@cyanheads/pubmed-mcp-server 2.3.5 → 2.3.7

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (16) 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/formatting/citation-formatter.d.ts.map +1 -1
  13. package/dist/services/ncbi/formatting/citation-formatter.js +101 -21
  14. package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
  15. package/package.json +6 -17
  16. 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:** 2.3.5
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+ **Version:** 2.3.7
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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-2.3.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![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-2.3.7-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-^1.27.1-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/formatting/citation-formatter.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,CAAC;AAoJ7D;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAgDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuD3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6ExD;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAWnF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
1
+ {"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,aAAa,EAAuB,MAAM,aAAa,CAAC;AAEtE,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,CAAC;AAiM7D;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA6CxD;AAMD;;;;;;;GAOG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAkDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA8E3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA4FxD;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAWnF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
package/dist/services/ncbi/formatting/citation-formatter.js CHANGED
@@ -9,25 +9,65 @@
9
9
  // ---------------------------------------------------------------------------
10
10
  /**
11
11
  * Extract the publication year from a ParsedArticle.
12
- * Falls back to 'n.d.' (no date) when unavailable.
12
+ * Prefers `journalInfo.publicationDate.year`; falls back to the earliest
13
+ * `articleDates` entry (typically the electronic pub date) before giving up.
14
+ * Returns 'n.d.' (no date) when no year is available.
13
15
  */
14
16
  function getYear(article) {
15
- return article.journalInfo?.publicationDate?.year ?? 'n.d.';
17
+ const journalYear = article.journalInfo?.publicationDate?.year;
18
+ if (journalYear)
19
+ return journalYear;
20
+ const articleYear = article.articleDates?.find((d) => d.year)?.year;
21
+ return articleYear ?? 'n.d.';
16
22
  }
17
23
  /**
18
24
  * Split a pages string like "45-67" into start and end components.
19
- * Handles en-dashes, em-dashes, and hyphens.
25
+ * Handles en-dashes, em-dashes, and hyphens. Expands PubMed's truncated-end
26
+ * convention (e.g., "737-8" → { start: "737", end: "738" }, "1639-41" →
27
+ * "1639"/"1641") so downstream RIS/BibTeX consumers see absolute page numbers.
20
28
  */
21
29
  function splitPages(pages) {
22
30
  if (!pages)
23
31
  return {};
24
- // Normalize hyphens, en-dashes, and em-dashes to a single separator
25
32
  const parts = pages.split(/[-\u2013\u2014]/).map((p) => p.trim());
26
- const [start, end] = parts;
33
+ let [start, end] = parts;
34
+ if (start && end && end.length < start.length) {
35
+ end = start.slice(0, start.length - end.length) + end;
36
+ }
27
37
  if (start && end)
28
38
  return { start, end };
29
39
  return start ? { start } : {};
30
40
  }
41
+ /**
42
+ * Collapse internal whitespace (including embedded newlines from structured
43
+ * abstracts) to single spaces. Strict RIS parsers treat blank lines as record
44
+ * terminators, so abstract text must be flattened before emission.
45
+ */
46
+ function collapseWhitespace(text) {
47
+ return text.replace(/\s+/g, ' ').trim();
48
+ }
49
+ /** PubMed `PublicationType` → BibTeX entry type. Defaults to `article`. */
50
+ const BIBTEX_ENTRY_TYPE = {
51
+ Book: 'book',
52
+ 'Book Chapter': 'inbook',
53
+ Preprint: 'misc',
54
+ };
55
+ /** PubMed `PublicationType` → RIS reference type. Defaults to `JOUR`. */
56
+ const RIS_REFERENCE_TYPE = {
57
+ Book: 'BOOK',
58
+ 'Book Chapter': 'CHAP',
59
+ Preprint: 'GEN',
60
+ };
61
+ function firstMappedType(types, map, fallback) {
62
+ if (!types?.length)
63
+ return fallback;
64
+ for (const t of types) {
65
+ const mapped = map[t];
66
+ if (mapped)
67
+ return mapped;
68
+ }
69
+ return fallback;
70
+ }
31
71
  /**
32
72
  * Escape characters that are special in LaTeX/BibTeX values.
33
73
  * Handles: & % $ # _ { } ~ ^
@@ -166,10 +206,11 @@ function formatAuthorBibtex(author) {
166
206
  */
167
207
  export function formatApa(article) {
168
208
  const parts = [];
169
- // Authors
209
+ // Authors — ensure trailing period (individual author initials end with '.',
210
+ // but collective names do not, which would otherwise produce "Name (Year).")
