@cyanheads/pubmed-mcp-server 2.3.4 → 2.3.6

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Files changed (20) hide show
  1. package/CLAUDE.md +1 -1
  2. package/README.md +2 -2
  3. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -2
  5. package/dist/mcp-server/tools/definitions/convert-ids.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 +1 -2
  8. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/search-articles.tool.js +1 -3
  11. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  12. package/dist/services/ncbi/ncbi-service.d.ts +1 -1
  13. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  14. package/dist/services/ncbi/ncbi-service.js +9 -3
  15. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  16. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  17. package/dist/services/ncbi/response-handler.js +28 -2
  18. package/dist/services/ncbi/response-handler.js.map +1 -1
  19. package/package.json +6 -17
  20. 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:** 2.3.4
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+ **Version:** 2.3.6
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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.
package/README.md CHANGED
@@ -7,9 +7,9 @@
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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-2.3.3-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-2.3.6-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/)
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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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+ [![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/)
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  </div>
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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA+EzB,CAAC"}
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+ {"version":3,"file":"convert-ids.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAGjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA8EzB,CAAC"}
package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED
@@ -13,8 +13,7 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
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  .array(z.string().min(1))
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  .min(1)
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  .max(50)
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- .describe('Article identifiers to convert. All IDs must be the same type. ' +
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- 'DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190".'),
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+ .describe('Article identifiers to convert. All IDs must be the same type. DOIs: "10.1093/nar/gks1195", PMIDs: "23193287", PMCIDs: "PMC3531190".'),
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  idtype: z
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  .enum(['pmcid', 'pmid', 'doi'])
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  .describe('The type of IDs being submitted. Required so the API can unambiguously resolve them.'),
package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"convert-ids.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/convert-ids.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,gQAAgQ;IAC7Q,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,sIAAsI,CACvI;QACH,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;aAC9B,QAAQ,CACP,sFAAsF,CACvF;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,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,mBAAmB,CAAC;YAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAChE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oCAAoC,CAAC;SAC7E,CAAC,CACH;aACA,QAAQ,CAAC,sCAAsC,CAAC;QACnD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KAC/D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,MAAM,CAAC,CAAC;QAEtE,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YAC9B,WAAW,EAAE,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC;YACtC,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;YACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;YACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;SAC5D,CAAC,CAAC,CAAC;QAEJ,MAAM,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC/D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,cAAc;YACd,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;IACvE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;YAClE,EAAE;YACF,uCAAuC;YACvC,uBAAuB;SACxB,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,IAAI,CAAC,CAAC,MAAM,EAAE,CAAC;gBACb,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,WAAW,qBAAqB,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC;YAClE,CAAC;iBAAM,CAAC;gBACN,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,IAAI,CAAC,CAAC;YAC9F,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAkO5B,CAAC"}
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+ {"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAiO5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -63,8 +63,7 @@ const SectionSchema = z.object({
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  subsections: z.array(SubsectionSchema).optional().describe('Nested subsections'),
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  });
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  export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
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- description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. ' +
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- 'Accepts PMC IDs directly or PubMed IDs (auto-resolved via ELink).',
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+ 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).',
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  annotations: { readOnlyHint: true, openWorldHint: true },
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  input: z.object({
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  pmcids: z
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsCjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8Q7B,CAAC"}
1
+ {"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsCjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA4Q7B,CAAC"}
package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED
@@ -40,9 +40,7 @@ const AppliedFiltersSchema = z.object({
40
40
  .describe('Species filter applied to the search'),
41
41
  });
42
42
  export const searchArticlesTool = tool('pubmed_search_articles', {
43
- description: 'Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. ' +
44
- 'Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), ' +
45
- 'and pagination via offset for paging through large result sets.',
43
+ description: 'Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.',
46
44
  annotations: { readOnlyHint: true, openWorldHint: true },
47
45
  input: z.object({
48
46
  query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/ncbi-service.d.ts CHANGED
@@ -42,7 +42,7 @@ export declare class NcbiService {
42
42
  private static readonly MAX_BACKOFF_MS;
43
43
  /**
44
44
  * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
45
- * Non-transient errors (validation, serialization) fail immediately.
45
+ * Non-transient McpErrors and unexpected plain Errors fail immediately.
46
46
  * Uses capped exponential backoff with jitter.
47
47
  */
48
48
  private withRetry;
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;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,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,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;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA8C3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;OAIG;YACW,SAAS;IAoCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;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,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,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;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA8C3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;OAIG;YACW,SAAS;IAuCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -145,7 +145,7 @@ export class NcbiService {
145
145
  static MAX_BACKOFF_MS = 30_000;
146
146
  /**
147
147
  * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
148
- * Non-transient errors (validation, serialization) fail immediately.
148
+ * Non-transient McpErrors and unexpected plain Errors fail immediately.
149
149
  * Uses capped exponential backoff with jitter.
