@cyanheads/pubmed-mcp-server 2.3.6 → 2.3.7

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** @cyanheads/pubmed-mcp-server
-**Version:** 2.3.6
+**Version:** 2.3.7
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 
 > **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.

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![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) [![Version](https://img.shields.io/badge/Version-2.3.6-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-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) [![Version](https://img.shields.io/badge/Version-2.3.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/) 
 
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![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/)
 

package/dist/services/ncbi/formatting/citation-formatter.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,CAAC;AAoJ7D;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAgDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuD3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6ExD;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAWnF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
+{"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,CAAC;AAiM7D;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA8E3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAWnF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}

package/dist/services/ncbi/formatting/citation-formatter.js

@@ -9,25 +9,65 @@
 // ---------------------------------------------------------------------------
 /**
  * Extract the publication year from a ParsedArticle.
- * Falls back to 'n.d.' (no date) when unavailable.
+ * Prefers `journalInfo.publicationDate.year`; falls back to the earliest
+ * `articleDates` entry (typically the electronic pub date) before giving up.
+ * Returns 'n.d.' (no date) when no year is available.
  */
 function getYear(article) {
-    return article.journalInfo?.publicationDate?.year ?? 'n.d.';
+    const journalYear = article.journalInfo?.publicationDate?.year;
+    if (journalYear)
+        return journalYear;
+    const articleYear = article.articleDates?.find((d) => d.year)?.year;
+    return articleYear ?? 'n.d.';
 }
 /**
  * Split a pages string like "45-67" into start and end components.
- * Handles en-dashes, em-dashes, and hyphens.
+ * Handles en-dashes, em-dashes, and hyphens. Expands PubMed's truncated-end
+ * convention (e.g., "737-8" → { start: "737", end: "738" }, "1639-41" →
+ * "1639"/"1641") so downstream RIS/BibTeX consumers see absolute page numbers.
  */
 function splitPages(pages) {
     if (!pages)
         return {};
-    // Normalize hyphens, en-dashes, and em-dashes to a single separator
     const parts = pages.split(/[-\u2013\u2014]/).map((p) => p.trim());
-    const [start, end] = parts;
+    let [start, end] = parts;
+    if (start && end && end.length < start.length) {
+        end = start.slice(0, start.length - end.length) + end;
+    }
     if (start && end)
         return { start, end };
     return start ? { start } : {};
 }
+/**
+ * Collapse internal whitespace (including embedded newlines from structured
+ * abstracts) to single spaces. Strict RIS parsers treat blank lines as record
+ * terminators, so abstract text must be flattened before emission.
+ */
+function collapseWhitespace(text) {
+    return text.replace(/\s+/g, ' ').trim();
+}
+/** PubMed `PublicationType` → BibTeX entry type. Defaults to `article`. */
+const BIBTEX_ENTRY_TYPE = {
+    Book: 'book',
+    'Book Chapter': 'inbook',
+    Preprint: 'misc',
+};
+/** PubMed `PublicationType` → RIS reference type. Defaults to `JOUR`. */
+const RIS_REFERENCE_TYPE = {
+    Book: 'BOOK',
+    'Book Chapter': 'CHAP',
+    Preprint: 'GEN',
+};
+function firstMappedType(types, map, fallback) {
+    if (!types?.length)
+        return fallback;
+    for (const t of types) {
+        const mapped = map[t];
+        if (mapped)
+            return mapped;
+    }
+    return fallback;
+}
 /**
  * Escape characters that are special in LaTeX/BibTeX values.
  * Handles: & % $ # _ { } ~ ^
@@ -166,10 +206,11 @@ function formatAuthorBibtex(author) {
  */
 export function formatApa(article) {
     const parts = [];
-    // Authors
+    // Authors — ensure trailing period (individual author initials end with '.',
+    // but collective names do not, which would otherwise produce "Name (Year).")
     const authorStr = article.authors?.length ? formatAuthorsApa(article.authors) : '';
     if (authorStr) {
-        parts.push(authorStr);
+        parts.push(authorStr.endsWith('.') ? authorStr : `${authorStr}.`);
     }
     // Year
     const year = getYear(article);
@@ -242,7 +283,9 @@ export function formatMla(article) {
             detailParts.push(year);
         }
         if (journal.pages) {
-            detailParts.push(`pp. ${journal.pages}`);
+            // MLA 9 §6.56: "p." for a single page, "pp." for a range
+            const isRange = /[-\u2013\u2014]/.test(journal.pages);
+            detailParts.push(`${isRange ? 'pp.' : 'p.'} ${journal.pages}`);
         }
