@atomic-ehr/codegen 0.0.15 → 0.0.16
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/README.md +22 -16
- package/assets/api/writer-generator/python/fhirpy_base_model.py +1 -0
- package/assets/api/writer-generator/python/profile_helpers.py +502 -0
- package/assets/api/writer-generator/python/resource_preprocessor.py +41 -0
- package/dist/cli/index.js +5 -5
- package/dist/index.d.ts +11 -0
- package/dist/index.js +1577 -422
- package/dist/index.js.map +1 -1
- package/package.json +8 -7
- package/assets/api/writer-generator/python/resource_family_validator.py +0 -92
package/dist/cli/index.js
CHANGED
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@@ -1,15 +1,15 @@
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#!/usr/bin/env node
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import T from'picocolors';import vn from'yargs';import {hideBin}from'yargs/helpers';import {mkdir,writeFile}from'fs/promises';import {dirname}from'path';import Pe from'assert';import {createHash}from'crypto';import {CanonicalManager}from'@atomic-ehr/fhir-canonical-manager';import*as he from'@atomic-ehr/fhirschema';import {isStructureDefinition}from'@atomic-ehr/fhirschema';var ie=e=>{console.log(),console.log(T.cyan(T.bold(`\u2501\u2501\u2501 ${e} \u2501\u2501\u2501`)));},re=(e,n,i)=>{let t=e;if(n&&(t+=` ${T.gray(`(${n}ms)`)}`),console.log(`${T.green("")} ${t}`),i)for(let[r,o]of Object.entries(i))console.log(T.gray(` ${r}: ${o}`));},F=(e,n="\u2022")=>{for(let i of e)console.log(T.gray(` ${n} ${i}`));};var oe={DEBUG:0,INFO:1,WARN:2,ERROR:3,SILENT:4};function k(e={}){let n=e.prefix??"",i=new Set(e.suppressTags??[]),t={},r=[],o=new Set,a=e.level??"INFO",s=p=>oe[p]>=oe[a],c={DEBUG:p=>p,INFO:p=>p,WARN:T.yellow,ERROR:T.red,SILENT:p=>p},l=(p,m,f,y)=>{let h=n?`${n}: `:"",S=y?` ${T.dim(`(${y})`)}`:"";return c[p](`${m} ${h}${f}`)+S},d=(p,m,f,y=false)=>{r.push({level:p,tag:f,message:m,suppressed:y,prefix:n,timestamp:Date.now()});},u=(p,m,f,y=false)=>(...h)=>{let S=h.length===2?h[0]:void 0,x=h.length===2?h[1]:h[0];S&&(t[S]=(t[S]??0)+1);let C=S!==void 0&&i.has(S);if(d(p,x,S,C),!C&&s(p)){if(y){let N=`${p}::${S??""}::${x}`;if(o.has(N))return;o.add(N);}f(l(p,m,x,S));}},g={warn:u("WARN","!",console.warn),dryWarn:u("WARN","!",console.warn,true),info:u("INFO","i",console.log),error:u("ERROR","X",console.error),debug:u("DEBUG","D",console.log),fork(p,m){let f=n?`${n}/${p}`:p,y=[...i,...m?.suppressTags??[]];return k({prefix:f,suppressTags:y,level:m?.level??a})},as(){return g},tagCounts(){return t},printTagSummary(){let p=Object.entries(t);if(p.length===0)return;let m=n?`${n}: `:"",f=p.filter(([h])=>!i.has(h)),y=p.filter(([h])=>i.has(h));if(f.length>0){let h=f.reduce((x,[,C])=>x+C,0),S=f.map(([x,C])=>`${x}: ${C}`).join(", ");console.warn(T.yellow(`! ${m}${h} warnings (${S})`));}if(y.length>0){let h=y.reduce((x,[,C])=>x+C,0),S=y.map(([x,C])=>`${x}: ${C}`).join(", ");console.log(T.dim(`i ${m}${h} suppressed (${S})`));}},buffer(){return r},bufferClear(){r.length=0;}};return g}var b="Use CodeableReference which is not provided by FHIR R4.",Ve="Use Availability which is not provided by FHIR R4.",A={"hl7.fhir.uv.extensions.r4":{"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-manipulation":b,"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-processing":b,"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":Ve,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":b,"http://hl7.org/fhir/StructureDefinition/specimen-additive":b,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":b,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":b,"http://hl7.org/fhir/StructureDefinition/workflow-reason":b},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. FHIR Schema generator output broken value in it, so we just skip it for now.","http://hl7.org/fhir/StructureDefinition/publishablecodesystem":"Uses R5-only base types not available in R4 generation."}};function v(e,n){let i=`${e.name}#${e.version}`,t=A[i]?.