@atomic-ehr/codegen 0.0.10 → 0.0.11

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

@@ -157,6 +157,18 @@ export const pushExtension = <E extends { url?: string }>(target: { extension?:
     (target.extension ??= []).push(ext);
 };
 
+/**
+ * Insert or replace an extension by URL on `target.extension`.
+ * If an extension with the same `url` already exists it is replaced in place;
+ * otherwise the new extension is appended (like {@link pushExtension}).
+ */
+export const upsertExtension = <E extends { url?: string }>(target: { extension?: E[] }, ext: E): void => {
+    const list = (target.extension ??= []);
+    const idx = list.findIndex((e) => e.url === ext.url);
+    if (idx >= 0) list[idx] = ext;
+    else list.push(ext);
+};
+
 // ---------------------------------------------------------------------------
 // Extension helpers
 // ---------------------------------------------------------------------------
@@ -191,19 +203,6 @@ export const extractComplexExtension = <T = Record<string, unknown>>(
 // Slice helpers
 // ---------------------------------------------------------------------------
 
-/**
- * Remove discriminator keys from a slice element, returning only the
- * user-supplied portion.  Used by slice getters so callers see a clean object
- * without the fixed discriminator values baked in.
- */
-export const stripMatchKeys = <T>(slice: object, matchKeys: string[]): T => {
-    const result = { ...slice } as Record<string, unknown>;
-    for (const key of matchKeys) {
-        delete result[key];
-    }
-    return result as T;
-};
-
 /**
  * Wrap a flat input object under a choice-type key before inserting into a
  * slice.  For example, a Quantity value destined for `valueQuantity` is
@@ -255,13 +254,6 @@ export const ensureSliceDefaults = <T>(items: T[], ...matches: Record<string, un
     return items;
 };
 
-/**
- * Cast an object literal to a FHIR resource type.  This centralises the single
- * `as unknown as T` that is unavoidable when constructing a resource from a
- * plain object (deep inheritance prevents direct structural compatibility).
- */
-export const buildResource = <T>(obj: object): T => obj as unknown as T;
-
 /**
  * Add `canonicalUrl` to `resource.meta.profile` if not already present.
  * Creates `meta` and `profile` when missing.
@@ -291,6 +283,26 @@ export const getArraySlice = <T>(list: readonly T[] | undefined, match: Record<s
     return list.find((item) => matchesValue(item, match));
 };
 
+/** Return all elements in `list` that satisfy the slice discriminator `match`. */
+export const getArraySliceAll = <T>(list: readonly T[] | undefined, match: Record<string, unknown>): T[] => {
+    if (!list) return [];
+    return list.filter((item) => matchesValue(item, match));
+};
+
+/**
+ * Replace all elements matching `match` in `list` with `newItems`.
+ * Each new item has the discriminator values applied via {@link applySliceMatch}
+ * before this call, so this helper only handles the array surgery.
+ */
+export const setArraySliceAll = <T>(list: T[], match: Record<string, unknown>, newItems: T[]): void => {
+    // Remove all existing items that match the discriminator
+    for (let i = list.length - 1; i >= 0; i--) {
+        if (matchesValue(list[i], match)) list.splice(i, 1);
+    }
+    // Append new items
+    list.push(...newItems);
+};
+
 // ---------------------------------------------------------------------------
 // Validation helpers
 //
@@ -353,6 +365,31 @@ export const validateSliceCardinality = (
     return errors;
 };
 
+/**
+ * Validate required fields within matched slice elements.
+ * For each array item matching the discriminator, checks that the listed fields are present.
+ */
+export const validateSliceFields = (
+    res: object,
+    profileName: string,
+    field: string,
+    match: Record<string, unknown>,
+    sliceName: string,
+    requiredFields: string[],
+): string[] => {
+    const items = (res as Record<string, unknown>)[field] as unknown[] | undefined;
+    const errors: string[] = [];
+    for (const item of (items ?? []).filter((item) => matchesValue(item, match))) {
+        const obj = item as Record<string, unknown>;
+        for (const rf of requiredFields) {
+            if (obj[rf] === undefined || obj[rf] === null) {
+                errors.push(`${profileName}.${field}[${sliceName}].${rf} is required`);
+            }
+        }
+    }
+    return errors;
+};
+
 /**
  * Checks that at least one of the listed choice-type variants is present.
  * E.g. `["effectiveDateTime", "effectivePeriod"]`.

