@cyanheads/pubmed-mcp-server 2.6.7 → 2.6.9

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Files changed (67) hide show
  1. package/CLAUDE.md +2 -2
  2. package/README.md +1 -1
  3. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +32 -2
  4. package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
  5. package/dist/mcp-server/tools/definitions/convert-ids.tool.js +3 -1
  6. package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
  7. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +12 -0
  8. package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +1 -1
  10. package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
  11. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +18 -0
  12. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  13. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +6 -2
  14. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  15. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +14 -8
  16. package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
  17. package/dist/mcp-server/tools/definitions/find-related.tool.js +46 -33
  18. package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
  19. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +31 -1
  20. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  21. package/dist/mcp-server/tools/definitions/format-citations.tool.js +2 -0
  22. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  23. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +31 -1
  24. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  25. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +3 -1
  26. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  27. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +31 -1
  28. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
  29. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +2 -0
  30. package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
  31. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +31 -1
  32. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  33. package/dist/mcp-server/tools/definitions/search-articles.tool.js +2 -0
  34. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  35. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +31 -1
  36. package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
  37. package/dist/mcp-server/tools/definitions/spell-check.tool.js +2 -0
  38. package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
  39. package/dist/services/error-contracts.d.ts +89 -0
  40. package/dist/services/error-contracts.d.ts.map +1 -0
  41. package/dist/services/error-contracts.js +97 -0
  42. package/dist/services/error-contracts.js.map +1 -0
  43. package/dist/services/ncbi/api-client.d.ts.map +1 -1
  44. package/dist/services/ncbi/api-client.js +3 -2
  45. package/dist/services/ncbi/api-client.js.map +1 -1
  46. package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
  47. package/dist/services/ncbi/formatting/citation-formatter.js +3 -4
  48. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  49. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  50. package/dist/services/ncbi/ncbi-service.js +50 -6
  51. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  52. package/dist/services/ncbi/request-queue.d.ts.map +1 -1
  53. package/dist/services/ncbi/request-queue.js +7 -1
  54. package/dist/services/ncbi/request-queue.js.map +1 -1
  55. package/dist/services/ncbi/response-handler.d.ts +7 -2
  56. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  57. package/dist/services/ncbi/response-handler.js +57 -12
  58. package/dist/services/ncbi/response-handler.js.map +1 -1
  59. package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
  60. package/dist/services/unpaywall/unpaywall-service.js +7 -2
  61. package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
  62. package/package.json +3 -3
  63. package/server.json +3 -3
  64. package/dist/mcp-server/tools/definitions/_error-contracts.d.ts +0 -41
  65. package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map +0 -1
  66. package/dist/mcp-server/tools/definitions/_error-contracts.js +0 -45
  67. package/dist/mcp-server/tools/definitions/_error-contracts.js.map +0 -1
package/CLAUDE.md CHANGED
@@ -1,8 +1,8 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.6.7
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.8.19`
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+ **Version:** 2.6.9
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.8.20`
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  **Engines:** Bun ≥1.3.2, Node ≥24.0.0
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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
@@ -7,7 +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-2.6.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-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-2.6.9-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-^1.29.0-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-^6.0.3-3178C6.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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package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts CHANGED
@@ -7,8 +7,8 @@ import { z } from '@cyanheads/mcp-ts-core';
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  export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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  ids: z.ZodArray<z.ZodString>;
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  idType: z.ZodEnum<{
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- pmcid: "pmcid";
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  pmid: "pmid";
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+ pmcid: "pmcid";
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  doi: "doi";
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  }>;
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  }, z.core.$strip>, z.ZodObject<{
@@ -21,5 +21,35 @@ export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefini
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  }, z.core.$strip>>;
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  totalConverted: z.ZodNumber;
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  totalSubmitted: z.ZodNumber;
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- }, z.core.$strip>, undefined>;