[n];if(t)return {shouldSkip:true,reason:t};let r=A[e.name]?.[n];return r?{shouldSkip:true,reason:r}:{shouldSkip:false}}var R=e=>`${e.name}#${e.version}`,ae=e=>`${e.name}@${e.version}`,se=e=>{let n=JSON.stringify(e);return createHash("sha256").update(n).digest("hex").slice(0,16)},ce=(e,n)=>{let i=e.derivation==="constraint"?"constraint":"specialization";return {...e,derivation:i,kind:e.kind,package_meta:e.package_meta||n,name:e.name,url:e.url,base:e.base}};var G=e=>e?.kind==="nested";var E=(...e)=>{let n=e.filter(t=>t!==void 0).flatMap(t=>t.map(r=>[r.url,r]));return n.length===0?void 0:Object.values(Object.fromEntries(n)).sort((t,r)=>t.url.localeCompare(r.url))};var le=e=>[...e.valueFieldTypes??[],...e.profile?[e.profile]:[],...e.subExtensions?.flatMap(n=>n.valueFieldType?[n.valueFieldType]:[])??[]];var pe=(e,n)=>{if(!e.url)throw new Error("ValueSet must have a URL");if(!e.name)throw new Error("ValueSet must have a name");return {...e,package_meta:e.package_meta||n,name:e.name,url:e.url}};function z(e){let n=e.split("|")[0];return n||e}function Be(e){return e.split("|")[1]}var Me=e=>({package:e.package_meta.name,version:e.package_meta.version,name:e.name,url:e.url});function I(e){let n=Me(e);return e.derivation==="constraint"?{kind:"profile",...n}:e.kind==="primitive-type"?{kind:"primitive-type",...n}:e.kind==="complex-type"?{kind:"complex-type",...n}:e.kind==="resource"?{kind:"resource",...n}:e.kind==="logical"?{kind:"logical",...n}:{kind:"resource",...n}}var je=e=>{let n=e.split("/"),i=n[n.length-1];return i&&i.length>0?i.split(/[-_]/).map(t=>t.charAt(0).toUpperCase()+t.slice(1).toLowerCase()).join(""):e};function L(e,n,i){let t=z(i),r=je(t),o={package_meta:{name:"missing_valuesets",version:Be(t)||"0.0.0"},id:i},a=e.resolveVs(n,t)||o,s=a?.id&&!/^[a-zA-Z0-9_-]{20,}$/.test(a.id)?a.id:r;return {kind:"value-set",package:a.package_meta.name,version:a.package_meta.version,name:s,url:t}}function H(e,n,i){let t=i.binding?.bindingName,r=n.join("."),[o,a,s]=t?[{name:"shared",version:"1.0.0"},t,`urn:fhir:binding:${t}`]:[e.package_meta,`${e.name}.${r}_binding`,`${e.url}#${r}_binding`];return {kind:"binding",package:o.name,version:o.version,name:a,url:s}}function q(e,n,i,t){let r=z(i)||i,o=e.resolveVs(n,r);if(o)return Ae(e,o)}function Ae(e,n,i){if(n.expansion?.contains)return n.expansion.contains.filter(r=>r.code!==void 0).map(r=>(Pe(r.code),{code:r.code,display:r.display,system:r.system}));let t=[];if(n.compose?.include){for(let r of n.compose.include)if(r.concept)for(let o of r.concept)t.push({system:r.system,code:o.code,display:o.display});else if(r.system&&!r.filter)try{let o=e.resolveAny(r.system);if(o?.concept){let a=(s,c)=>{for(let l of s)t.push({system:c,code:l.code,display:l.display}),l.concept&&a(l.concept,c);};a(o.concept,r.system);}}catch{}}return t.length>0?t:void 0}var de=100,Ge=new Set(["UNK"]),W=new Set(["code","Coding","CodeableConcept","CodeableReference","Quantity","string","uri","Duration"]);function K(e,n,i,t){if(!i.binding)return;let r=i.binding.strength,o=i.binding.valueSet;if(!o)return;if(!W.has(i.type??"")){t?.dryWarn("#binding",`eld-11: Binding on non-bindable type '${i.type}' (valueSet: ${o})`);return}if(!(r==="required"||r==="extensible"||r==="preferred"))return;let s=q(e,n.package_meta,o);if(!s||s.length===0)return;let c=s.map(d=>d.code).filter(d=>d&&typeof d=="string"&&d.trim().length>0),l=c.length===1?c[0]:void 0;if(l&&Ge.has(l)){t?.dryWarn("#placeholderValueSet",`Value set ${o} only expands to placeholder code '${l}'; skipping enum generation.`);return}if(c.length>de){t?.dryWarn("#largeValueSet",`Value set ${o} has ${c.length} which is more than ${de} codes, which may 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+
