@cyanheads/pubmed-mcp-server 2.3.2 → 2.3.3

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Files changed (21) hide show
  1. package/CLAUDE.md +1 -1
  2. package/README.md +4 -1
  3. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +3 -0
  4. package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
  5. package/dist/mcp-server/tools/definitions/format-citations.tool.js +21 -2
  6. package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
  7. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +6 -0
  8. package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
  9. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +28 -6
  10. package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
  11. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +23 -0
  12. package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
  13. package/dist/mcp-server/tools/definitions/search-articles.tool.js +110 -16
  14. package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
  15. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  16. package/dist/services/ncbi/ncbi-service.js +20 -5
  17. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  18. package/dist/services/ncbi/types.d.ts +4 -0
  19. package/dist/services/ncbi/types.d.ts.map +1 -1
  20. package/package.json +8 -5
  21. 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:** 2.3.2
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+ **Version:** 2.3.3
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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
@@ -7,7 +7,7 @@
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7
 
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  <div align="center">
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9
 
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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-2.3.2-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-2.3.3-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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  [![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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@@ -49,6 +49,7 @@ Search PubMed with full NCBI query syntax and filters.
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  - Sort by relevance, publication date, author, or journal
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  - Pagination via offset for paging through large result sets
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  - Optional brief summaries for top N results via ESummary
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+ - Returns the original query plus the fully applied PubMed query and normalized filter metadata
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  ---
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@@ -86,6 +87,7 @@ Generate formatted citations for articles.
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  - Request multiple styles per article in a single call
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  - Hand-rolled formatters — zero external dependencies, fully Workers-compatible
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  - Up to 50 articles per request
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+ - Reports formatted counts and unavailable PMIDs for partial-result handling
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  ---
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@@ -126,6 +128,7 @@ Resolve partial bibliographic references to PubMed IDs via NCBI ECitMatch.
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  - More fields = better match accuracy; at least one field required
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  - Batch up to 25 citations per request
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  - Deterministic matching — more reliable than free-text search for known references
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+ - Returns explicit `matched`, `not_found`, and `ambiguous` statuses with recovery detail
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  ---
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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts CHANGED
@@ -18,5 +18,8 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
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  title: z.ZodOptional<z.ZodString>;
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  citations: z.ZodRecord<z.ZodString, z.ZodString>;
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  }, z.core.$strip>>;
21
+ totalSubmitted: z.ZodNumber;
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+ totalFormatted: z.ZodNumber;
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+ unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
21
24
  }, z.core.$strip>>;
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  //# sourceMappingURL=format-citations.tool.d.ts.map
