@atomic-ehr/codegen 0.0.4-canary.20251211114058.39d4b3a → 0.0.4-canary.20251216132615.27719de

package/README.md

@@ -122,25 +122,47 @@ Actual examples of type generation and usage can be found here: [examples/typesc
 
 - `demo.ts` - a simple script that creates resources and demonstrates how to work with profiles
 - `generate.ts` - script to generate types
+- [`examples/local-structure-package.ts`](examples/local-structure-package.ts) - demonstrates loading local profiles, installing dependencies, and tree shaking the output
+- [`examples/local-package-folder/generate.ts`](examples/local-package-folder/generate.ts) - demonstrates pointing the builder at an existing FHIR package folder without publishing it
 
-### Generate Types for a Custom Profile (Draft)
+### Load Local StructureDefinitions, Local Packages & TGZ Archives
+
+Use the new `localPackage` helper to point the builder at an on-disk FHIR package folder (for example, an unpublished implementation guide). If you only have loose StructureDefinition JSON files, group them under a folder and pass it to `localStructureDefinitions`. Canonical Manager handles copying, indexing, and dependency installation in both scenarios, so the API builder only needs to describe where the files live and what upstream packages they depend on.
 
 ```typescript
-import { APIBuilder } from '@atomic-ehr/codegen';
+import { APIBuilder } from "@atomic-ehr/codegen";
 
 const builder = new APIBuilder();
 
-// Load custom profile
 await builder
-  .fromProfile('./profiles/my-patient-profile.json')
-  .withBaseProfile('http://hl7.org/fhir/StructureDefinition/Patient')
-  .typescript({
-    outputDir: './generated/profiles',
-    includeValidators: true,
+  .localPackage({
+    package: { name: "example.folder.structures", version: "0.0.1" },
+    path: "./packages/example-ig/package",
+    dependencies: [{ name: "hl7.fhir.r4.core", version: "4.0.1" }],
   })
+  .localStructureDefinitions({
+    package: { name: "example.local.structures", version: "0.0.1" },
+    path: "./custom-profiles",
+    dependencies: [{ name: "hl7.fhir.r4.core", version: "4.0.1" }],
+  })
+  .localTgzPackage("./packages/my-custom-ig.tgz")
+  .typescript({ generateIndex: true })
+  .treeShake({
+    "example.local.structures#0.0.1": {
+      "http://example.org/fhir/StructureDefinition/ExampleNotebook": {},
+    },
+    "hl7.fhir.r4.core#4.0.1": {
+      "http://hl7.org/fhir/StructureDefinition/Patient": {},
+    },
+  })
+  .outputTo("./generated/local-profiles")
   .generate();
 ```
 
+The example above points Canonical Manager at `./custom-profiles`, installs the HL7 R4 core dependency automatically, and then limits generation to the custom `ExampleNotebook` logical model plus the standard R4 `Patient` resource via tree shaking. The `localTgzPackage` helper registers `.tgz` artifacts that Canonical Manager already knows how to unpack.
+
+`localPackage` is ideal when you already have an extracted Implementation Guide on disk (for example, after running `fhirpack` or `npm pack`). The helper copies that folder into Canonical Manager's cache, synthesizes an index if necessary, and makes the package available to the rest of the pipeline without publishing it anywhere.
+
 ### Generate with Custom Templates (Draft)
 
 ```typescript

package/dist/cli/index.js

@@ -1,12 +1,12 @@
 #!/usr/bin/env node
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f},h=u=>{let f=d(u).find(S=>S.identifier.kind!=="profile");if(!f)throw new Error(`No non-constraint schema found in hierarchy for: ${u.identifier.name}`);return f};return {_schemaIndex:n,_relations:i,collectComplexTypes:()=>r.filter(rt),collectResources:()=>r.filter(w),collectLogicalModels:()=>r.filter(D),collectProfiles:()=>r.filter(oe),resolve:s,resolveByUrl:c,resourceChildren:a,tryHierarchy:l,hierarchy:d,findLastSpecialization:h,findLastSpecializationByIdentifier:u=>{let f=s(u);return f?h(f).identifier:u},flatProfile:u=>{let f=d(u),S=f.filter(P=>P.identifier.kind==="profile"),v=f.find(P=>P.identifier.kind!=="profile");if(!v)throw new Error(`No non-constraint schema found in hierarchy for ${u.identifier.name}`);let b={};for(let P of S.slice().reverse()){let ee=P;if(ee.fields)for(let[te,Ge]of Object.entries(ee.fields))b[te]?b[te]={...b[te],...Ge}:b[te]={...Ge};}let R={};for(let P of S.flatMap(ee=>ee.dependencies??[]))R[P.url]=P;let M=Object.values(R);return {...u,base:v.identifier,fields:b,dependencies:M}},isWithMetaField:u=>{let f=l(u);return f?f.filter(j).some(S=>S.fields?.meta!==void 0):false},exportTree:async u=>{let f={};for(let[v,b]of Object.entries(Le(r))){f[v]={"primitive-type":{},"complex-type":{},resource:{},"value-set":{},nested:{},binding:{},profile:{},logical:{}};for(let R of b)f[v][R.identifier.kind][R.identifier.url]={};}let S=u.endsWith(".yaml")?Tt.stringify(f):JSON.stringify(f,void 0,2);await L.mkdir(E.dirname(u),{recursive:true}),await L.writeFile(u,S);}}};var X=class{manager;options;logger;constructor(e={}){this.options={...e},this.manager=e.manager||CanonicalManager({packages:[],workingDir:"tmp/fhir"}),this.logger=e.logger||N({prefix:"TypeSchema"});}async registerFromPackageMetas(e){let t=e.map(C);return this.logger?.step(`Loading FHIR packages: ${t.join(", ")}`),await this.manager.init(),K(this.manager,{focusedPackages:e})}generateFhirSchemas(e){this.logger?.progress(`Converting ${e.length} StructureDefinitions to FHIRSchemas`);let t=[],n=0,o=0;for(let i of e)try{let s=gt.translate(i);t.push(s),n++,this.logger?.debug(`Converted StructureDefinition: ${i.name||i.id} (${i.resourceType})`);}catch(s){o++,this.logger?.warn(`Failed to convert StructureDefinition ${i.name||i.id}: ${s instanceof Error?s.message:String(s)}`);}return this.logger?.success(`FHIR Schema conversion completed: ${n}/${e.length} successful, ${o} failed`),t}async generateValueSetSchemas(e,t){e.length>0&&this.logger?.debug(`${e.length} ValueSets available for enum extraction`);let n=await K(this.manager,{logger:this.logger}),o=[];if(e.length>0){this.logger?.progress(`Converting ${e.length} ValueSets to TypeSchema`);let i=0,s=0;for(let c of e)try{let a=await fe(n,c,t);a&&(o.push(a),i++,this.logger?.debug(`Converted ValueSet: ${c.name||c.id}`));}catch(a){s++,this.logger?.warn(`Failed to convert ValueSet ${c.name||c.id}: ${a instanceof Error?a.message:String(a)}`);}this.logger?.success(`ValueSet conversion completed: ${i}/${e.length} successful, ${s} failed`);}return o}async generateFromPackage(e,t,n){let o={name:e,version:t||"latest"},i=await this.registerFromPackageMetas([o]),s=await this.generateValueSetSchemas(i.allVs(),n);return [...(await Promise.all(i.allFs().map(async l=>await ge(i,l,n)))).flat(),...s]}};var Y="Use CodeableReference which is not provided by FHIR R4.",fr="Use Availability which is not provided by FHIR R4.",Ft={"hl7.fhir.uv.extensions.r4#1.0.0":{"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":fr,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":Y,"http://hl7.org/fhir/StructureDefinition/specimen-additive":Y,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":Y,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":Y,"http://hl7.org/fhir/StructureDefinition/workflow-reason":Y},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. FHIR Schema generator output broken value in it, so we just skip it for now."}},wt=async(r,e)=>{let t=[];for(let n of r.allFs()){let o=C(n.package_meta);if(Ft[o]?.[n.url]){e?.dry_warn(`Skip ${n.url} from ${o}. Reason: ${Ft[o]?.[n.url]}`);continue}t.push(...await ge(r,n,e));}for(let n of r.allVs())t.push(await fe(r,n));return t};var gr={boolean:"boolean",instant:"string",time:"string",date:"string",dateTime:"string",decimal:"number",integer:"number",unsignedInt:"number",positiveInt:"number",integer64:"number",base64Binary:"string",uri:"string",url:"string",canonical:"string",oid:"string",uuid:"string",string:"string",code:"string",markdown:"string",id:"string",xhtml:"string"},$t=r=>{let e=gr[r];if(e===void 0)throw new Error(`Unknown primitive type ${r}`);return e},Pt=r=>Qe(r),je=r=>r.kind==="profile"?`${k(r)}_profile`:re(r.name),mr=r=>`${je(r)}.ts`,he=r=>`${Pt(r.package)}/${je(r)}`,Be=(r,e=true)=>{if(!r)return;let t=ie(r,e);if(t)return Ve(t)},k=r=>{if(r.kind==="nested"){let e=r.url,t=Be(e,false);if(!t)return "";let[n,o]=t.split("#"),i=ne((o??"").split(".")).join("");return Ve([n,i].join(""))}return Ve(r.name)},Nt=new Set(["class","function","return","if","for","while","const","let","var","import","export","interface"]),W=r=>Nt.has(r)?`"${r}"`:r.includes(" ")||r.includes("-")?`"${r}"`:r,Ve=r=>(Nt.has(r)&&(r=`${r}_`),r.replace(/[- ]/g,"_")),A=(r,e)=>e.startsWith('"')?`${r}[${e}]`:`${r}.${e}`,Et=r=>`(${r.map(e=>`"${e}"`).join(" | ")})`,ye=class extends z{tsImportType(e,...t){this.lineSM(`import type { ${t.join(", ")} } from "${e}"`);}generateFhirPackageIndexFile(e){this.cat("index.ts",()=>{let t=e.flatMap(n=>[{identifier:n.identifier,tsPackageName:je(n.identifier),resourceName:k(n.identifier),nestedTypes:w(n)&&n.nested||D(n)&&n.nested?n.nested.map(o=>k(o.identifier)):[],helpers:w(n)||D(n)?