@cyanheads/pubmed-mcp-server 2.1.0 → 2.1.2

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-2.1.0-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP Spec](https://img.shields.io/badge/MCP%20Spec-2025--11--25-8A2BE2.svg?style=flat-square)](https://modelcontextprotocol.io/specification/2025-11-25) 
+[![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-2.1.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP Spec](https://img.shields.io/badge/MCP%20Spec-2025--11--25-8A2BE2.svg?style=flat-square)](https://modelcontextprotocol.io/specification/2025-11-25) 
 
 [![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) [![Status](https://img.shields.io/badge/Status-Stable-brightgreen.svg?style=flat-square)](https://github.com/cyanheads/pubmed-mcp-server/issues) [![TypeScript](https://img.shields.io/badge/TypeScript-^5.9.3-3178C6.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/)
 
@@ -23,7 +23,7 @@ Seven tools for working with PubMed and NCBI data:
 |:---|:---|
 | `pubmed_search` | Search PubMed with full query syntax, field-specific filters, date ranges, pagination, and optional brief summaries |
 | `pubmed_fetch` | Fetch full article metadata by PMIDs — abstract, authors, journal, MeSH terms, grants |
-| `pmc_fetch` | Fetch full-text articles from PubMed Central — body sections, references, and metadata for open-access articles |
+| `pubmed_pmc_fetch` | Fetch full-text articles from PubMed Central — body sections, references, and metadata for open-access articles |
 | `pubmed_cite` | Generate formatted citations in APA 7th, MLA 9th, BibTeX, or RIS |
 | `pubmed_related` | Find similar articles, citing articles, or references for a given PMID |
 | `pubmed_spell` | Spell-check biomedical queries using NCBI's ESpell service |
@@ -56,7 +56,7 @@ Fetch full article metadata by PubMed IDs.
 
 ---
 
-### `pmc_fetch`
+### `pubmed_pmc_fetch`
 
 Fetch full-text articles from PubMed Central (PMC).
 