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+ }, z.core.$strip>, readonly [{
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+ readonly reason: "queue_full";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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+ readonly when: "Local NCBI request queue is at capacity.";
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+ readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
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+ readonly retryable: true;
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+ }, {
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+ readonly reason: "ncbi_unreachable";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
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+ readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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+ readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
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+ readonly retryable: true;
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+ }, {
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+ readonly reason: "ncbi_deadline_exceeded";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
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+ readonly when: "Total request deadline expired before NCBI returned a response.";
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+ readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
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+ readonly retryable: true;
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+ }, {
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+ readonly reason: "ncbi_invalid_response";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
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+ readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
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+ readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
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+ readonly retryable: true;
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+ }, {
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+ readonly reason: "ncbi_resource_not_found";
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+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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+ readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
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+ readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
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+ readonly retryable: false;
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+ }]>;
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  //# sourceMappingURL=convert-ids.tool.d.ts.map
package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"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;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;6BAyGzB,CAAC"}
1
+ {"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;AAcjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2GzB,CAAC"}
package/dist/mcp-server/tools/definitions/convert-ids.tool.js CHANGED
@@ -4,6 +4,7 @@
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  * @module src/mcp-server/tools/definitions/convert-ids.tool
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  */
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  import { tool, z } from '@cyanheads/mcp-ts-core';
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+ import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
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  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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  import { conceptMeta, EDAM_ACCESSION, EDAM_ID_MAPPING } from './_concepts.js';
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  /**
@@ -14,10 +15,11 @@ import { conceptMeta, EDAM_ACCESSION, EDAM_ID_MAPPING } from './_concepts.js';
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  const PMC_NOT_FOUND_RE = /^identifier not found in pmc$/i;
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  const PMC_NOT_FOUND_REWRITE = 'Not in PMC ID Converter. Article may still exist in PubMed — try pubmed_fetch_articles (PMID → DOI) or pubmed_search_articles.';
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  export const convertIdsTool = tool('pubmed_convert_ids', {
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- description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Uses the NCBI PMC ID Converter API — only resolves articles indexed in PubMed Central. For articles not in PMC, use pubmed_search_articles instead.`,
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+ description: `Convert between article identifiers (DOI, PMID, PMCID). Accepts up to 50 IDs of a single type per request. Only resolves articles indexed in PubMed Central — for articles not in PMC, use pubmed_search_articles instead.`,
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  annotations: { readOnlyHint: true, openWorldHint: true },
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  _meta: conceptMeta([EDAM_ID_MAPPING, EDAM_ACCESSION]),
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  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/convert-ids.tool.ts',
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+ errors: [...NCBI_SERVICE_ERRORS],
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  input: z.object({
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  ids: z
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  .array(z.string().min(1))
package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map CHANGED
@@ -1 +1 @@
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1