[`is${k(n.identifier)}`]:[]}]).sort((n,o)=>n.resourceName.localeCompare(o.resourceName));t=Array.from(new Map(t.map(n=>[n.resourceName.toLowerCase(),n])).values()).sort((n,o)=>n.resourceName.localeCompare(o.resourceName));for(let n of t)this.debugComment(n.identifier),this.lineSM(`export type { ${[n.resourceName,...n.nestedTypes].join(", ")} } from "./${n.tsPackageName}"`),n.helpers.length>0&&this.lineSM(`export { ${n.helpers.join(", ")} } from "./${n.tsPackageName}"`);});}generateDependenciesImports(e,t){if(t.dependencies){let n=[],o=[];for(let i of t.dependencies)if(["complex-type","resource","logical"].includes(i.kind))n.push({tsPackage:`../${he(i)}`,name:F(i.name),dep:i});else if(O(i)){let s={...i};s.name=Be(i.url),n.push({tsPackage:`../${he(s)}`,name:k(i),dep:i});}else o.push(i);n.sort((i,s)=>i.name.localeCompare(s.name));for(let i of n)this.debugComment(i.dep),this.tsImportType(i.tsPackage,i.name);for(let i of o)this.debugComment("skip:",i);if(this.line(),this.withPrimitiveTypeExtension(t)&&t.identifier.name!=="Element"&&t.dependencies.find(i=>i.name==="Element")===void 0){let i="http://hl7.org/fhir/StructureDefinition/Element",s=e.resolveByUrl(t.identifier.package,i);if(!s)throw new Error(`'${i}' not found for ${t.identifier.package}.`);this.tsImportType(`../${he(s.identifier)}`,"Element");}}}generateComplexTypeReexports(e){let t=e.dependencies?.filter(et).map(n=>({tsPackage:`../${he(n)}`,name:F(n.name)}));if(t&&t.length>0){for(let n of t)this.lineSM(`export type { ${n.name} } from "${n.tsPackage}"`);this.line();}}addFieldExtension(e){let t=W(`_${e}`);this.lineSM(`${t}?: Element`);}generateType(e,t){let n;t.identifier.name==="Reference"?n="Reference<T extends string = string>":(t.identifier.kind,n=k(t.identifier));let o;if(t.base&&(o=`extends ${Be(t.base.url)}`),this.debugComment(t.identifier),!t.fields&&!o&&!w(t)){this.lineSM(`export type ${n} = object`);return}this.curlyBlock(["export","interface",n,o],()=>{if(w(t)||D(t)){let s=[t.identifier];s.push(...e.resourceChildren(t.identifier));let c=this.opts.openResourceTypeSet&&s.length>1?" | string":"";this.lineSM(`resourceType: ${s.sort((a,l)=>a.name.localeCompare(l.name)).map(a=>`"${a.name}"`).join(" | ")}${c}`),this.line();}if(!t.fields)return;let i=Object.entries(t.fields).sort((s,c)=>s[0].localeCompare(c[0]));for(let[s,c]of i){if(U(c))continue;this.debugComment(s,":",c);let a=W(s),l;c.enum?l=Et(c.enum):t.identifier.name==="Reference"&&a==="reference"?l="`${T}/${string}`":c.reference&&c.reference.length>0?l=`Reference<${c.reference.map(p=>`"${p.name}"`).join(" | ")}>`:q(c.type)?l=$t(c.type.name):O(c.type)?l=k(c.type):l=c.type.name;let d=c.required?"":"?",h=c.array?"[]":"";this.lineSM(`${a}${d}: ${l}${h}`),this.withPrimitiveTypeExtension(t)&&q(c.type)&&this.addFieldExtension(s);}});}withPrimitiveTypeExtension(e){if(!this.opts.primitiveTypeExtension||!j(e))return  false;for(let t of Object.values(e.fields??{}))if(!U(t)&&q(t.type))return  true;return  false}generateResourceTypePredicate(e){if(!w(e)&&!D(e))return;let t=k(e.identifier);this.curlyBlock(["export","const",`is${t}`,"=",`(resource: unknown): resource is ${t}`,"=>"],()=>{this.lineSM(`return resource !== null && typeof resource === "object" && (resource as {resourceType: string}).resourceType === "${e.identifier.name}"`);});}generateNestedTypes(e,t){if(t.nested)for(let n of t.nested)this.generateType(e,n),this.line();}generateProfileType(e,t){this.debugComment("flatProfile",t);let n=k(t.identifier);this.debugComment("identifier",t.identifier),this.debugComment("base",t.base),this.curlyBlock(["export","interface",n],()=>{this.lineSM(`__profileUrl: "${t.identifier.url}"`),this.line();for(let[o,i]of Object.entries(t.fields??{})){if(U(i))continue;this.debugComment(o,i);let s=W(o),c;if(i.enum)c=Et(i.enum);else if(i.reference&&i.reference.length>0){let a=e.findLastSpecialization(t);if(!j(a))throw new Error(`Invalid specialization for ${t.identifier}`);let l=a.fields?.[o];if(l===void 0||U(l)||l.reference===void 0)throw new Error(`Invalid field declaration for ${o}`);let d=l.reference.map(m=>m.name),h=i.reference.map(m=>{let p=e.findLastSpecializationByIdentifier(m);return p.name!==m.name?`"${p.name}" /*${m.name}*/`:`'${m.name}'`}).join(" | ");d.length===1&&d[0]==="Resource"&&h!=='"Resource"'?c=`Reference<"Resource" /* ${h} */ >`:c=`Reference<${h}>`;}else if(O(i.type))c=k(i.type);else if(q(i.type))c=$t(i.type.name);else {if(i.type===void 0)throw new Error(`Undefined type for '${o}' field at ${Ze(t)}`);c=i.type.name;}this.lineSM(`${s}${i.required?"":"?"}: ${c}${i.array?"[]":""}`);}}),this.line();}generateAttachProfile(e){let t=k(e.base),n=k(e.identifier),o=Object.entries(e.fields||{}).filter(([i,s])=>s&&J(s)&&s.type!==void 0).map(([i])=>W(i));this.curlyBlock([`export const attach_${n}_to_${t} =`,`(resource: ${t}, profile: ${n}): ${t}`,"=>"],()=>{this.curlyBlock(["return"],()=>{this.line("...resource,"),this.curlyBlock(["meta:"],()=>{this.line(`profile: ['${e.identifier.url}']`);},[","]),o.forEach(i=>{this.line(`${i}: ${A("profile",i)},`);});});}),this.line();}generateExtractProfile(e,t){let n=k(t.base),o=k(t.identifier),i=Object.entries(t.fields||{}).filter(([a,l])=>J(l)&&l.type!==void 0).map(([a])=>a),s=e.findLastSpecialization(t);if(!j(s))throw new Error(`Specialization not found for ${t.identifier.url}`);let c={};this.curlyBlock([`export const extract_${o}_from_${n} =`,`(resource: ${n}): ${o}`,"=>"],()=>{i.forEach(a=>{let l=W(a),d=t.fields?.[a],h=s.fields?.[a];if(!J(d)||!J(h))return;d.required&&!h.required&&this.curlyBlock([`if (${A("resource",l)} === undefined)`],()=>this.lineSM(`throw new Error("'${l}' is required for ${t.identifier.url}")`));let m=d?.reference?.map(g=>g.name),p=h?.reference?.map(g=>g.name);if(m&&p&&m.length!==p.length){let g=`reference_is_valid_${l}`;this.curlyBlock(["const",g,"=","(ref?: Reference)","=>"],()=>{this.line("return !ref"),this.indentBlock(()=>{p.forEach(u=>{this.line(`|| ref.reference?.startsWith('${u}/')`);}),this.line(";");});});let y=d?.required?"":`!${A("resource",l)} || `;d.array?y+=`${A("resource",l)}.every( (ref) => ${g}(ref) )`:y+=`!${g}(${A("resource",l)})`,this.curlyBlock(["if (",y,")"],()=>{this.lineSM(`throw new Error("'${a}' has different references in profile and specialization")`);}),this.line(),c[a]=true;}}),this.curlyBlock(["return"],()=>{this.line(`__profileUrl: '${t.identifier.url}',`),i.forEach(a=>{let l=W(a);c[a]?this.line(`${l}:`,`${A("resource",l)} as ${o}['${l}'],`):this.line(`${l}:`,`${A("resource",l)},`);});});});}generateResourceModule(e,t){this.cat(`${mr(t.identifier)}`,()=>{if(this.generateDisclaimer(),["complex-type","resource","logical"].includes(t.identifier.kind))this.generateDependenciesImports(e,t),this.generateComplexTypeReexports(t),this.generateNestedTypes(e,t),this.comment("CanonicalURL:",t.identifier.url),this.generateType(e,t),this.generateResourceTypePredicate(t);else if(oe(t)){let n=e.flatProfile(t);this.generateDependenciesImports(e,n),this.comment("CanonicalURL:",t.identifier.url),this.generateProfileType(e,n),this.generateAttachProfile(n),this.generateExtractProfile(e,n);}else throw new Error(`Profile generation not implemented for kind: ${t.identifier.kind}`)});}async generate(e){let t=[...e.collectComplexTypes(),...e.collectResources(),...e.collectLogicalModels(),...this.opts.generateProfile?e.collectProfiles().filter(o=>e.isWithMetaField(o)):[]],n=Le(t);this.cd("/",()=>{for(let[o,i]of Object.entries(n)){let s=Pt(o);this.cd(s,()=>{for(let c of i)this.generateResourceModule(e,c);this.generateFhirPackageIndexFile(i);});}});}};var Ot=r=>{let e=r.replace(/[^a-zA-Z0-9\-_.@#()]/g,"");return e.length===0?"unknown":e},yr=async(r,e)=>{e.info("Cleaning outputs...");try{e.info(`Clean ${r.outputDir}`),T.rmSync(r.outputDir,{recursive:!0,force:!0}),r.typeSchemaOutputDir&&(e.info(`Clean ${r.typeSchemaOutputDir}`),T.rmSync(r.typeSchemaOutputDir,{recursive:!0,force:!0})),r.exportTypeTree&&(e.info(`Clean ${r.exportTypeTree}`),T.rmSync(r.exportTypeTree,{recursive:!0,force:!0}));}catch(t){e.warn(`Error cleaning output directory: ${t instanceof Error?t.message:String(t)}`);}},Sr=async(r,e,t)=>{await L.mkdir(e,{recursive:true}),t.info(`Writing TypeSchema files to ${e}/...`);let n={};for(let o of r){let i={name:o.identifier.package,version:o.identifier.version},s=Ot(C(i)),c=Ot(`${o.identifier.name}(${ie(o.identifier.url)})`),a=JSON.stringify(o,null,2),l=E.join(e,s,c);n[l]||(n[l]=[]),n[l]?.some(d=>d===a)||n[l].push(a);}for(let[o,i]of Object.entries(n))await Promise.all(i.map(async(s,c)=>{let a;c===0?a=`${o}.typeschema.json`:a=`${o}-${c}.typeschema.json`,await L.mkdir(E.dirname(a),{recursive:true}),await L.writeFile(a,s);}));},br=async(r,e,t)=>{t.info(`Writing TypeSchema files to: ${e}`),await L.mkdir(E.dirname(e),{recursive:true}),t.info(`Writing TypeSchemas to one file ${e}...`);for(let n of r){let o=JSON.stringify(n,null,2);await L.appendFile(e,`${o}
