npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.7.3 → 2.7.5 - Mend

@cyanheads/pubmed-mcp-server 2.7.3 → 2.7.5

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.

Files changed (16) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.6.12
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.4`
+**Version:** 2.7.5
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.10`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -35,6 +35,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
 - **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
 - **Secrets in env vars only** — never hardcoded.
+- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
 ---
@@ -146,6 +147,9 @@ Handlers receive a unified `ctx` object. Key properties:
 |:---------|:------------|
 | `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
 | `ctx.state` | Tenant-scoped KV — `.get(key)`, `.set(key, value, { ttl? })`, `.delete(key)`, `.list(prefix, { cursor, limit })`. Accepts any serializable value. |
+| `ctx.elicit` | Ask user for structured input. **Check for presence first:** `if (ctx.elicit) { ... }` |
+| `ctx.sample` | Request LLM completion from the client. **Check for presence first:** `if (ctx.sample) { ... }` |
+| `ctx.progress` | Task progress (present when `task: true`) — `.setTotal(n)`, `.increment()`, `.update(message)`. |
 | `ctx.recoveryFor(reason)` | Typed lookup of the contract `recovery` for a declared reason. Returns `{ recovery: { hint } }` for known reasons, `{}` otherwise. Spread into `ctx.fail` data to mirror the contract hint into `content[]`. |
 | `ctx.signal` | `AbortSignal` for cancellation. |
 | `ctx.requestId` | Unique request ID. |
@@ -262,6 +266,7 @@ Available skills:
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
 | `maintenance` | Investigate changelogs, adopt upstream changes, and sync skills after `bun update --latest` |
+| `git-wrapup` | Land working-tree changes as a versioned release commit + annotated tag (version bump, changelog, verify, commit, tag — no push/publish) |
 | `release-and-publish` | Ship a release: verification gate, push commits+tags, publish to npm / MCP Registry / GHCR / `.mcpb` bundle on GitHub Releases |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
 | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
@@ -353,4 +358,7 @@ import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
 - [ ] NCBI wrapping: tests include at least one sparse payload case with omitted upstream fields
 - [ ] Registered in `createApp()` arrays (directly or via barrel exports)
 - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
+- [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
 - [ ] `bun run devcheck` passes

package/README.md CHANGED Viewed

@@ -9,13 +9,13 @@
-[![Version](https://img.shields.io/badge/Version-2.7.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
+[![Version](https://img.shields.io/badge/Version-2.7.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![Docker](https://img.shields.io/badge/Docker-ghcr.io-2496ED?style=flat-square&logo=docker&logoColor=white)](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
 </div>
 <div align="center">
-[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubmed-mcp-server/releases/latest/download/pubmed-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubmed-mcp-server&config=eyJjb21tYW5kIjoibnB4IC15IEBjeWFuaGVhZHMvcHVibWVkLW1jcC1zZXJ2ZXIifQ%3D%3D) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubmed-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fpubmed-mcp-server%22%5D%7D)
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/pubmed-mcp-server/releases/latest/download/pubmed-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=pubmed-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvcHVibWVkLW1jcC1zZXJ2ZXIiXX0=) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22pubmed-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads%2Fpubmed-mcp-server%22%5D%7D)
 [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
@@ -94,7 +94,7 @@ Fetch full-text articles via a three-stage chain: NCBI PMC EFetch → Europe PMC
 Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than PubMed alone.
-- Surfaces records PubMed search can't reach: preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC (`PMC`)
+- Surfaces records PubMed search can't reach — preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC (`PMC`). On recent queries this can mean dozens of relevant hits with zero PubMed overlap.
 - Default sources `["MED", "PMC", "PPR"]`; pass `sources` to include `PAT` / `AGR`
 - Cursor-based pagination via `cursorMark` (unlike `pubmed_search_articles`, which uses offset) — `*` for the first page, return `nextCursorMark` for the next
 - Output discriminator on `source` plus optional `pmid` / `pmcId` / `doi` cross-walking
@@ -162,7 +162,7 @@ Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converte
 - Batch up to 50 IDs per request
 - Accepts DOIs, PMIDs, or PMCIDs (all IDs must be the same type)
 - Only resolves articles indexed in PubMed Central
-- Returns all available identifier mappings for each input ID
+- Per-ID success/error reporting — partial batches return resolved mappings alongside structured errors for unresolvable IDs, not a batch-level failure
 ## Resource and prompt
@@ -189,6 +189,12 @@ PubMed-specific:
 - NCBI-specific XML parser with `isArray` hints for PubMed's inconsistent XML structure
 - Hand-rolled citation formatters (APA, MLA, BibTeX, RIS) — zero deps, Workers-compatible
+Agent-friendly output:
+- Provenance on every response — source labels, license fields, best-effort warnings on Unpaywall results, and effective-query echo on searches so agents can reason about trust
+- Graceful partial failure — batch tools return per-item success/error rows instead of failing the request, with structured status codes and actionable next-step text
+- Discriminated output contracts — `source: "pmc" | "unpaywall"`, typed `unavailable` reasons, `viaSource` and `triedTiers` fields — callers branch on data, not string parsing
 ## Getting started
 ### Public Hosted Instance