+ {"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,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAC1D,MAAM,qBAAqB,GACzB,gIAAgI,CAAC;AAEnI,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,4NAA4N;IACzO,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,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;aACE,MAAM,CAAC;YACN,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACjF,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yHAAyH,CAC1H;SACJ,CAAC;aACD,QAAQ,CAAC,0BAA0B,CAAC,CACxC;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,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAE9F,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC5B,MAAM,WAAW,GAAG,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;YAC9C,IAAI,MAA0B,CAAC;YAC/B,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;gBAClC,IAAI,gBAAgB,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;oBACpC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,gCAAgC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC,CAAC;oBAC3E,MAAM,GAAG,qBAAqB,CAAC;gBACjC,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,QAAQ,CAAC;gBACpB,CAAC;YACH,CAAC;YACD,OAAO;gBACL,WAAW;gBACX,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,CAAC;aACxC,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,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,+CAA+C;YAC/C,4BAA4B;SAC7B,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,MAAM,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CACrG,CAAC;QACJ,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-articles.tool.d.ts CHANGED
@@ -87,6 +87,18 @@ export declare const fetchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDef
87
87
  readonly when: "Total request deadline expired before NCBI returned a response.";
88
88
  readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
89
89
  readonly retryable: true;
90
+ }, {
91
+ readonly reason: "ncbi_invalid_response";
92
+ readonly code: JsonRpcErrorCode.SerializationError;
93
+ readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
94
+ readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
95
+ readonly retryable: true;
96
+ }, {
97
+ readonly reason: "ncbi_resource_not_found";
98
+ readonly code: JsonRpcErrorCode.NotFound;
99
+ readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
100
+ readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
101
+ readonly retryable: false;
90
102
  }, {
91
103
  readonly reason: "invalid_efetch_response";
92
104
  readonly code: JsonRpcErrorCode.SerializationError;
package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0K5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js CHANGED
@@ -5,11 +5,11 @@
5
5
  */
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
7
7
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
8
+ import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
8
9
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
9
10
  import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
10
11
  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
11
12
  import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
12
- import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
13
13
  import { pmidStringSchema } from './_schemas.js';
14
14
  const AuthorSchema = z
15
15
  .object({
package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts CHANGED
@@ -109,6 +109,24 @@ export declare const fetchFulltextTool: import("@cyanheads/mcp-ts-core").ToolDef
109
109
  readonly when: "Total request deadline expired before NCBI returned a response.";
110
110
  readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
111
111
  readonly retryable: true;
112
+ }, {
113
+ readonly reason: "ncbi_invalid_response";
114
+ readonly code: JsonRpcErrorCode.SerializationError;
115
+ readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
116
+ readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
117
+ readonly retryable: true;
118
+ }, {
119
+ readonly reason: "ncbi_resource_not_found";
120
+ readonly code: JsonRpcErrorCode.NotFound;
121
+ readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
122
+ readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
123
+ readonly retryable: false;
124
+ }, {
125
+ readonly reason: "unpaywall_unreachable";
126
+ readonly code: JsonRpcErrorCode.ServiceUnavailable;
127
+ readonly when: "Unpaywall was unreachable when resolving a DOI or fetching content.";
128
+ readonly recovery: "Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.";
129
+ readonly retryable: true;
112
130
  }, {
113
131
  readonly reason: "invalid_pmc_efetch_response";
114
132
  readonly code: JsonRpcErrorCode.SerializationError;
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;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuP5B,CAAC"}
1
+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8P5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -9,6 +9,7 @@
9
9
  import { tool, z } from '@cyanheads/mcp-ts-core';
10
10
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
11
11
  import { htmlExtractor, pdfParser } from '@cyanheads/mcp-ts-core/utils';
12
+ import { NCBI_SERVICE_ERRORS, UNPAYWALL_SERVICE_ERRORS } from '../../../services/error-contracts.js';
12
13
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
13
14
  import { extractDoi, extractPmid } from '../../../services/ncbi/parsing/article-parser.js';
14
15
  import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
@@ -16,7 +17,6 @@ import { findAll, findOne } from '../../../services/ncbi/parsing/pmc-xml-helpers
16
17
  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
17
18
  import { getUnpaywallService } from '../../../services/unpaywall/unpaywall-service.js';
18
19
  import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
19
- import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
20
20
  import { pmidStringSchema } from './_schemas.js';
21
21
  function normalizePmcId(id) {
22
22
  return id.replace(/^PMC/i, '');
@@ -146,12 +146,13 @@ const UnavailableSchema = z
146
146
  .describe('One PMID that could not be returned with an explanation of why');
147
147
  // ─── Tool Definition ─────────────────────────────────────────────────────────
148
148
  export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
149
- description: 'Fetch full-text articles. Primary source is PubMed Central (structured JATS with sections and references). When a PMID has no PMC copy, transparently falls back to Unpaywall (open-access copies hosted by publishers or institutional repositories) and returns best-effort HTML-as-Markdown or PDF-as-text. Set UNPAYWALL_EMAIL to enable the fallback. Provide exactly one of `pmcids` (PMC IDs directly) or `pmids` (PubMed IDs, auto-resolved via the PMC ID Converter) — not both, not neither.',
149
+ description: 'Fetch full-text articles from PubMed Central with structured sections and references. When a PMID has no PMC copy, transparently falls back to publisher-hosted or institutional open-access copies as HTML-as-Markdown or PDF-as-text. Provide exactly one of `pmcids` (PMC IDs directly) or `pmids` (PubMed IDs, auto-resolved) — not both, not neither.',