package/dist/cli/index.js

@@ -1,6 +1,6 @@
 #!/usr/bin/env node
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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 T(e,n){let o=`${e.name}#${e.version}`,t=_[o]?.[n];if(t)return {shouldSkip:true,reason:t};let i=_[e.name]?.[n];return i?{shouldSkip:true,reason:i}:{shouldSkip:false}}var R=e=>`${e.name}#${e.version}`,ie=e=>`${e.name}@${e.version}`,oe=e=>{let n=JSON.stringify(e);return createHash("sha256").update(n).digest("hex").slice(0,16)},re=(e,n)=>{let o=e.derivation==="constraint"?"constraint":"specialization";return {...e,derivation:o,kind:e.kind,package_meta:e.package_meta||n,name:e.name,url:e.url,base:e.base}};var A=e=>e?.kind==="nested";var v=(...e)=>{let n=e.filter(t=>t!==void 0).flatMap(t=>t.map(i=>[i.url,i]));return n.length===0?void 0:Object.values(Object.fromEntries(n)).sort((t,i)=>t.url.localeCompare(i.url))};var 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t=[],r=n.elements?.extension?.slicing?.slices;if(!r||typeof r!="object")return t;for(let[a,l]of Object.entries(r)){let c=l,s=c.schema;if(!s)continue;let d;for(let[u,h]of Object.entries(s.elements??{})){let p=h;if(!(p.choiceOf!=="value"&&!u.startsWith("value"))&&(d=E(e,n,[u],p,o),d))break}t.push({name:a,url:c.match?.url??a,valueFieldType:d,min:s._required?1:s.min??0,max:s.max!==void 0?String(s.max):s.array?"*":"1"});}return t},en=(e,n,o,t)=>{let i=e.resolveFs(n.package_meta,o);if(!i?.elements)return;let r=Qe(e,i,t),a=Xe(e,i,t),l=[...r,...a];return l.length>0?l:void 0},ke=(e,n,o)=>{let t=[],i=(c,s,d)=>{let u=d.url,h=u?Ze(e,n,u,o):void 0,p=u?en(e,n,u,o):void 0;if(!u){let y=n.elements?.extension?.slicing?.slices?.[s]?.schema;if(y){u=y.elements?.url?.fixed?.value??s;for(let[S,x]of Object.entries(y.elements??{})){let k=x;if(k.choiceOf==="value"||S.startsWith("value")){let D=E(e,n,[S],k,o);if(D){h=[D];break}}}}}let m=p&&p.length>0,f=u?e.resolveFs(n.package_meta,u):void 0,g=f?I(f):void 0;t.push({name:s,path:[...c,"extension"].join("."),url:u,profile:g,min:d.min,max:d.max!==void 0?String(d.max):void 0,mustSupport:d.mustSupport,valueFieldTypes:h,subExtensions:p,isComplex:m});},r=(c,s)=>{if(s.extensions)for(let[d,u]of Object.entries(s.extensions))i(c,d,u);if(s.elements)for(let[d,u]of Object.entries(s.elements))r([...c,d],u);};r([],n);let a=new Set,l=t.filter(c=>{let s=`${c.url}:${c.path}`;return a.has(s)?false:(a.add(s),true)});return l.length===0?void 0:l};function nn(e,n,o,t,i){if(!t)return;let r={};for(let a of e.getAllElementKeys(t)){let l=[...o,a],c=e.resolveElementSnapshot(n,l),s=c.type?e.ensureSpecializationCanonicalUrl(c.type):void 0;if(s&&T(n.package_meta,s).shouldSkip){i?.warn("#skipCanonical",`Skipping field ${l} for ${s} due to skip hack ${T(n.package_meta,s).reason}`);continue}Y(e,n,l,c,t[a])?r[a]=j(e,n,l,c):r[a]=B(e,n,l,c,i,t[a]);}return r}function tn(e){let n=[];for(let o of Object.values(e))"type"in o&&o.type&&n.push(o.type),"binding"in o&&o.binding&&n.push(o.binding);return n}async function be(e,n,o){if(!n.url)throw new Error("ValueSet URL is required");let t=N(e,n.package_meta,n.url),i=z(e,n.package_meta,n.url);return {identifier:t,description:n.description,concept:i,compose:i?void 0:n.compose}}var Fe=(e,n,o)=>{let t=[];return e&&t.push(e),n&&t.push(...tn(n)),o&&t.push(...ye(o)),t},Ie=(e,n,o,t)=>{let r=Fe(n,o,t).filter(a=>!(a.url===e.url||A(a)));return v(r)},on=(e,n,o,t)=>{let r=Fe(n,o,t).filter(a=>a.url!==e.url);return v(r)};function Te(e,n,o){let t;if(n.base){let s=e.resolveFs(n.package_meta,e.ensureSpecializationCanonicalUrl(n.base));if(!s)throw new Error(`Base resource not found '${n.base}' for <${n.url}> from ${R(n.package_meta)}`);let d=I(s);Ce(!A(d),`Unexpected nested base for ${n.url}`),t=d;}let i=nn(e,n,[],n.elements,o),r=ge(e,n,o),a=le(e,n,o);if(n.derivation==="constraint"){let s=I(n);if(!t)throw new Error(`Profile ${n.url} must have a base type`);let d=ke(e,n,o),u=d?.flatMap(ae),h=on(s,t,i,r);return [{identifier:s,base:t,fields:i,nested:r,description:n.description,dependencies:v(h,u),extensions:d},...a]}if(n.kind==="primitive-type"){let s=I(n);return Ce(t,`Primitive type ${n.url} must have a base type`),[{identifier:s,description:n.description,base:t,dependencies:Ie(s,t,i,r)},...a]}let l=I(n);return [{identifier:l,base:t,fields:i,nested:r,description:n.description,dependencies:Ie(l,t,i,r),typeFamily:void 0},...a]}var rn=(e,n,o)=>{let t={};for(let a of e){let l=`${a.schema.identifier.url}|${a.schema.identifier.package}`,c=oe(a.schema);t[l]??