Unify FHIR package patching via preprocessPackage hook

CLAUDE.md

@@ -95,7 +95,7 @@ FHIR Package → TypeSchema Generator → TypeSchema Format → Code Generators
 - Uses strict TypeScript with latest ESNext features
 - Module format: ESM with `"type": "module"` in package.json
 - Build target: Node.js with Bun bundler
-- Biome for linting/formatting (tabs, double quotes)
+- Biome for linting/formatting (spaces, double quotes)
 
 ### Coding Style
 - Use arrow function syntax for new functions: `const foo = (): ReturnType => { ... }`

biome.json

@@ -16,6 +16,7 @@
       "biome.json",
       "package.json",
       "examples/*/*.ts",
+      "examples/*.ts",
       ".zed/*.json"
     ]
   },

examples/nodge-r4.ts

@@ -1,7 +1,7 @@
 // Run this script using Bun CLI with:
 // bun run scripts/generate-fhir-types.ts
 
-import { CanonicalManager, type PreprocessPackageContext } from "@atomic-ehr/fhir-canonical-manager";
+import type { PreprocessContext } from "@atomic-ehr/fhir-canonical-manager";
 import { APIBuilder, prettyReport } from "../src/api/builder";
 
 // Fix known package name typos (in-memory transformation)
@@ -21,8 +21,9 @@ const needsCoreDependency = (name: string): boolean => {
     );
 };
 
-const preprocessPackage = ({ packageJson }: PreprocessPackageContext): PreprocessPackageContext => {
-    let json = packageJson;
+const preprocessPackage = (ctx: PreprocessContext): PreprocessContext => {
+    if (ctx.kind !== "package") return ctx;
+    let json = ctx.packageJson;
     const name = json.name as string;
 
     // Fix package name typos
@@ -44,25 +45,20 @@ const preprocessPackage = ({ packageJson }: PreprocessPackageContext): Preproces
         }
     }
 
-    return { packageJson: json };
+    return { kind: "package", packageJson: json };
 };
 
 if (require.main === module) {
     console.log("📦 Generating FHIR R4 Core Types...");
 
-    const manager = CanonicalManager({
-        packages: [
-            "hl7.fhir.r4.core@4.0.1",
-            "ehelse.fhir.no.grunndata@2.3.5",
-            "hl7.fhir.no.basis@2.2.2",
-            "sfm.030322@2.0.1",
-        ],
-        workingDir: ".codegen-cache/canonical-manager-cache",
-        registry: "https://packages.simplifier.net",
+    const builder = new APIBuilder({
         preprocessPackage,
-    });
-
-    const builder = new APIBuilder({ manager })
+        registry: "https://packages.simplifier.net",
+    })
+        .fromPackage("hl7.fhir.r4.core", "4.0.1")
+        .fromPackage("ehelse.fhir.no.grunndata", "2.3.5")
+        .fromPackage("hl7.fhir.no.basis", "2.2.2")
+        .fromPackage("sfm.030322", "2.0.1")
         .throwException()
         .typescript({
             withDebugComment: false,

examples/typescript-ccda/generate.ts

@@ -1,32 +1,36 @@
 // Run this script using Bun CLI with:
 // bun run scripts/generate-fhir-types.ts
 
-import { registerFromPackageMetas } from "@root/typeschema/register";
+import { CanonicalManager, type PreprocessContext } from "@atomic-ehr/fhir-canonical-manager";
+import { registerFromManager } from "@root/typeschema/register";
 import { APIBuilder, prettyReport } from "../../src/api/builder";
 
+const preprocessPackage = (ctx: PreprocessContext): PreprocessContext => {
+    if (ctx.kind !== "resource") return ctx;
+    if (ctx.package.name !== "hl7.cda.uv.core") return ctx;
+    let str = JSON.stringify(ctx.resource);
+    str = str.replaceAll(
+        "http://hl7.org/cda/stds/core/StructureDefinition/IVL_TS",
+        "http://hl7.org/cda/stds/core/StructureDefinition/IVL-TS",
+    );
+    return { ...ctx, resource: JSON.parse(str) };
+};
+
 if (require.main === module) {
     console.log("📦 Generating CCDA Types...");
 
-    const registry = await registerFromPackageMetas(
-        [
-            { name: "hl7.fhir.r4.core", version: "4.0.1" },
-            { name: "hl7.cda.us.ccda", version: "5.0.0-ballot" },
-            // { name: "hl7.cda.uv.core", version: "2.0.2-sd" },
-        ],
-        {},
-    );
-    if (registry === undefined) throw new Error("Failed to register package");
-
-    registry.patchSd((pkg, sd) => {
-        if (pkg.name !== "hl7.cda.uv.core") return sd;
-        let str = JSON.stringify(sd);
-        str = str.replaceAll(
-            "http://hl7.org/cda/stds/core/StructureDefinition/IVL_TS",
-            "http://hl7.org/cda/stds/core/StructureDefinition/IVL-TS",
-        );
-        return JSON.parse(str);
+    const manager = CanonicalManager({
+        packages: [],
+        workingDir: ".codegen-cache/canonical-manager-cache",
+        preprocessPackage,
     });
 