-`);}},Cr=async(r,e,t)=>{if(e.typeSchemaOutputDir)try{E.extname(e.typeSchemaOutputDir)===".ndjson"?await br(r,e.typeSchemaOutputDir,t):await Sr(r,e.typeSchemaOutputDir,t),t.info("Writing TypeSchema - DONE");}catch(n){if(t.error("Failed to write TypeSchema output",n instanceof Error?n:new Error(String(n))),e.throwException)throw n}},Z=class{schemas=[];options;generators=new Map;logger;packages=[];progressCallback;typeSchemaConfig;constructor(e={}){this.options={outputDir:e.outputDir||"./generated",overwrite:e.overwrite??true,cache:e.cache??true,cleanOutput:e.cleanOutput??true,typeSchemaConfig:e.typeSchemaConfig,manager:e.manager||null,throwException:e.throwException||false,typeSchemaOutputDir:e.typeSchemaOutputDir,exportTypeTree:e.exportTypeTree,treeShake:e.treeShake},this.typeSchemaConfig=e.typeSchemaConfig,this.logger=e.logger||N({prefix:"API",level:e.logLevel});}fromPackage(e,t){let n=Re({name:e,version:t||"latest"});return this.packages.push(n),this}fromPackageRef(e){return this.packages.push(e),this}fromSchemas(e){return this.logger.debug(`Adding ${e.length} TypeSchemas to generation`),this.schemas=[...this.schemas,...e],this}typescript(e){let o={...{...{logger:this.logger,outputDir:E.join(this.options.outputDir,"/types"),tabSize:4,withDebugComment:false,commentLinePrefix:"//",generateProfile:true},openResourceTypeSet:false,primitiveTypeExtension:true},...Object.fromEntries(Object.entries(e).filter(([s,c])=>c!==void 0))},i=new ye(o);return this.generators.set("typescript",i),this.logger.debug(`Configured TypeScript generator (${JSON.stringify(o,void 0,2)})`),this}csharp(e,t){let n=new se({outputDir:E.join(this.options.outputDir,"/types"),staticSourceDir:t??void 0,targetNamespace:e,logger:new _({prefix:"C#",timestamp:true,suppressLoggingLevel:[]})});return this.generators.set("C#",n),this.logger.debug("Configured C# generator"),this}onProgress(e){return this.progressCallback=e,this}outputTo(e){this.logger.debug(`Setting output directory: ${e}`),this.options.outputDir=e;for(let t of this.generators.values())t.setOutputDir(e);return this}setLogLevel(e){return this.logger?.setLevel(e),this}throwException(e=true){return this.options.throwException=e,this}cleanOutput(e=true){return this.options.cleanOutput=e,this}writeTypeTree(e){return this.options.exportTypeTree=e,this}treeShake(e){return this.options.treeShake=e,this}writeTypeSchemas(e){return this.options.typeSchemaOutputDir=e,this}async generate(){let e=performance.now(),t={success:false,outputDir:this.options.outputDir,filesGenerated:[],errors:[],warnings:[],duration:0};this.logger.debug(`Starting generation with ${this.generators.size} generators`);try{this.options.cleanOutput&&yr(this.options,this.logger),this.logger.info("Initialize Canonical Manager");let n=CanonicalManager({packages:this.packages,workingDir:".codegen-cache/canonical-manager-cache"}),o=await n.init(),i=Object.values(o),s=await K(n,{logger:this.logger,focusedPackages:i}),c=await wt(s,this.logger);await Cr(c,this.options,this.logger);let a={resolutionTree:s.resolutionTree(),logger:this.logger},l=Me(c,a);this.options.treeShake&&(l=Rt(l,this.options.treeShake,a)),this.options.exportTypeTree&&await l.exportTree(this.options.exportTypeTree),this.logger.debug(`Executing ${this.generators.size} generators`),await this.executeGenerators(t,l),this.logger.info("Generation completed successfully"),t.success=t.errors.length===0,this.logger.debug(`Generation completed: ${t.filesGenerated.length} files`);}catch(n){if(this.logger.error("Code generation failed",n instanceof Error?n:new Error(String(n))),t.errors.push(n instanceof Error?n.message:String(n)),this.options.throwException)throw n}return {...t,success:t.errors.length===0,duration:performance.now()-e}}reset(){return this.schemas=[],this.generators.clear(),this.progressCallback=void 0,this}getSchemas(){return [...this.schemas]}getGenerators(){return Array.from(this.generators.keys())}async executeGenerators(e,t){for(let[n,o]of this.generators.entries()){this.logger.info(`Generating ${n}...`);try{await o.generate(t);let i=o.writtenFiles();e.filesGenerated.push(...i.map(s=>s.absPath)),this.logger.info(`Generating ${n} finished successfully`);}catch(i){if(e.errors.push(`${n} generator failed: ${i instanceof Error?i.message:String(i)}`),this.options.throwException)throw i}}}};var Ue={outputDir:"./generated",verbose:false,overwrite:true,validate:true,cache:true,cleanOutput:true,typescript:{moduleFormat:"esm",generateIndex:true,includeDocuments:false,namingConvention:"PascalCase",strictMode:true,includeProfiles:true,includeExtensions:false,includeCodeSystems:false,includeOperations:false,generateValueSets:false,valueSetDirectory:"valuesets",valueSetMode:"required-only",valueSetStrengths:["required"],includeValueSetHelpers:false,fhirVersion:"R4",resourceTypes:[],maxDepth:10,profileOptions:{generateKind:"interface",includeConstraints:true,includeDocumentation:true,strictMode:false,subfolder:"profiles"},generateBuilders:false,builderOptions:{includeValidation:true,includeFactoryMethods:true,includeInterfaces:true,generateNestedBuilders:true,includeHelperMethods:true,supportPartialBuild:true,includeJSDoc:true,generateFactories:true,includeTypeGuards:true,handleChoiceTypes:true,generateArrayHelpers:true},validatorOptions:{includeCardinality:true,includeTypes:true,includeConstraints:true,includeInvariants:false,validateRequired:true,allowAdditional:false,strictValidation:false,collectMetrics:false,generateAssertions:true,generatePartialValidators:true,optimizePerformance:true,includeJSDoc:true,generateCompositeValidators:true},guardOptions:{includeRuntimeValidation:true,includeErrorMessages:true,treeShakeable:true,targetTSVersion:"5.0",strictGuards:false,includeNullChecks:true,verbose:false}},typeSchema:{enablePersistence:true,cacheDir:".typeschema-cache",maxAge:1440*60*1e3,validateCached:true,forceRegenerate:false,shareCache:true,cacheKeyPrefix:"",treeshake:[],singleFile:false,profiles:{autoDetect:true}},packages:[],files:[],$schema:""},be=["atomic-codegen.config.ts","atomic-codegen.config","atomic-codegen.config.json",".atomic-codegenrc","atomic-codegen.json",".atomic-codegen.json","codegen.config.json","codegen.json"],He=class{validate(e){let t={valid:true,errors:[],warnings:[]};if(!e||typeof e!="object")return t.valid=false,t.errors.push({path:"root",message:"Configuration must be an object",value:e}),t;let n=e;n.outputDir!==void 0&&typeof n.outputDir!="string"&&t.errors.push({path:"outputDir",message:"outputDir must be a string",value:n.outputDir});let o=["verbose","overwrite","validate","cache"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.errors.push({path:i,message:`${i} must be a boolean`,value:n[i]});if(n.typescript!==void 0){let i=this.validateTypeScriptConfig(n.typescript);t.errors.push(...i);}if(n.typeSchema!==void 0){let i=this.validateTypeSchemaConfig(n.typeSchema);t.errors.push(...i);}return n.packages!==void 0&&(Array.isArray(n.packages)?n.packages.forEach((i,s)=>{typeof i!="string"&&t.errors.push({path:`packages[${s}]`,message:"package name must be a string",value:i});}):t.errors.push({path:"packages",message:"packages must be an array",value:n.packages})),n.files!==void 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n&&n.type&&e.push(n.type),"binding"in n&&n.binding&&e.push(n.binding);}return e}function bt(r,e,t){let n=t[t.length-1];if(!n)throw new Error(`Internal error: fieldName is missing for path ${t.join("/")}`);let o=t.slice(0,-1),i=r.resolveFsGenealogy(e.package_meta,e.url).flatMap(s=>{if(o.length===0)return s.required||[];if(!s.elements)return [];let c=s;for(let a of o)c=c?.elements?.[a];return c?.required||[]});return new Set(i).has(n)}function Ct(r,e,t){let n=t[t.length-1];if(!n)throw new Error(`Internal error: fieldName is missing for path ${t.join("/")}`);let o=t.slice(0,-1),i=r.resolveFsGenealogy(e.package_meta,e.url).flatMap(s=>{if(o.length===0)return s.excluded||[];if(!s.elements)return [];let c=s;for(let a of o)c=c?.elements?.[a];return c?.excluded||[]});return new Set(i).has(n)}var rr=(r,e,t)=>{if(t.refers)return t.refers.map(n=>{let o=r.ensureSpecializationCanonicalUrl(n),i=r.resolveFs(e.package_meta,o);if(!i)throw new Error(`Failed to resolve fs for ${o}`);return 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i=r.resolveAny(o.system);if(i?.concept){let s=(c,a)=>{for(let l of c)n.push({system:a,code:l.code,display:l.display}),l.concept&&s(l.concept,a);};s(i.concept,o.system);}}catch{}}return n.length>0?n:void 0}var vt=100;function Ne(r,e,t,n){if(!t.binding)return;let o=t.binding.strength,i=t.binding.valueSet;if(!i||!(o==="required"||o==="extensible"&&(t.type==="code"||t.type==="Coding")||o==="preferred"&&(t.type==="code"||t.type==="Coding")))return;let c=De(r,e.package_meta,i);if(!c||c.length===0)return;let a=c.map(l=>l.code).filter(l=>l&&typeof l=="string"&&l.trim().length>0);if(a.length>vt){n?.dry_warn(`Value set ${i} has ${a.length} which is more than ${vt} codes, which may cause issues with code generation.