package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;kBAmE9B,CAAC"}
1
+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBAuF9B,CAAC"}
package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED
@@ -26,6 +26,12 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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  citations: z.record(z.string(), z.string()).describe('Citations keyed by style'),
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  }))
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  .describe('Citations per article'),
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+ totalSubmitted: z.number().describe('Number of PMIDs submitted for citation formatting'),
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+ totalFormatted: z.number().describe('Number of PMIDs successfully formatted'),
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+ unavailablePmids: z
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+ .array(z.string())
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+ .optional()
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+ .describe('Requested PMIDs that did not return article metadata'),
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  }),
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  async handler(input, ctx) {
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  ctx.log.debug('Fetching articles for citation generation', {
@@ -45,10 +51,23 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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  citations: formatCitations(parsed, input.styles),
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  };
47
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  });
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- return { citations };
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+ const returnedPmids = new Set(citations.map((entry) => entry.pmid));
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+ const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
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+ return {
57
+ citations,
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+ totalSubmitted: input.pmids.length,
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+ totalFormatted: citations.length,
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+ ...(unavailablePmids.length > 0 && { unavailablePmids }),
61
+ };
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  },
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  format: (result) => {
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- const lines = ['# PubMed Citations'];
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+ const lines = [
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+ '# PubMed Citations',
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+ `**Formatted:** ${result.totalFormatted}/${result.totalSubmitted}`,
67
+ ];
68
+ if (result.unavailablePmids?.length) {
69
+ lines.push(`**Unavailable PMIDs:** ${result.unavailablePmids.join(', ')}`);
70
+ }
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  for (const entry of result.citations) {
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  lines.push(`\n## PMID ${entry.pmid}`);
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  if (entry.title)
package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED
@@ -1 +1 @@
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1
+ {"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,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,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,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,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACvF,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,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/lookup-citation.tool.d.ts CHANGED
@@ -18,6 +18,12 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
18
18
  key: z.ZodString;
19
19
  pmid: z.ZodOptional<z.ZodString>;
20
20
  matched: z.ZodBoolean;
21
+ status: z.ZodEnum<{
22
+ matched: "matched";
23
+ not_found: "not_found";
24
+ ambiguous: "ambiguous";
25
+ }>;
26
+ detail: z.ZodOptional<z.ZodString>;
21
27
  }, z.core.$strip>>;
22
28
  totalMatched: z.ZodNumber;
23
29
  totalSubmitted: z.ZodNumber;
package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;kBAkG7B,CAAC"}
1
+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBAyH7B,CAAC"}
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED
@@ -37,6 +37,13 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
37
37
  key: z.string().describe('Citation tracking key'),
38
38
  pmid: z.string().optional().describe('Matched PubMed ID'),
39
39
  matched: z.boolean().describe('Whether a PMID was found'),
40
+ status: z
41
+ .enum(['matched', 'not_found', 'ambiguous'])
42
+ .describe('Lookup outcome classification for this citation'),
