@atomic-ehr/codegen 0.0.7 → 0.0.8-canary.20260304203134.178662b

package/README.md

@@ -23,7 +23,6 @@
     - [Generation](#generation)
       - [1. Writer-Based Generation (Programmatic)](#1-writer-based-generation-programmatic)
       - [2. Mustache Template-Based Generation (Declarative)](#2-mustache-template-based-generation-declarative)
-  - [Roadmap](#roadmap)
   - [Support](#support)
 - [Footnotes](#footnotes)
 
@@ -41,14 +40,32 @@ Guides:
 
 ## Features
 
-- 🚀 **High-Performance** - Built with Bun runtime for blazing-fast generation
-- 🔧 **Extensible Architecture** - Three-stage pipeline:
-  - FHIR package management & canonical resolution
-  - Optimized intermediate FHIR data entities representation via Type Schema
-  - Generation for different programming languages
-- 📦 **Multi-Package Support** - Generate from a list of FHIR packages
-- 🎯 **Type-Safe** - Generates fully typed interfaces with proper inheritance
-- 🛠️ **Developer Friendly** - Fluent API
+- [x] **Multi-Package Support** — Load packages from the [FHIR registry](examples/typescript-r4/), [remote TGZ files](examples/typescript-sql-on-fhir/), or a [local folder with custom StructureDefinitions](examples/local-package-folder/)
+  - Tested with hl7.fhir.r4.core, US Core, C-CDA, SQL on FHIR, etc.
+- [x] **Resources & Complex Types** — Generates typed definitions with proper inheritance
+- [x] **Value Set Bindings** — Strongly-typed enums from FHIR terminology bindings
+- [x] **Profiles & Extensions** — Factory methods with auto-populated fixed values and required slices ([R4 profiles](examples/typescript-r4/profile-bp.test.ts), [US Core](examples/typescript-us-core/))
+  - Extensions — flat typed accessors (e.g. `setRace()` on US Core Patient), [standalone extension profiles](examples/typescript-r4/extension-profile.test.ts)
+  - Slicing — typed get/set accessors with discriminator matching
+  - Validation — runtime `validate()` for required fields, fixed values, slice cardinality, enums, references
+- [x] **Extensible Architecture** — Three-stage pipeline: FHIR packages → [TypeSchema](https://www.health-samurai.io/articles/type-schema-a-pragmatic-approach-to-build-fhir-sdk) IR → code generation
+  - TypeSchema is a universal intermediate representation — add a new language by writing only the final generation stage
+  - Built-in generators: TypeScript, Python/Pydantic, C#, and Mustache templates
+- [x] **TypeSchema Transformations**:
+  - [x] Tree Shaking — include only the resources and fields you need; automatically resolves dependencies
+  - [x] Logical Model Promotion — promote FHIR logical models (e.g. CDA ClinicalDocument) to first-class resources
+  - [ ] Renaming — custom naming conventions for generated types, fields, packages, etc.
+- [ ] **Search Builders** — type-safe FHIR search query construction
+- [ ] **Operation Generation** — type-safe FHIR operation calls
+
+| Feature | TypeSchema | TypeScript | Python | C# | Mustache |
+|---|---|---|---|---|---|
+| Resources & Complex Types | yes | yes | yes | yes | template |
+| Value Set Bindings | yes | inline | inline | enum | template |
+| Profiles & Extensions | yes | yes | no | no | no |
+| Tree Shaking | yes | 〃 | 〃 | 〃 | 〃 |
+| Logical Model Promotion | yes | 〃 | 〃 | 〃 | 〃 |
+
 
 ## Versions & Release Cycle
 
@@ -298,107 +315,61 @@ Templates enable flexible code generation for any language or format (Go, Rust,
 