package/dist/index.js

@@ -15776,7 +15776,7 @@ var require_util = __commonJS((exports) => {
       }
       path = url2.path;
     }
-    var isAbsolute = exports.isAbsolute(path);
+    var isAbsolute2 = exports.isAbsolute(path);
     var parts = [];
     var start = 0;
     var i = 0;
@@ -15811,7 +15811,7 @@ var require_util = __commonJS((exports) => {
     }
     path = parts.join("/");
     if (path === "") {
-      path = isAbsolute ? "/" : ".";
+      path = isAbsolute2 ? "/" : ".";
     }
     if (url2) {
       url2.path = path;
@@ -15820,7 +15820,7 @@ var require_util = __commonJS((exports) => {
     return path;
   });
   exports.normalize = normalize;
-  function join(aRoot, aPath) {
+  function join2(aRoot, aPath) {
     if (aRoot === "") {
       aRoot = ".";
     }
@@ -15852,7 +15852,7 @@ var require_util = __commonJS((exports) => {
     }
     return joined;
   }
-  exports.join = join;
+  exports.join = join2;
   exports.isAbsolute = function(aPath) {
     return aPath.charAt(0) === "/" || urlRegexp.test(aPath);
   };
@@ -16066,7 +16066,7 @@ var require_util = __commonJS((exports) => {
           parsed.path = parsed.path.substring(0, index + 1);
         }
       }
-      sourceURL = join(urlGenerate(parsed), sourceURL);
+      sourceURL = join2(urlGenerate(parsed), sourceURL);
     }
     return normalize(sourceURL);
   }
@@ -17440,7 +17440,7 @@ var require_source_map = __commonJS((exports) => {
 // node_modules/postcss/lib/previous-map.js
 var require_previous_map = __commonJS((exports, module) => {
   var { existsSync, readFileSync } = __require("fs");
-  var { dirname, join } = __require("path");
+  var { dirname: dirname2, join: join2 } = __require("path");
   var { SourceMapConsumer, SourceMapGenerator } = require_source_map();
   function fromBase64(str) {
     if (Buffer) {
@@ -17462,7 +17462,7 @@ var require_previous_map = __commonJS((exports, module) => {
         this.mapFile = opts.from;
       }
       if (this.mapFile)
-        this.root = dirname(this.mapFile);
+        this.root = dirname2(this.mapFile);
       if (text)
         this.text = text;
     }
@@ -17507,7 +17507,7 @@ var require_previous_map = __commonJS((exports, module) => {
       }
     }
     loadFile(path) {
-      this.root = dirname(path);
+      this.root = dirname2(path);
       if (existsSync(path)) {
         this.mapFile = path;
         return readFileSync(path, "utf-8").toString().trim();
@@ -17542,7 +17542,7 @@ var require_previous_map = __commonJS((exports, module) => {
       } else if (this.annotation) {
         let map2 = this.annotation;
         if (file2)
-          map2 = join(dirname(file2), map2);
+          map2 = join2(dirname2(file2), map2);
         return this.loadFile(map2);
       }
     }
@@ -17562,15 +17562,15 @@ var require_previous_map = __commonJS((exports, module) => {
 // node_modules/postcss/lib/input.js
 var require_input = __commonJS((exports, module) => {
   var { nanoid: nanoid3 } = require_non_secure();
-  var { isAbsolute, resolve } = __require("path");
+  var { isAbsolute: isAbsolute2, resolve } = __require("path");
   var { SourceMapConsumer, SourceMapGenerator } = require_source_map();
-  var { fileURLToPath, pathToFileURL } = __require("url");
+  var { fileURLToPath: fileURLToPath2, pathToFileURL } = __require("url");
   var CssSyntaxError = require_css_syntax_error();
   var PreviousMap = require_previous_map();
   var terminalHighlight = require_terminal_highlight();
   var lineToIndexCache = Symbol("lineToIndexCache");
   var sourceMapAvailable = Boolean(SourceMapConsumer && SourceMapGenerator);
-  var pathAvailable = Boolean(resolve && isAbsolute);
+  var pathAvailable = Boolean(resolve && isAbsolute2);
   function getLineToIndex(input) {
     if (input[lineToIndexCache])
       return input[lineToIndexCache];
@@ -17605,7 +17605,7 @@ var require_input = __commonJS((exports, module) => {
       if (opts.document)
         this.document = opts.document.toString();
       if (opts.from) {
-        if (!pathAvailable || /^\w+:\/\//.test(opts.from) || isAbsolute(opts.from)) {
+        if (!pathAvailable || /^\w+:\/\//.test(opts.from) || isAbsolute2(opts.from)) {
           this.file = opts.from;
         } else {
           this.file = resolve(opts.from);
@@ -17723,7 +17723,7 @@ var require_input = __commonJS((exports, module) => {
         to = consumer.originalPositionFor({ column: endColumn, line: endLine });
       }
       let fromUrl;
-      if (isAbsolute(from.source)) {
+      if (isAbsolute2(from.source)) {
         fromUrl = pathToFileURL(from.source);
       } else {
         fromUrl = new URL(from.source, this.map.consumer().sourceRoot || pathToFileURL(this.map.mapFile));
@@ -17736,8 +17736,8 @@ var require_input = __commonJS((exports, module) => {
         url: fromUrl.toString()
       };
       if (fromUrl.protocol === "file:") {
-        if (fileURLToPath) {
-          result.file = fileURLToPath(fromUrl);
+        if (fileURLToPath2) {
+          result.file = fileURLToPath2(fromUrl);
         } else {
           throw new Error(`file: protocol is not available in this PostCSS build`);
         }
@@ -17963,12 +17963,12 @@ var require_fromJSON = __commonJS((exports, module) => {
 
 // node_modules/postcss/lib/map-generator.js
 var require_map_generator = __commonJS((exports, module) => {
-  var { dirname, relative, resolve, sep } = __require("path");
+  var { dirname: dirname2, relative, resolve, sep } = __require("path");
   var { SourceMapConsumer, SourceMapGenerator } = require_source_map();
   var { pathToFileURL } = __require("url");
   var Input = require_input();
   var sourceMapAvailable = Boolean(SourceMapConsumer && SourceMapGenerator);
-  var pathAvailable = Boolean(dirname && resolve && relative && sep);
+  var pathAvailable = Boolean(dirname2 && resolve && relative && sep);
 
