@atomic-ehr/codegen 0.0.6 → 0.0.7-canary.20260224101452.ccac84d

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Files changed (5) hide show
  1. package/dist/cli/index.js +7 -7
  2. package/dist/index.d.ts +13 -7
  3. package/dist/index.js +910 -689
  4. package/dist/index.js.map +1 -1
  5. package/package.json +10 -7
package/dist/cli/index.js CHANGED
@@ -1,11 +1,11 @@
1
1
  #!/usr/bin/env node
2
- import x from'picocolors';import Ke from'yargs';import {hideBin}from'yargs/helpers';import {mkdir,writeFile}from'fs/promises';import {dirname}from'path';import {CanonicalManager}from'@atomic-ehr/fhir-canonical-manager';import*as re from'@atomic-ehr/fhirschema';import {isStructureDefinition}from'@atomic-ehr/fhirschema';import Ue from'assert';var L=class t{options;dryWarnSet=new Set;constructor(e={}){this.options={timestamp:false,level:1,...e};}shouldLog(e){let n=this.options.level??1;return e>=n}static consoleLevelsMap={1:console.log,2:console.warn,3:console.error,0:console.log,4:()=>{}};formatMessage(e,n,i){let r=this.options.timestamp?`${x.gray(new Date().toLocaleTimeString())} `:"",o=this.options.prefix?`${x.cyan(`[${this.options.prefix}]`)} `:"";return `${r}${i(e)} ${o}${n}`}isSuppressed(e){return this.options.suppressLoggingLevel==="all"||this.options.suppressLoggingLevel?.includes(e)||false}tryWriteToConsole(e,n){if(this.isSuppressed(e)||!this.shouldLog(e))return;(t.consoleLevelsMap[e]||console.log)(n);}success(e){this.tryWriteToConsole(1,this.formatMessage("",e,x.green));}error(e,n){if(this.isSuppressed(3)||!this.shouldLog(3))return;console.error(this.formatMessage("X",e,x.red));let i=this.options.level===0;n&&i&&(console.error(x.red(` ${n.message}`)),n.stack&&console.error(x.gray(n.stack)));}warn(e){this.tryWriteToConsole(2,this.formatMessage("!",e,x.yellow));}dry_warn(e){this.dryWarnSet.has(e)||(this.warn(e),this.dryWarnSet.add(e));}info(e){this.tryWriteToConsole(1,this.formatMessage("i",e,x.blue));}debug(e){this.shouldLog(0)&&this.tryWriteToConsole(0,this.formatMessage("\u{1F41B}",e,x.magenta));}step(e){this.tryWriteToConsole(1,this.formatMessage("\u{1F680}",e,x.cyan));}progress(e){this.tryWriteToConsole(1,this.formatMessage("\u23F3",e,x.blue));}plain(e,n=i=>i){let i=this.options.timestamp?`${x.gray(new Date().toLocaleTimeString())} `:"",r=this.options.prefix?`${x.cyan(`[${this.options.prefix}]`)} `:"";this.tryWriteToConsole(1,`${i}${r}${n(e)}`);}dim(e){this.plain(e,x.gray);}child(e){return new t({...this.options,prefix:this.options.prefix?`${this.options.prefix}:${e}`:e})}configure(e){this.options={...this.options,...e};}getLevel(){return this.options.level??1}setLevel(e){this.options.level=e;}},F=new L;function Re(t){F.success(t);}function b(t,e){F.error(t,e);}function O(t){F.info(t);}function Ce(t){F.dim(t);}function X(t){F.configure(t);}function w(t={}){return new L(t)}function Z(t){console.log(),console.log(x.cyan(x.bold(`\u2501\u2501\u2501 ${t} \u2501\u2501\u2501`)));}function Y(t,e,n){let i=t;e&&(i+=` ${x.gray(`(${e}ms)`)}`),Re(i),n&&Object.entries(n).forEach(([r,o])=>{Ce(` ${r}: ${o}`);});}function I(t,e="\u2022"){t.forEach(n=>{console.log(x.gray(` ${e} ${n}`));});}var B=t=>t!==null&&typeof t=="object"&&t.resourceType==="CodeSystem";var P=t=>t!==null&&typeof t=="object"&&t.resourceType==="ValueSet";var S=t=>`${t.name}#${t.version}`;var j=(t,e)=>(e||(e={name:"undefined",version:"undefined"}),{...t,package_meta:t.package_meta||e,name:t.name,url:t.url,base:t.base});var ee=t=>t?.kind==="nested",te=t=>t?.kind==="profile";var ne=(t,e)=>{if(!t.url)throw new Error("ValueSet must have a URL");if(!t.name)throw new Error("ValueSet must have a name");return {...t,package_meta:t.package_meta||e,name:t.name,url:t.url}};var ke=async(t,e)=>{let i=(await t.packageJson(e.name)).dependencies;return i!==void 0?Object.entries(i).map(([r,o])=>({name:r,version:o})):[]},oe=t=>({pkg:t,canonicalResolution:{},fhirSchemas:{},valueSets:{}}),ae=async(t,e,n,i,r)=>{let o=S(e);if(r?.info(`${" ".repeat(n*2)}+ ${o}`),i[o])return i[o];let a=oe(e);for(let s of await t.search({package:e})){let c=s.url;if(!c||!(isStructureDefinition(s)||P(s)||B(s)))continue;let u=c;a.canonicalResolution[u]&&r?.dry_warn(`Duplicate canonical URL: ${u} at ${o}.`),a.canonicalResolution[u]=[{deep:n,pkg:e,pkgId:o,resource:s}];}let l=await ke(t,e);for(let s of l){let{canonicalResolution:c}=await ae(t,s,n+1,i,r);for(let[u,m]of Object.entries(c)){let f=u;a.canonicalResolution[f]=[...a.canonicalResolution[f]||[],...m];}}for(let s of Object.values(a.canonicalResolution))s.sort((c,u)=>c.deep-u.deep);return i[o]=a,a},ie=(t,e)=>{for(let{pkg:n,canonicalResolution:i}of Object.values(t)){let r=S(n);if(!t[r])throw new Error(`Package ${r} not found`);for(let[a,l]of Object.entries(i)){let s=l[0];if(!s)throw new Error("Resource not found");let c=s.resource,u=s.pkg;if(isStructureDefinition(c)){let m=re.translate(c),f=j(m,u);t[r].fhirSchemas[f.url]=f;}if(P(c)){let m=ne(c,u);t[r].valueSets[m.url]=m;}}}},be=(t,e,n)=>{let i=Object.values(t).flatMap(r=>r.canonicalResolution[e]);if(!i)throw new Error(`No canonical resolution found for ${e} in any package`);return i[0]?.resource},_=async(t,{logger:e,fallbackPackageForNameResolution:n,focusedPackages:i})=>{let r=i??await t.packages(),o={};for(let p of r)await ae(t,p,0,o,e);ie(o);let a=(p,d)=>o[S(p)]?.fhirSchemas[d]||n&&o[S(n)]?.fhirSchemas[d],l=(p,d)=>o[S(p)]?.valueSets[d]||n&&o[S(n)]?.valueSets[d],s=p=>(p.includes("|")&&(p=p.split("|")[0]),p.match(/^[a-zA-Z0-9]+$/)?`http://hl7.org/fhir/StructureDefinition/${p}`:p),c=(p,d)=>{let g=a(p,d);if(g===void 0)throw new Error(`Failed to resolve FHIR Schema: '${d}'`);let y=[g];for(;g?.base;){let R=g.package_meta,C=s(g.base);if(g=a(R,C),g===void 0)throw new Error(`Failed to resolve FHIR Schema base for '${d}'. Problem: '${C}' from '${S(R)}'`);y.push(g);}return y},u=(p,d)=>c(p,d).filter(g=>g.derivation==="specialization"),m=(p,d)=>{let g=c(p.package_meta,p.url),y=Ie(g,d);return ve(y)},f=p=>{let d=new Set;for(let[g,y]of Object.entries(p)){d.add(g);for(let R of y?.choices||[])p[R]||d.add(R);}return Array.from(d)},h;return {testAppendFs(p){let d=j(p),g=S(d.package_meta);o[g]||(o[g]=oe(d.package_meta)),o[g].fhirSchemas[d.url]=d,h=void 0;},resolveFs:a,resolveFsGenealogy:c,resolveFsSpecializations:u,ensureSpecializationCanonicalUrl:s,resolveSd:(p,d)=>{let g=o[S(p)]?.canonicalResolution[d]?.