 ### Profile Classes
 
-When generating TypeScript with `generateProfile: true`, the generator creates profile wrapper classes that provide a fluent API for working with FHIR profiles (US Core, etc.). These classes handle complex profile constraints like slicing and extensions automatically.
+When generating TypeScript with `generateProfile: true`, the generator creates profile wrapper classes that provide a fluent API for working with FHIR profiles. These classes handle complex profile constraints like slicing and extensions automatically.
 
 ```typescript
-import { Patient } from "./fhir-types/hl7-fhir-r4-core/Patient";
-import { USCorePatientProfileProfile } from "./fhir-types/hl7-fhir-us-core/profiles/UscorePatientProfile";
-
-// Wrap a FHIR resource with a profile class
-const resource: Patient = { resourceType: "Patient" };
-const profile = new USCorePatientProfileProfile(resource);
+import { observation_bpProfile as bpProfile } from "./profiles/Observation_observation_bp";
 
-// Set extensions using flat API - complex extensions are simplified
-profile.setRace({
-    ombCategory: { system: "urn:oid:2.16.840.1.113883.6.238", code: "2106-3", display: "White" },
-    text: "White",
+// create() auto-sets fixed values (code, meta.profile) and required slice stubs
+const bp = bpProfile.create({
+    status: "final",
+    subject: { reference: "Patient/pt-1" },
 });
 
-// Set simple extensions directly
-profile.setSex({ system: "http://hl7.org/fhir/administrative-gender", code: "male" });
-
-// Get extension values - flat API returns simplified object
-const race = profile.getRace();
-console.log(race?.ombCategory?.display); // "White"
+// Slice setters — discriminator values (LOINC codes) applied automatically
+// Single-variant choice types (value[x] → valueQuantity) are flattened:
+bp.setVSCat({ text: "Vital Signs" })
+    .setSystolicBP({ value: 120, unit: "mmHg" })
+    .setDiastolicBP({ value: 80, unit: "mmHg" })
+    .setEffectiveDateTime("2024-06-15");
 
-// Get raw FHIR Extension when needed
-const raceExtension = profile.getRaceExtension();
-console.log(raceExtension?.url); // "http://hl7.org/fhir/us/core/StructureDefinition/us-core-race"
+bp.validate(); // [] — valid
 
-// Get the underlying resource
-const patientResource = profile.toResource();
+// Get plain FHIR JSON — ready for API calls, storage, etc.
+const obs = bp.toResource();
+// obs.component[0].valueQuantity.value === 120
+// obs.component[0].code.coding[0].code === "8480-6"
 ```
 
-**Slicing Support:**
-
-Profile classes also handle FHIR slicing, automatically applying discriminator values:
+**Slicing & Choice Type Flattening:**
 
 ```typescript
-import { Observation } from "./fhir-types/hl7-fhir-r4-core/Observation";
-import { USCoreBloodPressureProfileProfile } from "./fhir-types/hl7-fhir-us-core/profiles/UscoreBloodPressureProfile";
-
-const obs: Observation = { resourceType: "Observation", status: "final", code: {} };
-const bp = new USCoreBloodPressureProfileProfile(obs);
+// Simplified getter — discriminator stripped, choice type flattened
+bp.getSystolicBP();    // { value: 120, unit: "mmHg" }
 
-// Set slices - discriminator is applied automatically
-// No input needed when all fields are part of the discriminator
-bp.setSystolic({ valueQuantity: { value: 120, unit: "mmHg" } });
-bp.setDiastolic({ valueQuantity: { value: 80, unit: "mmHg" } });
-
-// Get simplified slice (without discriminator fields)
-const systolic = bp.getSystolic();
-console.log(systolic?.valueQuantity?.value); // 120
-
-// Get raw slice (includes discriminator)
-const systolicRaw = bp.getSystolicRaw();
-console.log(systolicRaw?.code?.coding?.[0]?.code); // "8480-6" (LOINC code for systolic BP)
+// Raw getter — full FHIR element including discriminator values
+bp.getSystolicBPRaw(); // { code: { coding: [...] }, valueQuantity: { value: 120, ... } }
 ```
 
-See [examples/typescript-us-core/](examples/typescript-us-core/) for complete profile usage examples.
-
-## Roadmap
-
-- [x] TypeScript generation
-- [x] FHIR R4 core package support
-- [x] Configuration file support
-- [x] Comprehensive test suite (72+ tests)
-- [x] **Value Set Generation** - Strongly-typed enums from FHIR bindings
-- [x] **Profile & Extension Support** - Basic parsing (US Core in development)
-- [ ] **Complete Multi-Package Support** - Custom packages and dependencies
-- [ ] **Smart Chained Search** - Intelligent search builders
+**Wrapping Existing Resources:**
 
-    ```typescript
-    // Intelligent search builders
-    const results = await client.Patient
-        .search()
-        .name().contains('Smith')
-        .birthdate().greaterThan('2000-01-01')
-        .address().city().equals('Boston')
-        .include('Patient:organization')
-        .sort('birthdate', 'desc')
-        .execute();
-    ```
+```typescript
+// Wrap any resource to read slices
+const bp2 = bpProfile.from(existingObservation);
+bp2.getSystolicBP();       // { value: 120, unit: "mmHg" }
+bp2.getVSCat();            // { text: "Vital Signs" }
+bp2.getEffectiveDateTime(); // "2024-06-15"
+```
 
