@cyanheads/pubmed-mcp-server 2.7.11 → 2.9.0

package/AGENTS.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.11
+**Version:** 2.9.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0
 

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.7.11
+**Version:** 2.9.0
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.21`
 **Engines:** Bun ≥1.3.2, Node ≥24.0.0
 

package/README.md

@@ -9,7 +9,7 @@
 
 
 
-[![Version](https://img.shields.io/badge/Version-2.7.11-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-2.9.0-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>
 
@@ -39,7 +39,7 @@
 | `pubmed_europepmc_search` | Search Europe PMC for preprints, patents, Agricola, and EPMC-only OA records that don't surface in PubMed. Cursor-based pagination. |
 | `pubmed_fetch_articles` | Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants |
 | `pubmed_fetch_fulltext` | Fetch full-text articles via a chain: NCBI PMC EFetch → Europe PMC `fullTextXML` → Unpaywall. Accepts PMIDs, PMCIDs, or DOIs. |
-| `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS |
+| `pubmed_format_citations` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, RIS, or Vancouver (ICMJE/NLM) |
 | `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
 | `pubmed_spell_check` | Spell-check biomedical queries using NCBI's ESpell service |
 | `pubmed_lookup_mesh` | Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms |
@@ -106,7 +106,7 @@ Search Europe PMC (EBI/EMBL-EBI), a broader open-access biomedical corpus than P
 
 Generate formatted citations for articles.
 
-- Four citation styles: APA 7th, MLA 9th, BibTeX, RIS
+- Five citation styles: APA 7th, MLA 9th, BibTeX, RIS, Vancouver (ICMJE/NLM)
 - Request multiple styles per article in a single call
 - Hand-rolled formatters — zero external dependencies, fully Workers-compatible
 - Up to 50 articles per request
@@ -187,7 +187,7 @@ PubMed-specific:
 - Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
 - Sequential request queue with configurable delay for NCBI rate limit compliance
 - 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
+- Hand-rolled citation formatters (APA, MLA, BibTeX, RIS, Vancouver) — zero deps, Workers-compatible
 
 Agent-friendly output:
 

package/dist/index.js

@@ -19,6 +19,7 @@ import { searchArticlesTool } from './mcp-server/tools/definitions/search-articl
 import { spellCheckTool } from './mcp-server/tools/definitions/spell-check.tool.js';
 import { initEuropePmcService } from './services/europe-pmc/europe-pmc-service.js';
 import { initNcbiService } from './services/ncbi/ncbi-service.js';
+import { initOpenAlexService } from './services/openalex/openalex-service.js';
 import { initUnpaywallService } from './services/unpaywall/unpaywall-service.js';
 const config = getServerConfig();
 const tools = [
@@ -66,6 +67,7 @@ await createApp({
         initNcbiService();
         initUnpaywallService();
         initEuropePmcService();
+        initOpenAlexService();
     },
 });
 //# sourceMappingURL=index.js.map

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,yBAAyB,EAAE,MAAM,gEAAgE,CAAC;AAC3G,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,oBAAoB,EAAE,MAAM,6CAA6C,CAAC;AACnF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAClE,OAAO,EAAE,mBAAmB,EAAE,MAAM,yCAAyC,CAAC;AAC9E,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AAEjF,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;AACjC,MAAM,KAAK,GAAG;IACZ,kBAAkB;IAClB,iBAAiB;IACjB,iBAAiB;IACjB,mBAAmB;IACnB,eAAe;IACf,cAAc;IACd,cAAc;IACd,kBAAkB;IAClB,cAAc;IACd,GAAG,CAAC,MAAM,CAAC,gBAAgB,CAAC,CAAC,CAAC,CAAC,yBAAyB,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;CAChE,CAAC;AAEF,MAAM,SAAS,CAAC;IACd,KAAK;IACL,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,YAAY,EACV,iqBAAiqB;IACnqB,OAAO,EAAE;QACP,WAAW,EAAE,KAAK;QAClB,OAAO,EACL,uGAAuG;QACzG,QAAQ,EAAE,gDAAgD;QAC1D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,kCAAkC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC7E;gBACE,KAAK,EAAE,kBAAkB;gBACzB,IAAI,EAAE,8CAA8C;gBACpD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,qBAAqB;gBAC5B,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD,EAAE,KAAK,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE,QAAQ,EAAE,IAAI,EAAE;SAC9E;QACD,UAAU,EAAE;YACV,YAAY,EAAE,mBAAmB;YACjC,gBAAgB,EAAE,iBAAiB;YACnC,eAAe,EAAE,iBAAiB;SACnC;KACF;IACD,KAAK;QACH,eAAe,EAAE,CAAC;QAClB,oBAAoB,EAAE,CAAC;QACvB,oBAAoB,EAAE,CAAC;QACvB,mBAAmB,EAAE,CAAC;IACxB,CAAC;CACF,CAAC,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts

@@ -104,5 +104,7 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: "NCBI EFetch returned a payload missing the PubmedArticleSet wrapper.";
     readonly recovery: "Retry once; if it persists, NCBI returned malformed data — try fewer PMIDs at once.";
-}], undefined>;
+}], {
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=fetch-articles.tool.d.ts.map

package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"fetch-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqL5B,CAAC"}

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js

@@ -121,6 +121,14 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             .optional()
             .describe('PMIDs that returned no article data'),
     }),
+    // Recovery guidance when no articles are returned — agent-facing context, surfaced via
+    // ctx.enrich.notice() to both structuredContent and content[]; absent on success.
+    enrichment: {
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when no articles were returned — points to discovery tools. Absent on successful fetches.'),
+    },
     async handler(input, ctx) {
         ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
         const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100, signal: ctx.signal });
@@ -150,6 +158,9 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
             requested: input.pmids.length,
             returned: articles.length,
         });
+        if (articles.length === 0) {
+            ctx.enrich.notice('No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs.');
+        }
         return {
             articles,
             totalReturned: articles.length,
@@ -161,9 +172,6 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
         if (result.unavailablePmids?.length) {
             lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
         }
-        if (result.totalReturned === 0) {
-            lines.push(`\n> No articles were returned. These PMIDs may be invalid, unpublished, or withdrawn. Try \`pubmed_search_articles\` to discover valid PMIDs.`);
-        }
         for (const a of result.articles) {
             lines.push(`\n### ${a.title ?? a.pmid ?? 'Unknown'}`);
             if (a.authors?.length) {

package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts

@@ -1,6 +1,8 @@
 /**
  * @fileoverview PubMed related articles tool — finds articles related to a
- * source article via NCBI ELink and enriches results with ESummary data.
+ * source article via a provider chain: NCBI ELink (primary) → Europe PMC →
+ * OpenAlex. First success wins; results are never merged across sources.
+ * Supports offset pagination on the returned window.
  * @module src/mcp-server/tools/definitions/find-related.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
@@ -12,6 +14,7 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         cited_by: "cited_by";
     }>>;
     maxResults: z.ZodDefault<z.ZodNumber>;
+    offset: z.ZodDefault<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     sourcePmid: z.ZodString;
     relationship: z.ZodEnum<{
@@ -19,6 +22,7 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         similar: "similar";
         cited_by: "cited_by";
     }>;
+    offset: z.ZodNumber;
     articles: z.ZodArray<z.ZodObject<{
         pmid: z.ZodString;
         title: z.ZodOptional<z.ZodString>;
@@ -56,8 +60,43 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
     readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
     readonly retryable: false;
+}, {
+    readonly reason: "europepmc_unreachable";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Europe PMC was unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly retryable: true;
+}, {
+    readonly reason: "europepmc_invalid_response";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
+    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
+    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly retryable: true;
+}, {
+    readonly reason: "europepmc_invalid_input";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).";
+    readonly recovery: "Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.";
+    readonly retryable: false;
+}, {
+    readonly reason: "openalex_unreachable";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "OpenAlex was unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.";
+    readonly retryable: true;
+}, {
+    readonly reason: "openalex_invalid_response";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
+    readonly when: "OpenAlex returned a body that could not be parsed (invalid JSON).";
+    readonly recovery: "Retry the request; OpenAlex returned a malformed response that could not be parsed.";
+    readonly retryable: true;
 }], {
     readonly totalFound: z.ZodNumber;
+    readonly source: z.ZodEnum<{
+        europepmc: "europepmc";
+        openalex: "openalex";
+        ncbi: "ncbi";
+    }>;
     readonly notice: z.ZodOptional<z.ZodString>;
 }>;
 //# sourceMappingURL=find-related.tool.d.ts.map

package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6KjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8W1B,CAAC"}