npm - @cyanheads/protein-mcp-server - Versions diffs - 0.4.0 → 0.4.1 - Mend

@cyanheads/protein-mcp-server 0.4.0 → 0.4.1

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Files changed (53) hide show

package/dist/services/shared/attribution.js CHANGED Viewed

@@ -8,8 +8,11 @@
  * `best_available` structures are federated through 3D-Beacons, an open set of
  * model providers (AlphaFold DB, SWISS-MODEL, BFVD, AlphaFill, …), so an uncurated
  * provider gets an honest fallback entry that asserts no license rather than a
- * fabricated one. Pure data + a projection helper; the Zod output schema and
- * renderer live in the tools' shared `_schemas.ts`.
+ * fabricated one. Computed structure models fetched by RCSB ID (`AF_*` / `MA_*`)
+ * credit their modelling provider (AlphaFold DB, ModelArchive) rather than the
+ * PDB — the RCSB entry endpoint serves them, but the license is the provider's.
+ * Pure data + a projection helper; the Zod output schema and renderer live in
+ * the tools' shared `_schemas.ts`.
  * @module services/shared/attribution
  */
 /**
@@ -22,6 +25,7 @@ export const CURATED_SOURCES = [
     'AlphaFold DB',
     'SWISS-MODEL',
     'BFVD',
+    'ModelArchive',
     'UniProt',
     'InterPro',
     'GO',
@@ -59,6 +63,12 @@ const ATTRIBUTIONS = {
         citation: 'Kim et al., "BFVD—a large repository of predicted viral protein structures," Nucleic Acids Research 53(D1):D340–D347 (2025). DOI: 10.1093/nar/gkae1119',
         homepage: 'https://bfvd.steineggerlab.workers.dev/',
     },
+    ModelArchive: {
+        source: 'ModelArchive',
+        license: 'CC BY 4.0',
+        citation: 'ModelArchive (SIB Swiss Institute of Bioinformatics / Biozentrum, University of Basel). Each deposited model carries its own DOI — cite the model accession alongside its depositors.',
+        homepage: 'https://www.modelarchive.org/',
+    },
     UniProt: {
         source: 'UniProt',
         license: 'CC BY 4.0',

package/dist/services/shared/attribution.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/shared/http.d.ts CHANGED Viewed

@@ -2,8 +2,7 @@
  * @fileoverview Shared HTTP layer for the protein data providers. Wraps the
  * framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
  * parse pipeline) and centralizes HTML-error-page / empty-body detection so each
- * service stays thin. The single `Context → RequestContext` cast the framework
- * utilities expect is isolated here.
+ * service stays thin.
  * @module services/shared/http
  */
 import type { Context } from '@cyanheads/mcp-ts-core';
@@ -13,6 +12,12 @@ export interface FetchOptions {
     baseDelayMs?: number;
     /** Request body (pre-serialized JSON string, FormData, etc.). */
     body?: RequestInit['body'];
+    /**
+     * Non-2xx statuses this caller treats as an outcome rather than a failure
+     * (e.g. 404 → "no such record"). They still throw a status-mapped `McpError`
+     * for the caller to branch on, but log at `debug` instead of `error`.
+     */
+    expectedStatuses?: number[];
     /** Request headers. */
     headers?: Record<string, string>;
     /** Human-readable provider label used in error messages. */