-- [ ] **Operation Generation** - Type-safe FHIR operations
+**Validation:**
 
-    ```typescript
-    // Type-safe FHIR operations
-    const result = await client.Patient
-        .operation('$match')
-        .withParameters({
-            resource: patient,
-            onlyCertainMatches: true
-        })
-        .execute();
-    ```
+```typescript
+const errors = bp.validate();
+// [] — empty means valid
+// ["effective: at least one of effectiveDateTime, effectivePeriod is required"]
+```
 
-- [x] **Python generation**
-- [x] **C# generation**
-- [ ] **Rust generation**
-- [ ] **GraphQL schema generation**
-- [ ] **OpenAPI specification generation**
-- [ ] **Validation functions**
-- [ ] **Mock data generation**
+See [examples/typescript-r4/](examples/typescript-r4/) for R4 profile tests and [examples/typescript-us-core/](examples/typescript-us-core/) for US Core profile examples.
 
 ## Support
 

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

@@ -1,4 +1,4 @@
-from typing import Any, Union, Optional, Iterator, Tuple, Dict
+from typing import Any, ClassVar, Type, Union, Optional, Iterator, Tuple, Dict
 from pydantic import BaseModel, Field
 from typing import Protocol
 
@@ -8,20 +8,23 @@ class ResourceProtocol(Protocol):
     id: Union[str, None]
 
 
+class ResourceTypeDescriptor:
+    def __get__(self, instance: Optional[BaseModel], owner: Type[BaseModel]) -> str:
+        field = owner.model_fields.get("resource_type")
+        if field is None:
+            raise ValueError("resource_type field not found")
+        if field.default is None:
+            raise ValueError("resource_type field default value is not set")
+        return str(field.default)
+
+
 class FhirpyBaseModel(BaseModel):
     """
     This class satisfies ResourceProtocol
     """
-    resource_type: str = Field(alias="resourceType")
     id: Optional[str] = Field(None, alias="id")
 
-    @property
-    def resourceType(self) -> str:
-        return self.resource_type
-
-    @resourceType.setter
-    def resourceType(self, value: str) -> None:
-        self.resource_type = value
+    resourceType: ClassVar[ResourceTypeDescriptor] = ResourceTypeDescriptor()
 
     def __iter__(self) -> Iterator[Tuple[str, Any]]:  # type: ignore[override]
         data = self.model_dump(mode='json', by_alias=True, exclude_none=True)

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

@@ -0,0 +1,23 @@
+from typing import Any, Union, Optional, Iterator, Tuple, Dict
+from pydantic import BaseModel, Field
+from typing import Protocol
+
+
+class ResourceProtocol(Protocol):
+    resourceType: Any
+    id: Union[str, None]
+
+
+class FhirpyBaseModel(BaseModel):
+    """
+    This class satisfies ResourceProtocol
+    """
+    id: Optional[str] = Field(None, alias="id")
+
+    def __iter__(self) -> Iterator[Tuple[str, Any]]:  # type: ignore[override]
+        data = self.model_dump(mode='json', by_alias=True, exclude_none=True)
+        return iter(data.items())
+
+    def serialize(self) -> Dict[str, Any]:
+        """Serialize to dict (compatible with fhirpy's serialize method)"""
+        return self.model_dump(mode='json', by_alias=True, exclude_none=True)