import T from'picocolors';import Dn from'yargs';import {hideBin}from'yargs/helpers';import {mkdir,writeFile}from'fs/promises';import {dirname}from'path';import Pe from'assert';import {createHash}from'crypto';import {CanonicalManager}from'@atomic-ehr/fhir-canonical-manager';import*as he from'@atomic-ehr/fhirschema';import {isStructureDefinition}from'@atomic-ehr/fhirschema';var ie=e=>{console.log(),console.log(T.cyan(T.bold(`\u2501\u2501\u2501 ${e} \u2501\u2501\u2501`)));},re=(e,n,i)=>{let t=e;if(n&&(t+=` ${T.gray(`(${n}ms)`)}`),console.log(`${T.green("")} ${t}`),i)for(let[r,o]of Object.entries(i))console.log(T.gray(` ${r}: ${o}`));},F=(e,n="\u2022")=>{for(let i of e)console.log(T.gray(` ${n} ${i}`));};var oe={DEBUG:0,INFO:1,WARN:2,ERROR:3,SILENT:4};function k(e={}){let n=e.prefix??"",i=new Set(e.suppressTags??[]),t={},r=[],o=new Set,a=e.level??"INFO",s=p=>oe[p]>=oe[a],c={DEBUG:p=>p,INFO:p=>p,WARN:T.yellow,ERROR:T.red,SILENT:p=>p},l=(p,m,f,y)=>{let h=n?`${n}: `:"",S=y?` ${T.dim(`(${y})`)}`:"";return c[p](`${m} ${h}${f}`)+S},d=(p,m,f,y=false)=>{r.push({level:p,tag:f,message:m,suppressed:y,prefix:n,timestamp:Date.now()});},u=(p,m,f,y=false)=>(...h)=>{let S=h.length===2?h[0]:void 0,x=h.length===2?h[1]:h[0];S&&(t[S]=(t[S]??0)+1);let C=S!==void 0&&i.has(S);if(d(p,x,S,C),!C&&s(p)){if(y){let N=`${p}::${S??""}::${x}`;if(o.has(N))return;o.add(N);}f(l(p,m,x,S));}},g={warn:u("WARN","!",console.warn),dryWarn:u("WARN","!",console.warn,true),info:u("INFO","i",console.log),error:u("ERROR","X",console.error),debug:u("DEBUG","D",console.log),fork(p,m){let f=n?`${n}/${p}`:p,y=[...i,...m?.suppressTags??[]];return k({prefix:f,suppressTags:y,level:m?.level??a})},as(){return g},tagCounts(){return t},printTagSummary(){let p=Object.entries(t);if(p.length===0)return;let m=n?`${n}: `:"",f=p.filter(([h])=>!i.has(h)),y=p.filter(([h])=>i.has(h));if(f.length>0){let h=f.reduce((x,[,C])=>x+C,0),S=f.map(([x,C])=>`${x}: ${C}`).join(", ");console.warn(T.yellow(`! ${m}${h} warnings (${S})`));}if(y.length>0){let h=y.reduce((x,[,C])=>x+C,0),S=y.map(([x,C])=>`${x}: ${C}`).join(", ");console.log(T.dim(`i ${m}${h} suppressed (${S})`));}},buffer(){return r},bufferClear(){r.length=0;}};return g}var b="Use CodeableReference which is not provided by FHIR R4.",Oe="Use Availability which is not provided by FHIR R4.",A={"hl7.fhir.uv.extensions.r4":{"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-manipulation":b,"http://hl7.org/fhir/StructureDefinition/biologicallyderivedproduct-processing":b,"http://hl7.org/fhir/StructureDefinition/extended-contact-availability":Oe,"http://hl7.org/fhir/StructureDefinition/immunization-procedure":b,"http://hl7.org/fhir/StructureDefinition/specimen-additive":b,"http://hl7.org/fhir/StructureDefinition/workflow-barrier":b,"http://hl7.org/fhir/StructureDefinition/workflow-protectiveFactor":b,"http://hl7.org/fhir/StructureDefinition/workflow-reason":b},"hl7.fhir.r5.core#5.0.0":{"http://hl7.org/fhir/StructureDefinition/shareablecodesystem":"FIXME: CodeSystem.concept.concept defined by ElementReference. 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le=e=>[...e.valueFieldTypes??[],...e.profile?[e.profile]:[],...e.subExtensions?.flatMap(n=>n.valueFieldType?[n.valueFieldType]:[])??[]];var pe=(e,n)=>{if(!e.url)throw new Error("ValueSet must have a URL");if(!e.name)throw new Error("ValueSet must have a name");return {...e,package_meta:e.package_meta||n,name:e.name,url:e.url}};function z(e){let n=e.split("|")[0];return n||e}function Be(e){return e.split("|")[1]}var Me=e=>({package:e.package_meta.name,version:e.package_meta.version,name:e.name,url:e.url});function I(e){let n=Me(e);return e.derivation==="constraint"?{kind:"profile",...n}:e.kind==="primitive-type"?{kind:"primitive-type",...n}:e.kind==="complex-type"?{kind:"complex-type",...n}:e.kind==="resource"?{kind:"resource",...n}:e.kind==="logical"?{kind:"logical",...n}:{kind:"resource",...n}}var je=/[-_]/,_e=/^[a-zA-Z0-9_-]{20,}$/,Ae=e=>{let n=e.split("/"),i=n[n.length-1];return i&&i.length>0?i.split(je).map(t=>t.charAt(0).toUpperCase()+t.slice(1).toLowerCase()).join(""):e};function 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t(e,0)},fe=e=>({candidates:Qe(e.name,e.path),recommended:""}),ge=(e,n)=>({candidates:Xe(e,n),recommended:""}),ye=e=>{let n=(e.extensions??