43
+ detail: z
44
+ .string()
45
+ .optional()
46
+ .describe('Additional detail returned by ECitMatch for non-exact matches'),
40
47
  }))
41
48
  .describe('Match results, one per input citation'),
42
49
  totalMatched: z.number().describe('Number of citations with PMID matches'),
@@ -61,7 +68,9 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
61
68
  const mapped = results.map((r) => ({
62
69
  key: r.key,
63
70
  matched: r.matched,
71
+ status: r.status,
64
72
  ...(r.pmid && { pmid: r.pmid }),
73
+ ...(r.detail && { detail: r.detail }),
65
74
  }));
66
75
  const totalMatched = mapped.filter((r) => r.matched).length;
67
76
  ctx.log.info('pubmed_lookup_citation completed', {
@@ -74,14 +83,27 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
74
83
  const lines = [
75
84
  `## Citation Lookup Results`,
76
85
  `**Matched:** ${result.totalMatched}/${result.totalSubmitted}`,
77
- '',
78
- '| Key | PMID | Status |',
79
- '|:---|:---|:---|',
80
86
  ];
81
87
  for (const r of result.results) {
82
- const pmid = r.pmid ?? '-';
83
- const status = r.matched ? 'Matched' : 'No match';
84
- lines.push(`| ${r.key} | ${pmid} | ${status} |`);
88
+ lines.push(`\n### ${r.key}`);
89
+ if (r.pmid)
90
+ lines.push(`**PMID:** ${r.pmid}`);
91
+ if (r.status === 'matched') {
92
+ lines.push(`**Status:** Matched`);
93
+ lines.push(`**Next Step:** PMID is ready for downstream PubMed fetch or citation tools.`);
94
+ continue;
95
+ }
96
+ if (r.status === 'ambiguous') {
97
+ lines.push(`**Status:** Ambiguous`);
98
+ if (r.detail)
99
+ lines.push(`**Detail:** ${r.detail}`);
100
+ lines.push(`**Next Step:** Add more citation fields such as journal, year, volume, firstPage, or authorName, then retry.`);
101
+ continue;
102
+ }
103
+ lines.push(`**Status:** No match`);
104
+ if (r.detail)
105
+ lines.push(`**Detail:** ${r.detail}`);
106
+ lines.push(`**Next Step:** Verify the citation details or try pubmed_search_articles.`);
85
107
  }
86
108
  return [{ type: 'text', text: lines.join('\n') }];
87
109
  },
package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,sPAAsP;IACnQ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;YACvE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACvD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8EAA8E,CAC/E;SACJ,CAAC,CACH;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SAC1D,CAAC,CACH;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YAChC,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;gBACxE,MAAM,IAAI,KAAK,CACb,gHAAgH,CACjH,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,OAAO,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;QAE5D,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjC,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;SAChC,CAAC,CAAC,CAAC;QAEJ,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAC5D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE;YAC/C,YAAY;YACZ,cAAc,EAAE,SAAS,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,cAAc,EAAE,SAAS,CAAC,MAAM,EAAE,CAAC;IAC7E,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,4BAA4B;YAC5B,gBAAgB,MAAM,CAAC,YAAY,IAAI,MAAM,CAAC,cAAc,EAAE;YAC9D,EAAE;YACF,yBAAyB;YACzB,kBAAkB;SACnB,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC;YAC3B,MAAM,MAAM,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC;YAClD,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,MAAM,IAAI,MAAM,MAAM,IAAI,CAAC,CAAC;QACnD,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"}
1
+ {"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,sPAAsP;IACnQ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;YACvE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACvD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8EAA8E,CAC/E;SACJ,CAAC,CACH;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YACzD,MAAM,EAAE,CAAC;iBACN,IAAI,CAAC,CAAC,SAAS,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC;iBAC3C,QAAQ,CAAC,iDAAiD,CAAC;YAC9D,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,+DAA+D,CAAC;SAC7E,CAAC,CACH;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YAChC,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;gBACxE,MAAM,IAAI,KAAK,CACb,gHAAgH,CACjH,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,OAAO,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;QAE5D,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjC,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,GAAG,CAAC,CAAC,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;SACtC,CAAC,CAAC,CAAC;QAEJ,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAC5D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE;YAC/C,YAAY;YACZ,cAAc,EAAE,SAAS,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,cAAc,EAAE,SAAS,CAAC,MAAM,EAAE,CAAC;IAC7E,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,4BAA4B;YAC5B,gBAAgB,MAAM,CAAC,YAAY,IAAI,MAAM,CAAC,cAAc,EAAE;SAC/D,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YAC7B,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC9C,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,6EAA6E,CAAC,CAAC;gBAC1F,SAAS;YACX,CAAC;YAED,IAAI,CAAC,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBAC7B,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;gBACpC,IAAI,CAAC,CAAC,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;gBACpD,KAAK,CAAC,IAAI,CACR,8GAA8G,CAC/G,CAAC;gBACF,SAAS;YACX,CAAC;YAED,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;YACnC,IAAI,CAAC,CAAC,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACpD,KAAK,CAAC,IAAI,CAAC,2EAA2E,CAAC,CAAC;QAC1F,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/search-articles.tool.d.ts CHANGED