package/dist/cli/index.js

@@ -1,11 +1,11 @@
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Object.entries(e.slices??{})){if(!o)continue;let{required:r,excluded:s,elements:a}=o.schema?We(o.schema):{};i[n]={min:o.min,max:o.max,match:qe(o.match)?Ke(e.discriminator??[],o.schema):o.match,required:r,excluded:s,elements:a};}return {discriminator:e.discriminator,rules:e.rules,ordered:e.ordered,slices:Object.keys(i).length>0?i:void 0}};function O(t,e,i,n,o){if(n.elementReference){let r=n.elementReference.slice(1).filter((s,a)=>a%2===1);return U(t,e,r)}else if(n.type){let r=t.ensureSpecializationCanonicalUrl(n.type),s=t.resolveFs(e.package_meta,r);if(!s)throw new Error(`Could not resolve field type: <${e.url}>.${i.join(".")}: <${n.type}> (pkg: '${x(e.package_meta)}'))`);return b(s)}else {if(n.choices)return;if(e.derivation==="constraint")return;o?.dryWarn(`Can't recognize element type: <${e.url}>.${i.join(".")} (pkg: '${x(e.package_meta)}'): missing type info`);return}}var H=(t,e,i,n,o,r)=>{let s,a;n.binding&&(s=L(e,i,n),_.has(n.type??"")&&(a=A(t,e,n,o)));let c=O(t,e,i,n,o);c||o?.dryWarn(`Field type not found for '${e.url}#${i.join(".")}' (${e.derivation})`);let l;n.pattern?l={kind:"pattern",type:n.pattern.type,value:n.pattern.value}:n.fixed&&(l={kind:"fixed",type:n.fixed.type,value:n.fixed.value});let d=r??n;if(!l&&d.elements?.coding?.slicing?.slices){let m=d.elements.coding.slicing.slices,y=Object.values(m);if(y.length>0&&y.every(u=>u.min!==void 0&&u.min>=1&&u.match&&typeof u.match=="object"&&Object.keys(u.match).length>0)){let u=y.map(f=>f.match);l={kind:"fixed",type:"CodeableConcept",value:{coding:u.length===1?[u[0]]:u}};}}return {type:c,required:he(t,e,i),excluded:Se(t,e,i),reference:Ge(t,e,n),array:n.array||false,min:n.min,max:n.max,slicing:Re(n),choices:n.choices,choiceOf:n.choiceOf,binding:s,enum:a,valueConstraint:l}};function V(t,e,i,n){return {type:U(t,e,i),array:n.array||false,required:he(t,e,i),excluded:Se(t,e,i),slicing:Re(n)}}var Je=(t,e,i,n)=>{let o=t.resolveFs(e.package_meta,i);if(!o?.elements)return;let r=[];for(let[s,a]of Object.entries(o.elements)){if(a.choiceOf!=="value"&&!s.startsWith("value"))continue;let c=O(t,o,[s],a,n);c&&r.push(c);}return F(r)},Qe=(t,e,i)=>{let n=[];if(!e.elements)return n;for(let[o,r]of Object.entries(e.elements)){if(!o.startsWith("extension:"))continue;let s=o.split(":")[1];if(!s)continue;let a;for(let[c,l]of Object.entries(r.elements??{}))if(!(l.choiceOf!=="value"&&!c.startsWith("value"))&&(a=O(t,e,[o,c],l,i),a))break;n.push({name:s,url:r.url??s,valueType:a,min:r.min,max:r.max!==void 0?String(r.max):void 0});}return n},Xe=t=>{let e=[],n=t.elements?.extension?.slicing?.slices;if(!n||typeof n!="object")return e;for(let[o,r]of Object.entries(n)){let s=r,a=s.schema;if(!a)continue;let c;for(let[l,d]of Object.entries(a.elements??{})){let m=d;if(!(m.choiceOf!=="value"&&!l.startsWith("value"))&&m.type){c={kind:"complex-type",package:t.package_meta.name,version:t.package_meta.version,name:m.type,url:`http://hl7.org/fhir/StructureDefinition/${m.type}`};break}}e.push({name:o,url:s.match?.url??o,valueType:c,min:a._required?1:a.min??0,max:a.max!==void 0?String(a.max):a.array?"*":"1"});}return e},Ye=(t,e,i,n)=>{let o=t.resolveFs(e.package_meta,i);if(!o?.elements)return;let r=Qe(t,o,n),s=Xe(o),a=[...r,...s];return a.length>0?a:void 0},ke=(t,e,i)=>{let n=[],o=(s,a,c)=>{let l=c.url,d=l?Je(t,e,l,i):void 0,m=l?Ye(t,e,l,i):void 0;if(!l){let p=e.elements?.extension?.slicing?.slices?.[a]?.schema;if(p){l=p.elements?.url?.fixed?.value??a;for(let[u,f]of Object.entries(p.elements??{})){let g=f;if(g.choiceOf==="value"&&g.type){d=[{kind:"complex-type",package:e.package_meta.name,version:e.package_meta.version,name:g.type,url:`http://hl7.org/fhir/StructureDefinition/${g.type}`}];break}}}}let y=m&&m.length>0;n.push({name:a,path:[...s,"extension"].join("."),url:l,min:c.min,max:c.max!==void 0?String(c.max):void 0,mustSupport:c.mustSupport,valueTypes:d,subExtensions:m,isComplex:y});},r=(s,a)=>{if(a.extensions)for(let[c,l]of Object.entries(a.extensions))o(s,c,l);if(a.elements)for(let[c,l]of Object.entries(a.elements))r([...s,c],l);};return r([],e),n.length===0?void 0:n};function Ze(t,e,i,n,o){if(!n)return;let r={};for(let s of t.getAllElementKeys(n)){let a=[...i,s],c=t.resolveElementSnapshot(e,a),l=c.type?t.ensureSpecializationCanonicalUrl(c.type):void 0;if(l&&C(e.package_meta,l).shouldSkip){o?.warn(`Skipping field ${a} for ${l} due to skip hack ${C(e.package_meta,l).reason}`);continue}q(t,e,a,c,n[s])?r[s]=V(t,e,a,c):r[s]=H(t,e,a,c,o,n[s]);}return r}function et(t){let e=[];for(let i of Object.values(t))"type"in i&&i.type&&e.push(i.type),"binding"in i&&i.binding&&e.push(i.binding);return e}async function Ce(t,e,i){if(!e.url)throw new Error("ValueSet URL is required");let n=D(t,e.package_meta,e.url),o=B(t,e.package_meta,e.url);return {identifier:n,description:e.description,concept:o,compose:o?void 0:e.compose}}function tt(t,e,i,n){let o=[];e&&o.push(e),i&&o.push(...et(i)),n&&o.push(...ye(n));let r=new Set(n?.map(a=>a.identifier.url)),s=o.filter(a=>a.url===t.url?false:se(t)||!re(a)?true:!r.has(a.url));return F(s)}function nt(t,e,i){let n=b(e),o;if(e.base){let y=t.resolveFs(e.package_meta,t.ensureSpecializationCanonicalUrl(e.base));if(!y)throw new Error(`Base resource not found '${e.base}' for <${e.url}> from ${x(e.package_meta)}`);o=b(y);}let r=Ze(t,e,[],e.elements,i),s=ge(t,e,i),a=e.derivation==="constraint"?ke(t,e,i):void 0,c=a?.flatMap(y=>y.valueTypes??