[]).filter(a=>a.url).map(a=>({key:`ext:${a.url}:${a.path}`,candidates:a.nameCandidates.candidates})),i=Object.entries(e.fields??{}).flatMap(([a,s])=>!("slicing"in s)||!s.slicing?.slices?[]:Object.entries(s.slicing.slices).map(([c,l])=>({key:`slice:${a}:${c}`,candidates:l.nameCandidates.candidates}))),t=new Set(Object.keys(e.fields??{}).map(w)),r=[...n,...i];if(r.length===0)return;let o=nn(r,t);for(let a of e.extensions??[]){if(!a.url)continue;let s=`ext:${a.url}:${a.path}`;o[s]&&(a.nameCandidates.recommended=o[s]);}for(let[a,s]of Object.entries(e.fields??{}))if(!(!("slicing"in s)||!s.slicing?.slices))for(let[c,l]of Object.entries(s.slicing.slices)){let d=`slice:${a}:${c}`;o[d]&&(l.nameCandidates.recommended=o[d]);}};var J=e=>e!==null&&typeof e=="object"&&e.resourceType==="CodeSystem";var U=e=>e!==null&&typeof 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a},an=(e,n)=>{for(let{pkg:i,canonicalResolution:t}of Object.values(e)){let r=R(i);if(!e[r])throw new Error(`Package ${r} not found`);let o=0;n?.info(`FHIR Schema conversion for '${R(i)}' begins...`);for(let[a,s]of Object.entries(t)){let c=s[0];if(!c)throw new Error("Resource not found");let l=c.resource,d=c.pkg;if(isStructureDefinition(l)){let u=he.translate(l),g=ce(u,d);o++,e[r].fhirSchemas[g.url]=g;}if(U(l)){let u=pe(l,d);e[r].valueSets[u.url]=u;}}n?.info(`FHIR Schema conversion for '${R(i)}' completed: ${o} successful`);}},sn=(e,n,i)=>{let t=Object.values(e).flatMap(r=>r.canonicalResolution[n]);if(!t)throw new Error(`No canonical resolution found for ${n} in any package`);return t[0]?.resource},cn=async(e,{logger:n,focusedPackages:i})=>{let t=i??await e.packages(),r={};for(let p of t)await Re(e,p,0,r,n);an(r,n);let o=(p,m)=>{let f=r[R(p)];if(f){let y=f.canonicalResolution[m]?.[0];if(y)return r[y.pkgId]?.fhirSchemas[m]}for(let y of Object.values(r)){let 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|
|
3
3
|
hint: '${i}' is an R5+ type and is not available when generating against R4.
|
|
4
|
-
Either skip this canonical via skip-hack.ts, or upgrade the target to R5.`;function be(e,n,i){let t=i[i.length-1];if(!t)throw new Error(`Internal error: fieldName is missing for path ${i.join("/")}`);let r=i.slice(0,-1),o=e.resolveFsGenealogy(n.package_meta,n.url).flatMap(a=>{if(r.length===0)return a.required||[];if(!a.elements)return [];let s=a;for(let c of r)s=s?.elements?.[c];return s?.required||[]});return new Set(o).has(t)}function Te(e,n,i){let t=i[i.length-1];if(!t)throw new Error(`Internal error: fieldName is missing for path ${i.join("/")}`);let r=i.slice(0,-1),o=e.resolveFsGenealogy(n.package_meta,n.url).flatMap(a=>{if(r.length===0)return a.excluded||[];if(!a.elements)return [];let s=a;for(let c of r)s=s?.elements?.[c];return s?.excluded||[]});return new Set(o).has(t)}var
|
|
4
|
+
Either skip this canonical via skip-hack.ts, or upgrade the target to R5.`;function be(e,n,i){let t=i[i.length-1];if(!t)throw new Error(`Internal error: fieldName is missing for path ${i.join("/")}`);let r=i.slice(0,-1),o=e.resolveFsGenealogy(n.package_meta,n.url).flatMap(a=>{if(r.length===0)return a.required||[];if(!a.elements)return [];let s=a;for(let c of r)s=s?.elements?.[c];return s?.required||[]});return new Set(o).has(t)}function Te(e,n,i){let t=i[i.length-1];if(!t)throw new Error(`Internal error: fieldName is missing for path ${i.join("/")}`);let r=i.slice(0,-1),o=e.resolveFsGenealogy(n.package_meta,n.url).flatMap(a=>{if(r.length===0)return a.excluded||[];if(!a.elements)return [];let s=a;for(let c of r)s=s?.elements?.[c];return s?.excluded||[]});return new Set(o).has(t)}var fn=(e,n,i)=>{if(i.refers)return i.refers.map(t=>{let r=e.ensureSpecializationCanonicalUrl(t),o=e.resolveFs(n.package_meta,r);if(!o)throw new Error(`Failed to resolve fs for ${r}`);return I(o)})},gn=e=>{let n=new Set,i=new Set;if(e.required)for(let r of e.required)n.add(r);if(e.excluded)for(let r of e.excluded)i.add(r);if(e.elements)for(let[r,o]of Object.entries(e.elements))o.min!