@@ -37,6 +37,29 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
37
37
  summaryCount: z.ZodDefault<z.ZodNumber>;
38
38
  }, z.core.$strip>, z.ZodObject<{
39
39
  query: z.ZodString;
40
+ effectiveQuery: z.ZodString;
41
+ appliedFilters: z.ZodObject<{
42
+ dateRange: z.ZodOptional<z.ZodObject<{
43
+ minDate: z.ZodString;
44
+ maxDate: z.ZodString;
45
+ dateType: z.ZodEnum<{
46
+ pdat: "pdat";
47
+ mdat: "mdat";
48
+ edat: "edat";
49
+ }>;
50
+ }, z.core.$strip>>;
51
+ publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
52
+ author: z.ZodOptional<z.ZodString>;
53
+ journal: z.ZodOptional<z.ZodString>;
54
+ meshTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
55
+ language: z.ZodOptional<z.ZodString>;
56
+ hasAbstract: z.ZodOptional<z.ZodBoolean>;
57
+ freeFullText: z.ZodOptional<z.ZodBoolean>;
58
+ species: z.ZodOptional<z.ZodEnum<{
59
+ humans: "humans";
60
+ animals: "animals";
61
+ }>>;
62
+ }, z.core.$strip>;
40
63
  totalFound: z.ZodNumber;
41
64
  offset: z.ZodNumber;
42
65
  pmids: z.ZodArray<z.ZodString>;
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;AAKjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAoM7B,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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8Q7B,CAAC"}
package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED
@@ -7,6 +7,38 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
7
7
  import { sanitization } from '@cyanheads/mcp-ts-core/utils';
8
8
  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
9
9
  import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
10
+ const AppliedFiltersSchema = z.object({
11
+ dateRange: z
12
+ .object({
13
+ minDate: z.string().describe('Applied minimum date'),
14
+ maxDate: z.string().describe('Applied maximum date'),
15
+ dateType: z
16
+ .enum(['pdat', 'mdat', 'edat'])
17
+ .describe('Applied date field used for the range filter'),
18
+ })
19
+ .optional()
20
+ .describe('Date range filter applied to the search'),
21
+ publicationTypes: z
22
+ .array(z.string())
23
+ .optional()
24
+ .describe('Publication type filters applied to the search'),
25
+ author: z.string().optional().describe('Author filter applied to the search'),
26
+ journal: z.string().optional().describe('Journal filter applied to the search'),
27
+ meshTerms: z.array(z.string()).optional().describe('MeSH term filters applied to the search'),
28
+ language: z.string().optional().describe('Language filter applied to the search'),
29
+ hasAbstract: z
30
+ .boolean()
31
+ .optional()
32
+ .describe('Whether results were restricted to articles with abstracts'),
33
+ freeFullText: z
34
+ .boolean()
35
+ .optional()
36
+ .describe('Whether results were restricted to free full-text articles'),
37
+ species: z
38
+ .enum(['humans', 'animals'])
39
+ .optional()
40
+ .describe('Species filter applied to the search'),
41
+ });
10
42
  export const searchArticlesTool = tool('pubmed_search_articles', {
11
43
  description: 'Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. ' +
12
44
  'Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), ' +
@@ -52,6 +84,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
52
84
  }),
53
85
  output: z.object({
54
86
  query: z.string().describe('Original query'),
87
+ effectiveQuery: z
88
+ .string()
89
+ .describe('Sanitized query sent to PubMed after applying all active filters'),
90
+ appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
55
91
  totalFound: z.number().describe('Total matching articles'),
56
92
  offset: z.number().describe('Result offset used'),
57
93
  pmids: z.array(z.string()).describe('PubMed IDs'),
@@ -74,27 +110,41 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
74
110
  ctx.log.info('Executing pubmed_search', { query: input.query });
75
111
  const ncbi = getNcbiService();
76
112
  let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
113
+ // Build filters — capture normalized values for both query construction and appliedFilters
114
+ let normalizedDateRange;
77
115
  if (input.dateRange?.minDate && input.dateRange?.maxDate) {
78
- const minDate = input.dateRange.minDate.replace(/-/g, '/');
79
- const maxDate = input.dateRange.maxDate.replace(/-/g, '/');
80