`);return}return a.length>0?a:void 0}function or(r,e,t,n,o){if(!n.binding?.valueSet)return;let i=pe(e,t,n.binding.bindingName),s=Ee(r,e,t,n,o),c=le(r,e.package_meta,n.binding.valueSet),a=[];s&&a.push(s),a.push(c);let l=Ne(r,e,n,o);return {identifier:i,type:s,valueset:c,strength:n.binding.strength,enum:l,dependencies:a}}function kt(r,e,t){let n=new Set;if(!e.elements)return [];let o=[];function i(a,l){for(let[p,h]of Object.entries(a)){let m=[...l,p],d=m.join(".");if(!n.has(d)){if(n.add(d),h.binding){let g=or(r,e,m,h,t);g&&o.push(g);}h.elements&&i(h.elements,m);}}}i(e.elements,[]),o.sort((a,l)=>a.identifier.name.localeCompare(l.identifier.name));let s=[],c=new Set;for(let a of o)c.has(a.identifier.url)||(c.add(a.identifier.url),s.push(a));return s}function sr(r,e,t,n,o){if(!n)return;let i={};for(let s of r.getAllElementKeys(n)){let c=[...t,s],a=r.resolveElementSnapshot(e,c);Q(a)?i[s]=fe(r,e,c,a,o):i[s]=ue(r,e,c,a,o);}return i}function ar(r){let e=[];for(let t of Object.values(r))"type"in t&&t.type&&e.push(t.type),"binding"in t&&t.binding&&e.push(t.binding);return e}function cr(r,e){return !!(r.base==="Extension"||r.base==="http://hl7.org/fhir/StructureDefinition/Extension"||r.url?.includes("/extension/")||r.url?.includes("-extension")||r.name?.toLowerCase().includes("extension")||r.type==="Extension")}async function ge(r,e,t){if(!e.url)throw new Error("ValueSet URL is required");let n=le(r,e.package_meta,e.url),o=De(r,e.package_meta,e.url);return {identifier:n,description:e.description,concept:o,compose:o?void 0:e.compose}}function Oe(r,e,t,n){let o=[];e&&o.push(e),t&&o.push(...ar(t)),n&&o.push(...St(n));let i={};for(let a of o)a.url!==r.url&&(i[a.url]=a);let s=new Set(n?.map(a=>a.identifier.url)),c=Object.values(i).filter(a=>tt(r)||!D(a)?true:!s.has(a.url)).sort((a,l)=>a.url.localeCompare(l.url));return c.length>0?c:void 0}function lr(r,e,t){let n=A(e),o;if(e.base&&e.type!=="Element"){let p=r.resolveFs(e.package_meta,r.ensureSpecializationCanonicalUrl(e.base));if(!p)throw new Error(`Base resource not found '${e.base}' for <${e.url}> from ${C(e.package_meta)}`);o=A(p);}let i=sr(r,e,[],e.elements,t),s=Pe(r,e,t),c=Oe(n,o,i,s),a={identifier:n,base:o,fields:i,nested:s,description:e.description,dependencies:c},l=kt(r,e,t);return [a,...l]}async function me(r,e,t){let n=lr(r,e,t);if(cr(e,A(e))){let o=n[0];if(!o)throw new Error("Expected schema to be defined");o.metadata={isExtension:true};}return n}var Le=r=>{let e={};for(let t of r){let n=t.identifier.package;e[n]||(e[n]=[]),e[n].push(t);}for(let[t,n]of Object.entries(e)){let o={};for(let s of n)o[JSON.stringify(s.identifier)]=s;let i=Object.values(o);i.sort((s,c)=>s.identifier.name.localeCompare(c.identifier.name)),e[t]=i;}return e},pr=(r,e,t)=>{if(r=structuredClone(r),nt(r)||ot(r)||it(r))return r;for(let n of e.ignoreFields??[]){if(r.fields&&!r.fields[n])throw new Error(`Field ${n} not found`);r.fields&&delete r.fields[n];}return r.dependencies=Oe(r.identifier,r.base,r.fields,r.nested),r},Rt=(r,e,{resolutionTree:t,logger:n})=>{let o=[];for(let[c,a]of Object.entries(e))for(let[l,p]of Object.entries(a)){let h=r.resolveByUrl(c,l);if(!h)throw new Error(`Schema not found for ${c} ${l}`);let m=pr(h,p);o.push(m);}let i=(c,a)=>{if(c.length===0)return Object.values(a);for(let p of c)a[JSON.stringify(p.identifier)]=p;let l=[];for(let p of c)if(j(p)){if(!p.dependencies)continue;if(p.dependencies.forEach(h=>{let m=r.resolve(h);if(!m)throw new Error(`Schema not found for ${h}`);let d=JSON.stringify(m.identifier);a[d]||l.push(m);}),p.nested)for(let h of p.nested){if(D(h.identifier))continue;let m=JSON.stringify(h.identifier);a[m]||l.push(h);}}return i(l,a)},s=i(o,{});return Me(s,{resolutionTree:t,logger:n})},dr=r=>{let e=r.filter(i=>$(i)||O(i)),t=[];for(let i of e)i.base&&t.push({parent:i.base,child:i.identifier});let n=[...t],o=i=>{let s=t.filter(a=>a.parent.name===i.name).map(a=>a.child),c=[];for(let a of s)c.push(...o(a));return [...s,...c]};for(let i of t){let s=o(i.child);for(let c of s)t.some(a=>a.parent.name===i.parent.name&&a.child.name===c.name)||n.push({parent:i.parent,child:c});}return n},Me=(r,{resolutionTree:e,logger:t})=>{let n={},o=u=>{let f=u.identifier.url,S=u.identifier.package;if(n[f]||(n[f]={}),n[f][u.identifier.package]&&S!=="shared"){let v=JSON.stringify(u.identifier,void 0,2),b=JSON.stringify(n[f][S]?.identifier,void 0,2);if(v!==b)throw new Error(`Duplicate schema: ${v} and ${b}`);return}n[f][S]=u;};for(let u of r)o(u);let i=dr(r),s=u=>n[u.url]?.[u.package],c=(u,f)=>{if(e){let S=e[u]?.[f]?.[0];if(S)return n[f]?.[S.pkg.name]}return n[f]?.[u]},a=u=>i.filter(f=>f.parent.name===u.name).map(f=>f.child),l=u=>{let f=[],S=u;for(;S;){f.push(S);let v=S.base;if(v===void 0)break;let b=s(v);if(!b){t?.warn(`Failed to resolve base type: ${f.map(R=>`${R.identifier.url} (${R.identifier.kind})`).join(", ")}`);return}S=b;}return f},p=u=>{let f=l(u);if(f===void 0)throw new Error(`Failed to resolve base type: ${u.identifier.url} (${u.identifier.kind})`);return f},h=u=>{let f=p(u).find(S=>S.identifier.kind!=="profile");if(!f)throw new Error(`No non-constraint schema found in hierarchy for: ${u.identifier.name}`);return f};return {_schemaIndex:n,_relations:i,collectComplexTypes:()=>r.filter(rt),collectResources:()=>r.filter($),collectLogicalModels:()=>r.filter(O),collectProfiles:()=>r.filter(se),resolve:s,resolveByUrl:c,resourceChildren:a,tryHierarchy:l,hierarchy:p,findLastSpecialization:h,findLastSpecializationByIdentifier:u=>{let f=s(u);return f?h(f).identifier:u},flatProfile:u=>{let f=p(u),S=f.filter(E=>E.identifier.kind==="profile"),v=f.find(E=>E.identifier.kind!=="profile");if(!v)throw new Error(`No non-constraint schema found in hierarchy for ${u.identifier.name}`);let b={};for(let E of S.slice().reverse()){let ee=E;if(ee.fields)for(let[te,Ge]of Object.entries(ee.fields))b[te]?b[te]={...b[te],...Ge}:b[te]={...Ge};}let R={};for(let E of S.flatMap(ee=>ee.dependencies??[]))R[E.url]=E;let M=Object.values(R);return {...u,base:v.identifier,fields:b,dependencies:M}},isWithMetaField:u=>{let f=l(u);return f?f.filter(j).some(S=>S.fields?.meta!==void 0):false},exportTree:async u=>{let f={};for(let[v,b]of Object.entries(Le(r))){f[v]={"primitive-type":{},"complex-type":{},resource:{},"value-set":{},nested:{},binding:{},profile:{},logical:{}};for(let R of b)f[v][R.identifier.kind][R.identifier.url]={};}let S=u.endsWith(".yaml")?Tt.stringify(f):JSON.stringify(f,void 0,2);await L.mkdir(F.dirname(u),{recursive:true}),await L.writeFile(u,S);}}};var X=class{manager;options;logger;constructor(e={}){this.options={...e},this.manager=e.manager||CanonicalManager({packages:[],workingDir:"tmp/fhir"}),this.logger=e.logger||N({prefix:"TypeSchema"});}async registerFromPackageMetas(e){let t=e.map(C);return this.logger?.step(`Loading FHIR packages: ${t.join(", ")}`),await this.manager.init(),K(this.manager,{focusedPackages:e})}generateFhirSchemas(e){this.logger?.progress(`Converting ${e.length} StructureDefinitions to 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successful, ${s} failed`);}return o}async generateFromPackage(e,t,n){let o={name:e,version:t||"latest"},i=await this.registerFromPackageMetas([o]),s=await this.generateValueSetSchemas(i.allVs(),n);return [...(await Promise.all(i.allFs().map(async l=>await me(i,l,n)))).flat(),...s]}};var Y="Use CodeableReference which is not provided by FHIR R4.",fr="Use Availability which is not provided by FHIR R4.",Ft={"hl7.fhir.uv.extensions.r4#1.0.0":{"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":fr,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":Y,"http://hl7.org/fhir/StructureDefinition/specimen-additive":Y,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":Y,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":Y,"http://hl7.org/fhir/StructureDefinition/workflow-reason":Y},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. 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Set(["class","function","return","if","for","while","const","let","var","import","export","interface"]),W=r=>Nt.has(r)?`"${r}"`:r.includes(" ")||r.includes("-")?`"${r}"`:r,Ve=r=>(Nt.has(r)&&(r=`${r}_`),r.replace(/[- ]/g,"_")),H=(r,e)=>e.startsWith('"')?`${r}[${e}]`:`${r}.${e}`,Pt=r=>`(${r.map(e=>`"${e}"`).join(" | ")})`,Se=class extends z{tsImportType(e,...t){this.lineSM(`import type { ${t.join(", ")} } from "${e}"`);}generateFhirPackageIndexFile(e){this.cat("index.ts",()=>{let t=e.flatMap(n=>[{identifier:n.identifier,tsPackageName:je(n.identifier),resourceName:x(n.identifier),nestedTypes:$(n)&&n.nested||O(n)&&n.nested?n.nested.map(o=>x(o.identifier)):[],helpers:$(n)||O(n)?[`is${x(n.identifier)}`]:[]}]).sort((n,o)=>n.resourceName.localeCompare(o.resourceName));t=Array.from(new Map(t.map(n=>[n.resourceName.toLowerCase(),n])).values()).sort((n,o)=>n.resourceName.localeCompare(o.resourceName));for(let n of t)this.debugComment(n.identifier),this.lineSM(`export type { ${[n.resourceName,...n.nestedTypes].join(", ")} } from "./${n.tsPackageName}"`),n.helpers.length>0&&this.lineSM(`export { ${n.helpers.join(", ")} } from "./${n.tsPackageName}"`);});}generateDependenciesImports(e,t){if(t.dependencies){let n=[],o=[];for(let i of t.dependencies)if(["complex-type","resource","logical"].includes(i.kind))n.push({tsPackage:`../${ye(i)}`,name:w(i.name),dep:i});else if(D(i)){let s={...i};s.name=Be(i.url),n.push({tsPackage:`../${ye(s)}`,name:x(i),dep:i});}else o.push(i);n.sort((i,s)=>i.name.localeCompare(s.name));for(let i of n)this.debugComment(i.dep),this.tsImportType(i.tsPackage,i.name);for(let i of o)this.debugComment("skip:",i);if(this.line(),this.withPrimitiveTypeExtension(t)&&t.identifier.name!