   class MapGenerator {
     constructor(stringify, root, opts, cssString) {
@@ -18005,7 +18005,7 @@ var require_map_generator = __commonJS((exports, module) => {
     applyPrevMaps() {
       for (let prev of this.previous()) {
         let from = this.toUrl(this.path(prev.file));
-        let root = prev.root || dirname(prev.file);
+        let root = prev.root || dirname2(prev.file);
         let map2;
         if (this.mapOpts.sourcesContent === false) {
           map2 = new SourceMapConsumer(prev.text);
@@ -18212,9 +18212,9 @@ var require_map_generator = __commonJS((exports, module) => {
       let cached2 = this.memoizedPaths.get(file2);
       if (cached2)
         return cached2;
-      let from = this.opts.to ? dirname(this.opts.to) : ".";
+      let from = this.opts.to ? dirname2(this.opts.to) : ".";
       if (typeof this.mapOpts.annotation === "string") {
-        from = dirname(resolve(from, this.mapOpts.annotation));
+        from = dirname2(resolve(from, this.mapOpts.annotation));
       }
       let path = relative(from, file2);
       this.memoizedPaths.set(file2, path);
@@ -40573,7 +40573,7 @@ var require_register = __commonJS((exports) => {
 var require_import_in_the_middle = __commonJS((exports, module) => {
   var path2 = __require("path");
   var moduleDetailsFromPath = require_module_details_from_path();
-  var { fileURLToPath } = __require("url");
+  var { fileURLToPath: fileURLToPath2 } = __require("url");
   var { MessageChannel } = __require("worker_threads");
   var { isBuiltin } = __require("module");
   if (!isBuiltin) {
@@ -40661,7 +40661,7 @@ var require_import_in_the_middle = __commonJS((exports, module) => {
         const stackTraceLimit = Error.stackTraceLimit;
         Error.stackTraceLimit = 0;
         try {
-          filePath = fileURLToPath(name2);
+          filePath = fileURLToPath2(name2);
           name2 = filePath;
         } catch (e) {}
         Error.stackTraceLimit = stackTraceLimit;
@@ -91725,12 +91725,12 @@ var require_fetch2 = __commonJS((exports, module) => {
 // node_modules/@protobufjs/path/index.js
 var require_path = __commonJS((exports) => {
   var path2 = exports;
-  var isAbsolute = path2.isAbsolute = function isAbsolute(path3) {
+  var isAbsolute2 = path2.isAbsolute = function isAbsolute(path3) {
     return /^(?:\/|\w+:)/.test(path3);
   };
   var normalize = path2.normalize = function normalize(path3) {
     path3 = path3.replace(/\\/g, "/").replace(/\/{2,}/g, "/");
-    var parts = path3.split("/"), absolute = isAbsolute(path3), prefix = "";
+    var parts = path3.split("/"), absolute = isAbsolute2(path3), prefix = "";
     if (absolute)
       prefix = parts.shift() + "/";
     for (var i2 = 0;i2 < parts.length; ) {
@@ -91751,7 +91751,7 @@ var require_path = __commonJS((exports) => {
   path2.resolve = function resolve(originPath, includePath, alreadyNormalized) {
     if (!alreadyNormalized)
       includePath = normalize(includePath);
-    if (isAbsolute(includePath))
+    if (isAbsolute2(includePath))
       return includePath;
     if (!alreadyNormalized)
       originPath = normalize(originPath);
@@ -121965,6 +121965,8 @@ if (shouldShowDeprecationWarning())
 
 // src/config/index.ts
 var import_dotenv = __toESM(require_main4(), 1);
+import { dirname, isAbsolute, join } from "node:path";
+import { fileURLToPath } from "node:url";
 
