@atomic-ehr/fhir-canonical-manager 0.0.25 → 0.0.26

package/README.md

@@ -1,7 +1,8 @@
 # @atomic-ehr/fhir-canonical-manager
 
-[![npm version](https://badge.fury.io/js/@atomic-ehr%2Ffhir-canonical-manager.svg)](https://www.npmjs.com/package/@atomic-ehr/fhir-canonical-manager)
 [![npm canary](https://img.shields.io/npm/v/@atomic-ehr/fhir-canonical-manager/canary.svg?label=canary)](https://www.npmjs.com/package/@atomic-ehr/fhir-canonical-manager/v/canary)
+[![npm version](https://img.shields.io/npm/v/@atomic-ehr/fhir-canonical-manager.svg)](https://www.npmjs.com/package/@atomic-ehr/fhir-canonical-manager)
+[![CI](https://github.com/atomic-ehr/fhir-canonical-manager/actions/workflows/ci.yml/badge.svg)](https://github.com/atomic-ehr/fhir-canonical-manager/actions/workflows/ci.yml)
 
 A TypeScript package manager for FHIR resources that provides canonical URL resolution. This library helps you discover, resolve, and manage FHIR packages and their resources through a simple, functional API.
 
@@ -360,9 +361,15 @@ const fixVersion: PackagePatch = (pkg, packageJson) => ({ ...packageJson, versio
 // patches: { packageJson: [fixVersion] }
 ```
 
-The bundled patch helpers (`excludeCanonical`, `applyPatches`, `matchPackage`) are exported
-from the `@atomic-ehr/fhir-canonical-manager/patch` subpath. `excludeCanonical` returns an
-`indexEntry` handler that drops a canonical (e.g. an R4 extension that references an R5-only type):
+The bundled patch helpers are exported from the `@atomic-ehr/fhir-canonical-manager/patch` subpath:
+
+- **Scoping combinators** — `inPackage(match, [handlers])` applies handlers only to matching packages (name, `{name, version}`, or predicate) and nests; `inResource(url, [handlers])` scopes resource handlers to one canonical.
+- **Manifest fixes** (`packageJson` phase) — `ensureDependency(deps)` makes a package declare each dependency at the given version (adds missing ones, adjusts mismatched ones, never adds a package to itself); `renamePackage(from, to)` fixes a typo'd manifest name.
+- **Resource fixes** (`fhirResource` phase) — `replaceText(from, to)` substitutes a string throughout the serialized body (typo'd canonicals, wrong reference targets, unavailable ValueSet bindings — scope it!); `ensureCodes(url, codes)` appends missing codes to a CodeSystem without touching existing concepts.
+- **Index fixes** (`indexEntry` phase) — `excludeCanonical({package?, url, reason})` drops a canonical from the index (output *and* resolution), recording the reason in `report()`.
+- **Plumbing** — `applyPatches`, `matchPackage`.
+
+For example, `excludeCanonical` dropping a canonical (e.g. an R4 extension that references an R5-only type):
 
 ```typescript
 import { CanonicalManager } from "@atomic-ehr/fhir-canonical-manager";

package/dist/patches.d.ts

@@ -1,4 +1,4 @@
-import type { EntryPatch, IndexEntry, PackageId, PatchReportSink, Resource } from "./types/index.js";
+import type { EntryPatch, IndexEntry, PackageId, PackagePatch, PatchReportSink, Resource, ResourcePatch } from "./types/index.js";
 export type PackageMatch = string | PackageId | ((pkg: PackageId) => boolean);
 export declare const matchPackage: (match: PackageMatch, pkg: PackageId) => boolean;
 export declare const applyPatches: <T extends Record<string, unknown> | IndexEntry | Resource>(handlers: ((pkg: PackageId, value: T, report: PatchReportSink) => T | null | undefined)[] | undefined, pkg: PackageId, value: T, report: PatchReportSink) => T | null;
@@ -7,4 +7,12 @@ export declare const excludeCanonical: (opts: {
     url: string;
     reason: string;
 }) => EntryPatch;
+type Handler<V> = (pkg: PackageId, value: V, report: PatchReportSink) => V | undefined;
+export declare const inPackage: <V>(match: PackageMatch, handlers: Handler<V>[]) => Handler<V>;
+export declare const inResource: (url: string, handlers: ResourcePatch[]) => ResourcePatch;
+export declare const replaceText: (from: string, to: string) => ResourcePatch;
+export declare const ensureCodes: (url: string, codes: string[]) => ResourcePatch;
+export declare const ensureDependency: (deps: Record<string, string>) => PackagePatch;
+export declare const renamePackage: (from: string, to: string) => PackagePatch;
+export {};
 //# sourceMappingURL=patches.d.ts.map