- effectiveQuery += ` AND (${minDate}[${input.dateRange.dateType}] : ${maxDate}[${input.dateRange.dateType}])`;
116
+ normalizedDateRange = {
117
+ minDate: input.dateRange.minDate.trim().replace(/[-.]/g, '/'),
118
+ maxDate: input.dateRange.maxDate.trim().replace(/[-.]/g, '/'),
119
+ dateType: input.dateRange.dateType,
120
+ };
121
+ effectiveQuery += ` AND (${normalizedDateRange.minDate}[${normalizedDateRange.dateType}] : ${normalizedDateRange.maxDate}[${normalizedDateRange.dateType}])`;
81
122
  }
123
+ let sanitizedPubTypes;
82
124
  if (input.publicationTypes?.length) {
83
- const sanitizedPts = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
84
- const ptQuery = sanitizedPts.map((pt) => `"${pt}"[Publication Type]`).join(' OR ');
85
- effectiveQuery += ` AND (${ptQuery})`;
125
+ sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
126
+ effectiveQuery += ` AND (${sanitizedPubTypes.map((pt) => `"${pt}"[Publication Type]`).join(' OR ')})`;
127
+ }
128
+ let sanitizedAuthor;
129
+ if (input.author) {
130
+ sanitizedAuthor = await sanitization.sanitizeString(input.author, { context: 'text' });
131
+ effectiveQuery += ` AND ${sanitizedAuthor}[Author]`;
132
+ }
133
+ let sanitizedJournal;
134
+ if (input.journal) {
135
+ sanitizedJournal = await sanitization.sanitizeString(input.journal, { context: 'text' });
136
+ effectiveQuery += ` AND "${sanitizedJournal}"[Journal]`;
86
137
  }
87
- if (input.author)
88
- effectiveQuery += ` AND ${await sanitization.sanitizeString(input.author, { context: 'text' })}[Author]`;
89
- if (input.journal)
90
- effectiveQuery += ` AND "${await sanitization.sanitizeString(input.journal, { context: 'text' })}"[Journal]`;
138
+ let sanitizedMeshTerms;
91
139
  if (input.meshTerms?.length) {
92
- const sanitizedTerms = await Promise.all(input.meshTerms.map((term) => sanitization.sanitizeString(term, { context: 'text' })));
93
- const meshQuery = sanitizedTerms.map((term) => `"${term}"[MeSH Terms]`).join(' AND ');
94
- effectiveQuery += ` AND (${meshQuery})`;
140
+ sanitizedMeshTerms = await Promise.all(input.meshTerms.map((term) => sanitization.sanitizeString(term, { context: 'text' })));
141
+ effectiveQuery += ` AND (${sanitizedMeshTerms.map((term) => `"${term}"[MeSH Terms]`).join(' AND ')})`;
142
+ }
143
+ let sanitizedLanguage;
144
+ if (input.language) {
145
+ sanitizedLanguage = await sanitization.sanitizeString(input.language, { context: 'text' });
146
+ effectiveQuery += ` AND ${sanitizedLanguage}[Language]`;
95
147
  }
96
- if (input.language)
97
- effectiveQuery += ` AND ${await sanitization.sanitizeString(input.language, { context: 'text' })}[Language]`;
98
148
  if (input.hasAbstract)
99
149
  effectiveQuery += ' AND hasabstract[text word]';
100
150
  if (input.freeFullText)
@@ -120,7 +170,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
120
170
  if (esResult.webEnv && esResult.queryKey) {
121
171
  eSummaryParams.WebEnv = esResult.webEnv;
122
172
  eSummaryParams.query_key = esResult.queryKey;
123
- eSummaryParams.retmax = input.summaryCount;
173
+ eSummaryParams.retmax = Math.min(input.summaryCount, pmids.length);
124
174
  eSummaryParams.retstart = input.offset;
125
175
  }
126
176
  else {
@@ -143,12 +193,25 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
143
193
  }
144
194
  }
145
195
  const searchUrl = `https://pubmed.ncbi.nlm.nih.gov/?term=${encodeURIComponent(effectiveQuery)}`;
196
+ const appliedFilters = {
197
+ ...(normalizedDateRange && { dateRange: normalizedDateRange }),
198
+ ...(sanitizedPubTypes?.length && { publicationTypes: sanitizedPubTypes }),
199
+ ...(sanitizedAuthor && { author: sanitizedAuthor }),
200
+ ...(sanitizedJournal && { journal: sanitizedJournal }),
201
+ ...(sanitizedMeshTerms?.length && { meshTerms: sanitizedMeshTerms }),
202
+ ...(sanitizedLanguage && { language: sanitizedLanguage }),
203
+ ...(input.hasAbstract && { hasAbstract: true }),
204
+ ...(input.freeFullText && { freeFullText: true }),
205
+ ...(input.species && { species: input.species }),
206
+ };
146
207
  ctx.log.info('pubmed_search completed', {
147
208
  totalFound: esResult.count,
148
209
  pmidCount: pmids.length,
149
210
  });
150
211
  return {
151
212
  query: input.query,
213
+ effectiveQuery,
214
+ appliedFilters,
152
215
  totalFound: esResult.count,
153
216
  offset: input.offset,
154
217
  pmids,
@@ -160,9 +223,40 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
160
223
  const lines = [
161
224
  `## PubMed Search Results`,
162
225
  `**Query:** ${result.query}`,
226
+ `**Effective Query:** ${result.effectiveQuery}`,
163
227
  `**Total Found:** ${result.totalFound} | **Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
164
228
  `**Search URL:** ${result.searchUrl}`,
165
229
  ];
230
+ if (Object.keys(result.appliedFilters).length > 0) {
231
+ lines.push('\n### Applied Filters');
232
+ if (result.appliedFilters.dateRange) {
233