150
150
  */
151
151
  async withRetry(execute, label) {
@@ -154,7 +154,10 @@ export class NcbiService {
154
154
  return await execute();
155
155
  }
156
156
  catch (error) {
157
- if (error instanceof McpError && !NcbiService.RETRYABLE_CODES.has(error.code)) {
157
+ if (!(error instanceof McpError)) {
158
+ throw error;
159
+ }
160
+ if (!NcbiService.RETRYABLE_CODES.has(error.code)) {
158
161
  throw error;
159
162
  }
160
163
  if (attempt < this.maxRetries) {
@@ -167,7 +170,10 @@ export class NcbiService {
167
170
  }
168
171
  const attempts = this.maxRetries + 1;
169
172
  const msg = error instanceof Error ? error.message : String(error);
170
- throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint: label, attempts });
173
+ throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
174
+ endpoint: label,
175
+ attempts,
176
+ });
171
177
  }
172
178
  }
173
179
  throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
1
- 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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;CAiGL"}
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;AA4GrD;;;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;CAoHL"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -60,6 +60,16 @@ const WARNING_PATHS = [
60
60
  'eSearchResult.WarningList.QuotedPhraseNotFound',
61
61
  'eSearchResult.WarningList.OutputMessage',
62
62
  ];
63
+ /**
64
+ * NCBI responses routinely contain numeric character references for punctuation
65
+ * and diacritics, especially in page ranges and author names. Keep entity
66
+ * processing enabled, but raise the aggregate expansion ceiling high enough for
67
+ * trusted PubMed payloads.
68
+ */
69
+ const NCBI_PROCESS_ENTITIES_OPTIONS = {
70
+ enabled: true,
71
+ maxTotalExpansions: 100_000,
72
+ };
63
73
  function resolvePath(obj, path) {
64
74
  let current = obj;
65
75
  for (const part of path.split('.')) {
@@ -109,7 +119,7 @@ export class NcbiResponseHandler {
109
119
  ignoreAttributes: false,
110
120
  attributeNamePrefix: '@_',
111
121
  parseTagValue: true,
112
- processEntities: true,
122
+ processEntities: NCBI_PROCESS_ENTITIES_OPTIONS,
113
123
  htmlEntities: true,
114
124
  isArray: (_name, jpath) => NCBI_ARRAY_JPATHS.has(jpath),
115
125
  });
@@ -159,7 +169,23 @@ export class NcbiResponseHandler {
159
169
  responseSnippet: responseText.substring(0, 200),
160
170
  });
161
171
  }
162
- const parsedXml = this.xmlParser.parse(responseText);
172
+ let parsedXml;
173
+ try {
174
+ parsedXml = this.xmlParser.parse(responseText);
175
+ }
176
+ catch (error) {
177
+ const parserError = error instanceof Error ? error.message : String(error);
178
+ logger.error('Failed to parse validated XML response from NCBI.', {
179
+ endpoint,
180
+ parserError,
181
+ responseSnippet: responseText.substring(0, 500),
182
+ });
183
+ throw new McpError(JsonRpcErrorCode.SerializationError, `Failed to parse XML response from NCBI: ${parserError}`, {
184
+ endpoint,
185
+ parserError,
186
+ responseSnippet: responseText.substring(0, 200),
187
+ });
188
+ }
163
189
  const hasError = ERROR_PATHS.some((path) => resolvePath(parsedXml, path) !== undefined);
164
190
  if (hasError) {
165
191
  const errorMessages = this.extractNcbiErrorMessages(parsedXml);
package/dist/services/ncbi/response-handler.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": "2.3.4",
3
+ "version": "2.3.6",
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",
@@ -66,32 +66,21 @@
66
66
  "publishConfig": {
67
67
  "access": "public"
68
68
  },
69
- "overrides": {
70
- "@hono/node-server": ">=1.19.13",
71
- "brace-expansion": ">=2.0.3",
72
- "express-rate-limit": ">=8.2.2",
73
- "hono": ">=4.12.12",
74
- "path-to-regexp": ">=8.4.0",
75
- "picomatch": ">=4.0.4",
76
- "vite": ">=8.0.8",
77
- "yaml": ">=2.8.3",
78
- "lodash": ">=4.17.24"
79
- },
80
69
  "dependencies": {
81
- "@cyanheads/mcp-ts-core": "^0.3.4",
82
- "fast-xml-parser": "^5.5.11",
70
+ "@cyanheads/mcp-ts-core": "^0.3.7",
71
+ "fast-xml-parser": "^5.7.1",
83
72
  "pino-pretty": "^13.1.3",
84
- "sanitize-html": "^2.17.2"
73
+ "sanitize-html": "^2.17.3"
85
74
  },
86
75
  "devDependencies": {
87
- "@biomejs/biome": "^2.4.11",
76
+ "@biomejs/biome": "^2.4.12",
88
77
  "@types/node": "^25.6.0",
89
78
  "@types/sanitize-html": "^2.16.1",
90
79
  "@vitest/coverage-istanbul": "^4.1.4",
91
80
  "depcheck": "^1.4.7",
92
81
  "ignore": "^7.0.5",
93
82
  "tsc-alias": "^1.8.16",
94
- "typescript": "^6.0.2",
83
+ "typescript": "^6.0.3",
95
84
  "vitest": "^4.1.4"
96
85
  }
97
86
  }
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": "2.3.4",
9
+ "version": "2.3.6",
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": "2.3.4",
22
+ "version": "2.3.6",
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": "2.3.4",
63
+ "version": "2.3.6",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",