@cyanheads/pubmed-mcp-server 2.2.3 → 2.2.5

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Files changed (12) hide show
  1. package/CLAUDE.md +3 -1
  2. package/README.md +2 -1
  3. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +22 -1
  5. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  6. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  7. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +38 -0
  8. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  9. package/dist/services/ncbi/parsing/article-parser.js +3 -3
  10. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  11. package/package.json +9 -5
  12. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.2.3
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+ **Version:** 2.2.5
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **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.
@@ -232,6 +232,8 @@ Available skills:
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  | `api-testing` | createMockContext, test patterns |
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  | `api-utils` | Formatting, parsing, security, pagination, scheduling |
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  | `api-workers` | Cloudflare Workers runtime |
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+ | `report-issue-framework` | File bug/feature request against @cyanheads/mcp-ts-core |
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+ | `report-issue-local` | File bug/feature request against this server's repo |
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  When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
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package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![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-2.2.3-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/)
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+ [![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-2.2.5-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/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.2-3178C6.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/)
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@@ -252,6 +252,7 @@ All configuration is validated at startup via Zod schemas in `src/config/server-
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  | `MCP_HTTP_PORT` | HTTP server port | `3010` |
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  | `MCP_AUTH_MODE` | Authentication: `none`, `jwt`, or `oauth` | `none` |
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  | `MCP_LOG_LEVEL` | Log level (`debug`, `info`, `warning`, `error`, etc.) | `info` |
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+ | `LOGS_DIR` | Directory for log files (Node.js only). | `<project-root>/logs` |
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  | `STORAGE_PROVIDER_TYPE` | Storage backend: `in-memory`, `filesystem`, `supabase`, `cloudflare-kv/r2/d1` | `in-memory` |
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  | `NCBI_API_KEY` | NCBI API key for higher rate limits (10 req/s vs 3 req/s) | none |
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  | `NCBI_ADMIN_EMAIL` | Contact email sent with NCBI requests (recommended by NCBI) | none |
package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED
@@ -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;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAmM5B,CAAC"}
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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;AAMjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsN5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -114,7 +114,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  if (!xmlData || !('PubmedArticleSet' in xmlData)) {
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  throw new Error('Invalid EFetch response from NCBI: missing PubmedArticleSet');
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  }
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- if (!xmlData.PubmedArticleSet || !xmlData.PubmedArticleSet.PubmedArticle) {
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+ if (!xmlData.PubmedArticleSet?.PubmedArticle) {
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  return { articles: [], totalReturned: 0 };
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  }
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  const xmlArticles = ensureArray(xmlData.PubmedArticleSet.PubmedArticle);
@@ -157,6 +157,8 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  const authorStr = a.authors.length > 3 ? `${first3}, et al.` : first3;
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  lines.push(`**Authors:** ${authorStr}`);
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  }
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+ if (a.affiliations?.length)
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+ lines.push(`**Affiliations:** ${a.affiliations.join('; ')}`);
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  const ji = a.journalInfo;
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  if (ji) {
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  const parts = [ji.isoAbbreviation ?? ji.title];
@@ -181,6 +183,25 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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  lines.push(`**PMC:** ${a.pmcUrl}`);
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  if (a.abstractText)
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  lines.push(`\n#### Abstract\n${a.abstractText}`);
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+ if (a.keywords?.length)
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+ lines.push(`\n**Keywords:** ${a.keywords.join(', ')}`);
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+ if (a.meshTerms?.length) {
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+ lines.push(`\n#### MeSH Terms`);
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+ for (const m of a.meshTerms) {
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+ const major = m.isMajorTopic ? ' *' : '';
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+ const qualifiers = m.qualifiers?.length
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+ ? ` (${m.qualifiers.map((q) => `${q.qualifierName}${q.isMajorTopic ? '*' : ''}`).join(', ')})`
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+ : '';
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+ lines.push(`- ${m.descriptorName}${major}${qualifiers}`);
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+ }
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+ }
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+ if (a.grantList?.length) {
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+ lines.push(`\n#### Grants`);
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+ for (const g of a.grantList) {
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+ const parts = [g.grantId, g.agency, g.country].filter(Boolean);