==void 0&&o.min>0&&n.add(r);let t=e.elements?Object.keys(e.elements):void 0;return {required:n.size>0?Array.from(n):void 0,excluded:i.size>0?Array.from(i):void 0,elements:t&&t.length>0?t:void 0}},yn=e=>!e||typeof e=="object"&&Object.keys(e).length===0,j=(e,n,i)=>{let t=e;for(let o=0;o<n.length-1;o++){let a=n[o];(!t[a]||typeof t[a]!="object")&&(t[a]={}),t=t[a];}let r=n[n.length-1];t[r]=i;},hn=(e,n)=>{let i=e;for(let t of n)if(i&&typeof i=="object"&&!Array.isArray(i))i=i[t];else return;return i},Fe=(e,n,i,t,r)=>{if(i>=n.length||!e.elements)return;let o=n[i],a=e.elements[o];if(a){if(i===n.length-1&&a.fixed?.value!==void 0){j(t,n,a.fixed.value);return}if(a.slicing?.slices){r.add(n.slice(0,i+1).join("."));let s=n.slice(i+1);for(let c of Object.values(a.slicing.slices)){if(!c.min||c.min<1||!c.match||typeof c.match!="object")continue;let l=c.match;if(Object.keys(l).length!==0)if(s.length>0){let d=hn(l,s);d!==void 0&&j(t,n,d);}else j(t,n.slice(0,i+1),l);}return}Fe(a,n,i+1,t,r);}},Sn=(e,n,i)=>{if(e==="$this")return;let t=e.split("."),r=n;for(let a of t)if(r=r?.elements?.[a],!r)return;let o=r.type;!o||o.includes("/")||j(i,t,{resourceType:o});},Rn=(e,n)=>{if(!n||!e||e.length===0)return;let i={},t=new Set;for(let r of e)if(r.type==="type")Sn(r.path,n,i);else {if(!n.elements)continue;let o=r.path.split(".");Fe(n,o,0,i,t);}if(Object.keys(i).length!==0){for(let r of t){let o=r.split("."),a=i;for(let c=0;c<o.length-1;c++){let l=a[o[c]];if(!l||typeof l!="object"||Array.isArray(l))break;a=l;}let s=o[o.length-1];a[s]&&typeof a[s]=="object"&&!Array.isArray(a[s])&&(a[s]=[a[s]]);}return i}},ve=(e,n)=>{let i=n.slicing;if(!i)return;let t={};for(let[r,o]of Object.entries(i.slices??{})){if(!o)continue;let{required:a,excluded:s,elements:c}=o.schema?gn(o.schema):{};t[r]={min:o.min,max:o.max,match:yn(o.match)?Rn(i.discriminator??[],o.schema):o.match,required:a,excluded:s,elements:c,nameCandidates:ge(e,r)};}return {discriminator:i.discriminator??[],rules:i.rules,ordered:i.ordered,slices:Object.keys(t).length>0?t:void 0}};function P(e,n,i,t,r){if(t.elementReference){let o=t.elementReference.slice(1).filter((a,s)=>s%2===1);return V(e,n,o)}if(t.type){let o=e.ensureSpecializationCanonicalUrl(t.type),a=e.resolveFs(n.package_meta,o);if(!a){let s=R(n.package_meta),c=i.join("."),l=un(e,n.package_meta,t.type);throw new Error(`Could not resolve field type:
|
|
5
5
|
package: ${s}
|
|
6
6
|
schema: ${n.url}
|
|
7
7
|
field: ${c}
|
|
8
|
-
type: ${t.type}${l}`)}return I(a)}
|
|
8
|
+
type: ${t.type}${l}`)}return I(a)}t.choices||n.derivation!=="constraint"&&r?.dryWarn("#fieldTypeNotFound",`Can't recognize element type: <${n.url}>.${i.join(".")} (pkg: '${R(n.package_meta)}'): missing type info`);}var B=(e,n,i,t,r,o)=>{let a,s;t.binding&&(a=H(n,i,t),W.has(t.type??"")&&(s=K(e,n,t,r)));let c=P(e,n,i,t,r);c||r?.dryWarn("#fieldTypeNotFound",`Field type not found for '${n.url}#${i.join(".")}' (${n.derivation})`);let l;t.pattern?l={kind:"pattern",type:t.pattern.type,value:t.pattern.value}:t.fixed&&(l={kind:"fixed",type:t.fixed.type,value:t.fixed.value});let d=o??t;if(!l&&d.elements?.coding?.slicing?.slices){let u=d.elements.coding.slicing.slices,g=Object.values(u);g.length>0&&g.every(m=>m.min!==void 0&&m.min>=1&&m.match&&typeof m.match=="object"&&Object.keys(m.match).length>0)&&(l={kind:"fixed",type:"CodeableConcept",value:{coding:g.flatMap(f=>f.match?[f.match]:[])}});}return {type:c,required:be(e,n,i),excluded:Te(e,n,i),reference:fn(e,n,t),array:t.array||false,min:t.min,max:t.max,slicing:ve(i[i.length-1]??"",t),choices:t.choices,choiceOf:t.choiceOf,binding:a,enum:s,valueConstraint:l,mustSupport:t.mustSupport}};function M(e,n,i,t){return {type:V(e,n,i),array:t.array||false,required:be(e,n,i),excluded:Te(e,n,i),slicing:ve(i[i.length-1]??"",t)}}var xn=(e,n,i,t)=>{let r=e.resolveFs(n.package_meta,i);if(!r?.elements)return;let o=[];for(let[a,s]of Object.entries(r.elements)){if(s.choiceOf!