[0]?.resource;if(isStructureDefinition(g))return g},allSd:()=>Object.values(o).flatMap(p=>Object.values(p.canonicalResolution).flatMap(d=>d.map(g=>{let y=g.resource;return y.package_name?y:{...y,package_name:p.pkg.name,package_version:p.pkg.version}}))).filter(p=>isStructureDefinition(p)).sort((p,d)=>p.url.localeCompare(d.url)),patchSd:p=>{Object.values(o).flatMap(d=>Object.values(d.canonicalResolution).forEach(g=>{g.forEach(y=>{if(isStructureDefinition(y.resource)){let R=y.resource,C=p(d.pkg,R);if(R.url!==C.url)throw new Error(`Patch update StructureDefinition URL: ${R.url} !== ${C.url}`);y.resource=C;}});})),ie(o),h=void 0;},allFs:()=>Object.values(o).flatMap(p=>Object.values(p.fhirSchemas)),allVs:()=>Object.values(o).flatMap(p=>Object.values(p.valueSets)),resolveVs:l,resolveAny:p=>be(o,p),resolveElementSnapshot:m,getAllElementKeys:f,resolver:o,resolutionTree:()=>{if(h)return h;let p={};for(let[d,g]of Object.entries(o)){let y=g.pkg.name;p[y]={};for(let[R,C]of Object.entries(g.canonicalResolution)){let J=R;p[y][J]=[];for(let Q of C)p[y][J].push({deep:Q.deep,pkg:Q.pkg});}}return h=p,p}}};var Ie=(t,e)=>{let[n,...i]=e;return n===void 0?[]:t.map(r=>{if(!r.elements)return;let o=r.elements?.[n];for(let a of i)o=o?.elements?.[a];return o}).filter(r=>r!==void 0)};function ve(t){let e=t.reverse(),n=Object.assign({},...e);return n.elements=void 0,n}var T="Use CodeableReference which is not provided by FHIR R4.",Fe="Use Availability which is not provided by FHIR R4.",se={"hl7.fhir.uv.extensions.r4":{"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":Fe,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":T,"http://hl7.org/fhir/StructureDefinition/specimen-additive":T,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":T,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":T,"http://hl7.org/fhir/StructureDefinition/workflow-reason":T},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. FHIR Schema generator output broken value in it, so we just skip it for now.","http://hl7.org/fhir/StructureDefinition/publishablecodesystem":"Uses R5-only base types not available in R4 generation."}};function A(t,e){let n=`${t.name}#${t.version}`,i=se[n]?.[e];if(i)return {shouldSkip:true,reason:i};let r=se[t.name]?.[e];return r?{shouldSkip:true,reason:r}:{shouldSkip:false}}function G(t){let e=t.split("|")[0];return e||t}function Ee(t){return t.split("|")[1]}function Te(t){return t.derivation==="constraint"?"profile":t.kind==="primitive-type"?"primitive-type":t.kind==="complex-type"?"complex-type":t.kind==="resource"?"resource":t.kind==="logical"?"logical":"resource"}function k(t){return {kind:Te(t),package:t.package_meta.name,version:t.package_meta.version,name:t.name,url:t.url}}var De=t=>{let e=t.split("/"),n=e[e.length-1];return n&&n.length>0?n.split(/[-_]/).map(i=>i.charAt(0).toUpperCase()+i.slice(1).toLowerCase()).join(""):t};function U(t,e,n){let i=G(n),r=De(i),o={package_meta:{name:"missing_valuesets",version:Ee(i)||"0.0.0"},id:n},a=t.resolveVs(e,i)||o,l=a?.id&&!/^[a-zA-Z0-9_-]{20,}$/.test(a.id)?a.id:r;return {kind:"value-set",package:a.package_meta.name,version:a.package_meta.version,name:l,url:i}}function N(t,e,n){let i=e.join("."),[r,o,a]=n?[{name:"shared",version:"1.0.0"},n,`urn:fhir:binding:${n}`]:[t.package_meta,`${t.name}.${i}_binding`,`${t.url}#${i}_binding`];return {kind:"binding",package:r.name,version:r.version,name:o,url:a}}function $(t,e,n,i){let r={};if(e.derivation==="constraint"){let m=t.resolveFsSpecializations(e.package_meta,e.url).map(f=>q(t,f,i)).filter(f=>f!==void 0).flat();for(let f of m.reverse())r[f.identifier.name]=f.identifier.url;}let o=n.join("."),a=r[o]??`${e.url}#${o}`,l=a.split("#")[0],c=t.resolveFs(e.package_meta,l)?.package_meta??e.package_meta;return {kind:"nested",package:c.name,version:c.version,name:o,url:a}}function ce(t,e,n){let i=[];for(let[r,o]of Object.entries(n)){let a=[...e,r];D(o)&&i.push([a,o]),o.elements&&i.push(...ce(t,a,o.elements));}return i}function Le(t,e,n,i,r){let o={};for(let[a,l]of Object.entries(i)){let s=[...n,a],c=t.resolveElementSnapshot(e,s);D(c)?o[a]=H(t,e,s,c,r):o[a]=V(t,e,s,c,r);}return o}function q(t,e,n){if(!e.elements)return;let i=ce(e,[],e.elements).filter(([o,a])=>a.elements&&Object.keys(a.elements).length>0),r=[];for(let[o,a]of i){let l=$(t,e,o,n),s;a.type==="BackboneElement"||!a.type?s="BackboneElement":s=a.type;let c=t.ensureSpecializationCanonicalUrl(s),u=t.resolveFs(e.package_meta,c);if(!u)throw new Error(`Could not resolve base type ${s}`);let m={kind:"complex-type",package:u.package_meta.name,version:u.package_meta.version,name:s,url:c},f=Le(t,e,o,a.elements??{},n),h={identifier:l,base:m,fields:f};r.push(h);}return r.sort((o,a)=>o.identifier.url.localeCompare(a.identifier.url)),r.length===0?void 0:r}function le(t){let e=[];for(let n of t){n.base&&e.push(n.base);for(let i of Object.values(n.fields||{}))"type"in i&&i.type&&e.push(i.type),"binding"in i&&i.binding&&e.push(i.binding);}return e}function pe(t,e,n){let i=n[n.length-1];if(!i)throw new Error(`Internal error: fieldName is missing for path ${n.join("/")}`);let r=n.slice(0,-1),o=t.resolveFsGenealogy(e.package_meta,e.url).flatMap(a=>{if(r.length===0)return a.required||[];if(!a.elements)return [];let l=a;for(let s of r)l=l?.elements?.[s];return l?.required||[]});return new Set(o).has(i)}function de(t,e,n){let i=n[n.length-1];if(!i)throw new Error(`Internal error: fieldName is missing for path ${n.join("/")}`);let r=n.slice(0,-1),o=t.resolveFsGenealogy(e.package_meta,e.url).flatMap(a=>{if(r.length===0)return a.excluded||[];if(!a.elements)return [];let l=a;for(let s of r)l=l?.elements?.[s];return l?.excluded||[]});return new Set(o).has(i)}var we=(t,e,n)=>{if(n.refers)return n.refers.map(i=>{let r=t.ensureSpecializationCanonicalUrl(i),o=t.resolveFs(e.package_meta,r);if(!o)throw new Error(`Failed to resolve fs for ${r}`);return 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{type:$(t,e,n,r),array:i.array||false,required:pe(t,e,n),excluded:de(t,e,n),slicing:ue(i)}}function W(t,e,n,i){let r=G(n)||n,o=t.resolveVs(e,r);if(o)return Ne(t,o)}function Ne(t,e,n){if(e.expansion?.contains)return e.expansion.contains.filter(r=>r.code!