 // node_modules/zod/v4/classic/external.js
 var exports_external = {};
@@ -135501,7 +135503,7 @@ config(en_default());
 // package.json
 var package_default = {
   name: "@cyanheads/pubmed-mcp-server",
-  version: "2.1.0",
+  version: "2.1.2",
   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.",
   main: "dist/index.js",
@@ -135579,7 +135581,7 @@ var package_default = {
     rollup: "4.59.0"
   },
   devDependencies: {
-    "@cloudflare/workers-types": "^4.20260301.1",
+    "@cloudflare/workers-types": "^4.20260305.1",
     "@biomejs/biome": "2.4.5",
     "@hono/mcp": "^0.2.4",
     "@traversable/registry": "^0.0.49",
@@ -136003,13 +136005,13 @@ var parseConfig = () => {
     ...rawConfig,
     pkg: parsedPkg,
     logsPath: hasFileSystemAccess ? (() => {
-      const depth = import.meta.url.includes("/dist/") ? ".." : "../..";
-      const p = new URL(depth, import.meta.url).pathname;
-      const root = p.endsWith("/") ? p.slice(0, -1) : p;
+      const thisFile = fileURLToPath(import.meta.url);
+      const depth = /[\\/]dist[\\/]/.test(thisFile) ? ".." : "../..";
+      const root = join(dirname(thisFile), depth);
       const logsDir = rawConfig.logsPath ?? "logs";
-      if (logsDir.startsWith("/"))
+      if (isAbsolute(logsDir))
         return logsDir;
-      return `${root}/${logsDir}`;
+      return join(root, logsDir);
     })() : undefined,
     mcpServerName: env.MCP_SERVER_NAME ?? parsedPkg.name,
     mcpServerVersion: env.MCP_SERVER_VERSION ?? parsedPkg.version,
@@ -139126,8 +139128,8 @@ function extractTextValues(source, prefix = "") {
   const items = Array.isArray(source) ? source : [source];
   const messages = [];
   for (const item of items) {
-    if (typeof item === "string") {
-      messages.push(`${prefix}${item}`);
+    if (typeof item === "string" || typeof item === "number" || typeof item === "boolean") {
+      messages.push(`${prefix}${String(item)}`);
     } else if (item && typeof item["#text"] === "string") {
       messages.push(`${prefix}${item["#text"]}`);
     }
@@ -139187,7 +139189,7 @@ class NcbiResponseHandler {
         });
       }
       const parsedXml = this.xmlParser.parse(responseText);
-      const hasError = resolvePath(parsedXml, "eLinkResult.ERROR") !== undefined || resolvePath(parsedXml, "eSummaryResult.ERROR") !== undefined || resolvePath(parsedXml, "PubmedArticleSet.ErrorList") !== undefined || resolvePath(parsedXml, "ERROR") !== undefined;
+      const hasError = ERROR_PATHS.some((path) => resolvePath(parsedXml, path) !== undefined);
       if (hasError) {
         const errorMessages = this.extractNcbiErrorMessages(parsedXml);
         logger.error("NCBI API returned an error in XML response.", {
@@ -151008,7 +151010,7 @@ function parsePmcArticle(xmlArticle) {
   const keywords = extractKeywords(articleMeta?.["kwd-group"]);
   const sections = extractBodySections(xmlArticle.body);
   const references = extractReferences(xmlArticle.back);
-  const normalizedPmcId = pmcId.startsWith("PMC") ? pmcId : `PMC${pmcId}`;
+  const normalizedPmcId = !pmcId ? "" : pmcId.startsWith("PMC") ? pmcId : `PMC${pmcId}`;
   return {
     pmcId: normalizedPmcId,
     ...pmid && { pmid },
@@ -151274,7 +151276,7 @@ function markdown() {
 