=="Element"&&t.dependencies.find(i=>i.name==="Element")===void 0){let i="http://hl7.org/fhir/StructureDefinition/Element",s=e.resolveByUrl(t.identifier.package,i);if(!s)throw new Error(`'${i}' not found for ${t.identifier.package}.`);this.tsImportType(`../${ye(s.identifier)}`,"Element");}}}generateComplexTypeReexports(e){let t=e.dependencies?.filter(et).map(n=>({tsPackage:`../${ye(n)}`,name:w(n.name)}));if(t&&t.length>0){for(let n of t)this.lineSM(`export type { ${n.name} } from "${n.tsPackage}"`);this.line();}}addFieldExtension(e){let t=W(`_${e}`);this.lineSM(`${t}?: Element`);}generateType(e,t){let n;t.identifier.name==="Reference"?n="Reference<T extends string = string>":(t.identifier.kind,n=x(t.identifier));let o;if(t.base&&(o=`extends ${Be(t.base.url)}`),this.debugComment(t.identifier),!t.fields&&!o&&!$(t)){this.lineSM(`export type ${n} = object`);return}this.curlyBlock(["export","interface",n,o],()=>{if($(t)||O(t)){let s=[t.identifier];s.push(...e.resourceChildren(t.identifier));let c=this.opts.openResourceTypeSet&&s.length>1?" | string":"";this.lineSM(`resourceType: ${s.sort((a,l)=>a.name.localeCompare(l.name)).map(a=>`"${a.name}"`).join(" | ")}${c}`),this.line();}if(!t.fields)return;let i=Object.entries(t.fields).sort((s,c)=>s[0].localeCompare(c[0]));for(let[s,c]of i){if(U(c))continue;this.debugComment(s,":",c);let a=W(s),l;c.enum?l=Pt(c.enum):t.identifier.name==="Reference"&&a==="reference"?l="`${T}/${string}`":c.reference&&c.reference.length>0?l=`Reference<${c.reference.map(d=>`"${d.name}"`).join(" | ")}>`:q(c.type)?l=$t(c.type.name):D(c.type)?l=x(c.type):l=c.type.name;let p=c.required?"":"?",h=c.array?"[]":"";this.lineSM(`${a}${p}: ${l}${h}`),this.withPrimitiveTypeExtension(t)&&q(c.type)&&this.addFieldExtension(s);}});}withPrimitiveTypeExtension(e){if(!this.opts.primitiveTypeExtension||!j(e))return  false;for(let t of Object.values(e.fields??{}))if(!U(t)&&q(t.type))return  true;return  false}generateResourceTypePredicate(e){if(!$(e)&&!O(e))return;let t=x(e.identifier);this.curlyBlock(["export","const",`is${t}`,"=",`(resource: unknown): resource is ${t}`,"=>"],()=>{this.lineSM(`return resource !== null && typeof resource === "object" && (resource as {resourceType: string}).resourceType === "${e.identifier.name}"`);});}generateNestedTypes(e,t){if(t.nested)for(let n of t.nested)this.generateType(e,n),this.line();}generateProfileType(e,t){this.debugComment("flatProfile",t);let n=x(t.identifier);this.debugComment("identifier",t.identifier),this.debugComment("base",t.base),this.curlyBlock(["export","interface",n],()=>{this.lineSM(`__profileUrl: "${t.identifier.url}"`),this.line();for(let[o,i]of Object.entries(t.fields??{})){if(U(i))continue;this.debugComment(o,i);let s=W(o),c;if(i.enum)c=Pt(i.enum);else if(i.reference&&i.reference.length>0){let a=e.findLastSpecialization(t);if(!j(a))throw new Error(`Invalid specialization for ${t.identifier}`);let l=a.fields?.[o];if(l===void 0||U(l)||l.reference===void 0)throw new Error(`Invalid field declaration for ${o}`);let p=l.reference.map(m=>m.name),h=i.reference.map(m=>{let d=e.findLastSpecializationByIdentifier(m);return d.name!==m.name?`"${d.name}" /*${m.name}*/`:`'${m.name}'`}).join(" | ");p.length===1&&p[0]==="Resource"&&h!=='"Resource"'?c=`Reference<"Resource" /* ${h} */ >`:c=`Reference<${h}>`;}else if(D(i.type))c=x(i.type);else if(q(i.type))c=$t(i.type.name);else {if(i.type===void 0)throw new Error(`Undefined type for '${o}' field at ${Ze(t)}`);c=i.type.name;}this.lineSM(`${s}${i.required?"":"?"}: ${c}${i.array?"[]":""}`);}}),this.line();}generateAttachProfile(e){let t=x(e.base),n=x(e.identifier),o=Object.entries(e.fields||{}).filter(([i,s])=>s&&J(s)&&s.type!==void 0).map(([i])=>W(i));this.curlyBlock([`export const attach_${n}_to_${t} =`,`(resource: ${t}, profile: ${n}): ${t}`,"=>"],()=>{this.curlyBlock(["return"],()=>{this.line("...resource,"),this.curlyBlock(["meta:"],()=>{this.line(`profile: ['${e.identifier.url}']`);},[","]),o.forEach(i=>{this.line(`${i}: ${H("profile",i)},`);});});}),this.line();}generateExtractProfile(e,t){let n=x(t.base),o=x(t.identifier),i=Object.entries(t.fields||{}).filter(([a,l])=>J(l)&&l.type!==void 0).map(([a])=>a),s=e.findLastSpecialization(t);if(!j(s))throw new Error(`Specialization not found for ${t.identifier.url}`);let c={};this.curlyBlock([`export const extract_${o}_from_${n} =`,`(resource: ${n}): ${o}`,"=>"],()=>{i.forEach(a=>{let l=W(a),p=t.fields?.[a],h=s.fields?.[a];if(!J(p)||!J(h))return;p.required&&!h.required&&this.curlyBlock([`if (${H("resource",l)} === undefined)`],()=>this.lineSM(`throw new Error("'${l}' is required for ${t.identifier.url}")`));let m=p?.reference?.map(g=>g.name),d=h?.reference?.map(g=>g.name);if(m&&d&&m.length!==d.length){let g=`reference_is_valid_${l}`;this.curlyBlock(["const",g,"=","(ref?: Reference)","=>"],()=>{this.line("return !ref"),this.indentBlock(()=>{d.forEach(u=>{this.line(`|| ref.reference?.startsWith('${u}/')`);}),this.line(";");});});let y=p?.required?"":`!${H("resource",l)} || `;p.array?y+=`${H("resource",l)}.every( (ref) => ${g}(ref) 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n=e.flatProfile(t);this.generateDependenciesImports(e,n),this.comment("CanonicalURL:",t.identifier.url),this.generateProfileType(e,n),this.generateAttachProfile(n),this.generateExtractProfile(e,n);}else throw new Error(`Profile generation not implemented for kind: ${t.identifier.kind}`)});}async generate(e){let t=[...e.collectComplexTypes(),...e.collectResources(),...e.collectLogicalModels(),...this.opts.generateProfile?e.collectProfiles().filter(o=>e.isWithMetaField(o)):[]],n=Le(t);this.cd("/",()=>{for(let[o,i]of Object.entries(n)){let s=Et(o);this.cd(s,()=>{for(let c of i)this.generateResourceModule(e,c);this.generateFhirPackageIndexFile(i);});}});}};var Dt=r=>{let e=r.replace(/[^a-zA-Z0-9\-_.@#()]/g,"");return e.length===0?"unknown":e},yr=async(r,e)=>{e.info("Cleaning outputs...");try{e.info(`Clean ${r.outputDir}`),T.rmSync(r.outputDir,{recursive:!0,force:!0}),r.typeSchemaOutputDir&&(e.info(`Clean 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this.packages.push(n),this}fromPackageRef(e){return this.packages.push(e),this}localStructureDefinitions(e){return this.localStructurePackages.push(e),this}localTgzPackage(e){return this.localTgzArchives.push(F.resolve(e)),this}fromSchemas(e){return this.logger.debug(`Adding ${e.length} TypeSchemas to generation`),this.schemas=[...this.schemas,...e],this}typescript(e){let o={...{...{logger:this.logger,outputDir:F.join(this.options.outputDir,"/types"),tabSize:4,withDebugComment:false,commentLinePrefix:"//",generateProfile:true},openResourceTypeSet:false,primitiveTypeExtension:true},...Object.fromEntries(Object.entries(e).filter(([s,c])=>c!==void 0))},i=new Se(o);return this.generators.set("typescript",i),this.logger.debug(`Configured TypeScript generator (${JSON.stringify(o,void 0,2)})`),this}csharp(e,t){let n=new ae({outputDir:F.join(this.options.outputDir,"/types"),staticSourceDir:t??void 0,targetNamespace:e,logger:new _({prefix:"C#",timestamp:true,suppressLoggingLevel:[]})});return this.generators.set("C#",n),this.logger.debug("Configured C# generator"),this}onProgress(e){return this.progressCallback=e,this}outputTo(e){this.logger.debug(`Setting output directory: ${e}`),this.options.outputDir=e;for(let t of this.generators.values())t.setOutputDir(e);return this}setLogLevel(e){return this.logger?.setLevel(e),this}throwException(e=true){return this.options.throwException=e,this}cleanOutput(e=true){return this.options.cleanOutput=e,this}writeTypeTree(e){return this.options.exportTypeTree=e,this}treeShake(e){return this.options.treeShake=e,this}writeTypeSchemas(e){return this.options.typeSchemaOutputDir=e,this}async generate(){let e=performance.now(),t={success:false,outputDir:this.options.outputDir,filesGenerated:[],errors:[],warnings:[],duration:0};this.logger.debug(`Starting generation with ${this.generators.size} generators`);try{this.options.cleanOutput&&yr(this.options,this.logger),this.logger.info("Initialize Canonical Manager");let n=this.options.manager||CanonicalManager({packages:this.packages,workingDir:".codegen-cache/canonical-manager-cache"});if(this.localStructurePackages.length>0)for(let p of this.localStructurePackages)this.logger.info(`Registering local StructureDefinitions for ${p.package.name}@${p.package.version}`),await n.addLocalPackage({name:p.package.name,version:p.package.version,path:p.path,dependencies:p.dependencies?.map(h=>oe(h))});for(let p of this.localTgzArchives)this.logger.info(`Registering local tgz package: ${p}`),await n.addTgzPackage({archivePath:p});let o=await n.init(),i=Object.values(o),s=await K(n,{logger:this.logger,focusedPackages:i}),c=await wt(s,this.logger);await Cr(c,this.options,this.logger);let a={resolutionTree:s.resolutionTree(),logger:this.logger},l=Me(c,a);this.options.treeShake&&(l=Rt(l,this.options.treeShake,a)),this.options.exportTypeTree&&await l.exportTree(this.options.exportTypeTree),this.logger.debug(`Executing ${this.generators.size} generators`),await this.executeGenerators(t,l),this.logger.info("Generation completed successfully"),t.success=t.errors.length===0,this.logger.debug(`Generation completed: ${t.filesGenerated.length} files`);}catch(n){if(this.logger.error("Code generation failed",n instanceof Error?n:new Error(String(n))),t.errors.push(n instanceof Error?n.message:String(n)),this.options.throwException)throw n}return {...t,success:t.errors.length===0,duration:performance.now()-e}}reset(){return this.schemas=[],this.generators.clear(),this.progressCallback=void 0,this.packages=[],this.localStructurePackages=[],this.localTgzArchives=[],this}getSchemas(){return [...this.schemas]}getGenerators(){return Array.from(this.generators.keys())}async executeGenerators(e,t){for(let[n,o]of this.generators.entries()){this.logger.info(`Generating ${n}...