={},t[l][c]??={typeSchema:a.schema,sources:[]},t[l][c].sources.push(a);}let i=[],r={};for(let a of Object.values(t)){let l=Object.values(a).sort((s,d)=>d.sources.length-s.sources.length),c=l[0];if(c)if(l.length>1){let s=c.typeSchema.identifier.url,d=c.typeSchema.identifier.package;o?.dryWarn("#duplicateSchema",`'${s}' from '${d}' has ${l.length} versions`),i.push(c.typeSchema);r[d]??={},r[d][s]=l.flatMap(h=>h.sources.map(p=>({typeSchema:h.typeSchema,sourcePackage:p.sourcePackage,sourceCanonical:p.sourceCanonical})));}else i.push(c.typeSchema);}return {schemas:i,collisions:r}},ve=async(e,n,o)=>{let t=[];for(let i of e.allFs()){let r=R(i.package_meta),a=T(i.package_meta,i.url);if(a.shouldSkip){o?.dryWarn("#skipCanonical",`Skip ${i.url} from ${r}. Reason: ${a.reason}`);continue}for(let l of Te(e,i,o))t.push({schema:l,sourcePackage:r,sourceCanonical:i.url});}for(let i of e.allVs())t.push({schema:await be(e,i),sourcePackage:R(i.package_meta),sourceCanonical:i.url});return rn(t,n,o)};var Ee={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=C({prefix:"TypeSchema"});try{n.info("Generating TypeSchema from FHIR packages"),n.info(`Packages: ${e.packages.join(", ")}`),n.info(`Output: ${e.output}`);let o=e.singleFile?"ndjson":e.format;n.debug(`Format: ${o}${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(),i=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: ${i.map(d=>`${d.name}@${d.version}`).join(", ")}`);let r=await ue(i,{logger:n,registry:e.registry,focusedPackages:i}),{schemas:a}=await ve(r,void 0,n);if(a.length===0)throw new Error("No schemas were generated from the specified packages");let l=e.output;if(!l)throw new Error("Output format not specified");await mkdir(dirname(l),{recursive:!0});let c;o==="json"?c=JSON.stringify(a,null,2):c=a.map(d=>JSON.stringify(d)).join(`
+`),await writeFile(l,c,"utf-8");let s=Date.now()-t;if(ne(`Generated ${a.length} TypeSchema definitions`,s,{schemas:a.length}),n.info(`Output: ${l}`),e.verbose){n.debug("Generated schemas:");let d=a.map(u=>`${u.identifier?.name||"Unknown"} (${u.identifier?.kind||"unknown"})`);F(d);}}catch(o){n.error(`Failed to generate TypeSchema: ${o instanceof Error?o.message:String(o)}`),process.exit(1);}}};var Q=C({prefix:"typeschema"}),De={command:"typeschema [subcommand]",describe:"TypeSchema operations - generate, validate and merge schemas",builder:e=>e.command(Ee).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){Q.info("Available typeschema subcommands:"),F(["generate    Generate TypeSchema files from FHIR packages"]),console.log(`
 Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),console.log(`
 Examples:`),F(["atomic-codegen typeschema generate hl7.fhir.r4.core@4.0.1 -o schemas.ndjson","atomic-codegen typeschema validate schemas.ndjson","atomic-codegen typeschema merge schema1.ndjson schema2.ndjson -o merged.ndjson"]);return}e.subcommand&&!["generate","validate","merge"].includes(e.subcommand)&&(Q.error(`Unknown typeschema subcommand: ${e.subcommand}`),Q.info("Available typeschema subcommands:"),F(["generate    Generate TypeSchema files from FHIR packages","validate    Validate TypeSchema files for correctness and consistency","merge       Merge multiple TypeSchema files into a single file"]),console.log(`
 Use 'atomic-codegen typeschema <subcommand> --help' for more information about a subcommand.`),process.exit(1));}};var M=C({prefix:"cli"});async function dn(e){let n=e.logLevel??(e.debug||e.verbose?"DEBUG":"INFO");M=C({prefix:"cli",level:n});}function mn(){return ln(hideBin(process.argv)).scriptName("atomic-codegen").usage("$0 <command> [options]").middleware(dn).command(De).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&&(ee("Welcome to Atomic Codegen!"),console.log("Available commands:"),console.log("  typeschema   Generate, validate and merge TypeSchema files"),console.log(`

package/dist/index.d.ts

@@ -988,6 +988,7 @@ type CSharpGeneratorOptions = WriterOptions & {
 type StringFormatKey = "snake_case" | "PascalCase" | "camelCase";
 interface PythonGeneratorOptions extends WriterOptions {
     allowExtraFields?: boolean;
+    primitiveTypeExtension?: boolean;
     rootPackageName: string;
     fieldFormat: StringFormatKey;
     fhirpyClient?: boolean;