package/dist/patches.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"patches.d.ts","sourceRoot":"","sources":["../src/patches.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EAAE,UAAU,EAAE,UAAU,EAAE,SAAS,EAAE,eAAe,EAAE,QAAQ,EAAE,MAAM,kBAAkB,CAAC;AAGrG,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,SAAS,GAAG,CAAC,CAAC,GAAG,EAAE,SAAS,KAAK,OAAO,CAAC,CAAC;AAE9E,eAAO,MAAM,YAAY,GAAI,OAAO,YAAY,EAAE,KAAK,SAAS,KAAG,OAIlE,CAAC;AAOF,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,GAAG,QAAQ,EAClF,UAAU,CAAC,CAAC,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,eAAe,KAAK,CAAC,GAAG,IAAI,GAAG,SAAS,CAAC,EAAE,GAAG,SAAS,EACrG,KAAK,SAAS,EACd,OAAO,CAAC,EACR,QAAQ,eAAe,KACxB,CAAC,GAAG,IAQN,CAAC;AAMF,eAAO,MAAM,gBAAgB,GACxB,MAAM;IAAE,OAAO,CAAC,EAAE,YAAY,CAAC;IAAC,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,KAAG,UAMhE,CAAC"}
+{"version":3,"file":"patches.d.ts","sourceRoot":"","sources":["../src/patches.ts"],"names":[],"mappings":"AAIA,OAAO,KAAK,EACR,UAAU,EACV,UAAU,EACV,SAAS,EACT,YAAY,EACZ,eAAe,EACf,QAAQ,EACR,aAAa,EAChB,MAAM,kBAAkB,CAAC;AAG1B,MAAM,MAAM,YAAY,GAAG,MAAM,GAAG,SAAS,GAAG,CAAC,CAAC,GAAG,EAAE,SAAS,KAAK,OAAO,CAAC,CAAC;AAE9E,eAAO,MAAM,YAAY,GAAI,OAAO,YAAY,EAAE,KAAK,SAAS,KAAG,OAIlE,CAAC;AAOF,eAAO,MAAM,YAAY,GAAI,CAAC,SAAS,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,GAAG,QAAQ,EAClF,UAAU,CAAC,CAAC,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,eAAe,KAAK,CAAC,GAAG,IAAI,GAAG,SAAS,CAAC,EAAE,GAAG,SAAS,EACrG,KAAK,SAAS,EACd,OAAO,CAAC,EACR,QAAQ,eAAe,KACxB,CAAC,GAAG,IAQN,CAAC;AAMF,eAAO,MAAM,gBAAgB,GACxB,MAAM;IAAE,OAAO,CAAC,EAAE,YAAY,CAAC;IAAC,GAAG,EAAE,MAAM,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,KAAG,UAMhE,CAAC;AAKN,KAAK,OAAO,CAAC,CAAC,IAAI,CAAC,GAAG,EAAE,SAAS,EAAE,KAAK,EAAE,CAAC,EAAE,MAAM,EAAE,eAAe,KAAK,CAAC,GAAG,SAAS,CAAC;AAmBvF,eAAO,MAAM,SAAS,GAAI,CAAC,EAAE,OAAO,YAAY,EAAE,UAAU,OAAO,CAAC,CAAC,CAAC,EAAE,KAAG,OAAO,CAAC,CAAC,CAKnF,CAAC;AAGF,eAAO,MAAM,UAAU,GAAI,KAAK,MAAM,EAAE,UAAU,aAAa,EAAE,KAAG,aAKnE,CAAC;AAWF,eAAO,MAAM,WAAW,GACnB,MAAM,MAAM,EAAE,IAAI,MAAM,KAAG,aAK3B,CAAC;AAON,eAAO,MAAM,WAAW,GACnB,KAAK,MAAM,EAAE,OAAO,MAAM,EAAE,KAAG,aAS/B,CAAC;AAON,eAAO,MAAM,gBAAgB,GACxB,MAAM,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,KAAG,YAQ/B,CAAC;AAGN,eAAO,MAAM,aAAa,GACrB,MAAM,MAAM,EAAE,IAAI,MAAM,KAAG,YAI3B,CAAC"}