package/dist/services/shared/http.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"http.d.ts","sourceRoot":"","sources":["../../../src/services/shared/http.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AAmBtD,qDAAqD;AACrD,MAAM,WAAW,YAAY;IAC3B,yCAAyC;IACzC,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,iEAAiE;IACjE,IAAI,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAC3B;;;;OAIG;IACH,gBAAgB,CAAC,EAAE,MAAM,EAAE,CAAC;IAC5B,uBAAuB;IACvB,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,4DAA4D;IAC5D,KAAK,EAAE,MAAM,CAAC;IACd,wDAAwD;IACxD,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,kCAAkC;IAClC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,oDAAoD;IACpD,SAAS,EAAE,MAAM,CAAC;IAClB,wCAAwC;IACxC,SAAS,CAAC,EAAE,MAAM,CAAC;CACpB;AAED;;;;GAIG;AACH,wBAAgB,SAAS,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,KAAK,EAAE,MAAM,GAAG,CAAC,CAgB3D;AAED;;;;;;GAMG;AACH,wBAAgB,SAAS,CAAC,CAAC,EACzB,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,OAAO,EACZ,IAAI,EAAE,YAAY,GAAG;IAAE,WAAW,CAAC,EAAE,MAAM,CAAC,CAAA;CAAE,GAC7C,OAAO,CAAC,CAAC,CAAC,CAyBZ;AAED,wGAAwG;AACxG,wBAAgB,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,EAAE,YAAY,GAAG,OAAO,CAAC,MAAM,CAAC,CAqBxF;AAED;;;;;GAKG;AACH,wBAAgB,aAAa,CAC3B,GAAG,EAAE,MAAM,EACX,GAAG,EAAE,OAAO,EACZ,IAAI,EAAE;IACJ,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,IAAI,CAAC,EAAE,WAAW,CAAC,MAAM,CAAC,CAAC;IAC3B,OAAO,CAAC,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;IACjC,SAAS,EAAE,MAAM,CAAC;IAClB,SAAS,CAAC,EAAE,MAAM,CAAC;IACnB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,UAAU,CAAC,EAAE,MAAM,CAAC;CACrB,GACA,OAAO,CAAC,QAAQ,CAAC,CAoBnB"}

package/dist/services/shared/http.js CHANGED Viewed

@@ -2,8 +2,7 @@
  * @fileoverview Shared HTTP layer for the protein data providers. Wraps the
  * framework's `fetchWithTimeout` + `withRetry` (retry covers the full fetch +
  * parse pipeline) and centralizes HTML-error-page / empty-body detection so each
- * service stays thin. The single `Context → RequestContext` cast the framework
- * utilities expect is isolated here.
+ * service stays thin.
  * @module services/shared/http
  */
 import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
@@ -20,14 +19,6 @@ const USER_AGENT = 'protein-mcp-server (+https://github.com/cyanheads/protein-mc
 function withDefaultHeaders(headers) {
     return { 'User-Agent': USER_AGENT, ...headers };
 }
-/**
- * The framework HTTP utilities type their context parameter as `RequestContext`;
- * the handler `Context` is runtime-compatible (the logger strips non-serializable
- * fields). Cast once here so callers pass `ctx` unchanged.
- */
-function asRequestContext(ctx) {
-    return ctx;
-}
 /**
  * Parse a JSON body, first rejecting HTML error pages and empty responses as
  * transient `ServiceUnavailable` (so `withRetry` retries them rather than feeding
@@ -55,12 +46,12 @@ export function parseJson(text, label) {
  * Content` rather than an empty hit list.
  */
 export function fetchJson(url, ctx, opts) {
-    const rctx = asRequestContext(ctx);
     const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
     return withRetry(async () => {
-        const res = await fetchWithTimeout(url, timeoutMs, rctx, {
+        const res = await fetchWithTimeout(url, timeoutMs, ctx, {
             method: opts.method ?? 'GET',
             ...(opts.body !== undefined && { body: opts.body }),
+            ...(opts.expectedStatuses && { expectedStatuses: opts.expectedStatuses }),
             headers: withDefaultHeaders(opts.headers),
             signal: ctx.signal,
         });
@@ -71,7 +62,7 @@ export function fetchJson(url, ctx, opts) {
         return parseJson(text, opts.label);
     }, {
         operation: opts.operation,
-        context: rctx,
+        context: ctx,
         baseDelayMs: opts.baseDelayMs ?? 400,
         ...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
         signal: ctx.signal,
@@ -79,19 +70,19 @@ export function fetchJson(url, ctx, opts) {
 }
 /** Fetch raw text (coordinate files, etc.) with retry. Throws a status-mapped `McpError` on non-2xx. */
 export function fetchText(url, ctx, opts) {
-    const rctx = asRequestContext(ctx);
     const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
     return withRetry(async () => {
-        const res = await fetchWithTimeout(url, timeoutMs, rctx, {
+        const res = await fetchWithTimeout(url, timeoutMs, ctx, {
             method: opts.method ?? 'GET',
             ...(opts.body !== undefined && { body: opts.body }),
+            ...(opts.expectedStatuses && { expectedStatuses: opts.expectedStatuses }),
             headers: withDefaultHeaders(opts.headers),
             signal: ctx.signal,
         });
         return res.text();
     }, {
         operation: opts.operation,
-        context: rctx,
+        context: ctx,
         baseDelayMs: opts.baseDelayMs ?? 400,
         ...(opts.maxRetries !== undefined && { maxRetries: opts.maxRetries }),
         signal: ctx.signal,
@@ -104,7 +95,6 @@ export function fetchText(url, ctx, opts) {
  * through. Combines `ctx.signal` with a per-attempt timeout.
  */
 export function fetchResponse(url, ctx, opts) {
-    const rctx = asRequestContext(ctx);
     const timeoutMs = opts.timeoutMs ?? DEFAULT_TIMEOUT_MS;
     return withRetry(() => {
         const signal = AbortSignal.any([ctx.signal, AbortSignal.timeout(timeoutMs)]);
@@ -116,7 +106,7 @@ export function fetchResponse(url, ctx, opts) {
         });
     }, {
         operation: opts.operation,
-        context: rctx,
+        context: ctx,
         baseDelayMs: opts.baseDelayMs ?? 400,
         maxRetries: opts.maxRetries ?? 2,
         signal: ctx.signal,