==void 0).map(r=>(Ue(r.code),{code:r.code,display:r.display,system:r.system}));let i=[];if(e.compose?.include){for(let r of e.compose.include)if(r.concept)for(let o of r.concept)i.push({system:r.system,code:o.code,display:o.display});else if(r.system&&!r.filter)try{let o=t.resolveAny(r.system);if(o?.concept){let a=(l,s)=>{for(let c of l)i.push({system:s,code:c.code,display:c.display}),c.concept&&a(c.concept,s);};a(o.concept,r.system);}}catch{}}return i.length>0?i:void 0}var me=100;function z(t,e,n,i){if(!n.binding)return;let r=n.binding.strength,o=n.binding.valueSet;if(!o||!(r==="required"||r==="extensible"&&(n.type==="code"||n.type==="Coding")||r==="preferred"&&(n.type==="code"||n.type==="Coding")))return;let l=W(t,e.package_meta,o);if(!l||l.length===0)return;let s=l.map(c=>c.code).filter(c=>c&&typeof c=="string"&&c.trim().length>0);if(s.length>me){i?.dry_warn(`Value set ${o} has ${s.length} which is more than ${me} codes, which may cause issues with code generation.`);return}return s.length>0?s:void 0}function $e(t,e,n,i,r){if(!i.binding?.valueSet)return;let o=N(e,n,i.binding.bindingName),a=v(t,e,n,i,r),l=U(t,e.package_meta,i.binding.valueSet),s=[];a&&s.push(a),s.push(l);let c=z(t,e,i,r);return {identifier:o,type:a,valueset:l,strength:i.binding.strength,enum:c,dependencies:s}}function fe(t,e,n){let i=new Set;if(!e.elements)return [];let r=[];function o(s,c){for(let[u,m]of Object.entries(s)){let f=[...c,u],h=f.join("."),p=t.resolveElementSnapshot(e,f);if(!i.has(h)){if(i.add(h),p.binding){let d=$e(t,e,f,p,n);d&&r.push(d);}m.elements&&o(m.elements,f);}}}o(e.elements,[]),r.sort((s,c)=>s.identifier.name.localeCompare(c.identifier.name));let a=[],l=new Set;for(let s of 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{identifier:i,description:e.description,concept:r,compose:r?void 0:e.compose}}function Oe(t,e,n,i){let r=[];e&&r.push(e),n&&r.push(...He(n)),i&&r.push(...le(i));let o={};for(let s of r)s.url!==t.url&&(o[s.url]=s);let a=new Set(i?.map(s=>s.identifier.url)),l=Object.values(o).filter(s=>te(t)||!ee(s)?true:!a.has(s.url)).sort((s,c)=>s.url.localeCompare(c.url));return l.length>0?l:void 0}function Be(t,e,n){let i=k(e),r;if(e.base&&e.type!=="Element"){let h=t.resolveFs(e.package_meta,t.ensureSpecializationCanonicalUrl(e.base));if(!h)throw new Error(`Base resource not found '${e.base}' for <${e.url}> from ${S(e.package_meta)}`);r=k(h);}let o=Ve(t,e,[],e.elements,n),a=q(t,e,n),l=e.derivation==="constraint"?Ae(t,e,n):void 0,s=Oe(i,r,o,a),c=l?.flatMap(h=>h.valueTypes??[])??[],u=(()=>{if(!s&&c.length===0)return s;let h={};for(let p of s??[])h[p.url]=p;for(let p of c)h[p.url]=p;return Object.values(h)})(),m={identifier:i,base:r,fields:o,nested:a,description:e.description,dependencies:u,...l&&l.length>0?{extensions:l}:{}},f=fe(t,e,n);return [m,...f]}function je(t,e,n,i){let r=t.resolveFs(e.package_meta,n);if(!r?.elements)return;let o=[];for(let[l,s]of Object.entries(r.elements)){if(s.choiceOf!=="value"&&!l.startsWith("value"))continue;let c=v(t,r,[l],s,i);c&&o.push(c);}if(o.length===0)return;let a=new Map(o.map(l=>[l.url,l]));return Array.from(a.values())}function _e(t,e,n,i){let r=t.resolveFs(e.package_meta,n);if(!r?.elements)return;let o=[];for(let[s,c]of Object.entries(r.elements)){if(!s.startsWith("extension:"))continue;let u=s.split(":")[1];if(!u)continue;let m=c.url??u,f;for(let[h,p]of Object.entries(c.elements??{}))if(!(p.choiceOf!=="value"&&!h.startsWith("value"))&&(f=v(t,r,[s,h],p,i),f))break;o.push({name:u,url:m,valueType:f,min:c.min,max:c.max!==void 0?String(c.max):void 0});}let l=r.elements.extension?.slicing?.slices;if(l&&typeof l=="object")for(let[s,c]of Object.entries(l)){let u=c,m=u.schema;if(!m)continue;let f=u.match?.url??s,h,p=m.elements??{};for(let[d,g]of Object.entries(p)){let y=g;if(!(y.choiceOf!=="value"&&!d.startsWith("value"))&&y.type){h={kind:"complex-type",package:r.package_meta.name,version:r.package_meta.version,name:y.type,url:`http://hl7.org/fhir/StructureDefinition/${y.type}`};break}}o.push({name:s,url:f,valueType:h,min:m._required?1:m.min??0,max:m.max!==void 0?String(m.max):m.array?"*":"1"});}return o.length>0?o:void 0}function Ae(t,e,n){let i=[],r=(a,l,s)=>{let c=s.url,u=c?je(t,e,c,n):void 0,m=c?_e(t,e,c,n):void 0,f=m!==void 0&&m.length>0;i.push({name:l,path:[...a,"extension"].join("."),url:c,min:s.min,max:s.max!==void 0?String(s.max):void 0,mustSupport:s.mustSupport,valueTypes:u,subExtensions:m,isComplex:f});},o=(a,l)=>{if(l.extensions)for(let[s,c]of Object.entries(l.extensions))r(a,s,c);if(l.elements)for(let[s,c]of Object.entries(l.elements))o([...a,s],c);};if(e.extensions)for(let[a,l]of Object.entries(e.extensions))r([],a,l);if(e.elements)for(let[a,l]of Object.entries(e.elements))o([a],l);return i}async function he(t,e,n){let i=Be(t,e,n);if(Me(e,k(e))){let r=i[0];if(!r)throw new Error("Expected schema to be defined");r.metadata={isExtension:true};}return i}var M=class{manager;options;logger;constructor(e){this.options={...e},this.manager=e.manager,this.logger=e.logger||w({prefix:"TypeSchema"});}async registerFromPackageMetas(e){let n=e.map(S);return this.logger?.step(`Loading FHIR packages: ${n.join(", ")}`),await this.manager.init(),_(this.manager,{focusedPackages:e})}generateFhirSchemas(e){this.logger?.progress(`Converting ${e.length} StructureDefinitions to FHIRSchemas`);let n=[],i=0,r=0;for(let o of e)try{let a=re.translate(o);n.push(a),i++,this.logger?.debug(`Converted StructureDefinition: ${o.name||o.id} (${o.resourceType})`);}catch(a){r++,this.logger?.warn(`Failed to convert StructureDefinition ${o.name||o.id}: ${a instanceof Error?a.message:String(a)}`);}return this.logger?.success(`FHIR Schema conversion completed: ${i}/${e.length} successful, ${r} failed`),n}async generateValueSetSchemas(e,n){e.length>0&&this.logger?.debug(`${e.length} ValueSets available for enum extraction`);let i=await _(this.manager,{logger:this.logger}),r=[];if(e.length>0){this.logger?.progress(`Converting ${e.length} ValueSets to TypeSchema`);let o=0,a=0;for(let l of e)try{let s=await ge(i,l,n);s&&(r.push(s),o++,this.logger?.debug(`Converted ValueSet: ${l.name||l.id}`));}catch(s){a++,this.logger?.warn(`Failed to convert ValueSet ${l.name||l.id}: ${s instanceof Error?s.message:String(s)}`);}this.logger?.success(`ValueSet conversion completed: ${o}/${e.length} successful, ${a} failed`);}return r}async generateFromPackage(e,n,i){let r={name:e,version:n||"latest"},o=await this.registerFromPackageMetas([r]),a=await this.generateValueSetSchemas(o.allVs(),i);return [...