@cyanheads/pubmed-mcp-server 2.2.2 → 2.2.4

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 (23) 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/api-client.d.ts +4 -3
  10. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  11. package/dist/services/ncbi/api-client.js +22 -34
  12. package/dist/services/ncbi/api-client.js.map +1 -1
  13. package/dist/services/ncbi/ncbi-service.d.ts +8 -1
  14. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  15. package/dist/services/ncbi/ncbi-service.js +41 -5
  16. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  17. package/dist/services/ncbi/parsing/article-parser.js +3 -3
  18. package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
  19. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  20. package/dist/services/ncbi/response-handler.js +7 -0
  21. package/dist/services/ncbi/response-handler.js.map +1 -1
  22. package/package.json +9 -5
  23. 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:** 2.2.2
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+ **Version:** 2.2.4
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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-2.2.2-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-2.2.4-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/api-client.d.ts CHANGED
@@ -1,19 +1,20 @@
1
1
  /**
2
2
  * @fileoverview Core HTTP client for NCBI E-utility requests. Handles URL construction,
3
- * API key injection, GET/POST selection based on payload size, and exponential backoff retries.
3
+ * API key injection, and GET/POST selection based on payload size. Single-attempt only;
4
+ * retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
4
5
  * @module src/services/ncbi/api-client
5
6
  */
6
7
  import { type NcbiRequestOptions, type NcbiRequestParams } from './types.js';
7
8
  export interface NcbiApiClientConfig {
8
9
  adminEmail?: string;
9
10
  apiKey?: string;
10
- maxRetries: number;
11
11
  timeoutMs: number;
12
12
  toolIdentifier: string;
13
13
  }
14
14
  /**
15
15
  * Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
16
- * chooses GET/POST, and retries with exponential backoff.
16
+ * and chooses GET/POST based on payload size. Single-attempt — retry logic lives
17
+ * in {@link NcbiService.performRequest} so it covers both HTTP and XML-level errors.
17
18
  */
18
19
  export declare class NcbiApiClient {
19
20
  private readonly config;
package/dist/services/ncbi/api-client.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,UAAU,EAAE,MAAM,CAAC;IACnB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;GAGG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAyDlB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
1
+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAiClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
package/dist/services/ncbi/api-client.js CHANGED
@@ -1,6 +1,7 @@
1
1
  /**
2
2
  * @fileoverview Core HTTP client for NCBI E-utility requests. Handles URL construction,
3
- * API key injection, GET/POST selection based on payload size, and exponential backoff retries.
3
+ * API key injection, and GET/POST selection based on payload size. Single-attempt only;
4
+ * retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
4
5
  * @module src/services/ncbi/api-client
5
6
  */
6
7
  import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
@@ -10,7 +11,8 @@ import { NCBI_EUTILS_BASE_URL } from './types.js';
10
11
  const POST_THRESHOLD = 2000;
11
12
  /**
12
13
  * Low-level HTTP client for NCBI E-utilities. Constructs URLs, injects credentials,
13
- * chooses GET/POST, and retries with exponential backoff.
14
+ * and chooses GET/POST based on payload size. Single-attempt — retry logic lives
15
+ * in {@link NcbiService.performRequest} so it covers both HTTP and XML-level errors.