=="value"&&!a.startsWith("value"))continue;let c=P(e,r,[a],s,t);c&&o.push(c);}return E(o)},Cn=(e,n,i)=>{let t=[];if(!n.elements)return t;for(let[r,o]of Object.entries(n.elements)){if(!r.startsWith("extension:"))continue;let a=r.split(":")[1];if(!a)continue;let s;for(let[c,l]of Object.entries(o.elements??{}))if(!(l.choiceOf!=="value"&&!c.startsWith("value"))&&(s=P(e,n,[r,c],l,i),s))break;t.push({name:a,url:o.url??a,valueFieldType:s,min:o.min,max:o.max!==void 0?String(o.max):void 0});}return t},kn=(e,n,i)=>{let t=[],o=n.elements?.extension?.slicing?.slices;if(!o||typeof o!="object")return t;for(let[a,s]of Object.entries(o)){let c=s,l=c.schema;if(!l)continue;let d;for(let[u,g]of Object.entries(l.elements??{})){let p=g;if(!(p.choiceOf!=="value"&&!u.startsWith("value"))&&(d=P(e,n,[u],p,i),d))break}t.push({name:a,url:c.match?.url??a,valueFieldType:d,min:l._required?1:l.min??0,max:l.max!==void 0?String(l.max):l.array?"*":"1"});}return t},In=(e,n,i,t)=>{let r=e.resolveFs(n.package_meta,i);if(!r?.elements)return;let o=Cn(e,r,t),a=kn(e,r,t),s=[...o,...a];return s.length>0?s:void 0},Ee=(e,n,i)=>{let t=[],r=(c,l,d)=>{let u=d.url,g=u?xn(e,n,u,i):void 0,p=u?In(e,n,u,i):void 0;if(!u){let S=n.elements?.extension?.slicing?.slices?.[l]?.schema;if(S){u=S.elements?.url?.fixed?.value??l;for(let[x,C]of Object.entries(S.elements??{})){let N=C;if(N.choiceOf==="value"||x.startsWith("value")){let te=P(e,n,[x],N,i);if(te){g=[te];break}}}}}let m=p&&p.length>0,f=u?e.resolveFs(n.package_meta,u):void 0,y=f?I(f):void 0,h=[...c,"extension"].join(".");t.push({name:l,path:h,url:u,profile:y,min:d.min,max:d.max!==void 0?String(d.max):void 0,mustSupport:d.mustSupport,valueFieldTypes:g,subExtensions:p,isComplex:m,nameCandidates:fe({name:l,path:h})});},o=(c,l)=>{if(l.extensions)for(let[d,u]of Object.entries(l.extensions))r(c,d,u);if(l.elements)for(let[d,u]of Object.entries(l.elements))o([...c,d],u);};o([],n);let a=new Set,s=t.filter(c=>{let l=`${c.url}:${c.path}`;return a.has(l)?false:(a.add(l),true)});return s.length===0?void 0:s};function bn(e,n,i,t,r){if(!t)return;let o={};for(let a of e.getAllElementKeys(t)){let s=[...i,a],c=e.resolveElementSnapshot(n,s),l=c.type?e.ensureSpecializationCanonicalUrl(c.type):void 0;if(l&&v(n.package_meta,l).shouldSkip){r?.warn("#skipCanonical",`Skipping field ${s} for ${l} due to skip hack ${v(n.package_meta,l).reason}`);continue}Q(e,n,s,c,t[a])?o[a]=M(e,n,s,c):o[a]=B(e,n,s,c,r,t[a]);}return o}function Tn(e){let n=[];for(let i of Object.values(e))"type"in i&&i.type&&n.push(i.type),"binding"in i&&i.binding&&n.push(i.binding);return n}async function De(e,n,i){if(!n.url)throw new Error("ValueSet URL is required");let t=L(e,n.package_meta,n.url),r=q(e,n.package_meta,n.url);return {identifier:t,description:n.description,concept:r,compose:r?void 0:n.compose}}var Le=(e,n,i)=>{let t=[];return e&&t.push(e),n&&t.push(...Tn(n)),i&&t.push(...Ie(i)),t},Ne=(e,n,i,t)=>{let o=Le(n,i,t).filter(a=>!(a.url===e.url||G(a)));return E(o)},Fn=(e,n,i,t)=>{let o=Le(n,i,t).filter(a=>a.url!==e.url);return E(o)};function He(e,n,i){let t;if(n.base){let l=e.resolveFs(n.package_meta,e.ensureSpecializationCanonicalUrl(n.base));if(!l)throw new Error(`Base resource not found '${n.base}' for <${n.url}> from ${R(n.package_meta)}`);let d=I(l);Pe(!G(d),`Unexpected nested base for ${n.url}`),t=d;}let r=bn(e,n,[],n.elements,i),o=ke(e,n,i),a=me(e,n,i);if(n.derivation==="constraint"){let l=I(n);if(!t)throw new Error(`Profile ${n.url} must have a base type`);let d=Ee(e,n,i),u=d?.flatMap(le),g=Fn(l,t,r,o),p={identifier:l,base:t,fields:r,nested:o,description:n.description,dependencies:E(g,u),extensions:d};return ye(p),[p,...a]}if(n.kind==="primitive-type"){let l=I(n);return Pe(t,`Primitive type ${n.url} must have a base type`),[{identifier:l,description:n.description,base:t,dependencies:Ne(l,t,r,o)},...a]}let s=I(n);return [{identifier:s,base:t,fields:r,nested:o,description:n.description,dependencies:Ne(s,t,r,o),typeFamily:void 0},...a]}var vn=(e,n,i)=>{let t={};for(let a of e){let s=`${a.schema.identifier.url}|${a.schema.identifier.package}`,c=se(a.schema);t[s]??