150
150
  annotations: { readOnlyHint: true, openWorldHint: true },
151
151
  _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
152
152
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
153
153
  errors: [
154
154
  ...NCBI_SERVICE_ERRORS,
155
+ ...UNPAYWALL_SERVICE_ERRORS,
155
156
  {
156
157
  reason: 'invalid_pmc_efetch_response',
157
158
  code: JsonRpcErrorCode.SerializationError,
@@ -348,6 +349,9 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
348
349
  if (result.unavailablePmcIds?.length) {
349
350
  lines.push(`**Unavailable PMC IDs:** ${result.unavailablePmcIds.join(', ')}`);
350
351
  }
352
+ if (result.totalReturned === 0) {
353
+ lines.push(`\n> No full-text articles returned. Articles must be open-access and indexed in PMC (or recoverable via Unpaywall) to retrieve full text. For metadata and abstracts only, use \`pubmed_fetch_articles\`.`);
354
+ }
351
355
  for (const a of result.articles) {
352
356
  lines.push('');
353
357
  if (a.source === 'pmc')
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED
@@ -4,7 +4,6 @@
4
4
  * @module src/mcp-server/tools/definitions/find-related.tool
5
5
  */
6
6
  import { z } from '@cyanheads/mcp-ts-core';
7
- import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
8
7
  export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
9
8
  pmid: z.ZodString;
10
9
  relationship: z.ZodDefault<z.ZodEnum<{
@@ -32,26 +31,33 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
32
31
  notice: z.ZodOptional<z.ZodString>;
33
32
  }, z.core.$strip>, readonly [{
34
33
  readonly reason: "queue_full";
35
- readonly code: JsonRpcErrorCode.RateLimited;
34
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
36
35
  readonly when: "Local NCBI request queue is at capacity.";
37
36
  readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
38
37
  readonly retryable: true;
39
38
  }, {
40
39
  readonly reason: "ncbi_unreachable";
41
- readonly code: JsonRpcErrorCode.ServiceUnavailable;
40
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
42
41
  readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
43
42
  readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
44
43
  readonly retryable: true;
45
44
  }, {
46
45
  readonly reason: "ncbi_deadline_exceeded";
47
- readonly code: JsonRpcErrorCode.Timeout;
46
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
48
47
  readonly when: "Total request deadline expired before NCBI returned a response.";
49
48
  readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
50
49
  readonly retryable: true;
51
50
  }, {
52
- readonly reason: "elink_error";
53
- readonly code: JsonRpcErrorCode.ServiceUnavailable;
54
- readonly when: "NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.";
55
- readonly recovery: "Verify the source PMID exists or try a different relationship type.";
51
+ readonly reason: "ncbi_invalid_response";
52
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
53
+ readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
54
+ readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
55
+ readonly retryable: true;
56
+ }, {
57
+ readonly reason: "ncbi_resource_not_found";
58
+ readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
59
+ readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
60
+ readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
61
+ readonly retryable: false;
56
62
  }]>;
57
63
  //# sourceMappingURL=find-related.tool.d.ts.map
package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmN1B,CAAC"}
1
+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAuCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgO1B,CAAC"}
package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED
@@ -4,12 +4,12 @@
4
4
  * @module src/mcp-server/tools/definitions/find-related.tool
5
5
  */
6
6
  import { tool, z } from '@cyanheads/mcp-ts-core';
7
- import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
7
+ import { McpError } from '@cyanheads/mcp-ts-core/errors';
8
+ import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
8
9
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
9
10
  import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
10
11
  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
11
12
  import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
12
- import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
13
13
  import { pmidStringSchema } from './_schemas.js';
14
14
  function extractValue(field) {
15
15
  if (field === undefined || field === null)
@@ -24,15 +24,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
24
24
  annotations: { readOnlyHint: true, openWorldHint: true },
25
25
  _meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
26
26
  sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/find-related.tool.ts',
27
- errors: [
28
- ...NCBI_SERVICE_ERRORS,
29
- {
30
- reason: 'elink_error',
31
- code: JsonRpcErrorCode.ServiceUnavailable,
32
- when: 'NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.',
33
- recovery: 'Verify the source PMID exists or try a different relationship type.',
34
- },
35
- ],
27
+ errors: [...NCBI_SERVICE_ERRORS],
36
28
  input: z.object({
37
29
  pmid: pmidStringSchema.describe('Source PubMed ID'),
38
30
  relationship: z
@@ -63,7 +55,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
63
55
  notice: z
64
56
  .string()
65
57
  .optional()
66
- .describe('Optional guidance when results are empty due to a known limitation — e.g. references for a non-PMC source. Absent on successful result pages.'),
58
+ .describe('Optional guidance when results are empty — e.g. invalid source PMID, or references requested for a non-PMC source. Absent on successful result pages.'),
67
59
  }),
68
60
  async handler(input, ctx) {
69
61
  const ncbi = getNcbiService();
@@ -93,15 +85,16 @@ export const findRelatedTool = tool('pubmed_find_related', {
93
85
  const eLinkResult = (await ncbi.eLink(eLinkParams, { signal: ctx.signal }));
94
86
  const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
95
87
  const firstResult = eLinkResultsArray[0];
88
+ // NCBI ELink stamps `<ERROR>` for invalid PMIDs alongside an absent or empty
89
+ // LinkSet — the same observable shape as a valid PMID with no related links.