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+ lines.push(`- ${parts.join(' — ')}`);
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+ }
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+ }
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  }
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  return [{ type: 'text', text: lines.join('\n') }];
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  },
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
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{"version":3,"file":"fetch-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,uBAAuB,EAAE;IAC7D,WAAW,EACT,mIAAmI;IACrI,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;QACzF,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACrE,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACjD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YAC7D,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;YACzF,OAAO,EAAE,CAAC;iBACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;gBACrD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;gBAC7D,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC3D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;gBAC9E,kBAAkB,EAAE,CAAC;qBAClB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;qBACjB,QAAQ,EAAE;qBACV,QAAQ,CAAC,+CAA+C,CAAC;gBAC5D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;aAC1D,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,aAAa,CAAC;YAC1B,WAAW,EAAE,CAAC;iBACX,MAAM,CAAC;gBACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;gBAC3D,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;gBAC3E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;gBAClD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;gBACvD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;gBACrD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;gBAClE,eAAe,EAAE,CAAC;qBACf,MAAM,CAAC;oBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;oBACxD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;oBAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;oBACtD,WAAW,EAAE,CAAC;yBACX,MAAM,EAAE;yBACR,QAAQ,EAAE;yBACV,QAAQ,CAAC,+CAA+C,CAAC;iBAC7D,CAAC;qBACD,QAAQ,EAAE;qBACV,QAAQ,CAAC,0BAA0B,CAAC;aACxC,CAAC;iBACD,QAAQ,EAAE;iBACV,QAAQ,CAAC,qBAAqB,CAAC;YAClC,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;YAC1C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC;YAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;YAC/D,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC3D,gBAAgB,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9E,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC;YAC7D,SAAS,EAAE,CAAC;iBACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;gBACtE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;gBACzE,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;gBAClF,UAAU,EAAE,CAAC;qBACV,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;oBACP,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;oBAC/D,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;oBAClE,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;iBAC9E,CAAC,CACH;qBACA,QAAQ,EAAE;qBACV,QAAQ,CAAC,6BAA6B,CAAC;aAC3C,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,YAAY,CAAC;YACzB,SAAS,EAAE,CAAC;iBACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;gBAC3D,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;gBACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;gBACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;aAC1D,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,mBAAmB,CAAC;YAChC,YAAY,EAAE,CAAC;iBACZ,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;gBACrD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC;gBAC5C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC;gBAC9C,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;aAC3C,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,eAAe,CAAC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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8FjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4M5B,CAAC"}
1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8FjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA6O5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -221,14 +221,45 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
221
221
  const lines = [`## PMC Full-Text Articles`, `**Articles Returned:** ${result.totalReturned}`];
222
222
  if (result.unavailablePmids?.length)
223
223
  lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
224
+ if (result.unavailablePmcIds?.length)
225
+ lines.push(`**Unavailable PMC IDs:** ${result.unavailablePmcIds.join(', ')}`);
224
226
  for (const a of result.articles) {
225
227
  lines.push(`\n### ${a.title ?? a.pmcId}`);
228
+ if (a.authors?.length) {
229
+ const fmtAuthor = (au) => au.collectiveName ??
230
+ `${au.lastName ?? ''}${au.givenNames ? ` ${au.givenNames}` : ''}`.trim();
231
+ const first3 = a.authors.slice(0, 3).map(fmtAuthor).join(', ');
232
+ const authorStr = a.authors.length > 3 ? `${first3}, et al.` : first3;
233
+ lines.push(`**Authors:** ${authorStr}`);
234
+ }
235
+ if (a.affiliations?.length)
236
+ lines.push(`**Affiliations:** ${a.affiliations.join('; ')}`);
237
+ if (a.journal) {
238
+ const parts = [a.journal.title];
239
+ if (a.journal.volume)
240
+ parts.push(`**${a.journal.volume}**${a.journal.issue ? `(${a.journal.issue})` : ''}`);
241
+ if (a.journal.pages)
242
+ parts.push(a.journal.pages);
243
+ lines.push(`**Journal:** ${parts.filter(Boolean).join(', ')}`);
244
+ }
245
+ if (a.articleType)
246
+ lines.push(`**Type:** ${a.articleType}`);
247
+ if (a.publicationDate) {
248
+ const d = a.publicationDate;
249
+ const dateParts = [d.year, d.month, d.day].filter(Boolean);
250
+ if (dateParts.length)
251
+ lines.push(`**Published:** ${dateParts.join('-')}`);
252
+ }
226
253
  lines.push(`**PMCID:** ${a.pmcId}`);
227
254
  if (a.pmid)
228
255
  lines.push(`**PMID:** ${a.pmid}`);
229
256
  if (a.doi)
230
257
  lines.push(`**DOI:** ${a.doi}`);
231
258
  lines.push(`**PMC:** ${a.pmcUrl}`);
259
+ if (a.pubmedUrl)
260
+ lines.push(`**PubMed:** ${a.pubmedUrl}`);
261
+ if (a.keywords?.length)
262
+ lines.push(`**Keywords:** ${a.keywords.join(', ')}`);
232
263
  if (a.abstract)
233
264
  lines.push(`\n#### Abstract\n${a.abstract}`);
234
265
  for (const sec of a.sections) {
@@ -245,6 +276,13 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
245
276
  }
246
277
  }
247
278
  }
279
+ if (a.references?.length) {
280
+ lines.push(`\n#### References (${a.references.length})`);
281
+ for (const ref of a.references) {
282
+ const label = ref.label ?? ref.id ?? '';
283
+ lines.push(`- ${label ? `[${label}] ` : ''}${ref.citation}`);
284
+ }
285
+ }
248
286
  }
249
287
  return [{ type: 'text', text: lines.join('\n') }];
250
288
  },
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/services/ncbi/parsing/article-parser.js CHANGED
@@ -274,7 +274,7 @@ export function extractKeywords(keywordListsXml) {
274
274
  * @returns The abstract text string, or undefined if not found or empty.