         parts.push(`${detailParts.join(', ')}.`);
     }
@@ -270,6 +313,7 @@ export function formatMla(article) {
  */
 export function formatBibtex(article) {
     const key = `pmid${article.pmid}`;
+    const entryType = firstMappedType(article.publicationTypes, BIBTEX_ENTRY_TYPE, 'article');
     const fields = [];
     // Authors
     if (article.authors?.length) {
@@ -277,9 +321,10 @@ export function formatBibtex(article) {
         if (authorStr)
             fields.push(['author', authorStr]);
     }
-    // Title
+    // Title — strip trailing period; biblatex styles append their own
     if (article.title) {
-        fields.push(['title', `{${escapeBibtex(article.title)}}`]);
+        const title = article.title.replace(/\.\s*$/, '');
+        fields.push(['title', `{${escapeBibtex(title)}}`]);
     }
     // Journal
     const journal = article.journalInfo;
@@ -303,16 +348,36 @@ export function formatBibtex(article) {
     if (journal?.pages) {
         fields.push(['pages', escapeBibtex(journal.pages)]);
     }
+    // ISSN
+    const issn = journal?.issn ?? journal?.eIssn;
+    if (issn) {
+        fields.push(['issn', escapeBibtex(issn)]);
+    }
     // DOI
     if (article.doi) {
         fields.push(['doi', article.doi]);
     }
     // PMID
     fields.push(['pmid', article.pmid]);
+    // PMCID
+    if (article.pmcId) {
+        fields.push(['pmcid', article.pmcId]);
+    }
+    // Keywords — merge article keywords with MeSH descriptor names
+    const keywordSet = new Set();
+    for (const k of article.keywords ?? [])
+        keywordSet.add(k);
+    for (const m of article.meshTerms ?? []) {
+        if (m.descriptorName)
+            keywordSet.add(m.descriptorName);
+    }
+    if (keywordSet.size > 0) {
+        fields.push(['keywords', escapeBibtex([...keywordSet].join(', '))]);
+    }
     // Build entry
     const maxKeyLen = Math.max(...fields.map(([k]) => k.length));
     const fieldLines = fields.map(([k, v]) => `  ${k.padEnd(maxKeyLen)} = {${v}}`).join(',\n');
-    return `@article{${key},\n${fieldLines}\n}`;
+    return `@${entryType}{${key},\n${fieldLines}\n}`;
 }
 // ---------------------------------------------------------------------------
 // RIS
@@ -329,8 +394,9 @@ export function formatRis(article) {
         if (value)
             lines.push(`${code}  - ${value}`);
     };
-    // Type of reference
-    lines.push('TY  - JOUR');
+    // Type of reference — map from PubMed publication types
+    const refType = firstMappedType(article.publicationTypes, RIS_REFERENCE_TYPE, 'JOUR');
+    lines.push(`TY  - ${refType}`);
     // Authors — one AU tag per author
     if (article.authors?.length) {
         for (const author of article.authors) {
@@ -364,26 +430,40 @@ export function formatRis(article) {
     // Volume & Issue
     tag('VL', journal?.volume);
     tag('IS', journal?.issue);
-    // Pages — split into start/end
+    // Pages — split into start/end, expanding PubMed's truncated-end convention
     if (journal?.pages) {
         const { start, end } = splitPages(journal.pages);
         tag('SP', start);
         tag('EP', end);
     }
+    // ISSN — prefer print ISSN, fall back to electronic
+    tag('SN', journal?.issn ?? journal?.eIssn);
     // DOI (without URL prefix — RIS DO tag holds the bare DOI)
     tag('DO', article.doi);
     // Accession number (PMID)
     tag('AN', article.pmid);
     // PubMed URL
     lines.push(`UR  - https://pubmed.ncbi.nlm.nih.gov/${article.pmid}/`);
-    // Keywords
-    if (article.keywords?.length) {
-        for (const kw of article.keywords) {
-            tag('KW', kw);
-        }
+    // PMC URL (when available)
+    if (article.pmcId) {
+        lines.push(`UR  - https://pmc.ncbi.nlm.nih.gov/articles/${article.pmcId}/`);
+    }
+    // Keywords — merge article keywords with MeSH descriptor names
+    const keywordSet = new Set();
+    for (const k of article.keywords ?? [])
+        keywordSet.add(k);
+    for (const m of article.meshTerms ?? []) {
+        if (m.descriptorName)
+            keywordSet.add(m.descriptorName);
+    }
+    for (const kw of keywordSet) {
+        tag('KW', kw);
+    }
+    // Abstract — collapse internal whitespace so blank lines don't break strict
+    // RIS parsers that terminate records at blank lines
+    if (article.abstractText) {
+        tag('AB', collapseWhitespace(article.abstractText));
     }
-    // Abstract
-    tag('AB', article.abstractText);
     // End of record (trailing space per RIS spec)
     lines.push('ER  - ');
     return lines.join('\n');

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.3.6",
+  "version": "2.3.7",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
   "type": "module",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.3.6",
+  "version": "2.3.7",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.6",
+      "version": "2.3.7",
       "packageArguments": [
         {
           "type": "positional",
@@ -60,7 +60,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.3.6",
+      "version": "2.3.7",
       "packageArguments": [
         {
           "type": "positional",