}}let u=d&&d.length>0,f=m?e.resolveFs(n.package_meta,m):void 0,y=f?k(f):void 0,h=[...c,"extension"].join(".");t.push({name:l,path:h,url:m,profile:y,min:p.min,max:p.max!==void 0?String(p.max):void 0,mustSupport:p.mustSupport,valueFieldTypes:g,subExtensions:d,isComplex:u,nameCandidates:xe({name:l,path:h})});},o=(c,l)=>{if(l.extensions)for(let[p,m]of Object.entries(l.extensions))r(c,p,m);if(l.elements)for(let[p,m]of Object.entries(l.elements))o([...c,p],m);};o([],n);let s=new Set,a=t.filter(c=>{let l=`${c.url}:${c.path}`;return s.has(l)?false:(s.add(l),true)});return a.length===0?void 0:a};function Pn(e,n,i,t,r){if(!t)return {};let o={},s={};for(let a of e.getAllElementKeys(t)){let c=[...i,a],l=e.resolveElementSnapshot(n,c),p=l.type?e.ensureSpecializationCanonicalUrl(l.type):void 0;if(p&&v(n.package_meta,p).shouldSkip){r?.warn("#skipCanonical",`Skipping field ${c} for ${p} due to skip hack ${v(n.package_meta,p).reason}`);continue}ne(e,n,c,l,t[a])?o[a]=_(e,n,c,l):o[a]=j(e,n,c,l,r,t[a]);let m=M(a,l);m&&(s[a]=m);}return {fields:o,slicing:Object.keys(s).length>0?s:void 0}}function Nn(e){let n=[];for(let i of Object.values(e))"type"in i&&i.type&&n.push(i.type),"binding"in i&&i.binding&&n.push(i.binding);return n}async function $e(e,n,i){if(!n.url)throw new Error("ValueSet URL is required");let t=H(e,n.package_meta,n.url),r=Y(e,n.package_meta,n.url);return {identifier:t,description:n.description,concept:r,compose:r?void 0:n.compose}}var Ve=(e,n,i)=>{let t=[];return e&&t.push(e),n&&t.push(...Nn(n)),i&&t.push(...Pe(i)),t},Ue=(e,n,i,t)=>{let o=Ve(n,i,t).filter(s=>!(s.url===e.url||W(s)));return E(o)},Dn=(e,n,i,t)=>{let o=Ve(n,i,t).filter(s=>s.url!==e.url);return E(o)};function Oe(e,n,i){let t;if(n.base){let p=e.resolveFs(n.package_meta,e.ensureSpecializationCanonicalUrl(n.base));if(!p)throw new Error(`Base resource not found '${n.base}' for <${n.url}> from ${R(n.package_meta)}`);let m=k(p);we(!W(m),`Unexpected nested base for ${n.url}`),t=m;}let{fields:r,slicing:o}=Pn(e,n,[],n.elements,i),s=Ee(e,n,i),a=Se(e,n,i);if(n.derivation==="constraint"){let p=k(n);if(!t)throw new Error(`Profile ${n.url} must have a base type`);let m=He(e,n,i),g=m?.flatMap(ge),d=Dn(p,t,r,s),u={identifier:p,base:t,fields:r,slicing:o,nested:s,description:n.description,dependencies:E(d,g),extensions:m};return ke(u),[u,...a]}if(n.kind==="primitive-type"){let p=k(n);return we(t,`Primitive type ${n.url} must have a base type`),[{identifier:p,description:n.description,base:t,dependencies:Ue(p,t,r,s)},...a]}let c=k(n);return [{identifier:c,base:t,fields:r,slicing:o,nested:s,description:n.description,dependencies:Ue(c,t,r,s),typeFamily:void 0},...a]}var Ln=(e,n,i)=>{let t={};for(let s of e){let a=`${s.schema.identifier.url}|${s.schema.identifier.package}`,c=me(s.schema);t[a]??={},t[a][c]??={typeSchema:s.schema,sources:[]},t[a][c].sources.push(s);}let r=[],o={};for(let s of Object.values(t)){let a=Object.entries(s).map(([l,p])=>({...p,schemaHash:l,sources:[...p.sources].sort(z)})).sort(pe),c=a[0];if(c)if(a.length>1){let l=c.typeSchema.identifier.url,p=c.typeSchema.identifier.package;i?.dryWarn("#duplicateSchema",`'${l}' from '${p}' has ${a.length} versions`),r.push(c.typeSchema);o[p]??={},o[p][l]=a.flatMap(g=>g.sources.map(d=>({typeSchema:g.typeSchema,sourcePackage:d.sourcePackage,sourceCanonical:d.sourceCanonical})));}else r.push(c.typeSchema);}return {schemas:r,collisions:o}},Be=async(e,n,i)=>{let t=[];for(let r of e.allFs()){let o=R(r.package_meta),s=v(r.package_meta,r.url);if(s.shouldSkip){i?.dryWarn("#skipCanonical",`Skip ${r.url} from ${o}. Reason: ${s.reason}`);continue}for(let a of Oe(e,r,i))t.push({schema:a,sourcePackage:o,sourceCanonical:r.url});}for(let r of e.allVs())t.push({schema:await $e(e,r),sourcePackage:R(r.package_meta),sourceCanonical:r.url});return Ln(t,n,i)};var Me={command:"generate <packages..>",describe:"Generate TypeSchema files from FHIR packages",builder:{packages:{type:"string",array:true,demandOption:true,describe:"FHIR packages to process (e.g., hl7.fhir.r4.core@4.0.1)"},output:{alias:"o",type:"string",describe:"Output file or directory",default:"./schemas.ndjson"},format:{alias:"f",type:"string",choices:["ndjson","json"],default:"ndjson",describe:"Output format for TypeSchema files"},treeshake:{alias:"t",type:"string",array:true,describe:"Only generate TypeSchemas for specific ResourceTypes (treeshaking)"},singleFile:{alias:"s",type:"boolean",default:false,describe:"Generate single TypeSchema file instead of multiple files (NDJSON format)"},verbose:{alias:"v",type:"boolean",default:false,describe:"Enable verbose output"},registry:{alias:"r",type:"string",describe:"Custom FHIR package registry URL (default: https://fs.get-ig.org/pkgs/)"}},handler:async e=>{let n=I({prefix:"TypeSchema"});try{n.info("Generating TypeSchema from FHIR packages"),n.info(`Packages: ${e.packages.join(", ")}`),n.info(`Output: ${e.output}`);let i=e.singleFile?"ndjson":e.format;n.debug(`Format: ${i}${e.singleFile&&e.format==="json"?" (forced from json due to singleFile)":""}`),e.treeshake&&e.treeshake.length>0&&n.info(`Treeshaking enabled for ResourceTypes: ${e.treeshake.join(", ")}`),e.singleFile&&n.info("Single file output enabled (NDJSON format)"),e.registry&&n.info(`Using custom registry: ${e.registry}`);let t=Date.now(),r=e.packages.map(p=>{if(p.includes("@")){let m=p.lastIndexOf("@");return {name:p.slice(0,m),version:p.slice(m+1)||"latest"}}return {name:p,version:"latest"}});n.info(`Processing packages: ${r.map(p=>`${p.name}@${p.version}`).join(", ")}`);let o=await Te(r,{logger:n,registry:e.registry,focusedPackages:r}),{schemas:s}=await Be(o,void 0,n);if(s.length===0)throw new Error("No schemas were generated from the specified packages");let a=e.output;if(!a)throw new Error("Output format not specified");await mkdir(dirname(a),{recursive:!0});let c;i==="json"?c=JSON.stringify(s,null,2):c=s.map(p=>JSON.stringify(p)).join(`