275
275
  */
276
276
  export function extractAbstractText(abstractXml) {
277
- if (!abstractXml || !abstractXml.AbstractText)
277
+ if (!abstractXml?.AbstractText)
278
278
  return;
279
279
  const abstractTexts = ensureArray(abstractXml.AbstractText);
280
280
  if (abstractTexts.length === 0)
@@ -304,7 +304,7 @@ export function extractAbstractText(abstractXml) {
304
304
  * @returns The PMID string or undefined.
305
305
  */
306
306
  export function extractPmid(medlineCitationXml) {
307
- if (!medlineCitationXml || !medlineCitationXml.PMID)
307
+ if (!medlineCitationXml?.PMID)
308
308
  return;
309
309
  return getText(medlineCitationXml.PMID);
310
310
  }
@@ -314,7 +314,7 @@ export function extractPmid(medlineCitationXml) {
314
314
  * @returns An array of parsed article dates.
315
315
  */
316
316
  export function extractArticleDates(articleXml) {
317
- if (!articleXml || !articleXml.ArticleDate)
317
+ if (!articleXml?.ArticleDate)
318
318
  return [];
319
319
  const articleDatesXml = ensureArray(articleXml.ArticleDate);
320
320
  return articleDatesXml.map((ad) => ({
package/dist/services/ncbi/parsing/article-parser.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.2.3",
3
+ "version": "2.2.5",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
6
6
  "type": "module",
@@ -67,23 +67,27 @@
67
67
  "access": "public"
68
68
  },
69
69
  "overrides": {
70
+ "brace-expansion": ">=2.0.3",
70
71
  "express-rate-limit": ">=8.2.2",
71
- "hono": ">=4.12.7"
72
+ "hono": ">=4.12.7",
73
+ "path-to-regexp": ">=8.4.0",
74
+ "picomatch": ">=4.0.4",
75
+ "yaml": ">=2.8.3"
72
76
  },
73
77
  "dependencies": {
74
- "@cyanheads/mcp-ts-core": "^0.1.29",
78
+ "@cyanheads/mcp-ts-core": "^0.2.8",
75
79
  "fast-xml-parser": "^5.5.9",
76
80
  "pino-pretty": "^13.1.3",
77
81
  "sanitize-html": "^2.17.2"
78
82
  },
79
83
  "devDependencies": {
80
- "@biomejs/biome": "^2.4.8",
84
+ "@biomejs/biome": "^2.4.9",
81
85
  "@types/node": "^25.5.0",
82
86
  "@types/sanitize-html": "^2.16.1",
83
87
  "depcheck": "^1.4.7",
84
88
  "ignore": "^7.0.5",
85
89
  "tsc-alias": "^1.8.16",
86
90
  "typescript": "^6.0.2",
87
- "vitest": "^4.1.1"
91
+ "vitest": "^4.1.2"
88
92
  }
89
93
  }
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.2.3",
9
+ "version": "2.2.5",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.2.3",
22
+ "version": "2.2.5",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -60,7 +60,7 @@
60
60
  "registryBaseUrl": "https://registry.npmjs.org",
61
61
  "identifier": "@cyanheads/pubmed-mcp-server",
62
62
  "runtimeHint": "bun",
63
- "version": "2.2.3",
63
+ "version": "2.2.5",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",