package/dist/patches.js

@@ -24,4 +24,62 @@ export const excludeCanonical = (opts) => (pkg, entry, report) => {
     report({ kind: "exclusion", package: pkg, url: opts.url, reason: opts.reason });
     return null;
 };
+const run = (handlers, pkg, value, report) => {
+    let acc = value;
+    let changed = false;
+    for (const handler of handlers) {
+        const result = handler(pkg, acc, report);
+        if (result !== undefined) {
+            acc = result;
+            changed = true;
+        }
+    }
+    if (!changed)
+        return undefined;
+    return acc;
+};
+export const inPackage = (match, handlers) => {
+    return (pkg, value, report) => {
+        if (!matchPackage(match, pkg))
+            return undefined;
+        return run(handlers, pkg, value, report);
+    };
+};
+export const inResource = (url, handlers) => {
+    return (pkg, resource, report) => {
+        if (resource.url !== url)
+            return undefined;
+        return run(handlers, pkg, resource, report);
+    };
+};
+export const replaceText = (from, to) => (_pkg, resource) => {
+    const str = JSON.stringify(resource);
+    if (!str.includes(from))
+        return undefined;
+    return JSON.parse(str.replaceAll(from, to));
+};
+export const ensureCodes = (url, codes) => (_pkg, resource) => {
+    if (resource.resourceType !== "CodeSystem" || resource.url !== url)
+        return undefined;
+    const concept = resource.concept;
+    if (!concept)
+        return undefined;
+    const existing = new Set(concept.map((c) => c.code));
+    const missing = codes.filter((code) => !existing.has(code));
+    if (missing.length === 0)
+        return undefined;
+    return { ...resource, concept: [...concept, ...missing.map((code) => ({ code }))] };
+};
+export const ensureDependency = (deps) => (pkg, pkgJson) => {
+    const existing = pkgJson.dependencies ?? {};
+    const updates = Object.entries(deps).filter(([name, version]) => name !== pkg.name && existing[name] !== version);
+    if (updates.length === 0)
+        return undefined;
+    return { ...pkgJson, dependencies: { ...existing, ...Object.fromEntries(updates) } };
+};
+export const renamePackage = (from, to) => (pkg, pkgJson) => {
+    if (pkg.name !== from)
+        return undefined;
+    return { ...pkgJson, name: to };
+};
 //# sourceMappingURL=patches.js.map