(await Promise.all(o.allFs().map(async c=>await he(o,c,i)))).flat(),...a]}};var Se={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=w({prefix:"TypeSchema"});try{e.step("Generating TypeSchema from FHIR packages"),e.info(`Packages: ${t.packages.join(", ")}`),e.info(`Output: ${t.output}`);let n=t.singleFile?"ndjson":t.format;e.debug(`Format: ${n}${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 i=Date.now(),r=new M({treeshake:t.treeshake,registry:t.registry,manager:CanonicalManager({packages:[],workingDir:".codegen-cache/canonical-manager-cache",registry:t.registry})}),o=[];for(let c of t.packages){let[u,m]=c.includes("@")?c.split("@"):[c,void 0];e.progress(`Processing package: ${u}${m?`@${m}`:""}`);let f=await r.generateFromPackage(u,m,e);o.push(...f);}if(o.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 l;n==="json"?l=JSON.stringify(o,null,2):l=o.map(c=>JSON.stringify(c)).join(`
3
- `),await writeFile(a,l,"utf-8");let s=Date.now()-i;if(Y(`Generated ${o.length} TypeSchema definitions`,s,{schemas:o.length}),e.dim(`Output: ${a}`),t.verbose){e.debug("Generated schemas:");let c=o.map(u=>`${u.identifier?.name||"Unknown"} (${u.identifier?.kind||"unknown"})`);I(c);}}catch(n){e.error("Failed to generate TypeSchema",n instanceof Error?n:new Error(String(n))),process.exit(1);}}};var xe={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:t=>t.command(Se).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:t=>{if(!t.subcommand&&t._.length===1){O("Available typeschema subcommands:"),I(["generate Generate TypeSchema files from FHIR packages"]),console.log(`
2
+ import S from'picocolors';import Ze from'yargs';import {hideBin}from'yargs/helpers';import {mkdir,writeFile}from'fs/promises';import {dirname}from'path';import {createHash}from'crypto';import Te from'assert';import {CanonicalManager}from'@atomic-ehr/fhir-canonical-manager';import*as ge from'@atomic-ehr/fhirschema';import {isStructureDefinition}from'@atomic-ehr/fhirschema';var D=class e{options;dryWarnSet=new Set;constructor(t={}){this.options={timestamp:false,level:1,...t};}shouldLog(t){let o=this.options.level??1;return t>=o}static consoleLevelsMap={1:console.log,2:console.warn,3:console.error,0:console.log,4:()=>{}};formatMessage(t,o,i){let n=this.options.timestamp?`${S.gray(new Date().toLocaleTimeString())} `:"",r=this.options.prefix?`${S.cyan(`[${this.options.prefix}]`)} `:"";return `${n}${i(t)} ${r}${o}`}isSuppressed(t){return this.options.suppressLoggingLevel==="all"||this.options.suppressLoggingLevel?.includes(t)||false}tryWriteToConsole(t,o){if(this.isSuppressed(t)||!this.shouldLog(t))return;(e.consoleLevelsMap[t]||console.log)(o);}success(t){this.tryWriteToConsole(1,this.formatMessage("",t,S.green));}error(t,o){if(this.isSuppressed(3)||!this.shouldLog(3))return;console.error(this.formatMessage("X",t,S.red));let i=this.options.level===0;o&&i&&(console.error(S.red(` ${o.message}`)),o.stack&&console.error(S.gray(o.stack)));}warn(t){this.tryWriteToConsole(2,this.formatMessage("!",t,S.yellow));}dryWarn(t){this.dryWarnSet.has(t)||(this.warn(t),this.dryWarnSet.add(t));}info(t){this.tryWriteToConsole(1,this.formatMessage("i",t,S.blue));}debug(t){this.shouldLog(0)&&this.tryWriteToConsole(0,this.formatMessage("\u{1F41B}",t,S.magenta));}step(t){this.tryWriteToConsole(1,this.formatMessage("\u{1F680}",t,S.cyan));}progress(t){this.tryWriteToConsole(1,this.formatMessage("\u23F3",t,S.blue));}plain(t,o=i=>i){let i=this.options.timestamp?`${S.gray(new Date().toLocaleTimeString())} `:"",n=this.options.prefix?`${S.cyan(`[${this.options.prefix}]`)} `:"";this.tryWriteToConsole(1,`${i}${n}${o(t)}`);}dim(t){this.plain(t,S.gray);}child(t){return new e({...this.options,prefix:this.options.prefix?`${this.options.prefix}:${t}`:t})}configure(t){this.options={...this.options,...t};}getLevel(){return this.options.level??1}setLevel(t){this.options.level=t;}},v=new D;function Ce(e){v.success(e);}function C(e,t){v.error(e,t);}function H(e){v.info(e);}function ke(e){v.dim(e);}function K(e){v.configure(e);}function J(e={}){return new D(e)}function Q(e){console.log(),console.log(S.cyan(S.bold(`\u2501\u2501\u2501 ${e} \u2501\u2501\u2501`)));}function X(e,t,o){let i=e;t&&(i+=` ${S.gray(`(${t}ms)`)}`),Ce(i),o&&Object.entries(o).forEach(([n,r])=>{ke(` ${n}: ${r}`);});}function k(e,t="\u2022"){e.forEach(o=>{console.log(S.gray(` ${t} ${o}`));});}var F="Use CodeableReference which is not provided by FHIR R4.",be="Use Availability which is not provided by FHIR R4.",O={"hl7.fhir.uv.extensions.r4":{"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":be,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":F,"http://hl7.org/fhir/StructureDefinition/specimen-additive":F,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":F,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":F,"http://hl7.org/fhir/StructureDefinition/workflow-reason":F},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. FHIR Schema generator output broken value in it, so we just skip it for now.","http://hl7.org/fhir/StructureDefinition/publishablecodesystem":"Uses R5-only base types not available in R4 generation."}};function b(e,t){let o=`${e.name}#${e.version}`,i=O[o]?.[t];if(i)return {shouldSkip:true,reason:i};let n=O[e.name]?.[t];return n?