90
+ // Fall through to the empty-LinkSet path below; the ESummary disambiguation
91
+ // there distinguishes "unknown PMID" from "valid PMID, no relations" and
92
+ // produces a notice in either case. Log the raw payload for telemetry.
96
93
  if (firstResult?.ERROR) {
97
- const detail = typeof firstResult.ERROR === 'string'
98
- ? firstResult.ERROR
99
- : 'NCBI returned a non-string ERROR payload';
100
- throw ctx.fail('elink_error', `ELink error: ${detail}`, {
94
+ ctx.log.debug('NCBI ELink returned <ERROR>; disambiguating via ESummary', {
101
95
  pmid: input.pmid,
102
96
  relationship: input.relationship,
103
97
  ncbiError: firstResult.ERROR,
104
- ...ctx.recoveryFor('elink_error'),
105
98
  });
106
99
  }
107
100
  const linkSet = firstResult?.LinkSet;
@@ -125,24 +118,44 @@ export const findRelatedTool = tool('pubmed_find_related', {
125
118
  }
126
119
  const totalFound = foundPmids.length;
127
120
  if (foundPmids.length === 0) {
128
- // NCBI's pubmed_pubmed_refs ELink only resolves reference lists for
129
- // PMC-indexed sources, so a valid PMID without a PMCID looks identical
130
- // to "this article cites nothing". Look up the source's PMCID so the
131
- // caller gets a relationship-aware recovery hint.
132
- let notice;
133
- if (input.relationship === 'references') {
134
- try {
135
- const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: input.pmid }, { signal: ctx.signal });
136
- const summaries = await extractBriefSummaries(summaryResult);
137
- const sourcePmcId = summaries[0]?.pmcId;
138
- notice = sourcePmcId
139
- ? `No reference list found in PMC for PMID ${input.pmid} (PMCID ${sourcePmcId}).`
140
- : `Reference lists require the source article to be indexed in PMC. PMID ${input.pmid} has no PMCID — references unavailable. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
141
- }
142
- catch (err) {
143
- ctx.log.debug('Failed to look up source PMCID for references hint', { err });
121
+ // ELink returns an empty LinkSet for both invalid source PMIDs and valid
122
+ // PMIDs that simply have no related articles, so a single ESummary on the
123
+ // source disambiguates the two cases for every relationship type. NCBI's
124
+ // pubmed_pubmed_refs ELink also only resolves references for PMC-indexed
125
+ // sources, so the same lookup yields the PMCID for the references hint.
126
+ let sourceSummary;
127
+ let sourceConfirmedMissing = false;
128
+ try {
129
+ const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: input.pmid }, { signal: ctx.signal });
130
+ const summaries = await extractBriefSummaries(summaryResult);
131
+ sourceSummary = summaries[0];
132
+ // ESummary succeeded but returned nothing parseable — PMID is unknown.
133
+ if (!sourceSummary?.title)
134
+ sourceConfirmedMissing = true;
135
+ }
136
+ catch (err) {
137
+ ctx.log.debug('Source PMID ESummary failed', { err });
138
+ // Key off the contract reason rather than the JSON-RPC code: the service
139
+ // layer stamps `ncbi_resource_not_found` for "unknown UID" responses,
140
+ // while transient transport failures keep their ServiceUnavailable code
141
+ // with no such reason.
142
+ const reason = err instanceof McpError
143
+ ? err.data?.reason
144
+ : undefined;
145
+ if (reason === 'ncbi_resource_not_found') {
146
+ sourceConfirmedMissing = true;
144
147
  }
145
148
  }
149
+ let notice;
150
+ if (sourceConfirmedMissing) {
151
+ notice = `Source PMID ${input.pmid} not found in PubMed. Verify the ID with \`pubmed_fetch_articles\` or \`pubmed_search_articles\`.`;
152
+ }
153
+ else if (sourceSummary?.title && input.relationship === 'references') {
154
+ const sourcePmcId = sourceSummary.pmcId;
155
+ notice = sourcePmcId
156
+ ? `No reference list found in PMC for PMID ${input.pmid} (PMCID ${sourcePmcId}).`
157
+ : `Reference lists require the source article to be indexed in PMC. PMID ${input.pmid} has no PMCID — references unavailable. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
158
+ }
146
159
  return {
147
160
  sourcePmid: input.pmid,
148
161
  relationship: input.relationship,