={},t[s][c]??={typeSchema:a.schema,sources:[]},t[s][c].sources.push(a);}let r=[],o={};for(let a of Object.values(t)){let s=Object.values(a).sort((l,d)=>d.sources.length-l.sources.length),c=s[0];if(c)if(s.length>1){let l=c.typeSchema.identifier.url,d=c.typeSchema.identifier.package;i?.dryWarn("#duplicateSchema",`'${l}' from '${d}' has ${s.length} versions`),r.push(c.typeSchema);o[d]??={},o[d][l]=s.flatMap(g=>g.sources.map(p=>({typeSchema:g.typeSchema,sourcePackage:p.sourcePackage,sourceCanonical:p.sourceCanonical})));}else r.push(c.typeSchema);}return {schemas:r,collisions:o}},we=async(e,n,i)=>{let t=[];for(let r of e.allFs()){let o=R(r.package_meta),a=v(r.package_meta,r.url);if(a.shouldSkip){i?.dryWarn("#skipCanonical",`Skip ${r.url} from ${o}. Reason: ${a.reason}`);continue}for(let s of He(e,r,i))t.push({schema:s,sourcePackage:o,sourceCanonical:r.url});}for(let r of e.allVs())t.push({schema:await De(e,r),sourcePackage:R(r.package_meta),sourceCanonical:r.url});return vn(t,n,i)};var Ue={command:"generate <packages..>",describe:"Generate TypeSchema files from FHIR packages",builder:{packages:{type:"string",array:true,demandOption:true,describe:"FHIR packages to process (e.g., hl7.fhir.r4.core@4.0.1)"},output:{alias:"o",type:"string",describe:"Output file or directory",default:"./schemas.ndjson"},format:{alias:"f",type:"string",choices:["ndjson","json"],default:"ndjson",describe:"Output format for TypeSchema files"},treeshake:{alias:"t",type:"string",array:true,describe:"Only generate TypeSchemas for specific ResourceTypes (treeshaking)"},singleFile:{alias:"s",type:"boolean",default:false,describe:"Generate single TypeSchema file instead of multiple files (NDJSON format)"},verbose:{alias:"v",type:"boolean",default:false,describe:"Enable verbose output"},registry:{alias:"r",type:"string",describe:"Custom FHIR package registry URL (default: https://fs.get-ig.org/pkgs/)"}},handler:async e=>{let n=k({prefix:"TypeSchema"});try{n.info("Generating TypeSchema from FHIR packages"),n.info(`Packages: ${e.packages.join(", ")}`),n.info(`Output: ${e.output}`);let i=e.singleFile?"ndjson":e.format;n.debug(`Format: ${i}${e.singleFile&&e.format==="json"?" (forced from json due to singleFile)":""}`),e.treeshake&&e.treeshake.length>0&&n.info(`Treeshaking enabled for ResourceTypes: ${e.treeshake.join(", ")}`),e.singleFile&&n.info("Single file output enabled (NDJSON format)"),e.registry&&n.info(`Using custom registry: ${e.registry}`);let t=Date.now(),r=e.packages.map(d=>{if(d.includes("@")){let u=d.lastIndexOf("@");return {name:d.slice(0,u),version:d.slice(u+1)||"latest"}}return {name:d,version:"latest"}});n.info(`Processing packages: ${r.map(d=>`${d.name}@${d.version}`).join(", ")}`);let o=await xe(r,{logger:n,registry:e.registry,focusedPackages:r}),{schemas:a}=await we(o,void 0,n);if(a.length===0)throw new Error("No schemas were generated from the specified packages");let s=e.output;if(!s)throw new Error("Output format not specified");await mkdir(dirname(s),{recursive:!0});let c;i==="json"?c=JSON.stringify(a,null,2):c=a.map(d=>JSON.stringify(d)).join(`
|
|
9
9
|
`),await writeFile(s,c,"utf-8");let l=Date.now()-t;if(re(`Generated ${a.length} TypeSchema definitions`,l,{schemas:a.length}),n.info(`Output: ${s}`),e.verbose){n.debug("Generated schemas:");let d=a.map(u=>`${u.identifier?.name||"Unknown"} (${u.identifier?.kind||"unknown"})`);F(d);}}catch(i){n.error(`Failed to generate TypeSchema: ${i instanceof Error?i.message:String(i)}`),process.exit(1);}}};var ee=k({prefix:"typeschema"}),$e={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:e=>e.command(Ue).help().example("$0 typeschema generate hl7.fhir.r4.core@4.0.1","Generate TypeSchema from FHIR R4 core package"),handler:e=>{if(!e.subcommand&&e._.length===1){ee.info("Available typeschema subcommands:"),F(["generate Generate TypeSchema files from FHIR packages"]),console.log(`