+`),await writeFile(a,c,"utf-8");let l=Date.now()-t;if(ae(`Generated ${s.length} TypeSchema definitions`,l,{schemas:s.length}),n.info(`Output: ${a}`),e.verbose){n.debug("Generated schemas:");let p=s.map(m=>`${m.identifier?.name||"Unknown"} (${m.identifier?.kind||"unknown"})`);T(p);}}catch(i){n.error(`Failed to generate TypeSchema: ${i instanceof Error?i.message:String(i)}`),process.exit(1);}}};var ie=I({prefix:"typeschema"}),je={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:e=>e.command(Me).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:e=>{if(!e.subcommand&&e._.length===1){ie.info("Available typeschema subcommands:"),T(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
 Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
-Examples:`),F(["atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","atomic-codegen typeschema validate schemas.ndjson","atomic-codegen typeschema merge schema1.ndjson schema2.ndjson -o merged.ndjson"]);return}e.subcommand&&!["generate","validate","merge"].includes(e.subcommand)&&(ee.error(`Unknown typeschema subcommand: ${e.subcommand}`),ee.info("Available typeschema subcommands:"),F(["generate    Generate TypeSchema files from FHIR packages","validate    Validate TypeSchema files for correctness and consistency","merge       Merge multiple TypeSchema files into a single file"]),console.log(`
-Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};var _=k({prefix:"cli"});async function Hn(e){let n=e.logLevel??(e.debug||e.verbose?"DEBUG":"INFO");_=k({prefix:"cli",level:n});}function wn(){return Dn(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(Hn).command($e).option("verbose",{alias:"v",type:"boolean",description:"Enable verbose output",default:false,global:true}).option("debug",{alias:"d",type:"boolean",description:"Enable debug output with detailed logging",default:false,global:true}).option("log-level",{alias:"l",type:"string",choices:["DEBUG","INFO","WARN","ERROR","SILENT"],description:"Set the log level (default: INFO)",global:true}).demandCommand(0).middleware(e=>{e._.length===0&&(ie("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log(`
+Examples:`),T(["atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","atomic-codegen typeschema validate schemas.ndjson","atomic-codegen typeschema merge schema1.ndjson schema2.ndjson -o merged.ndjson"]);return}e.subcommand&&!["generate","validate","merge"].includes(e.subcommand)&&(ie.error(`Unknown typeschema subcommand: ${e.subcommand}`),ie.info("Available typeschema subcommands:"),T(["generate    Generate TypeSchema files from FHIR packages","validate    Validate TypeSchema files for correctness and consistency","merge       Merge multiple TypeSchema files into a single file"]),console.log(`
+Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};var G=I({prefix:"cli"});async function On(e){let n=e.logLevel??(e.debug||e.verbose?"DEBUG":"INFO");G=I({prefix:"cli",level:n});}function Bn(){return $n(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(On).command(je).option("verbose",{alias:"v",type:"boolean",description:"Enable verbose output",default:false,global:true}).option("debug",{alias:"d",type:"boolean",description:"Enable debug output with detailed logging",default:false,global:true}).option("log-level",{alias:"l",type:"string",choices:["DEBUG","INFO","WARN","ERROR","SILENT"],description:"Set the log level (default: INFO)",global:true}).demandCommand(0).middleware(e=>{e._.length===0&&(se("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log(`
 Use 'atomic-codegen <command> --help' for more information about a command.`),console.log(`
 Quick examples:`),console.log("  atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson"),console.log(`
-Use 'atomic-codegen --help' to see all options.`),process.exit(0));}).help().version("0.1.0").example("$0 typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","Generate TypeSchemas from FHIR package").fail((e,n,i)=>{_.error(n?n.message:e),_.error("Use --help for usage information"),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function ne(){await wn().parseAsync();}import.meta.main&&ne().catch(e=>{_.error(String(e)),process.exit(1);});ne().catch(e=>{console.error("CLI Error:",e instanceof Error?e.message:e),process.exit(1);});
+Use 'atomic-codegen --help' to see all options.`),process.exit(0));}).help().version("0.1.0").example("$0 typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","Generate TypeSchemas from FHIR package").fail((e,n,i)=>{G.error(n?n.message:e),G.error("Use --help for usage information"),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function re(){await Bn().parseAsync();}import.meta.main&&re().catch(e=>{G.error(String(e)),process.exit(1);});re().catch(e=>{console.error("CLI Error:",e instanceof Error?e.message:e),process.exit(1);});