{shouldSkip:true,reason:n}:{shouldSkip:false}}var x=e=>`${e.name}#${e.version}`,Y=e=>`${e.name}@${e.version}`;var Z=e=>{let t=JSON.stringify(e);return createHash("sha256").update(t).digest("hex").slice(0,16)},ee=(e,t)=>({...e,package_meta:e.package_meta||t,name:e.name,url:e.url,base:e.base});var te=e=>e?.kind==="nested",ne=e=>e?.kind==="profile";var ie=(e,t)=>{if(!e.url)throw new Error("ValueSet must have a URL");if(!e.name)throw new Error("ValueSet must have a name");return {...e,package_meta:e.package_meta||t,name:e.name,url:e.url}};function M(e){let t=e.split("|")[0];return t||e}function ve(e){return e.split("|")[1]}function Fe(e){return e.derivation==="constraint"?"profile":e.kind==="primitive-type"?"primitive-type":e.kind==="complex-type"?"complex-type":e.kind==="resource"?"resource":e.kind==="logical"?"logical":"resource"}function I(e){return {kind:Fe(e),package:e.package_meta.name,version:e.package_meta.version,name:e.name,url:e.url}}var Ee=e=>{let t=e.split("/"),o=t[t.length-1];return o&&o.length>0?o.split(/[-_]/).map(i=>i.charAt(0).toUpperCase()+i.slice(1).toLowerCase()).join(""):e};function L(e,t,o){let i=M(o),n=Ee(i),r={package_meta:{name:"missing_valuesets",version:ve(i)||"0.0.0"},id:o},s=e.resolveVs(t,i)||r,c=s?.id&&!/^[a-zA-Z0-9_-]{20,}$/.test(s.id)?s.id:n;return {kind:"value-set",package:s.package_meta.name,version:s.package_meta.version,name:c,url:i}}function P(e,t,o){let i=o.binding?.bindingName,n=t.join("."),[r,s,c]=i?[{name:"shared",version:"1.0.0"},i,`urn:fhir:binding:${i}`]:[e.package_meta,`${e.name}.${n}_binding`,`${e.url}#${n}_binding`];return {kind:"binding",package:r.name,version:r.version,name:s,url:c}}function B(e,t,o,i){let n=M(o)||o,r=e.resolveVs(t,n);if(r)return De(e,r)}function De(e,t,o){if(t.expansion?.contains)return t.expansion.contains.filter(n=>n.code!==void 0).map(n=>(Te(n.code),{code:n.code,display:n.display,system:n.system}));let i=[];if(t.compose?.include){for(let n of t.compose.include)if(n.concept)for(let r of n.concept)i.push({system:n.system,code:r.code,display:r.display});else if(n.system&&!n.filter)try{let r=e.resolveAny(n.system);if(r?.concept){let s=(c,a)=>{for(let l of c)i.push({system:a,code:l.code,display:l.display}),l.concept&&s(l.concept,a);};s(r.concept,n.system);}}catch{}}return i.length>0?i:void 0}var oe=100,j=new Set(["code","Coding","CodeableConcept","CodeableReference","Quantity","string","uri","Duration"]);function _(e,t,o,i){if(!o.binding)return;let n=o.binding.strength,r=o.binding.valueSet;if(!r)return;if(!j.has(o.type??"")){i?.dryWarn(`eld-11: Binding on non-bindable type '${o.type}' (valueSet: ${r})`);return}if(!(n==="required"||n==="extensible"||n==="preferred"))return;let c=B(e,t.package_meta,r);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>oe){i?.dryWarn(`Value set ${r} has ${a.length} which is more than ${oe} codes, which may cause issues with code generation.`);return}if(a.length!==0)return {isOpen:n!=="required",values:a}}function Le(e,t,o,i,n){if(!i.binding?.valueSet)return;let r=P(t,o,i),s=L(e,t.package_meta,i.binding.valueSet),c=_(e,t,i,n);return {identifier:r,valueset:s,strength:i.binding.strength,enum:c,dependencies:[s]}}function re(e,t,o){let i=new Set;if(!t.elements)return [];let n=[];function r(a,l){for(let[u,m]of Object.entries(a)){let h=[...l,u],p=h.join("."),d=e.resolveElementSnapshot(t,h);if(!i.has(p)){if(i.add(p),d.binding){let f=Le(e,t,h,d,o);f&&n.push(f);}m.elements&&r(m.elements,h);}}}r(t.elements,[]),n.sort((a,l)=>a.identifier.name.localeCompare(l.identifier.name));let s=[],c=new Set;for(let a of n)c.has(a.identifier.url)||(c.add(a.identifier.url),s.push(a));return s}function N(e,t,o,i){let n={};if(t.derivation==="constraint"){let m=e.resolveFsSpecializations(t.package_meta,t.url).map(h=>A(e,h,i)).filter(h=>h!==void 0).flat();for(let h of m.reverse())n[h.identifier.name]=h.identifier.url;}let r=o.join("."),s=n[r]??`${t.url}#${r}`,c=s.split("#")[0],l=e.resolveFs(t.package_meta,c)?.package_meta??t.package_meta;return {kind:"nested",package:l.name,version:l.version,name:r,url:s}}function se(e,t,o){let i=[];for(let[n,r]of Object.entries(o)){let s=[...t,n];E(r)&&i.push([s,r]),r.elements&&i.push(...se(e,s,r.elements));}return i}function Pe(e,t,o,i,n){let r={};for(let[s,c]of Object.entries(i)){let a=[...o,s],l=e.resolveElementSnapshot(t,a);E(l)?r[s]=U(e,t,a,l,n):r[s]=w(e,t,a,l,n);}return r}function A(e,t,o){if(!t.elements)return;let i=se(t,[],t.elements).filter(([r,s])=>s.elements&&Object.keys(s.elements).length>0),n=[];for(let[r,s]of i){let c=N(e,t,r,o),a;s.type==="BackboneElement"||!s.type?a="BackboneElement":a=s.type;let l=e.ensureSpecializationCanonicalUrl(a),u=e.resolveFs(t.package_meta,l);if(!u)throw new Error(`Could not resolve base type ${a}`);let m={kind:"complex-type",package:u.package_meta.name,version:u.package_meta.version,name:a,url:l},h=Pe(e,t,r,s.elements??{},o),p={identifier:c,base:m,fields:h};n.push(p);}return n.sort((r,s)=>r.identifier.url.localeCompare(s.identifier.url)),n.length===0?void 0:n}function ae(e){let t=[];for(let o of e){o.base&&t.push(o.base);for(let i of Object.values(o.fields||{}))"type"in i&&i.type&&t.push(i.type),"binding"in i&&i.binding&&t.push(i.binding);}return t}function ce(e,t,o){let i=o[o.length-1];if(!i)throw new Error(`Internal error: fieldName is missing for path ${o.join("/")}`);let n=o.slice(0,-1),r=e.resolveFsGenealogy(t.package_meta,t.url).flatMap(s=>{if(n.length===0)return s.required||[];if(!s.elements)return [];let c=s;for(let a of n)c=c?.elements?.[a];return c?.required||[]});return new Set(r).has(i)}function le(e,t,o){let i=o[o.length-1];if(!i)throw new Error(`Internal error: fieldName is missing for path ${o.join("/")}`);let n=o.slice(0,-1),r=e.resolveFsGenealogy(t.package_meta,t.url).flatMap(s=>{if(n.length===0)return s.excluded||[];if(!s.elements)return [];let c=s;for(let a of n)c=c?.elements?.[a];return c?.excluded||[]});return new Set(r).has(i)}var Ne=(e,t,o)=>{if(o.refers)return o.refers.map(i=>{let n=e.ensureSpecializationCanonicalUrl(i),r=e.resolveFs(t.package_meta,n);if(!r)throw new Error(`Failed to resolve fs for ${n}`);return I(r)})},we=e=>{let t=new Set,o=new Set;if(e.required)for(let i of e.required)t.add(i);if(e.excluded)for(let i of e.excluded)o.add(i);if(e.elements)for(let[i,n]of Object.entries(e.elements))n.min!==void 0&&n.min>0&&t.add(i);return {required:t.size>0?Array.from(t):void 0,excluded:o.size>0?Array.from(o):void 0}},pe=e=>{let t=e.slicing;if(!t)return;let o={};for(let[i,n]of Object.entries(t.slices??