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED Viewed

@@ -234,7 +234,9 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
     input: z
         .object({
         pmcids: z
-            .array(z.string())
+            .array(z
+            .string()
+            .regex(/^(?:PMC)?\d+$/i, 'PMC ID must be digits, optionally prefixed with "PMC" (e.g. "PMC9575052" or "9575052")'))
             .min(1)
             .max(10)
             .optional()
@@ -620,7 +622,10 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
             for (const u of result.unavailable) {
                 lines.push(`- [${u.idType}] ${u.id} — ${u.reason}`);
                 const chain = u.triedTiers
-                    .map((t) => `${t.tier}:${t.outcome}${t.detail ? ` (${t.detail})` : ''}`)
+                    .map((t) => {
+                    const detail = t.detail ? sanitizeChainDetail(t.detail) : undefined;
+                    return `${t.tier}:${t.outcome}${detail ? ` (${detail})` : ''}`;
+                })
                     .join(' → ');
                 if (chain)
                     lines.push(`  chain: ${chain}`);
@@ -1126,4 +1131,14 @@ function formatPmcAuthor(au) {
 function formatHeading(label, title) {
     return label ? `${label} ${title}` : title;
 }
+/**
+ * Strip absolute URLs from chain detail strings. Upstream errors (e.g.
+ * `Fetch failed for <eutils URL>. Status: 400`) leak endpoint paths and query
+ * strings without adding actionable signal — the status code is the useful
+ * part. The raw detail is preserved in `structuredContent` for clients that
+ * want it.
+ */
+function sanitizeChainDetail(detail) {
+    return detail.replace(/https?:\/\/\S+/g, '<upstream>');
+}
 //# sourceMappingURL=fetch-fulltext.tool.js.map

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -20,7 +20,7 @@ function extractValue(field) {
 }
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const findRelatedTool = tool('pubmed_find_related', {
-    description: 'Find articles related to a source article — similar content, citing articles, or references.',
+    description: 'Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/find-related.tool.ts',

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -13,7 +13,7 @@ import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_conc
 import { pmidStringSchema } from './_schemas.js';
 const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris']);
 export const formatCitationsTool = tool('pubmed_format_citations', {
-    description: 'Get formatted citations for PubMed articles in one or more styles (APA, MLA, BibTeX, RIS). Pass a single style as a string or multiple as an array.',
+    description: 'Get formatted citations for PubMed articles in one or more styles (apa, mla, bibtex, ris). Pass a single style as a string or multiple as an array.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     _meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
     sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

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

@@ -132,9 +132,11 @@ export class EuropePmcService {
         }
         const hits = ensureArray(parsed.resultList?.result);
         const echoed = parsed.request?.queryString ?? params.query;
-        // EPMC echoes back the input cursor mark on the final page, so absence of
-        // an explicit "next" or equality with the request's cursor marks the end.
-        const cursorMark = parsed.request?.cursorMark ?? params.cursorMark ?? '*';
+        // EPMC's `request.cursorMark` echo is URL-encoded (the wire form), while
+        // `nextCursorMark` in the JSON body is raw. Use the caller's input as the
+        // current cursor so the echo is consistent and the equality check below
+        // (used to detect "no more pages") compares like-for-like.
+        const cursorMark = params.cursorMark ?? '*';
         const nextCursor = parsed.nextCursorMark && parsed.nextCursorMark !== cursorMark
             ? parsed.nextCursorMark
             : undefined;

package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/ncbi/request-queue.js CHANGED Viewed

@@ -5,7 +5,7 @@
  * abort-during-wait so callers' deadlines can bound queue time end-to-end.
  * @module src/services/ncbi/request-queue
  */
-import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { rateLimited } from '@cyanheads/mcp-ts-core/errors';
 import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { recoveryFor } from '../../services/error-contracts.js';
 const DEFAULT_MAX_CONCURRENT = 8;
@@ -40,7 +40,7 @@ export class NcbiRequestQueue {
     }
     enqueue(task, endpoint, params, signal) {
         if (this.waiters.length >= this.maxQueueSize) {
-            return Promise.reject(new McpError(JsonRpcErrorCode.RateLimited, `NCBI request queue is full (max ${this.maxQueueSize}).`, {
+            return Promise.reject(rateLimited(`NCBI request queue is full (max ${this.maxQueueSize}).`, {
                 reason: 'queue_full',
                 endpoint,
                 queueSize: this.waiters.length,

package/dist/services/ncbi/request-queue.js.map CHANGED Viewed

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

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.7.3",
+  "version": "2.7.5",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
   "type": "module",
@@ -40,6 +40,7 @@
     "model-context-protocol",
     "mcp-server",
     "typescript",
+    "bun",
     "ai-agent",
     "e-utilities",
     "open-access",
@@ -76,7 +77,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.4",
+    "@cyanheads/mcp-ts-core": "^0.9.10",
     "defuddle": "^0.18.1",
     "fast-xml-parser": "^5.8.0",
     "linkedom": "^0.18.12",
@@ -86,7 +87,7 @@
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.15",
+    "@biomejs/biome": "^2.4.16",
     "@types/node": "^25.9.1",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.7",

package/server.json CHANGED Viewed

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.7.3",
+  "version": "2.7.5",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.3",
+      "version": "2.7.5",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.7.3",
+      "version": "2.7.5",
       "packageArguments": [
         {
           "type": "positional",