package/dist/patches.js.map

@@ -1 +1 @@
-{"version":3,"file":"patches.js","sourceRoot":"","sources":["../src/patches.ts"],"names":[],"mappings":"AASA,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,KAAmB,EAAE,GAAc,EAAW,EAAE;IACzE,IAAI,OAAO,KAAK,KAAK,UAAU;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACnD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC,IAAI,KAAK,KAAK,CAAC;IACzD,OAAO,GAAG,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,KAAK,SAAS,IAAI,GAAG,CAAC,OAAO,KAAK,KAAK,CAAC,OAAO,CAAC,CAAC;AACrG,CAAC,CAAC;AAOF,MAAM,CAAC,MAAM,YAAY,GAAG,CACxB,QAAqG,EACrG,GAAc,EACd,KAAQ,EACR,MAAuB,EACf,EAAE;IACV,IAAI,GAAG,GAAG,KAAK,CAAC;IAChB,KAAK,MAAM,OAAO,IAAI,QAAQ,IAAI,EAAE,EAAE,CAAC;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;QACzC,IAAI,MAAM,KAAK,IAAI;YAAE,OAAO,IAAI,CAAC;QACjC,IAAI,MAAM,KAAK,SAAS;YAAE,GAAG,GAAG,MAAM,CAAC;IAC3C,CAAC;IACD,OAAO,GAAG,CAAC;AACf,CAAC,CAAC;AAMF,MAAM,CAAC,MAAM,gBAAgB,GACzB,CAAC,IAA6D,EAAc,EAAE,CAC9E,CAAC,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;IACnB,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,CAAC,GAAG;QAAE,OAAO,SAAS,CAAC;IAC7C,IAAI,IAAI,CAAC,OAAO,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,CAAC;QAAE,OAAO,SAAS,CAAC;IACvE,MAAM,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IAChF,OAAO,IAAI,CAAC;AAChB,CAAC,CAAC"}
+{"version":3,"file":"patches.js","sourceRoot":"","sources":["../src/patches.ts"],"names":[],"mappings":"AAiBA,MAAM,CAAC,MAAM,YAAY,GAAG,CAAC,KAAmB,EAAE,GAAc,EAAW,EAAE;IACzE,IAAI,OAAO,KAAK,KAAK,UAAU;QAAE,OAAO,KAAK,CAAC,GAAG,CAAC,CAAC;IACnD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC,IAAI,KAAK,KAAK,CAAC;IACzD,OAAO,GAAG,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,CAAC,KAAK,CAAC,OAAO,KAAK,SAAS,IAAI,GAAG,CAAC,OAAO,KAAK,KAAK,CAAC,OAAO,CAAC,CAAC;AACrG,CAAC,CAAC;AAOF,MAAM,CAAC,MAAM,YAAY,GAAG,CACxB,QAAqG,EACrG,GAAc,EACd,KAAQ,EACR,MAAuB,EACf,EAAE;IACV,IAAI,GAAG,GAAG,KAAK,CAAC;IAChB,KAAK,MAAM,OAAO,IAAI,QAAQ,IAAI,EAAE,EAAE,CAAC;QACnC,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;QACzC,IAAI,MAAM,KAAK,IAAI;YAAE,OAAO,IAAI,CAAC;QACjC,IAAI,MAAM,KAAK,SAAS;YAAE,GAAG,GAAG,MAAM,CAAC;IAC3C,CAAC;IACD,OAAO,GAAG,CAAC;AACf,CAAC,CAAC;AAMF,MAAM,CAAC,MAAM,gBAAgB,GACzB,CAAC,IAA6D,EAAc,EAAE,CAC9E,CAAC,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;IACnB,IAAI,KAAK,CAAC,GAAG,KAAK,IAAI,CAAC,GAAG;QAAE,OAAO,SAAS,CAAC;IAC7C,IAAI,IAAI,CAAC,OAAO,IAAI,CAAC,YAAY,CAAC,IAAI,CAAC,OAAO,EAAE,GAAG,CAAC;QAAE,OAAO,SAAS,CAAC;IACvE,MAAM,CAAC,EAAE,IAAI,EAAE,WAAW,EAAE,OAAO,EAAE,GAAG,EAAE,GAAG,EAAE,IAAI,CAAC,GAAG,EAAE,MAAM,EAAE,IAAI,CAAC,MAAM,EAAE,CAAC,CAAC;IAChF,OAAO,IAAI,CAAC;AAChB,CAAC,CAAC;AAQN,MAAM,GAAG,GAAG,CAAI,QAAsB,EAAE,GAAc,EAAE,KAAQ,EAAE,MAAuB,EAAiB,EAAE;IACxG,IAAI,GAAG,GAAG,KAAK,CAAC;IAChB,IAAI,OAAO,GAAG,KAAK,CAAC;IACpB,KAAK,MAAM,OAAO,IAAI,QAAQ,