`);try{await o.generate(t);let i=o.writtenFiles();e.filesGenerated.push(...i.map(s=>s.absPath)),this.logger.info(`Generating ${n} finished successfully`);}catch(i){if(e.errors.push(`${n} 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Ue={outputDir:"./generated",verbose:false,overwrite:true,validate:true,cache:true,cleanOutput:true,typescript:{moduleFormat:"esm",generateIndex:true,includeDocuments:false,namingConvention:"PascalCase",strictMode:true,includeProfiles:true,includeExtensions:false,includeCodeSystems:false,includeOperations:false,generateValueSets:false,valueSetDirectory:"valuesets",valueSetMode:"required-only",valueSetStrengths:["required"],includeValueSetHelpers:false,fhirVersion:"R4",resourceTypes:[],maxDepth:10,profileOptions:{generateKind:"interface",includeConstraints:true,includeDocumentation:true,strictMode:false,subfolder:"profiles"},generateBuilders:false,builderOptions:{includeValidation:true,includeFactoryMethods:true,includeInterfaces:true,generateNestedBuilders:true,includeHelperMethods:true,supportPartialBuild:true,includeJSDoc:true,generateFactories:true,includeTypeGuards:true,handleChoiceTypes:true,generateArrayHelpers:true},validatorOptions:{includeCardinality:true,includeTypes:true,includeConstraints:true,includeInvariants:false,validateRequired:true,allowAdditional:false,strictValidation:false,collectMetrics:false,generateAssertions:true,generatePartialValidators:true,optimizePerformance:true,includeJSDoc:true,generateCompositeValidators:true},guardOptions:{includeRuntimeValidation:true,includeErrorMessages:true,treeShakeable:true,targetTSVersion:"5.0",strictGuards:false,includeNullChecks:true,verbose:false}},typeSchema:{enablePersistence:true,cacheDir:".typeschema-cache",maxAge:1440*60*1e3,validateCached:true,forceRegenerate:false,shareCache:true,cacheKeyPrefix:"",treeshake:[],singleFile:false,profiles:{autoDetect:true}},packages:[],files:[],$schema:""},Ce=["atomic-codegen.config.ts","atomic-codegen.config","atomic-codegen.config.json",".atomic-codegenrc","atomic-codegen.json",".atomic-codegen.json","codegen.config.json","codegen.json"],Ae=class{validate(e){let t={valid:true,errors:[],warnings:[]};if(!e||typeof e!="object")return t.valid=false,t.errors.push({path:"root",message:"Configuration must be an object",value:e}),t;let n=e;n.outputDir!==void 0&&typeof n.outputDir!="string"&&t.errors.push({path:"outputDir",message:"outputDir must be a string",value:n.outputDir});let o=["verbose","overwrite","validate","cache"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.errors.push({path:i,message:`${i} must be a boolean`,value:n[i]});if(n.typescript!==void 0){let i=this.validateTypeScriptConfig(n.typescript);t.errors.push(...i);}if(n.typeSchema!==void 0){let i=this.validateTypeSchemaConfig(n.typeSchema);t.errors.push(...i);}return n.packages!==void 0&&(Array.isArray(n.packages)?n.packages.forEach((i,s)=>{typeof i!="string"&&t.errors.push({path:`packages[${s}]`,message:"package name must be a string",value:i});}):t.errors.push({path:"packages",message:"packages must be an array",value:n.packages})),n.files!==void 0&&(Array.isArray(n.files)?n.files.forEach((i,s)=>{typeof i!="string"&&t.errors.push({path:`files[${s}]`,message:"file path must be a string",value:i});}):t.errors.push({path:"files",message:"files must be an array",value:n.files})),t.valid=t.errors.length===0,t.valid&&(t.config=n),t}validateTypeScriptConfig(e){let t=[];if(typeof e!="object"||e===null)return t.push({path:"typescript",message:"typescript config must be an object",value:e}),t;let n=e;n.moduleFormat!==void 0&&(["esm","cjs"].includes(n.moduleFormat)||t.push({path:"typescript.moduleFormat",message:'moduleFormat must be "esm" or "cjs"',value:n.moduleFormat})),n.namingConvention!==void 0&&(["PascalCase","camelCase"].includes(n.namingConvention)||t.push({path:"typescript.namingConvention",message:'namingConvention must be "PascalCase" or "camelCase"',value:n.namingConvention}));let o=["generateIndex","includeDocuments","strictMode","includeProfiles","includeExtensions","includeCodeSystems","includeOperations","generateValueSets","includeValueSetHelpers"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.push({path:`typescript.${i}`,message:`${i} must be a boolean`,value:n[i]});if(n.validatorOptions!==void 0){let i=this.validateValidatorOptions(n.validatorOptions);t.push(...i);}if(n.guardOptions!==void 0){let i=this.validateGuardOptions(n.guardOptions);t.push(...i);}if(n.profileOptions!==void 0){let i=this.validateProfileOptions(n.profileOptions);t.push(...i);}return t}validateValidatorOptions(e){let t=[];if(typeof e!="object"||e===null)return t.push({path:"typescript.validatorOptions",message:"validatorOptions must be an object",value:e}),t;let n=e,o=["includeCardinality","includeTypes","includeConstraints","includeInvariants","validateRequired","allowAdditional","strictValidation","collectMetrics","generateAssertions","generatePartialValidators","optimizePerformance","includeJSDoc","generateCompositeValidators"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.push({path:`typescript.validatorOptions.${i}`,message:`${i} must be a boolean`,value:n[i]});return t}validateGuardOptions(e){let t=[];if(typeof e!="object"||e===null)return t.push({path:"typescript.guardOptions",message:"guardOptions must be an object",value:e}),t;let n=e;n.targetTSVersion!==void 0&&(["3.8","4.0","4.5","5.0"].includes(n.targetTSVersion)||t.push({path:"typescript.guardOptions.targetTSVersion",message:'targetTSVersion must be one of: "3.8", "4.0", "4.5", "5.0"',value:n.targetTSVersion}));let o=["includeRuntimeValidation","includeErrorMessages","treeShakeable","strictGuards","includeNullChecks","verbose"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.push({path:`typescript.guardOptions.${i}`,message:`${i} must be a boolean`,value:n[i]});return t}validateProfileOptions(e){let t=[];if(typeof e!="object"||e===null)return t.push({path:"typescript.profileOptions",message:"profileOptions must be an object",value:e}),t;let n=e;n.generateKind!==void 0&&(["interface","type","both"].includes(n.generateKind)||t.push({path:"typescript.profileOptions.generateKind",message:'generateKind must be "interface", "type", or "both"',value:n.generateKind})),n.subfolder!==void 0&&typeof n.subfolder!="string"&&t.push({path:"typescript.profileOptions.subfolder",message:"subfolder must be a string",value:n.subfolder});let o=["includeConstraints","includeDocumentation","strictMode"];for(let i of o)n[i]!==void 0&&typeof n[i]!="boolean"&&t.push({path:`typescript.profileOptions.${i}`,message:`${i} must be a boolean`,value:n[i]});return t}validateTypeSchemaConfig(e){let t=[];if(typeof e!="object"||e===null)return t.push({path:"typeSchema",message:"typeSchema config must be an object",value:e}),t;let n=e,o=["enablePersistence","validateCached","forceRegenerate","shareCache"];for(let s of o)n[s]!==void 0&&typeof n[s]!="boolean"&&t.push({path:`typeSchema.${s}`,message:`${s} must be a boolean`,value:n[s]});let i=["cacheDir","cacheKeyPrefix"];for(let s of i)n[s]!==void 0&&typeof n[s]!="string"&&t.push({path:`typeSchema.${s}`,message:`${s} must be a string`,value:n[s]});if(n.maxAge!==void 0&&(typeof n.maxAge!="number"||n.maxAge<=0)&&t.push({path:"typeSchema.maxAge",message:"maxAge must be a positive number",value:n.maxAge}),n.profiles!==void 0)if(typeof n.profiles!="object"||n.profiles===null)t.push({path:"typeSchema.profiles",message:"profiles must be an object",value:n.profiles});else {let s=n.profiles;s.autoDetect!==void 0&&typeof s.autoDetect!="boolean"&&t.push({path:"typeSchema.profiles.autoDetect",message:"autoDetect must be a boolean",value:s.autoDetect});}return t}},He=class{validator=new Ae;async autoload(e=process.cwd()){let t=await this.findConfigFile(e);return t?this.loadFromFile(t):{...Ue}}async loadFromFile(e){try{let t;if(e.endsWith(".ts")||e.endsWith("")){let i=await import(resolve(e));t=i.default||i;}else {let o=await readFile(e,"utf-8");t=JSON.parse(o);}let n=this.validator.validate(t);if(!n.valid){let o=n.errors.map(i=>`${i.path}: ${i.message}`).join(`
 `);throw new Error(`Configuration validation failed:
-${o}`)}if(!n.config)throw new Error("Invalid configuration");return this.mergeWithDefaults(n.config)}catch(t){throw t instanceof Error?new Error(`Failed to load config from ${e}: ${t.message}`):t}}async findConfigFile(e){for(let t of be){let n=resolve(e,t);if(existsSync(n))return n}return null}mergeWithDefaults(e){return {...Ue,...e,typescript:{...Ue.typescript,...e.typescript}}}},Tr=new Ae;async function Ce(r){return Tr.autoload(r)}var Lt={command:"generate",describe:"Generate code based on configuration file settings",builder:r=>r.option("verbose",{alias:"v",type:"boolean",default:false,description:"Enable verbose output"}).example("$0 generate","Generate code using settings from config file").example("$0 generate --verbose","Generate with verbose output"),handler:async r=>{if(r._.length>1){let s=r._.slice(1).join(" ");I(`Invalid syntax: 'atomic-codegen generate ${s}'
+${o}`)}if(!n.config)throw new Error("Invalid configuration");return this.mergeWithDefaults(n.config)}catch(t){throw t instanceof Error?new Error(`Failed to load config from ${e}: ${t.message}`):t}}async findConfigFile(e){for(let t of Ce){let n=resolve(e,t);if(existsSync(n))return n}return null}mergeWithDefaults(e){return {...Ue,...e,typescript:{...Ue.typescript,...e.typescript}}}},Tr=new He;async function ve(r){return Tr.autoload(r)}var Lt={command:"generate",describe:"Generate code based on configuration file settings",builder:r=>r.option("verbose",{alias:"v",type:"boolean",default:false,description:"Enable verbose output"}).example("$0 generate","Generate code using settings from config file").example("$0 generate --verbose","Generate with verbose output"),handler:async r=>{if(r._.length>1){let s=r._.slice(1).join(" ");I(`Invalid syntax: 'atomic-codegen generate ${s}'
 
 The CLI has been simplified and no longer uses subcommands.
 
@@ -14,7 +14,7 @@ The CLI has been simplified and no longer uses subcommands.
 \u274C Old: atomic-codegen generate typescript
 
 All generation settings are now configured in your config file.
-Create an atomic-codegen.config.ts file to get started.`),process.exit(1);}let e=process.cwd(),t=await Fr(e);if(!t){let s=be.map(c=>`  - ${c}`).join(`
+Create an atomic-codegen.config.ts file to get started.`),process.exit(1);}let e=process.cwd(),t=await Fr(e);if(!t){let s=Ce.map(c=>`  - ${c}`).join(`
 `);I(`No configuration file found. Please create one of the following files in your project root:
 ${s}
 
@@ -27,12 +27,12 @@ export default defineConfig({
   typescript: {
     generateIndex: true
   }
-});`),process.exit(1);}let n=await Ce(e),o=r.verbose??n.verbose??false,i=N({prefix:"Generate"});try{We("Starting generation from config"),o&&(i.info(`Config file: ${t}`),i.info(`Output directory: ${n.outputDir||"./generated"}`),i.info(`Packages: ${n.packages?.length||0}`),i.info(`Files: ${n.files?.length||0}`),i.info(`TypeScript generation: ${n.typescript?"enabled":"disabled"}`));let s=new Z({outputDir:n.outputDir||"./generated",overwrite:n.overwrite??!0,cache:n.cache??!0,typeSchemaConfig:n.typeSchema,logger:i});if(n.packages&&n.packages.length>0){i.info(`Loading packages from config: ${n.packages.join(", ")}`);for(let a of n.packages){let[l,d]=a.includes("@")?a.split("@"):[a,void 0];s.fromPackage(l,d);}}else throw n.files&&n.files.length>0?(i.info(`Loading files from config: ${n.files.join(", ")}`),new Error("Not Implemented")):new Error("No data source specified in config. Please configure 'packages' or 'files' in your config file.");if(n.typescript)throw new Error("Not Implemented");if(!n.typescript)throw new Error("No generators configured. Please enable 'typescript' in your config file.");o&&s.onProgress((a,l,d,h)=>{let m=Math.round(l/d*100);i.progress(`[${a}] ${m}% - ${h||"Processing..."}`);}),i.step("Executing generation...");let c=await s.generate();if(c.success){if(ve(`Generated ${c.filesGenerated.length} files in ${c.duration.toFixed(2)}ms`),i.dim(`Output directory: ${c.outputDir}`),c.warnings.length>0)for(let a of c.warnings)ze(a);}else {I(`Generation failed with ${c.errors.length} errors`);for(let a of c.errors)i.dim(`  ${a}`);process.exit(1);}}catch(s){I("Generation failed with unexpected error",s instanceof Error?s:new Error(String(s))),process.exit(1);}}};async function Fr(r){for(let e of be){let t=resolve(r,e);if(existsSync(t))return t}return null}var Mt={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"}},handler:async r=>{let e=N({prefix:"TypeSchema"});try{let t=await Ce(process.cwd());e.step("Generating TypeSchema from FHIR packages"),e.info(`Packages: ${r.packages.join(", ")}`),e.info(`Output: ${r.output}`);let n=r.singleFile!==void 0?r.singleFile:t.typeSchema?.singleFile??!1,o=n?"ndjson":r.format;e.debug(`Format: ${o}${n&&r.format==="json"?" (forced from json due to singleFile)":""}`);let i=r.treeshake&&r.treeshake.length>0?r.treeshake:t.typeSchema?.treeshake;i&&i.length>0&&e.info(`Treeshaking enabled for ResourceTypes: ${i.join(", ")}`),n&&e.info("Single file output enabled (NDJSON format)");let s=Date.now(),c=new X({treeshake:i}),a=[];for(let m of r.packages){let[p,g]=m.includes("@")?m.split("@"):[m,void 0];e.progress(`Processing package: ${p}${g?`@${g}`:""}`);let y=await c.generateFromPackage(p,g,e);a.push(...y);}if(a.length===0)throw new Error("No schemas were generated from the specified packages");let l=r.output;if(!l)throw new Error("Output format not specified");await mkdir(dirname(l),{recursive:!0});let d;o==="json"?d=JSON.stringify(a,null,2):d=a.map(m=>JSON.stringify(m)).join(`
-`),await writeFile(l,d,"utf-8");let h=Date.now()-s;if(Ke(`Generated ${a.length} TypeSchema definitions`,h,{schemas:a.length}),e.dim(`Output: ${l}`),r.verbose){e.debug("Generated schemas:");let m=a.map(p=>`${p.identifier?.name||"Unknown"} (${p.identifier?.kind||"unknown"})`);G(m);}}catch(t){e.error("Failed to generate TypeSchema",t instanceof Error?t:new Error(String(t))),process.exit(1);}}};var Bt={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:r=>r.command(Mt).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:r=>{if(!r.subcommand&&r._.length===1){xe("Available typeschema subcommands:"),G(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
+});`),process.exit(1);}let n=await ve(e),o=r.verbose??n.verbose??false,i=N({prefix:"Generate"});try{We("Starting generation from config"),o&&(i.info(`Config file: ${t}`),i.info(`Output directory: ${n.outputDir||"./generated"}`),i.info(`Packages: ${n.packages?.length||0}`),i.info(`Files: ${n.files?.length||0}`),i.info(`TypeScript generation: ${n.typescript?"enabled":"disabled"}`));let s=new Z({outputDir:n.outputDir||"./generated",overwrite:n.overwrite??!0,cache:n.cache??!0,typeSchemaConfig:n.typeSchema,logger:i});if(n.packages&&n.packages.length>0){i.info(`Loading packages from config: ${n.packages.join(", ")}`);for(let a of n.packages){let[l,p]=a.includes("@")?a.split("@"):[a,void 0];s.fromPackage(l,p);}}else throw n.files&&n.files.length>0?(i.info(`Loading files from config: ${n.files.join(", ")}`),new Error("Not Implemented")):new Error("No data source specified in config. Please configure 'packages' or 'files' in your config file.");if(n.typescript)throw new Error("Not Implemented");if(!n.typescript)throw new Error("No generators configured. Please enable 'typescript' in your config file.");o&&s.onProgress((a,l,p,h)=>{let m=Math.round(l/p*100);i.progress(`[${a}] ${m}% - ${h||"Processing..."}`);}),i.step("Executing generation...");let c=await s.generate();if(c.success){if(ke(`Generated ${c.filesGenerated.length} files in ${c.duration.toFixed(2)}ms`),i.dim(`Output directory: ${c.outputDir}`),c.warnings.length>0)for(let a of c.warnings)ze(a);}else {I(`Generation failed with ${c.errors.length} errors`);for(let a of c.errors)i.dim(`  ${a}`);process.exit(1);}}catch(s){I("Generation failed with unexpected error",s instanceof Error?s:new Error(String(s))),process.exit(1);}}};async function Fr(r){for(let e of Ce){let t=resolve(r,e);if(existsSync(t))return t}return null}var Mt={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"}},handler:async r=>{let e=N({prefix:"TypeSchema"});try{let t=await ve(process.cwd());e.step("Generating TypeSchema from FHIR packages"),e.info(`Packages: ${r.packages.join(", ")}`),e.info(`Output: ${r.output}`);let n=r.singleFile!==void 0?r.singleFile:t.typeSchema?.singleFile??!1,o=n?"ndjson":r.format;e.debug(`Format: ${o}${n&&r.format==="json"?" (forced from json due to singleFile)":""}`);let i=r.treeshake&&r.treeshake.length>0?r.treeshake:t.typeSchema?.treeshake;i&&i.length>0&&e.info(`Treeshaking enabled for ResourceTypes: ${i.join(", ")}`),n&&e.info("Single file output enabled (NDJSON format)");let s=Date.now(),c=new X({treeshake:i}),a=[];for(let m of r.packages){let[d,g]=m.includes("@")?m.split("@"):[m,void 0];e.progress(`Processing package: ${d}${g?`@${g}`:""}`);let y=await c.generateFromPackage(d,g,e);a.push(...y);}if(a.length===0)throw new Error("No schemas were generated from the specified packages");let l=r.output;if(!l)throw new Error("Output format not specified");await mkdir(dirname(l),{recursive:!0});let p;o==="json"?p=JSON.stringify(a,null,2):p=a.map(m=>JSON.stringify(m)).join(`