14
16
  */
15
17
  export class NcbiApiClient {
16
18
  config;
@@ -21,40 +23,26 @@ export class NcbiApiClient {
21
23
  const finalParams = this.buildParams(params);
22
24
  const usePost = this.shouldPost(finalParams, options);
23
25
  const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}.fcgi`;
24
- for (let attempt = 0; attempt <= this.config.maxRetries; attempt++) {
25
- try {
26
- logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
27
- endpoint,
28
- attempt: attempt + 1,
29
- });
30
- const response = usePost
31
- ? await this.postRequest(url, finalParams)
32
- : await this.getRequest(url, finalParams);
33
- return await response.text();
34
- }
35
- catch (error) {
36
- if (error instanceof McpError) {
37
- if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
38
- error.code !== JsonRpcErrorCode.Timeout) {
39
- throw error;
40
- }
41
- }
42
- if (attempt < this.config.maxRetries) {
43
- const retryDelay = 2 ** attempt * 200;
44
- logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.config.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
45
- await new Promise((r) => setTimeout(r, retryDelay));
46
- continue;
47
- }
48
- if (error instanceof McpError)
49
- throw error;
50
- const msg = error instanceof Error ? error.message : String(error);
51
- logger.error(`NCBI request to ${endpoint} failed after ${this.config.maxRetries} retries.`, { endpoint, errorMessage: msg });
52
- throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed after retries: ${msg}`, { endpoint });
26
+ try {
27
+ logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
28
+ endpoint,
29
+ });
30
+ const response = usePost
31
+ ? await this.postRequest(url, finalParams)
32
+ : await this.getRequest(url, finalParams);
33
+ if (!response.ok) {
34
+ throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI API returned HTTP ${response.status}.`, { endpoint, status: response.status });
53
35
  }
36
+ return await response.text();
37
+ }
38
+ catch (error) {
39
+ if (error instanceof McpError)
40
+ throw error;
41
+ const msg = error instanceof Error ? error.message : String(error);
42
+ throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed: ${msg}`, {
43
+ endpoint,
44
+ });
54
45
  }
55
- throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
56
- endpoint,
57
- });
58
46
  }
59
47
  buildParams(params) {
60
48
  const raw = {
package/dist/services/ncbi/api-client.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,OAAO,CAAC;QAEvD,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EAAE;gBACpE,QAAQ;aACA,CAAC,CAAC;YAEZ,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,CAAC;gBAC1C,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,WAAW,CAAC,CAAC;YAE5C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,0BAA0B,QAAQ,CAAC,MAAM,GAAG,EAC5C,EAAE,QAAQ,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CACtC,CAAC;YACJ,CAAC;YAED,OAAO,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAE3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,QAAQ;aACT,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAEO,WAAW,CAAC,MAAyB;QAC3C,MAAM,GAAG,GAAgD;YACvD,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU;YAC7B,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM;YAC3B,GAAG,MAAM;SACV,CAAC;QAEF,MAAM,MAAM,GAA2B,EAAE,CAAC;QAC1C,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;gBAClB,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEO,UAAU,CAAC,MAA8B,EAAE,OAA4B;QAC7E,IAAI,OAAO,EAAE,OAAO;YAAE,OAAO,IAAI,CAAC;QAClC,MAAM,WAAW,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAC3D,OAAO,WAAW,CAAC,MAAM,GAAG,cAAc,CAAC;IAC7C,CAAC;IAEO,UAAU,CAAC,GAAW,EAAE,MAA8B;QAC5D,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAClD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAC1C,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC;QAC/F,OAAO,gBAAgB,CAAC,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IAC/D,CAAC;IAEO,WAAW,CAAC,GAAW,EAAE,MAA8B;QAC7D,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QACpD,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,CAAC;QACvF,OAAO,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;YACvD,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;SACL,CAAC,CAAC;IACL,CAAC;CACF"}
package/dist/services/ncbi/ncbi-service.d.ts CHANGED
@@ -16,7 +16,8 @@ export declare class NcbiService {
16
16
  private readonly apiClient;
17
17
  private readonly queue;
18
18
  private readonly responseHandler;
19
- constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler);
19
+ private readonly maxRetries;
20
+ constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler, maxRetries: number);
20
21
  eSearch(params: NcbiRequestParams): Promise<ESearchResult>;
21
22
  eSummary(params: NcbiRequestParams): Promise<ESummaryResult>;
22
23
  eFetch<T = {
@@ -25,6 +26,12 @@ export declare class NcbiService {
25
26
  eLink<T = Record<string, unknown>>(params: NcbiRequestParams): Promise<T>;
26
27
  eSpell(params: NcbiRequestParams): Promise<ESpellResult>;
27
28
  eInfo(params: NcbiRequestParams): Promise<unknown>;
29
+ /**
30
+ * Enqueues a request with retry logic that covers both HTTP-level failures
31
+ * (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
32
+ * with an error structure in the response body, e.g. connection resets
33
+ * surfaced as C++ exception traces).
34
+ */
28
35
  private performRequest;
29
36
  }
30
37
  /** Initialize the NCBI service. Call from `setup()` in createApp. */
package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,KAAK,EAEV,aAAa,EAEb,YAAY,EAEZ,cAAc,EACd,kBAAkB,EAClB,iBAAiB,EACjB,mBAAmB,EACpB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAFf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB;IAGjD,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD,OAAO,CAAC,cAAc;CAcvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAiBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
1
+ {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,KAAK,EAEV,aAAa,EAEb,YAAY,EAEZ,cAAc,EACd,kBAAkB,EAClB,iBAAiB,EACjB,mBAAmB,EACpB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAqDvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -4,6 +4,7 @@
4
4
  * typed methods for each E-utility endpoint. Uses init/accessor pattern.