{})){if(!n)continue;let{required:r,excluded:s}=n.schema?we(n.schema):{};o[i]={min:n.min,max:n.max,match:n.match,required:r,excluded:s};}return {discriminator:t.discriminator,rules:t.rules,ordered:t.ordered,slices:Object.keys(o).length>0?o:void 0}};function $(e,t,o,i,n){if(i.elementReference){let r=i.elementReference.slice(1).filter((s,c)=>c%2===1);return N(e,t,r,n)}else if(i.type){let r=e.ensureSpecializationCanonicalUrl(i.type),s=e.resolveFs(t.package_meta,r);if(!s)throw new Error(`Could not resolve field type: <${t.url}>.${o.join(".")}: <${i.type}> (pkg: '${x(t.package_meta)}'))`);return I(s)}else {if(i.choices)return;if(t.derivation==="constraint")return;n?.dryWarn(`Can't recognize element type: <${t.url}>.${o.join(".")} (pkg: '${x(t.package_meta)}'): missing type info`);return}}var w=(e,t,o,i,n)=>{let r,s;i.binding&&(r=P(t,o,i),j.has(i.type??"")&&(s=_(e,t,i,n)));let c=$(e,t,o,i,n);return c||n?.dryWarn(`Field type not found for '${t.url}#${o.join(".")}' 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o&&o.type&&t.push(o.type),"binding"in o&&o.binding&&t.push(o.binding);return t}async function de(e,t,o){if(!t.url)throw new Error("ValueSet URL is required");let i=L(e,t.package_meta,t.url),n=B(e,t.package_meta,t.url);return {identifier:i,description:t.description,concept:n,compose:n?void 0:t.compose}}function Ve(e,t,o,i){let n=[];t&&n.push(t),o&&n.push(...$e(o)),i&&n.push(...ae(i));let r={};for(let a of n)a.url!==e.url&&(r[a.url]=a);let s=new Set(i?.map(a=>a.identifier.url)),c=Object.values(r).filter(a=>ne(e)||!te(a)?true:!s.has(a.url)).sort((a,l)=>a.url.localeCompare(l.url));return c.length>0?c:void 0}function He(e,t,o){let i=I(t),n;if(t.base&&t.type!=="Element"){let p=e.resolveFs(t.package_meta,e.ensureSpecializationCanonicalUrl(t.base));if(!p)throw new Error(`Base resource not found '${t.base}' for <${t.url}> from ${x(t.package_meta)}`);n=I(p);}let r=Ue(e,t,[],t.elements,o),s=A(e,t,o),c=t.derivation==="constraint"?_e(e,t,o):void 0,a=Ve(i,n,r,s),l=c?.flatMap(p=>p.valueTypes??[])??[],u=(()=>{if(!a&&l.length===0)return a;let p={};for(let d of a??[])p[d.url]=d;for(let d of l)p[d.url]=d;return Object.values(p)})(),m={identifier:i,base:n,fields:r,nested:s,description:t.description,dependencies:u,...c&&c.length>0?{extensions:c}:{}},h=re(e,t,o);return [m,...h]}function Oe(e,t,o,i){let n=e.resolveFs(t.package_meta,o);if(!n?.elements)return;let r=[];for(let[c,a]of Object.entries(n.elements)){if(a.choiceOf!=="value"&&!c.startsWith("value"))continue;let l=$(e,n,[c],a,i);l&&r.push(l);}if(r.length===0)return;let s=new Map(r.map(c=>[c.url,c]));return Array.from(s.values())}var Me=(e,t,o)=>{let i=[];if(!t.elements)return i;for(let[n,r]of Object.entries(t.elements)){if(!n.startsWith("extension:"))continue;let s=n.split(":")[1];if(!s)continue;let c;for(let[a,l]of Object.entries(r.elements??{}))if(!(l.choiceOf!=="value"&&!a.startsWith("value"))&&(c=$(e,t,[n,a],l,o),c))break;i.push({name:s,url:r.url??s,valueType:c,min:r.min,max:r.max!==void 0?String(r.max):void 0});}return i},Be=e=>{let t=[],i=e.elements?.extension?.slicing?.slices;if(!i||typeof i!="object")return t;for(let[n,r]of Object.entries(i)){let s=r,c=s.schema;if(!c)continue;let a;for(let[l,u]of Object.entries(c.elements??{})){let m=u;if(!(m.choiceOf!=="value"&&!l.startsWith("value"))&&m.type){a={kind:"complex-type",package:e.package_meta.name,version:e.package_meta.version,name:m.type,url:`http://hl7.org/fhir/StructureDefinition/${m.type}`};break}}t.push({name:n,url:s.match?.url??n,valueType:a,min:c._required?1:c.min??0,max:c.max!==void 0?String(c.max):c.array?"*":"1"});}return t},je=(e,t,o,i)=>{let n=e.resolveFs(t.package_meta,o);if(!n?.elements)return;let r=Me(e,n,i),s=Be(n),c=[...r,...s];return c.length>0?c:void 0};function _e(e,t,o){let i=[],n=(s,c,a)=>{let l=a.url,u=l?Oe(e,t,l,o):void 0,m=l?je(e,t,l,o):void 0,h=m!==void 0&&m.length>0;i.push({name:c,path:[...s,"extension"].join("."),url:l,min:a.min,max:a.max!==void 0?String(a.max):void 0,mustSupport:a.mustSupport,valueTypes:u,subExtensions:m,isComplex:h});},r=(s,c)=>{if(c.extensions)for(let[a,l]of Object.entries(c.extensions))n(s,a,l);if(c.elements)for(let[a,l]of Object.entries(c.elements))r([...s,a],l);};if(t.extensions)for(let[s,c]of Object.entries(t.extensions))n([],s,c);if(t.elements)for(let[s,c]of Object.entries(t.elements))r([s],c);return i}async function ue(e,t,o){return He(e,t,o)}var Ae=(e,t)=>{let o={};for(let r of e){let s=`${r.schema.identifier.url}|${r.schema.identifier.package}`,c=Z(r.schema);o[s]??={},o[s][c]??={typeSchema:r.schema,sources:[]},o[s][c].sources.push(r);}let i=[],n={};for(let r of Object.values(o)){let s=Object.values(r).sort((a,l)=>l.sources.length-a.sources.length),c=s[0];if(c&&(i.push(c.typeSchema),s.length>1)){let a=c.typeSchema.identifier.package,l=c.typeSchema.identifier.url;t?.dryWarn(`'${l}' from '${a}'' has ${s.length} versions`),n[a]??={},n[a][l]=s.flatMap(u=>u.sources.map(m=>({typeSchema:u.typeSchema,sourcePackage:m.sourcePackage,sourceCanonical:m.sourceCanonical})));}}return {schemas:i,collisions:n}},me=async(e,t)=>{let o=[];for(let i of e.allFs()){let n=x(i.package_meta),r=b(i.package_meta,i.url);if(r.shouldSkip){t?.dryWarn(`Skip ${i.url} from ${n}. Reason: ${r.reason}`);continue}for(let s of await ue(e,i,t))o.push({schema:s,sourcePackage:n,sourceCanonical:i.url});}for(let i of e.allVs())o.push({schema:await de(e,i),sourcePackage:x(i.package_meta),sourceCanonical:i.url});return Ae(o,t)};var G=e=>e!==null&&typeof e=="object"&&e.resourceType==="CodeSystem";var V=e=>e!==null&&typeof e=="object"&&e.resourceType==="ValueSet";var We=async(e,t)=>{let o=await e.packageJson(t.name);if(!o)return [];let i=o.dependencies;return i!==void 0?Object.entries(i).map(([n,r])=>({name:n,version:r})):[]},he=e=>({pkg:e,canonicalResolution:{},fhirSchemas:{},valueSets:{}}),ye=async(e,t,o,i,n)=>{let r=x(t);if(n?.info(`${" ".repeat(o*2)}+ ${r}`),i[r])return i[r];let s=he(t);for(let a of await e.search({package:t})){let l=a.url;if(!l||!(isStructureDefinition(a)||V(a)||G(a)))continue;let u=l;s.canonicalResolution[u]&&n?.dryWarn(`Duplicate canonical URL: ${u} at ${r}.