package/dist/services/shared/http.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/uniprot/uniprot-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/uniprot/uniprot-service.js CHANGED Viewed

@@ -70,6 +70,7 @@ export class UniProtService {
                 operation: 'UniProtService.getInterPro',
                 label: 'InterPro',
                 baseDelayMs: 400,
+                expectedStatuses: [404],
             });
         }
         catch (err) {

package/dist/services/uniprot/uniprot-service.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/protein-mcp-server",
-  "version": "0.4.0",
+  "version": "0.4.1",
   "mcpName": "io.github.cyanheads/protein-mcp-server",
   "description": "Federated protein structure & annotation across experimental (PDB) and predicted (AlphaFold) models via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -70,7 +70,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server/issues"
   },
   "homepage": "https://github.com/cyanheads/protein-mcp-server#readme",
-  "author": "cyanheads <casey@caseyjhand.com> (https://github.com/cyanheads/protein-mcp-server#readme)",
+  "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
   "funding": [
     {
       "type": "github",
@@ -82,7 +82,7 @@
     }
   ],
   "license": "Apache-2.0",
-  "packageManager": "bun@1.3.2",
+  "packageManager": "bun@1.3.14",
   "engines": {
     "bun": ">=1.3.0",
     "node": ">=24.0.0"
@@ -91,17 +91,18 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.10.10",
+    "@cyanheads/mcp-ts-core": "^0.11.5",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "2.5.2",
-    "@types/node": "26.1.0",
+    "@biomejs/biome": "2.5.8",
+    "@socketsecurity/bun-security-scanner": "^1.1.2",
+    "@types/node": "26.2.0",
     "depcheck": "^1.4.7",
-    "ignore": "^7.0.5",
-    "tsc-alias": "^1.8.17",
-    "typescript": "^6.0.3",
-    "vitest": "^4.1.9"
+    "ignore": "^7.0.6",
+    "tsc-alias": "^1.9.1",
+    "typescript": "^7.0.2",
+    "vitest": "^4.1.10"
   }
 }

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/protein-mcp-server",
     "source": "github"
   },
-  "version": "0.4.0",
+  "version": "0.4.1",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.0",
+      "version": "0.4.1",
       "packageArguments": [
         {
           "type": "positional",
@@ -48,7 +48,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/protein-mcp-server",
       "runtimeHint": "node",
-      "version": "0.4.0",
+      "version": "0.4.1",
       "packageArguments": [
         {
           "type": "positional",