5
5
  * @module src/services/ncbi/ncbi-service
6
6
  */
7
+ import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
7
8
  import { logger } from '@cyanheads/mcp-ts-core/utils';
8
9
  import { getServerConfig } from '../../config/server-config.js';
9
10
  import { NcbiApiClient } from './api-client.js';
@@ -17,10 +18,12 @@ export class NcbiService {
17
18
  apiClient;
18
19
  queue;
19
20
  responseHandler;
20
- constructor(apiClient, queue, responseHandler) {
21
+ maxRetries;
22
+ constructor(apiClient, queue, responseHandler, maxRetries) {
21
23
  this.apiClient = apiClient;
22
24
  this.queue = queue;
23
25
  this.responseHandler = responseHandler;
26
+ this.maxRetries = maxRetries;
24
27
  }
25
28
  async eSearch(params) {
26
29
  const response = await this.performRequest('esearch', params, {
@@ -74,10 +77,44 @@ export class NcbiService {
74
77
  eInfo(params) {
75
78
  return this.performRequest('einfo', params, { retmode: 'xml' });
76
79
  }
80
+ /**
81
+ * Enqueues a request with retry logic that covers both HTTP-level failures
82
+ * (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
83
+ * with an error structure in the response body, e.g. connection resets
84
+ * surfaced as C++ exception traces).
85
+ */
77
86
  performRequest(endpoint, params, options) {
78
87
  return this.queue.enqueue(async () => {
79
- const text = await this.apiClient.makeRequest(endpoint, params, options);
80
- return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
88
+ for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
89
+ try {
90
+ const text = await this.apiClient.makeRequest(endpoint, params, options);
91
+ return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
92
+ }
93
+ catch (error) {
94
+ // Only retry transient errors (ServiceUnavailable, Timeout).
95
+ // Validation, serialization, and other errors fail immediately.
96
+ if (error instanceof McpError) {
97
+ if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
98
+ error.code !== JsonRpcErrorCode.Timeout) {
99
+ throw error;
100
+ }
101
+ }
102
+ if (attempt < this.maxRetries) {
103
+ const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
104
+ logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
105
+ await new Promise((r) => setTimeout(r, retryDelay));
106
+ continue;
107
+ }
108
+ // Final attempt exhausted — surface retry context so the caller
109
+ // knows this wasn't a single failed request.
110
+ const attempts = this.maxRetries + 1;
111
+ const msg = error instanceof Error ? error.message : String(error);
112
+ throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint, attempts });
113
+ }
114
+ }
115
+ throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
116
+ endpoint,
117
+ });
81
118
  }, endpoint, params);
82
119
  }
83
120
  }
@@ -88,14 +125,13 @@ export function initNcbiService() {
88
125
  const config = getServerConfig();
89
126
  const apiClient = new NcbiApiClient({
90
127
  toolIdentifier: config.toolIdentifier,
91
- maxRetries: config.maxRetries,
92
128
  timeoutMs: config.timeoutMs,
93
129
  ...(config.apiKey && { apiKey: config.apiKey }),
94
130
  ...(config.adminEmail && { adminEmail: config.adminEmail }),
95
131
  });
96
132
  const queue = new NcbiRequestQueue(config.requestDelayMs);
97
133
  const responseHandler = new NcbiResponseHandler();
98
- _service = new NcbiService(apiClient, queue, responseHandler);
134
+ _service = new NcbiService(apiClient, queue, responseHandler, config.maxRetries);
99
135
  logger.info('NCBI service initialized.', {
100
136
  toolIdentifier: config.toolIdentifier,
101
137
  hasApiKey: !!config.apiKey,
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -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 @@
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package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiGrD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;;IAa1C,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CAqFL"}
1
+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiGrD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;;IAa1C,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CAiGL"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -143,6 +143,13 @@ export class NcbiResponseHandler {
143
143
  const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
144
144
  const validationResult = XMLValidator.validate(xmlForValidation);
145
145
  if (validationResult !== true) {
146
+ const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
147
+ if (isHtml) {
148
+ logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', {
149
+ endpoint,
150
+ });
151
+ throw new McpError(JsonRpcErrorCode.ServiceUnavailable, 'NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
152
+ }
146
153
  logger.error('Invalid XML response from NCBI.', {
147
154
  endpoint,
148
155
  responseSnippet: responseText.substring(0, 500),
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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1
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.2.2",
3
+ "version": "2.2.4",
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": "^0.2.3",
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": "2.2.2",
9
+ "version": "2.2.4",
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": "2.2.2",
22
+ "version": "2.2.4",
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": "2.2.2",
63
+ "version": "2.2.4",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",