[])??[],l=tt(n,o,r,s),d={identifier:n,base:o,fields:r,nested:s,description:e.description,dependencies:F(l,c),extensions:a},m=le(t,e,i);return [d,...m]}async function be(t,e,i){return nt(t,e,i)}var it=(t,e)=>{let i={};for(let r of t){let s=`${r.schema.identifier.url}|${r.schema.identifier.package}`,a=ie(r.schema);i[s]??={},i[s][a]??={typeSchema:r.schema,sources:[]},i[s][a].sources.push(r);}let n=[],o={};for(let r of Object.values(i)){let s=Object.values(r).sort((c,l)=>l.sources.length-c.sources.length),a=s[0];if(a&&(n.push(a.typeSchema),s.length>1)){let c=a.typeSchema.identifier.package,l=a.typeSchema.identifier.url;e?.dryWarn(`'${l}' from '${c}'' has ${s.length} versions`),o[c]??={},o[c][l]=s.flatMap(d=>d.sources.map(m=>({typeSchema:d.typeSchema,sourcePackage:m.sourcePackage,sourceCanonical:m.sourceCanonical})));}}return {schemas:n,collisions:o}},Ie=async(t,e)=>{let i=[];for(let n of t.allFs()){let o=x(n.package_meta),r=C(n.package_meta,n.url);if(r.shouldSkip){e?.dryWarn(`Skip ${n.url} from ${o}. Reason: ${r.reason}`);continue}for(let s of await be(t,n,e))i.push({schema:s,sourcePackage:o,sourceCanonical:n.url});}for(let n of t.allVs())i.push({schema:await Ce(t,n),sourcePackage:x(n.package_meta),sourceCanonical:n.url});return it(i,e)};var ve={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 t=>{let e=Z({prefix:"TypeSchema"});try{e.step("Generating TypeSchema from FHIR packages"),e.info(`Packages: ${t.packages.join(", ")}`),e.info(`Output: ${t.output}`);let i=t.singleFile?"ndjson":t.format;e.debug(`Format: ${i}${t.singleFile&&t.format==="json"?" (forced from json due to singleFile)":""}`),t.treeshake&&t.treeshake.length>0&&e.info(`Treeshaking enabled for ResourceTypes: ${t.treeshake.join(", ")}`),t.singleFile&&e.info("Single file output enabled (NDJSON format)"),t.registry&&e.info(`Using custom registry: ${t.registry}`);let n=Date.now(),o=t.packages.map(d=>{if(d.includes("@")){let m=d.lastIndexOf("@");return {name:d.slice(0,m),version:d.slice(m+1)||"latest"}}return {name:d,version:"latest"}});e.progress(`Processing packages: ${o.map(d=>`${d.name}@${d.version}`).join(", ")}`);let r=await me(o,{logger:e,registry:t.registry,focusedPackages:o}),{schemas:s}=await Ie(r,e);if(s.length===0)throw new Error("No schemas were generated from the specified packages");let a=t.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(d=>JSON.stringify(d)).join(`
+`),await writeFile(a,c,"utf-8");let l=Date.now()-n;if(te(`Generated ${s.length} TypeSchema definitions`,l,{schemas:s.length}),e.dim(`Output: ${a}`),t.verbose){e.debug("Generated schemas:");let d=s.map(m=>`${m.identifier?.name||"Unknown"} (${m.identifier?.kind||"unknown"})`);k(d);}}catch(i){e.error("Failed to generate TypeSchema",i instanceof Error?i:new Error(String(i))),process.exit(1);}}};var Fe={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:t=>t.command(ve).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:t=>{if(!t.subcommand&&t._.length===1){$("Available typeschema subcommands:"),k(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
 Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
-Examples:`),b(["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)&&(k(`Unknown typeschema subcommand: ${e.subcommand}
-`),V("Available typeschema subcommands:"),b(["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));}};function nt(e){return e?{debug:0,info:1,warn:2,error:3,silent:4}[e.toLowerCase()]:void 0}async function it(e){let t=nt(e.logLevel);t===void 0&&(e.debug||e.verbose?t=0:t=1),K({timestamp:e.debug,level:t});}function ot(){return et(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(it).command(Re).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&&(Q("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log(`
+Examples:`),k(["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}t.subcommand&&!["generate","validate","merge"].includes(t.subcommand)&&(R(`Unknown typeschema subcommand: ${t.subcommand}
+`),$("Available typeschema subcommands:"),k(["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));}};function lt(t){return t?{debug:0,info:1,warn:2,error:3,silent:4}[t.toLowerCase()]:void 0}async function pt(t){let e=lt(t.logLevel);e===void 0&&(t.debug||t.verbose?e=0:e=1),Y({timestamp:t.debug,level:e});}function dt(){return at(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(pt).command(Fe).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(t=>{t._.length===0&&(ee("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,t,o)=>{t?k(t.message,t):k(e),k(`
-Use --help for usage information`),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function W(){await ot().parseAsync();}import.meta.main&&W().catch(e=>{e("Unexpected error:",e),process.exit(1);});W().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((t,e,i)=>{e?R(e.message,e):R(t),R(`
+Use --help for usage information`),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function J(){await dt().parseAsync();}import.meta.main&&J().catch(t=>{t("Unexpected error:",t),process.exit(1);});J().catch(t=>{console.error("CLI Error:",t instanceof Error?t.message:t),process.exit(1);});