EAAE,CAAC;QAC7B,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;QACzC,IAAI,MAAM,KAAK,SAAS,EAAE,CAAC;YACvB,GAAG,GAAG,MAAM,CAAC;YACb,OAAO,GAAG,IAAI,CAAC;QACnB,CAAC;IACL,CAAC;IACD,IAAI,CAAC,OAAO;QAAE,OAAO,SAAS,CAAC;IAC/B,OAAO,GAAG,CAAC;AACf,CAAC,CAAC;AAIF,MAAM,CAAC,MAAM,SAAS,GAAG,CAAI,KAAmB,EAAE,QAAsB,EAAc,EAAE;IACpF,OAAO,CAAC,GAAG,EAAE,KAAK,EAAE,MAAM,EAAE,EAAE;QAC1B,IAAI,CAAC,YAAY,CAAC,KAAK,EAAE,GAAG,CAAC;YAAE,OAAO,SAAS,CAAC;QAChD,OAAO,GAAG,CAAC,QAAQ,EAAE,GAAG,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC;IAC7C,CAAC,CAAC;AACN,CAAC,CAAC;AAGF,MAAM,CAAC,MAAM,UAAU,GAAG,CAAC,GAAW,EAAE,QAAyB,EAAiB,EAAE;IAChF,OAAO,CAAC,GAAG,EAAE,QAAQ,EAAE,MAAM,EAAE,EAAE;QAC7B,IAAI,QAAQ,CAAC,GAAG,KAAK,GAAG;YAAE,OAAO,SAAS,CAAC;QAC3C,OAAO,GAAG,CAAC,QAAQ,EAAE,GAAG,EAAE,QAAQ,EAAE,MAAM,CAAC,CAAC;IAChD,CAAC,CAAC;AACN,CAAC,CAAC;AAWF,MAAM,CAAC,MAAM,WAAW,GACpB,CAAC,IAAY,EAAE,EAAU,EAAiB,EAAE,CAC5C,CAAC,IAAI,EAAE,QAAQ,EAAE,EAAE;IACf,MAAM,GAAG,GAAG,IAAI,CAAC,SAAS,CAAC,QAAQ,CAAC,CAAC;IACrC,IAAI,CAAC,GAAG,CAAC,QAAQ,CAAC,IAAI,CAAC;QAAE,OAAO,SAAS,CAAC;IAC1C,OAAO,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,UAAU,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC;AAChD,CAAC,CAAC;AAON,MAAM,CAAC,MAAM,WAAW,GACpB,CAAC,GAAW,EAAE,KAAe,EAAiB,EAAE,CAChD,CAAC,IAAI,EAAE,QAAQ,EAAE,EAAE;IACf,IAAI,QAAQ,CAAC,YAAY,KAAK,YAAY,IAAI,QAAQ,CAAC,GAAG,KAAK,GAAG;QAAE,OAAO,SAAS,CAAC;IACrF,MAAM,OAAO,GAAI,QAA6C,CAAC,OAAO,CAAC;IACvE,IAAI,CAAC,OAAO;QAAE,OAAO,SAAS,CAAC;IAC/B,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,CAAC;IACrD,MAAM,OAAO,GAAG,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;IAC5D,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,SAAS,CAAC;IAC3C,OAAO,EAAE,GAAG,QAAQ,EAAE,OAAO,EAAE,CAAC,GAAG,OAAO,EAAE,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;AACxF,CAAC,CAAC;AAON,MAAM,CAAC,MAAM,gBAAgB,GACzB,CAAC,IAA4B,EAAgB,EAAE,CAC/C,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;IACb,MAAM,QAAQ,GAAI,OAAO,CAAC,YAAmD,IAAI,EAAE,CAAC;IACpF,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,MAAM,CACvC,CAAC,CAAC,IAAI,EAAE,OAAO,CAAC,EAAE,EAAE,CAAC,IAAI,KAAK,GAAG,CAAC,IAAI,IAAI,QAAQ,CAAC,IAAI,CAAC,KAAK,OAAO,CACvE,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,SAAS,CAAC;IAC3C,OAAO,EAAE,GAAG,OAAO,EAAE,YAAY,EAAE,EAAE,GAAG,QAAQ,EAAE,GAAG,MAAM,CAAC,WAAW,CAAC,OAAO,CAAC,EAAE,EAAE,CAAC;AACzF,CAAC,CAAC;AAGN,MAAM,CAAC,MAAM,aAAa,GACtB,CAAC,IAAY,EAAE,EAAU,EAAgB,EAAE,CAC3C,CAAC,GAAG,EAAE,OAAO,EAAE,EAAE;IACb,IAAI,GAAG,CAAC,IAAI,KAAK,IAAI;QAAE,OAAO,SAAS,CAAC;IACxC,OAAO,EAAE,GAAG,OAAO,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC;AACpC,CAAC,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@atomic-ehr/fhir-canonical-manager",
-  "version": "0.0.25",
+  "version": "0.0.26",
   "license": "MIT",
   "type": "module",
   "main": "./dist/index.js",