`),s.canonicalResolution[u]=[{deep:o,pkg:t,pkgId:r,resource:a}];}let c=await We(e,t);for(let a of c){let{canonicalResolution:l}=await ye(e,a,o+1,i,n);for(let[u,m]of Object.entries(l)){let h=u;s.canonicalResolution[h]=[...s.canonicalResolution[h]||[],...m];}}for(let a of Object.values(s.canonicalResolution))a.sort((l,u)=>l.deep-u.deep);return i[r]=s,s},fe=(e,t)=>{for(let{pkg:o,canonicalResolution:i}of Object.values(e)){let n=x(o);if(!e[n])throw new Error(`Package ${n} not found`);for(let[s,c]of Object.entries(i)){let a=c[0];if(!a)throw new Error("Resource not found");let l=a.resource,u=a.pkg;if(isStructureDefinition(l)){let m=ge.translate(l),h=ee(m,u);e[n].fhirSchemas[h.url]=h;}if(V(l)){let m=ie(l,u);e[n].valueSets[m.url]=m;}}}},qe=(e,t,o)=>{let i=Object.values(e).flatMap(n=>n.canonicalResolution[t]);if(!i)throw new Error(`No canonical resolution found for ${t} in any package`);return i[0]?.resource},ze=async(e,{logger:t,focusedPackages:o})=>{let i=o??await e.packages(),n={};for(let p of i)await ye(e,p,0,n,t);fe(n);let r=(p,d)=>{let f=n[x(p)];if(f){let g=f.canonicalResolution[d]?.[0];if(g)return n[g.pkgId]?.fhirSchemas[d]}for(let g of Object.values(n)){let y=g.fhirSchemas[d];if(y&&y.package_meta.name===p.name)return y}for(let g of Object.values(n)){let y=g.fhirSchemas[d];if(y)return y}},s=(p,d)=>{let f=n[x(p)];if(f){let g=f.canonicalResolution[d]?.[0];if(g)return n[g.pkgId]?.valueSets[d]}for(let g of Object.values(n)){let y=g.valueSets[d];if(y&&y.package_meta.name===p.name)return y}for(let g of Object.values(n)){let y=g.valueSets[d];if(y)return y}},c=p=>(p.includes("|")&&(p=p.split("|")[0]),p.match(/^[a-zA-Z0-9]+$/)?`http://hl7.org/fhir/StructureDefinition/${p}`:p),a=(p,d)=>{let f=r(p,d);if(f===void 0)throw new Error(`Failed to resolve FHIR Schema: '${d}'`);let g=[f];for(;f?.base;){let y=f.package_meta,R=c(f.base);if(f=r(y,R),f===void 0)throw new Error(`Failed to resolve FHIR Schema base for '${d}'. Problem: '${R}' from '${x(y)}'`);g.push(f);}return g},l=(p,d)=>a(p,d).filter(f=>f.derivation==="specialization"),u=(p,d)=>{let f=a(p.package_meta,p.url),g=Ke(f,d);return Je(g)},m=p=>{let d=new Set;for(let[f,g]of Object.entries(p)){d.add(f);for(let y of g?.choices||[])p[y]||d.add(y);}return Array.from(d)},h;return {testAppendFs(p){let d=x(p.package_meta);n[d]||(n[d]=he(p.package_meta)),n[d].fhirSchemas[p.url]=p,h=void 0;},resolveFs:r,resolveFsGenealogy:a,resolveFsSpecializations:l,ensureSpecializationCanonicalUrl:c,resolveSd:(p,d)=>{let f=n[x(p)]?.canonicalResolution[d]?.[0]?.resource;if(isStructureDefinition(f))return f},allSd:()=>Object.values(n).flatMap(p=>Object.values(p.canonicalResolution).flatMap(d=>d.map(f=>{let g=f.resource;return g.package_name?g:{...g,package_name:p.pkg.name,package_version:p.pkg.version}}))).filter(p=>isStructureDefinition(p)).sort((p,d)=>p.url.localeCompare(d.url)),patchSd:p=>{Object.values(n).flatMap(d=>Object.values(d.canonicalResolution).forEach(f=>{f.forEach(g=>{if(isStructureDefinition(g.resource)){let y=g.resource,R=p(d.pkg,y);if(y.url!==R.url)throw new Error(`Patch update StructureDefinition URL: ${y.url} !== ${R.url}`);g.resource=R;}});})),fe(n),h=void 0;},allFs:()=>Object.values(n).flatMap(p=>Object.values(p.fhirSchemas)),allVs:()=>Object.values(n).flatMap(p=>Object.values(p.valueSets)),resolveVs:s,resolveAny:p=>qe(n,p),resolveElementSnapshot:u,getAllElementKeys:m,resolver:n,resolutionTree:()=>{if(h)return h;let p={};for(let[d,f]of Object.entries(n)){let g=f.pkg.name;p[g]={};for(let[y,R]of Object.entries(f.canonicalResolution)){let q=y;p[g][q]=[];for(let z of R)p[g][q].push({deep:z.deep,pkg:z.pkg});}}return h=p,p}}},Se=async(e,t)=>{let o=e.map(Y);t?.logger?.step(`Loading FHIR packages: ${o.join(", ")}`);let i=CanonicalManager({packages:o,workingDir:"tmp/fhir",registry:t.registry||void 0});return await i.init(),await ze(i,{...t,focusedPackages:e})},Ke=(e,t)=>{let[o,...i]=t;return o===void 0?[]:e.map(n=>{if(!n.elements)return;let r=n.elements?.[o];for(let s of i)r=r?.elements?.[s];return r}).filter(n=>n!==void 0)};function Je(e){let t=e.reverse(),o=Object.assign({},...t);return o.elements=void 0,o}var xe={command:"generate <packages..>",describe:"Generate TypeSchema files from FHIR packages",builder:{packages:{type:"string",array:true,demandOption:true,describe:"FHIR packages to process (e.g., hl7.fhir.r4.core@4.0.1)"},output:{alias:"o",type:"string",describe:"Output file or directory",default:"./schemas.ndjson"},format:{alias:"f",type:"string",choices:["ndjson","json"],default:"ndjson",describe:"Output format for TypeSchema files"},treeshake:{alias:"t",type:"string",array:true,describe:"Only generate TypeSchemas for specific ResourceTypes (treeshaking)"},singleFile:{alias:"s",type:"boolean",default:false,describe:"Generate single TypeSchema file instead of multiple files (NDJSON format)"},verbose:{alias:"v",type:"boolean",default:false,describe:"Enable verbose output"},registry:{alias:"r",type:"string",describe:"Custom FHIR package registry URL (default: https://fs.get-ig.org/pkgs/)"}},handler:async e=>{let t=J({prefix:"TypeSchema"});try{t.step("Generating TypeSchema from FHIR packages"),t.info(`Packages: ${e.packages.join(", ")}`),t.info(`Output: ${e.output}`);let o=e.singleFile?"ndjson":e.format;t.debug(`Format: ${o}${e.singleFile&&e.format==="json"?" (forced from json due to singleFile)":""}`),e.treeshake&&e.treeshake.length>0&&t.info(`Treeshaking enabled for ResourceTypes: ${e.treeshake.join(", ")}`),e.singleFile&&t.info("Single file output enabled (NDJSON format)"),e.registry&&t.info(`Using custom registry: ${e.registry}`);let i=Date.now(),n=e.packages.map(u=>{if(u.includes("@")){let m=u.lastIndexOf("@");return {name:u.slice(0,m),version:u.slice(m+1)||"latest"}}return {name:u,version:"latest"}});t.progress(`Processing packages: ${n.map(u=>`${u.name}@${u.version}`).join(", ")}`);let r=await Se(n,{logger:t,registry:e.registry,focusedPackages:n}),{schemas:s}=await me(r,t);if(s.length===0)throw new Error("No schemas were generated from the specified packages");let c=e.output;if(!c)throw new Error("Output format not specified");await mkdir(dirname(c),{recursive:!0});let a;o==="json"?a=JSON.stringify(s,null,2):a=s.map(u=>JSON.stringify(u)).join(`