+ lines.push(`- **Date Range (${result.appliedFilters.dateRange.dateType}):** ${result.appliedFilters.dateRange.minDate} to ${result.appliedFilters.dateRange.maxDate}`);
234
+ }
235
+ if (result.appliedFilters.publicationTypes?.length) {
236
+ lines.push(`- **Publication Types:** ${result.appliedFilters.publicationTypes.join(', ')}`);
237
+ }
238
+ if (result.appliedFilters.author) {
239
+ lines.push(`- **Author:** ${result.appliedFilters.author}`);
240
+ }
241
+ if (result.appliedFilters.journal) {
242
+ lines.push(`- **Journal:** ${result.appliedFilters.journal}`);
243
+ }
244
+ if (result.appliedFilters.meshTerms?.length) {
245
+ lines.push(`- **MeSH Terms:** ${result.appliedFilters.meshTerms.join(', ')}`);
246
+ }
247
+ if (result.appliedFilters.language) {
248
+ lines.push(`- **Language:** ${result.appliedFilters.language}`);
249
+ }
250
+ if (result.appliedFilters.hasAbstract) {
251
+ lines.push(`- **Has Abstract:** Yes`);
252
+ }
253
+ if (result.appliedFilters.freeFullText) {
254
+ lines.push(`- **Free Full Text:** Yes`);
255
+ }
256
+ if (result.appliedFilters.species) {
257
+ lines.push(`- **Species:** ${result.appliedFilters.species}`);
258
+ }
259
+ }
166
260
  if (result.pmids.length > 0)
167
261
  lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
168
262
  if (result.summaries?.length) {
package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED
@@ -1 +1 @@
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package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED
@@ -1 +1 @@
1
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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;;;OAGG;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
@@ -93,11 +93,26 @@ export class NcbiService {
93
93
  .map((line) => {
94
94
  const parts = line.split('|');
95
95
  const key = parts[5]?.trim() ?? '';
96
- const pmidField = parts[6]?.trim() ?? '';
97
- const pmid = pmidField && !pmidField.startsWith('NOT_FOUND') && !pmidField.startsWith('AMBIGUOUS')
98
- ? pmidField
99
- : null;
100
- return { key, matched: pmid !== null, pmid };
96
+ const rawOutcome = parts[6]?.trim() ?? '';
97
+ if (/^\d+$/.test(rawOutcome)) {
98
+ return { key, matched: true, pmid: rawOutcome, status: 'matched' };
99
+ }
100
+ if (rawOutcome.startsWith('AMBIGUOUS')) {
101
+ return {
102
+ key,
103
+ matched: false,
104
+ pmid: null,
105
+ status: 'ambiguous',
106
+ detail: rawOutcome,
107
+ };
108
+ }
109
+ return {
110
+ key,
111
+ matched: false,
112
+ pmid: null,
113
+ status: 'not_found',
114
+ ...(rawOutcome && { detail: rawOutcome }),
115
+ };
101
116
  });
102
117
  }
103
118
  /**
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/types.d.ts CHANGED
@@ -612,12 +612,16 @@ export interface ECitMatchCitation {
612
612
  }
613
613
  /** Single result from ECitMatch lookup. */
614
614
  export interface ECitMatchResult {
615
+ /** Raw non-match detail returned by ECitMatch when present */
616
+ detail?: string;
615
617
  /** The tracking key from the input citation */
616
618
  key: string;
617
619
  /** Whether a PMID was found */
618
620
  matched: boolean;
619
621
  /** Matched PubMed ID, or null if no match */
620
622
  pmid: string | null;
623
+ /** Lookup outcome classification for recovery guidance */
624
+ status: 'matched' | 'not_found' | 'ambiguous';
621
625
  }
622
626
  /** Single record from the PMC ID Converter API response. */
623
627
  export interface IdConvertRecord {
package/dist/services/ncbi/types.d.ts.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": "2.3.2",
3
+ "version": "2.3.3",
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",
@@ -67,17 +67,19 @@
67
67
  "access": "public"
68
68
  },
69
69
  "overrides": {
70
+ "@hono/node-server": ">=1.19.13",
70
71
  "brace-expansion": ">=2.0.3",
71
72
  "express-rate-limit": ">=8.2.2",
72
- "hono": ">=4.12.7",
73
+ "hono": ">=4.12.12",
73
74
  "path-to-regexp": ">=8.4.0",
74
75
  "picomatch": ">=4.0.4",
76
+ "vite": ">=8.0.8",
75
77
  "yaml": ">=2.8.3",
76
78
  "lodash": ">=4.17.24"
77
79
  },
78
80
  "dependencies": {
79
- "@cyanheads/mcp-ts-core": "^0.2.12",
80
- "fast-xml-parser": "^5.5.10",
81
+ "@cyanheads/mcp-ts-core": "^0.3.4",
82
+ "fast-xml-parser": "^5.5.11",
81
83
  "pino-pretty": "^13.1.3",
82
84
  "sanitize-html": "^2.17.2"
83
85
  },
@@ -85,10 +87,11 @@
85
87
  "@biomejs/biome": "^2.4.10",
86
88
  "@types/node": "^25.5.2",
87
89
  "@types/sanitize-html": "^2.16.1",
90
+ "@vitest/coverage-istanbul": "^4.1.4",
88
91
  "depcheck": "^1.4.7",
89
92
  "ignore": "^7.0.5",
90
93
  "tsc-alias": "^1.8.16",
91
94
  "typescript": "^6.0.2",
92
- "vitest": "^4.1.2"
95
+ "vitest": "^4.1.4"
93
96
  }
94
97
  }
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": "2.3.2",
9
+ "version": "2.3.3",
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": "2.3.2",
22
+ "version": "2.3.3",
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": "2.3.2",
63
+ "version": "2.3.3",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",