+`),await writeFile(l,p,"utf-8");let h=Date.now()-s;if(Ke(`Generated ${a.length} TypeSchema definitions`,h,{schemas:a.length}),e.dim(`Output: ${l}`),r.verbose){e.debug("Generated schemas:");let m=a.map(d=>`${d.identifier?.name||"Unknown"} (${d.identifier?.kind||"unknown"})`);G(m);}}catch(t){e.error("Failed to generate TypeSchema",t instanceof Error?t:new Error(String(t))),process.exit(1);}}};var Bt={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:r=>r.command(Mt).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:r=>{if(!r.subcommand&&r._.length===1){xe("Available typeschema subcommands:"),G(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
 Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
 Examples:`),G(["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}r.subcommand&&!["generate","validate","merge"].includes(r.subcommand)&&(I(`Unknown typeschema subcommand: ${r.subcommand}
 `),xe("Available typeschema subcommands:"),G(["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 Or(r){return r?{debug:0,info:1,warn:2,error:3,silent:4}[r.toLowerCase()]:void 0}async function Dr(r){let e=Or(r.logLevel);e===void 0&&(r.debug||r.verbose?e=0:e=1),qe({timestamp:r.debug,level:e});}function Lr(){return Pr(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(Dr).command(Bt).command(Lt).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}).option("config",{alias:"c",type:"string",description:"Path to configuration file (.atomic-codegen.json by default)",global:true}).demandCommand(0).middleware(r=>{r._.length===0&&(Je("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log("  generate     Generate code based on configuration file"),console.log(`
+Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};function Dr(r){return r?{debug:0,info:1,warn:2,error:3,silent:4}[r.toLowerCase()]:void 0}async function Or(r){let e=Dr(r.logLevel);e===void 0&&(r.debug||r.verbose?e=0:e=1),qe({timestamp:r.debug,level:e});}function Lr(){return Er(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(Or).command(Bt).command(Lt).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}).option("config",{alias:"c",type:"string",description:"Path to configuration file (.atomic-codegen.json by default)",global:true}).demandCommand(0).middleware(r=>{r._.length===0&&(Je("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log("  generate     Generate code based on configuration file"),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("  atomic-codegen generate  # Uses atomic-codegen.config.ts"),console.log(`
 Use 'atomic-codegen --help' to see all options.`),process.exit(0));}).help().version("0.1.0").example("$0 generate","Generate code using atomic-codegen.config.ts").example("$0 generate --verbose","Generate with detailed progress output").example("$0 --config custom-config.ts generate","Use custom configuration file").example("$0 typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","Generate TypeSchemas from FHIR package").fail((r,e,t)=>{e?I(e.message,e):I(r),I(`

package/dist/index.d.ts

@@ -133,6 +133,10 @@ type Name = string & {
 type CanonicalUrl = string & {
     readonly __brand: unique symbol;
 };
+interface PackageMeta {
+    name: string;
+    version: string;
+}
 type IdentifierBase = {
     name: Name;
     url: CanonicalUrl;
@@ -582,6 +586,11 @@ interface GenerationResult {
     warnings: string[];
     duration: number;
 }
+interface LocalStructureDefinitionConfig {
+    package: PackageMeta;
+    path: string;
+    dependencies?: PackageMeta[];
+}
 /**
  * High-Level API Builder class
  *
@@ -594,11 +603,15 @@ declare class APIBuilder {
     private generators;
     private logger;
     private packages;
+    private localStructurePackages;
+    private localTgzArchives;
     progressCallback: any;
     private typeSchemaConfig?;
     constructor(options?: APIBuilderOptions);
     fromPackage(packageName: string, version?: string): APIBuilder;
     fromPackageRef(packageRef: string): APIBuilder;
+    localStructureDefinitions(config: LocalStructureDefinitionConfig): APIBuilder;
+    localTgzPackage(archivePath: string): APIBuilder;
     fromSchemas(schemas: TypeSchema[]): APIBuilder;
     typescript(userOpts: Partial<TypeScriptOptions>): this;
     csharp(namespace: string, staticSourceDir?: string | undefined): APIBuilder;
@@ -638,4 +651,4 @@ type CSharpGeneratorOptions = WriterOptions & {
     targetNamespace: string;
 };
 
-export { APIBuilder, type APIBuilderOptions, CONFIG_FILE_NAMES, type CSharpGeneratorOptions, type Config, ConfigLoader, type ConfigValidationError, type ConfigValidationResult, ConfigValidator, DEFAULT_CONFIG, LogLevel, type TypeSchemaConfig, type TypeScriptGeneratorConfig, type TypeScriptOptions, configLoader, defineConfig, isConfig, loadConfig };
+export { APIBuilder, type APIBuilderOptions, CONFIG_FILE_NAMES, type CSharpGeneratorOptions, type Config, ConfigLoader, type ConfigValidationError, type ConfigValidationResult, ConfigValidator, DEFAULT_CONFIG, type LocalStructureDefinitionConfig, LogLevel, type TypeSchemaConfig, type TypeScriptGeneratorConfig, type TypeScriptOptions, configLoader, defineConfig, isConfig, loadConfig };

package/dist/index.js

@@ -1560,7 +1560,7 @@ var mkTypeSchemaIndex = (schemas, { resolutionTree, logger }) => {
     append(schema);
   }
   const relations = resourceRelatives(schemas);
-  const resolve3 = (id) => index[id.url]?.[id.package];
+  const resolve4 = (id) => index[id.url]?.[id.package];
   const resolveByUrl = (pkgName, url) => {
     if (resolutionTree) {
       const resolution = resolutionTree[pkgName]?.[url]?.[0];
@@ -1580,7 +1580,7 @@ var mkTypeSchemaIndex = (schemas, { resolutionTree, logger }) => {
       res.push(cur);
       const base = cur.base;
       if (base === void 0) break;
-      const resolved = resolve3(base);
+      const resolved = resolve4(base);
       if (!resolved) {
         logger?.warn(
           `Failed to resolve base type: ${res.map((e) => `${e.identifier.url} (${e.identifier.kind})`).join(", ")}`
@@ -1606,7 +1606,7 @@ var mkTypeSchemaIndex = (schemas, { resolutionTree, logger }) => {
     return nonConstraintSchema;
   };
   const findLastSpecializationByIdentifier = (id) => {
-    const schema = resolve3(id);
+    const schema = resolve4(id);
     if (!schema) return id;
     return findLastSpecialization(schema).identifier;
   };
@@ -1678,7 +1678,7 @@ var mkTypeSchemaIndex = (schemas, { resolutionTree, logger }) => {
     collectResources: () => schemas.filter(isResourceTypeSchema),
     collectLogicalModels: () => schemas.filter(isLogicalTypeSchema),
     collectProfiles: () => schemas.filter(isProfileTypeSchema),
-    resolve: resolve3,
+    resolve: resolve4,
     resolveByUrl,
     resourceChildren,
     tryHierarchy,
@@ -2251,6 +2251,8 @@ var APIBuilder = class {
   generators = /* @__PURE__ */ new Map();
   logger;
   packages = [];
+  localStructurePackages = [];
+  localTgzArchives = [];
   progressCallback;
   typeSchemaConfig;
   constructor(options = {}) {
@@ -2281,6 +2283,14 @@ var APIBuilder = class {
     this.packages.push(packageRef);
     return this;
   }
+  localStructureDefinitions(config) {
+    this.localStructurePackages.push(config);
+    return this;
+  }
+  localTgzPackage(archivePath) {
+    this.localTgzArchives.push(Path4.resolve(archivePath));
+    return this;
+  }
   fromSchemas(schemas) {
     this.logger.debug(`Adding ${schemas.length} TypeSchemas to generation`);
     this.schemas = [...this.schemas, ...schemas];
@@ -2380,10 +2390,27 @@ var APIBuilder = class {
     try {
       if (this.options.cleanOutput) cleanup(this.options, this.logger);
       this.logger.info("Initialize Canonical Manager");
-      const manager = CanonicalManager({
+      const manager = this.options.manager || CanonicalManager({
         packages: this.packages,
         workingDir: ".codegen-cache/canonical-manager-cache"
       });
+      if (this.localStructurePackages.length > 0) {
+        for (const config of this.localStructurePackages) {
+          this.logger.info(
+            `Registering local StructureDefinitions for ${config.package.name}@${config.package.version}`
+          );
+          await manager.addLocalPackage({
+            name: config.package.name,
+            version: config.package.version,
+            path: config.path,
+            dependencies: config.dependencies?.map((dep) => packageMetaToNpm(dep))
+          });
+        }
+      }
+      for (const archivePath of this.localTgzArchives) {
+        this.logger.info(`Registering local tgz package: ${archivePath}`);
+        await manager.addTgzPackage({ archivePath });
+      }
       const ref2meta = await manager.init();
       const packageMetas = Object.values(ref2meta);
       const register = await registerFromManager(manager, {
@@ -2422,6 +2449,9 @@ var APIBuilder = class {
     this.schemas = [];
     this.generators.clear();
     this.progressCallback = void 0;
+    this.packages = [];
+    this.localStructurePackages = [];
+    this.localTgzArchives = [];
     return this;
   }
   /**