3
+ `),await writeFile(c,a,"utf-8");let l=Date.now()-i;if(X(`Generated ${s.length} TypeSchema definitions`,l,{schemas:s.length}),t.dim(`Output: ${c}`),e.verbose){t.debug("Generated schemas:");let u=s.map(m=>`${m.identifier?.name||"Unknown"} (${m.identifier?.kind||"unknown"})`);k(u);}}catch(o){t.error("Failed to generate TypeSchema",o instanceof Error?o:new Error(String(o))),process.exit(1);}}};var Re={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:e=>e.command(xe).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:e=>{if(!e.subcommand&&e._.length===1){H("Available typeschema subcommands:"),k(["generate Generate TypeSchema files from FHIR packages"]),console.log(`
4
4
  Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
5
- Examples:`),I(["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)&&(b(`Unknown typeschema subcommand: ${t.subcommand}
6
- `),O("Available typeschema subcommands:"),I(["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(`
7
- Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};function Qe(t){return t?{debug:0,info:1,warn:2,error:3,silent:4}[t.toLowerCase()]:void 0}async function Xe(t){let e=Qe(t.logLevel);e===void 0&&(t.debug||t.verbose?e=0:e=1),X({timestamp:t.debug,level:e});}function Ze(){return Ke(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(Xe).command(xe).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&&(Z("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log(" typeschema Generate, validate and merge TypeSchema files"),console.log(`
5
+ 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}e.subcommand&&!["generate","validate","merge"].includes(e.subcommand)&&(C(`Unknown typeschema subcommand: ${e.subcommand}
6
+ `),H("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(`
7
+ Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};function tt(e){return e?{debug:0,info:1,warn:2,error:3,silent:4}[e.toLowerCase()]:void 0}async function nt(e){let t=tt(e.logLevel);t===void 0&&(e.debug||e.verbose?t=0:t=1),K({timestamp:e.debug,level:t});}function it(){return Ze(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(nt).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(`
8
8
  Use 'atomic-codegen <command> --help' for more information about a command.`),console.log(`
9
9
  Quick examples:`),console.log(" atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson"),console.log(`
10
- 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,n)=>{e?b(e.message,e):b(t),b(`
11
- Use --help for usage information`),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function K(){await Ze().parseAsync();}import.meta.main&&K().catch(t=>{t("Unexpected error:",t),process.exit(1);});K().catch(t=>{console.error("CLI Error:",t instanceof Error?t.message:t),process.exit(1);});
10
+ 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?C(t.message,t):C(e),C(`
11
+ Use --help for usage information`),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function W(){await it().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);});
package/dist/index.d.ts CHANGED
@@ -49,7 +49,7 @@ declare class CodegenLogger {
49
49
  * Warning message with warning sign
50
50
  */
51
51
  warn(message: string): void;
52
- dry_warn(message: string): void;
52
+ dryWarn(message: string): void;
53
53
  /**
54
54
  * Info message with info icon
55
55
  */
@@ -801,7 +801,9 @@ type Register = {
801
801
  resolveFsSpecializations(pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichFHIRSchema[];
802
802
  allSd(): RichStructureDefinition[];
803
803
  patchSd(fn: (pkg: PackageMeta, sd: StructureDefinition$1) => StructureDefinition$1): void;
804
+ /** Returns all FHIRSchemas from all packages in the resolver */
804
805
  allFs(): RichFHIRSchema[];
806
+ /** Returns all ValueSets from all packages in the resolver */
805
807
  allVs(): RichValueSet[];
806
808
  resolveVs(_pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichValueSet | undefined;
807
809
  resolveAny(canonicalUrl: CanonicalUrl): any | undefined;
@@ -830,6 +832,13 @@ type ResolutionTree = Record<PkgName, Record<CanonicalUrl, {
830
832
  deep: number;
831
833
  pkg: PackageMeta;
832
834
  }[]>>;
835
+ type RegisterConfig = {
836
+ logger?: CodegenLogger;
837
+ focusedPackages?: PackageMeta[];
838
+ /** Custom FHIR package registry URL */
839
+ registry?: string;
840
+ };
841
+ declare const registerFromPackageMetas: (packageMetas: PackageMeta[], conf: RegisterConfig) => Promise<Register>;
833
842
 
834
843
  type FileSystemWriterOptions = {
835
844
  outputDir: string;
@@ -949,6 +958,8 @@ interface APIBuilderOptions {
949
958
  logLevel: LogLevel;
950
959
  /** Custom FHIR package registry URL (default: https://fs.get-ig.org/pkgs/) */
951
960
  registry: string | undefined;
961
+ /** Drop the canonical manager cache */
962
+ dropCanonicalManagerCache: boolean;
952
963
  }
953
964
  type GenerationReport = {
954
965
  success: boolean;
@@ -984,11 +995,6 @@ declare class APIBuilder {
984
995
  });
985
996
  fromPackage(packageName: string, version?: string): APIBuilder;
986
997
  fromPackageRef(packageRef: string): APIBuilder;
987
- /**
988
- * Set a custom FHIR package registry URL
989
- * @param url The registry URL (default: https://fs.get-ig.org/pkgs/)
990
- */
991
- registry(url: string): APIBuilder;
992
998
  localStructureDefinitions(config: LocalStructureDefinitionConfig): APIBuilder;
993
999
  localTgzPackage(archivePath: string): APIBuilder;
994
1000
  introspection(userOpts?: Partial<IntrospectionWriterOptions>): APIBuilder;
@@ -1017,4 +1023,4 @@ declare class APIBuilder {
1017
1023
  private executeGenerators;
1018
1024
  }
1019
1025
 
1020
- export { APIBuilder, type APIBuilderOptions, type CSharpGeneratorOptions, type IrConf, type LocalStructureDefinitionConfig, LogLevel, type LogicalPromotionConf, type TreeShakeConf, type TypeScriptOptions, prettyReport };
1026
+ export { APIBuilder, type APIBuilderOptions, type CSharpGeneratorOptions, type IrConf, type LocalStructureDefinitionConfig, LogLevel, type LogicalPromotionConf, type TreeShakeConf, type TypeScriptOptions, prettyReport, registerFromPackageMetas };