+    // Initialize manager with packages to discover CDA resources
+    await manager.addPackages("hl7.fhir.r4.core@4.0.1", "hl7.cda.us.ccda@5.0.0-ballot");
+    const ref2meta = await manager.init();
+    const packageMetas = Object.values(ref2meta);
+
+    const registry = await registerFromManager(manager, { focusedPackages: packageMetas });
     const cdaResources = registry
         .allSd()
         .filter((sd) => {

package.json

@@ -65,7 +65,7 @@
   },
   "homepage": "https://github.com/atomic-ehr/codegen#readme",
   "dependencies": {
-    "@atomic-ehr/fhir-canonical-manager": "^0.0.20",
+    "@atomic-ehr/fhir-canonical-manager": "^0.0.21",
     "@atomic-ehr/fhirschema": "^0.0.8",
     "mustache": "^4.2.0",
     "picocolors": "^1.1.1",

src/api/builder.ts

@@ -8,7 +8,12 @@
 import assert from "node:assert";
 import * as fs from "node:fs";
 import * as Path from "node:path";
-import { CanonicalManager, type LocalPackageConfig, type TgzPackageConfig } from "@atomic-ehr/fhir-canonical-manager";
+import {
+    CanonicalManager,
+    type LocalPackageConfig,
+    type PreprocessContext,
+    type TgzPackageConfig,
+} from "@atomic-ehr/fhir-canonical-manager";
 import { CSharp, type CSharpGeneratorOptions } from "@root/api/writer-generator/csharp/csharp";
 import { Python, type PythonGeneratorOptions } from "@root/api/writer-generator/python";
 import { generateTypeSchemas } from "@root/typeschema";
@@ -127,6 +132,7 @@ export class APIBuilder {
         userOpts: Partial<APIBuilderOptions> & {
             manager?: ReturnType<typeof CanonicalManager>;
             register?: Register;
+            preprocessPackage?: (context: PreprocessContext) => PreprocessContext;
             logger?: CodegenLogger;
         } = {},
     ) {
@@ -144,7 +150,12 @@ export class APIBuilder {
             ...defaultOpts,
             ...Object.fromEntries(
                 Object.entries(userOpts).filter(
-                    ([k, v]) => v !== undefined && k !== "manager" && k !== "register" && k !== "logger",
+                    ([k, v]) =>
+                        v !== undefined &&
+                        k !== "manager" &&
+                        k !== "register" &&
+                        k !== "preprocessPackage" &&
+                        k !== "logger",
                 ),
             ),
         };
@@ -166,6 +177,7 @@ export class APIBuilder {
                 workingDir: ".codegen-cache/canonical-manager-cache",
                 registry: userOpts.registry,
                 dropCache: userOpts.dropCanonicalManagerCache,
+                preprocessPackage: userOpts.preprocessPackage,
             });
         this.logger = userOpts.logger ?? createLogger({ prefix: "API", level: opts.logLevel });
         this.options = opts;

src/typeschema/register.ts

@@ -26,7 +26,6 @@ export type Register = {
     resolveFsGenealogy(pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichFHIRSchema[];
     resolveFsSpecializations(pkg: PackageMeta, canonicalUrl: CanonicalUrl): RichFHIRSchema[];
     allSd(): RichStructureDefinition[];
-    patchSd(fn: (pkg: PackageMeta, sd: StructureDefinition) => StructureDefinition): void;
     /** Returns all FHIRSchemas from all packages in the resolver */
     allFs(): RichFHIRSchema[];
     /** Returns all ValueSets from all packages in the resolver */
@@ -312,23 +311,6 @@ export const registerFromManager = async (
                 )
                 .filter((r): r is RichStructureDefinition => isStructureDefinition(r))
                 .sort((sd1, sd2) => sd1.url.localeCompare(sd2.url)),
-        patchSd: (fn: (pkg: PackageMeta, sd: StructureDefinition) => StructureDefinition) => {
-            Object.values(resolver).flatMap((pkgIndex) =>
-                Object.values(pkgIndex.canonicalResolution).forEach((resolutions) => {
-                    resolutions.forEach((e) => {
-                        if (isStructureDefinition(e.resource)) {
-                            const sd = e.resource as StructureDefinition;
-                            const newSd = fn(pkgIndex.pkg, sd);
-                            if (sd.url !== newSd.url)
-                                throw new Error(`Patch update StructureDefinition URL: ${sd.url} !== ${newSd.url}`);
-                            e.resource = newSd;
-                        }
-                    });
-                }),
-            );
-            enrichResolver(resolver);
-            cachedResolutionTree = undefined;
-        },
         allFs: () => Object.values(resolver).flatMap((pkgIndex) => Object.values(pkgIndex.fhirSchemas)),
         allVs: () => Object.values(resolver).flatMap((pkgIndex) => Object.values(pkgIndex.valueSets)),
         resolveVs,