package/dist/index.d.ts

@@ -871,15 +871,22 @@ type CollisionResolution = {
 type ResolveCollisionsConf = Record<string, CollisionResolution>;
 type IrConf = {
     treeShake?: TreeShakeConf;
+    /** Rule defaults applied to every treeShake root; a rule's own value wins. */
+    treeShakeDefaults?: TreeShakeDefaults;
     promoteLogical?: LogicalPromotionConf;
     resolveCollisions?: ResolveCollisionsConf;
 };
+type TreeShakeDefaults = Pick<TreeShakeRule, "followReferences">;
 type LogicalPromotionConf = Record<PkgName$1, CanonicalUrl[]>;
 type TreeShakeConf = Record<string, Record<string, TreeShakeRule>>;
 type TreeShakeRule = {
     ignoreFields?: string[];
     selectFields?: string[];
     ignoreExtensions?: string[];
+    /** Also generate types for the schema's reference targets (base resources
+     *  and target profiles). Non-transitive: followed types keep their own
+     *  reference targets as plain string literals. Default: false. */
+    followReferences?: boolean;
 };
 
 type LogLevel = "DEBUG" | "INFO" | "WARN" | "ERROR" | "SILENT";
@@ -913,7 +920,7 @@ type LoggerOptions<T extends string> = {
     level?: LogLevel;
 };
 
-type CodegenTag = "#binding" | "#largeValueSet" | "#placeholderValueSet" | "#fieldTypeNotFound" | "#skipCanonical" | "#duplicateSchema" | "#duplicateCanonical" | "#resolveBase" | "#resolveCollisionMiss";
+type CodegenTag = "#binding" | "#largeValueSet" | "#placeholderValueSet" | "#fieldTypeNotFound" | "#skipCanonical" | "#duplicateSchema" | "#duplicateCanonical" | "#resolveBase" | "#resolveCollisionMiss" | "#nonMonotonicChoice";
 type CodegenLog = Log<CodegenTag>;
 type CodegenLogManager = LogManager<CodegenTag>;
 declare const mkCodegenLogger: (opts?: LoggerOptions<CodegenTag>) => LogManager<CodegenTag>;
@@ -1006,7 +1013,12 @@ interface PythonGeneratorOptions extends WriterOptions {
 }
 
 interface IntrospectionWriterOptions extends FileSystemWriterOptions {
-    typeSchemas?: string /** if .ndjson -- put in one file, else -- split into separated files*/;
+    /** if target is .ndjson -- put in one file, else -- split into separated files;
+     *  profileSnapshots additionally exports flattened profile snapshots next to profiles as <name>.snapshot.json */
+    typeSchemas?: string | {
+        target: string;
+        profileSnapshots?: boolean;
+    };
     typeTree?: string /** .json or .yaml file */;
     fhirSchemas?: string /** if .ndjson -- put in one file, else -- split into separated files*/;
     structureDefinitions?: string /** if .ndjson -- put in one file, else -- split into separated files*/;