|
|
10
10
|
Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
|
|
11
11
|
Examples:`),F(["atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","atomic-codegen typeschema validate schemas.ndjson","atomic-codegen typeschema merge schema1.ndjson schema2.ndjson -o merged.ndjson"]);return}e.subcommand&&!["generate","validate","merge"].includes(e.subcommand)&&(ee.error(`Unknown typeschema subcommand: ${e.subcommand}`),ee.info("Available typeschema subcommands:"),F(["generate Generate TypeSchema files from FHIR packages","validate Validate TypeSchema files for correctness and consistency","merge Merge multiple TypeSchema files into a single file"]),console.log(`
|
|
12
|
-
Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};var _=k({prefix:"cli"});async function
|
|
12
|
+
Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};var _=k({prefix:"cli"});async function Hn(e){let n=e.logLevel??(e.debug||e.verbose?"DEBUG":"INFO");_=k({prefix:"cli",level:n});}function wn(){return Dn(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(Hn).command($e).option("verbose",{alias:"v",type:"boolean",description:"Enable verbose output",default:false,global:true}).option("debug",{alias:"d",type:"boolean",description:"Enable debug output with detailed logging",default:false,global:true}).option("log-level",{alias:"l",type:"string",choices:["DEBUG","INFO","WARN","ERROR","SILENT"],description:"Set the log level (default: INFO)",global:true}).demandCommand(0).middleware(e=>{e._.length===0&&(ie("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log(" typeschema Generate, validate and merge TypeSchema files"),console.log(`
|
|
13
13
|
Use 'atomic-codegen <command> --help' for more information about a command.`),console.log(`
|
|
14
14
|
Quick examples:`),console.log(" atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson"),console.log(`
|
|
15
|
-
Use 'atomic-codegen --help' to see all options.`),process.exit(0));}).help().version("0.1.0").example("$0 typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","Generate TypeSchemas from FHIR package").fail((e,n,i)=>{_.error(n?n.message:e),_.error("Use --help for usage information"),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function ne(){await
|
|
15
|
+
Use 'atomic-codegen --help' to see all options.`),process.exit(0));}).help().version("0.1.0").example("$0 typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","Generate TypeSchemas from FHIR package").fail((e,n,i)=>{_.error(n?n.message:e),_.error("Use --help for usage information"),process.exit(1);}).wrap(Math.min(120,process.stdout.columns||80))}async function ne(){await wn().parseAsync();}import.meta.main&&ne().catch(e=>{_.error(String(e)),process.exit(1);});ne().catch(e=>{console.error("CLI Error:",e instanceof Error?e.message:e),process.exit(1);});
|
package/dist/index.d.ts
CHANGED
|
@@ -989,8 +989,19 @@ type StringFormatKey = "snake_case" | "PascalCase" | "camelCase";
|
|
|
989
989
|
interface PythonGeneratorOptions extends WriterOptions {
|
|
990
990
|
allowExtraFields?: boolean;
|
|
991
991
|
primitiveTypeExtension?: boolean;
|
|
992
|
+
generateProfile?: boolean;
|
|
992
993
|
rootPackageName: string;
|
|
993
994
|
fieldFormat: StringFormatKey;
|
|
995
|
+
/**
|
|
996
|
+
* Which client integration to generate into the output models.
|
|
997
|
+
* - `"fhirpy"` — models extend `FhirpyBaseModel` for use with the fhirpy async client (default).
|
|
998
|
+
* - `"none"` — plain Pydantic models with no client-specific code.
|
|
999
|
+
*/
|
|
1000
|
+
client?: "fhirpy" | "none";
|
|
1001
|
+
/**
|
|
1002
|
+
* @deprecated Use `client` instead: `fhirpyClient: true` → `client: "fhirpy"`,
|
|
1003
|
+
* `fhirpyClient: false` → `client: "none"`.
|
|
1004
|
+
*/
|
|
994
1005
|
fhirpyClient?: boolean;
|
|
995
1006
|
}
|
|
996
1007
|
|