package/dist/index.d.ts

@@ -1,6 +1,6 @@
 import * as FS from '@atomic-ehr/fhirschema';
 import { FHIRSchema, StructureDefinition as StructureDefinition$1, FHIRSchemaElement } from '@atomic-ehr/fhirschema';
-import { CanonicalManager } from '@atomic-ehr/fhir-canonical-manager';
+import { CanonicalManager, PreprocessContext } from '@atomic-ehr/fhir-canonical-manager';
 
 /**
  * CodeGen Logger
@@ -800,7 +800,6 @@ type Register = {
     resolveFsGenealogy(pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichFHIRSchema[];
     resolveFsSpecializations(pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichFHIRSchema[];
     allSd(): RichStructureDefinition[];
-    patchSd(fn: (pkg: PackageMeta, sd: StructureDefinition$1) => StructureDefinition$1): void;
     /** Returns all FHIRSchemas from all packages in the resolver */
     allFs(): RichFHIRSchema[];
     /** Returns all ValueSets from all packages in the resolver */
@@ -991,6 +990,7 @@ declare class APIBuilder {
     constructor(userOpts?: Partial<APIBuilderOptions> & {
         manager?: ReturnType<typeof CanonicalManager>;
         register?: Register;
+        preprocessPackage?: (context: PreprocessContext) => PreprocessContext;
         logger?: CodegenLogger;
     });
     fromPackage(packageName: string, version?: string): APIBuilder;