 // src/mcp-server/tools/definitions/pmc-fetch.tool.ts
 var ncbi2 = () => container.resolve(NcbiServiceToken);
-var TOOL_NAME = "pmc_fetch";
+var TOOL_NAME = "pubmed_pmc_fetch";
 var TOOL_TITLE = "PMC Full-Text Fetch";
 var TOOL_DESCRIPTION = "Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via ELink). Only articles available in PMC will return full text.";
 var TOOL_ANNOTATIONS = {
@@ -151383,7 +151385,7 @@ function filterSections(sections, sectionFilter) {
   });
 }
 async function logic(input, appContext, _sdkContext) {
-  logger.info("Executing pmc_fetch tool", {
+  logger.info("Executing pubmed_pmc_fetch tool", {
     ...appContext,
     hasPmcids: !!input.pmcids,
     hasPmids: !!input.pmids,
@@ -151444,7 +151446,7 @@ async function logic(input, appContext, _sdkContext) {
       return rest;
     });
   }
-  logger.notice("pmc_fetch completed", {
+  logger.notice("pubmed_pmc_fetch completed", {
     ...appContext,
     requested: pmcIds.length,
     returned: articles.length
@@ -151516,7 +151518,7 @@ var pmcFetchTool = {
   annotations: TOOL_ANNOTATIONS,
   description: TOOL_DESCRIPTION,
   inputSchema: InputSchema,
-  logic: withToolAuth(["tool:pmc_fetch:read"], logic),
+  logic: withToolAuth(["tool:pubmed_pmc_fetch:read"], logic),
   name: TOOL_NAME,
   outputSchema: OutputSchema2,
   responseFormatter,
@@ -151531,30 +151533,35 @@ function splitPages(pages) {
   if (!pages)
     return {};
   const parts = pages.split(/[-\u2013\u2014]/).map((p) => p.trim());
-  if (parts.length >= 2) {
-    const start2 = parts[0];
-    const end = parts[1];
-    return {
-      ...start2 !== undefined && { start: start2 },
-      ...end !== undefined && { end }
-    };
-  }
-  const start = parts[0];
-  return start !== undefined ? { start } : {};
+  const [start, end] = parts;
+  if (start && end)
+    return { start, end };
+  return start ? { start } : {};
 }
 function escapeBibtex(text) {
-  return text.replace(/\\/g, "\\textbackslash{}").replace(/&/g, "\\&").replace(/%/g, "\\%").replace(/\$/g, "\\$").replace(/#/g, "\\#").replace(/_/g, "\\_").replace(/\{/g, "\\{").replace(/\}/g, "\\}").replace(/~/g, "\\textasciitilde{}").replace(/\^/g, "\\textasciicircum{}");
+  return text.replace(/[\\&%$#_{}~^]/g, (ch) => {
+    switch (ch) {
+      case "\\":
+        return "\\textbackslash{}";
+      case "~":
+        return "\\textasciitilde{}";
+      case "^":
+        return "\\textasciicircum{}";
+      default:
+        return `\\${ch}`;
+    }
+  });
 }
 function formatAuthorApa(author) {
   if (author.collectiveName)
     return author.collectiveName;
   const last = author.lastName ?? "";
-  const initials = author.initials ?? author.firstName?.split(/[\s-]+/).map((part) => `${part[0]}.`).join(" ");
-  if (!last)
-    return initials ?? "";
+  const initials = author.initials ?? author.firstName?.split(/[\s-]+/).filter(Boolean).map((part) => `${part[0]}.`).join(" ");
   if (!initials)
     return last;
   const formatted = initials.replace(/[^A-Za-z]/g, "").split("").map((c) => `${c}.`).join(" ");
+  if (!last)
+    return formatted;
   return `${last}, ${formatted}`;
 }
 function formatAuthorsApa(authors) {
@@ -151846,6 +151853,9 @@ function extractJournalInfo(journalXml, articleXml) {
   const issnType = getAttribute(issnElement, "IssnType");
   const issn = issnType === "Electronic" ? undefined : issnValue || undefined;
   const eIssn = issnType === "Electronic" ? issnValue || undefined : undefined;
+  const month = getText(pubDate?.Month);
+  const day = getText(pubDate?.Day);
+  const medlineDate = getText(pubDate?.MedlineDate);
   return {
     title: getText(journalXml.Title),
     isoAbbreviation: getText(journalXml.ISOAbbreviation),
@@ -151856,9 +151866,9 @@ function extractJournalInfo(journalXml, articleXml) {
     pages: getText(articleXml?.Pagination?.MedlinePgn),
     publicationDate: {
       ...year && { year },
-      ...getText(pubDate?.Month) && { month: getText(pubDate?.Month) },
-      ...getText(pubDate?.Day) && { day: getText(pubDate?.Day) },
-      ...getText(pubDate?.MedlineDate) && { medlineDate: getText(pubDate?.MedlineDate) }
+      ...month && { month },
+      ...day && { day },
+      ...medlineDate && { medlineDate }
     }
   };
 }

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.1.0",
+  "version": "2.1.2",
   "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.",
   "main": "dist/index.js",
@@ -78,7 +78,7 @@
     "rollup": "4.59.0"
   },
   "devDependencies": {
-    "@cloudflare/workers-types": "^4.20260301.1",
+    "@cloudflare/workers-types": "^4.20260305.1",
     "@biomejs/biome": "2.4.5",
     "@hono/mcp": "^0.2.4",
     "@traversable/registry": "^0.0.49",