170
211
  const authorStr = article.authors?.length ? formatAuthorsApa(article.authors) : '';
171
212
  if (authorStr) {
172
- parts.push(authorStr);
213
+ parts.push(authorStr.endsWith('.') ? authorStr : `${authorStr}.`);
173
214
  }
174
215
  // Year
175
216
  const year = getYear(article);
@@ -242,7 +283,9 @@ export function formatMla(article) {
242
283
  detailParts.push(year);
243
284
  }
244
285
  if (journal.pages) {
245
- detailParts.push(`pp. ${journal.pages}`);
286
+ // MLA 9 §6.56: "p." for a single page, "pp." for a range
287
+ const isRange = /[-\u2013\u2014]/.test(journal.pages);
288
+ detailParts.push(`${isRange ? 'pp.' : 'p.'} ${journal.pages}`);
246
289
  }
247
290
  parts.push(`${detailParts.join(', ')}.`);
248
291
  }
@@ -270,6 +313,7 @@ export function formatMla(article) {
270
313
  */
271
314
  export function formatBibtex(article) {
272
315
  const key = `pmid${article.pmid}`;
316
+ const entryType = firstMappedType(article.publicationTypes, BIBTEX_ENTRY_TYPE, 'article');
273
317
  const fields = [];
274
318
  // Authors
275
319
  if (article.authors?.length) {
@@ -277,9 +321,10 @@ export function formatBibtex(article) {
277
321
  if (authorStr)
278
322
  fields.push(['author', authorStr]);
279
323
  }
280
- // Title
324
+ // Title — strip trailing period; biblatex styles append their own
281
325
  if (article.title) {
282
- fields.push(['title', `{${escapeBibtex(article.title)}}`]);
326
+ const title = article.title.replace(/\.\s*$/, '');
327
+ fields.push(['title', `{${escapeBibtex(title)}}`]);
283
328
  }
284
329
  // Journal
285
330
  const journal = article.journalInfo;
@@ -303,16 +348,36 @@ export function formatBibtex(article) {
303
348
  if (journal?.pages) {
304
349
  fields.push(['pages', escapeBibtex(journal.pages)]);
305
350
  }
351
+ // ISSN
352
+ const issn = journal?.issn ?? journal?.eIssn;
353
+ if (issn) {
354
+ fields.push(['issn', escapeBibtex(issn)]);
355
+ }
306
356
  // DOI
307
357
  if (article.doi) {
308
358
  fields.push(['doi', article.doi]);
309
359
  }
310
360
  // PMID
311
361
  fields.push(['pmid', article.pmid]);
362
+ // PMCID
363
+ if (article.pmcId) {
364
+ fields.push(['pmcid', article.pmcId]);
365
+ }
366
+ // Keywords — merge article keywords with MeSH descriptor names
367
+ const keywordSet = new Set();
368
+ for (const k of article.keywords ?? [])
369
+ keywordSet.add(k);
370
+ for (const m of article.meshTerms ?? []) {
371
+ if (m.descriptorName)
372
+ keywordSet.add(m.descriptorName);
373
+ }
374
+ if (keywordSet.size > 0) {
375
+ fields.push(['keywords', escapeBibtex([...keywordSet].join(', '))]);
376
+ }
312
377
  // Build entry
313
378
  const maxKeyLen = Math.max(...fields.map(([k]) => k.length));
314
379
  const fieldLines = fields.map(([k, v]) => ` ${k.padEnd(maxKeyLen)} = {${v}}`).join(',\n');
315
- return `@article{${key},\n${fieldLines}\n}`;
380
+ return `@${entryType}{${key},\n${fieldLines}\n}`;
316
381
  }
317
382
  // ---------------------------------------------------------------------------
318
383
  // RIS
@@ -329,8 +394,9 @@ export function formatRis(article) {
329
394
  if (value)
330
395
  lines.push(`${code} - ${value}`);
331
396
  };
332
- // Type of reference
333
- lines.push('TY - JOUR');
397
+ // Type of reference — map from PubMed publication types
398
+ const refType = firstMappedType(article.publicationTypes, RIS_REFERENCE_TYPE, 'JOUR');
399
+ lines.push(`TY - ${refType}`);
334
400
  // Authors — one AU tag per author
335
401
  if (article.authors?.length) {
336
402
  for (const author of article.authors) {
@@ -364,26 +430,40 @@ export function formatRis(article) {
364
430
  // Volume & Issue
365
431
  tag('VL', journal?.volume);
366
432
  tag('IS', journal?.issue);
367
- // Pages — split into start/end
433
+ // Pages — split into start/end, expanding PubMed's truncated-end convention
368
434
  if (journal?.pages) {
369
435
  const { start, end } = splitPages(journal.pages);
370
436
  tag('SP', start);
371
437
  tag('EP', end);
372
438
  }
439
+ // ISSN — prefer print ISSN, fall back to electronic
440
+ tag('SN', journal?.issn ?? journal?.eIssn);
373
441
  // DOI (without URL prefix — RIS DO tag holds the bare DOI)
374
442
  tag('DO', article.doi);
375
443
  // Accession number (PMID)
376
444
  tag('AN', article.pmid);
377
445
  // PubMed URL
378
446
  lines.push(`UR - https://pubmed.ncbi.nlm.nih.gov/${article.pmid}/`);
379
- // Keywords
380
- if (article.keywords?.length) {
381
- for (const kw of article.keywords) {
382
- tag('KW', kw);
383
- }
447
+ // PMC URL (when available)
448
+ if (article.pmcId) {
449
+ lines.push(`UR - https://pmc.ncbi.nlm.nih.gov/articles/${article.pmcId}/`);
450
+ }
451
+ // Keywords — merge article keywords with MeSH descriptor names
452
+ const keywordSet = new Set();
453
+ for (const k of article.keywords ?? [])
454
+ keywordSet.add(k);
455
+ for (const m of article.meshTerms ?? []) {
456
+ if (m.descriptorName)
457
+ keywordSet.add(m.descriptorName);
458
+ }
459
+ for (const kw of keywordSet) {
460
+ tag('KW', kw);
461
+ }
462
+ // Abstract — collapse internal whitespace so blank lines don't break strict
463
+ // RIS parsers that terminate records at blank lines
464
+ if (article.abstractText) {
465
+ tag('AB', collapseWhitespace(article.abstractText));
384
466
  }
385
- // Abstract
386
- tag('AB', article.abstractText);
387
467
  // End of record (trailing space per RIS spec)
388
468
  lines.push('ER - ');
389
469
  return lines.join('\n');
package/dist/services/ncbi/formatting/citation-formatter.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": "2.3.5",
3
+ "version": "2.3.7",
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": "^0.3.5",
82
- "fast-xml-parser": "^5.5.12",
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": "2.3.5",
9
+ "version": "2.3.7",
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": "2.3.5",
22
+ "version": "2.3.7",
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": "2.3.5",
63
+ "version": "2.3.7",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",