@cyanheads/pubmed-mcp-server 2.6.0 → 2.6.2
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.
- package/CLAUDE.md +2 -2
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +28 -7
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +1 -0
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +27 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +3 -0
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +18 -0
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +87 -1
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +8 -5
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
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@@ -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.
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**Version:** 2.6.2
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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.
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@@ -301,7 +301,7 @@ import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
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## Checklist
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- [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, `z.bigint()`, `z.symbol()`, `z.void()`, `z.map()`, `z.set()`, `z.function()`, `z.nan()`)
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- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`)
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- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`). When regex/length constraints matter, use `z.union([z.literal(''), z.string().regex(...).describe(...)])` — literal variants are exempt from `describe-on-fields`.
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- [ ] JSDoc `@fileoverview` + `@module` on every file
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- [ ] `ctx.log` for logging, `ctx.state` for storage
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- [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
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package/README.md
CHANGED
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@@ -7,7 +7,7 @@
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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@@ -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;
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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;AAajD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;kBA8FzB,CAAC"}
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@@ -6,6 +6,13 @@
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import { tool, z } from '@cyanheads/mcp-ts-core';
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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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/**
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* NCBI's PMC ID Converter returns this exact wording for any non-PMC ID — even
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* articles that exist in PubMed and have a recoverable DOI. Rewrite to point
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* the caller at the recovery path; the original is logged at debug.
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*/
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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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annotations: { readOnlyHint: true, openWorldHint: true },
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@@ -43,13 +50,27 @@ export const convertIdsTool = tool('pubmed_convert_ids', {
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});
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const raw = await getNcbiService().idConvert(input.ids, input.idtype, { signal: ctx.signal });
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// NCBI returns pmid as a number in JSON — coerce all ID fields to strings
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const records = raw.map((r) =>
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requestedId
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const records = raw.map((r) => {
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const requestedId = String(r['requested-id']);
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let errmsg;
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if (r.errmsg !== undefined) {
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const original = String(r.errmsg);
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if (PMC_NOT_FOUND_RE.test(original)) {
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ctx.log.debug('Rewriting PMC-not-found errmsg', { requestedId, original });
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errmsg = PMC_NOT_FOUND_REWRITE;
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}
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else {
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errmsg = original;
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}
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}
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return {
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requestedId,
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...(r.pmid !== undefined && { pmid: String(r.pmid) }),
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...(r.pmcid !== undefined && { pmcid: String(r.pmcid) }),
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...(r.doi !== undefined && { doi: String(r.doi) }),
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...(errmsg !== undefined && { errmsg }),
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};
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});
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const totalConverted = records.filter((r) => !r.errmsg).length;
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ctx.log.info('pubmed_convert_ids completed', {
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totalConverted,
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@@ -1 +1 @@
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-
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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;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,gQAAgQ;IAC7Q,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,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,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;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"}
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score: z.ZodOptional<z.ZodNumber>;
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}, z.core.$strip>>;
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totalFound: z.ZodNumber;
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notice: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>>;
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//# sourceMappingURL=find-related.tool.d.ts.map
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{"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;AAoCjD,eAAO,MAAM,eAAe
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{"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;AAoCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;kBAkM1B,CAAC"}
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.describe('Related article with enriched summary'))
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.describe('Related articles'),
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totalFound: z.number().describe('Total related articles found before truncation'),
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notice: z
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.string()
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.optional()
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.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.'),
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}),
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async handler(input, ctx) {
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}
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const totalFound = foundPmids.length;
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if (foundPmids.length === 0) {
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// NCBI's pubmed_pubmed_refs ELink only resolves reference lists for
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// PMC-indexed sources, so a valid PMID without a PMCID looks identical
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// to "this article cites nothing". Look up the source's PMCID so the
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// caller gets a relationship-aware recovery hint.
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let notice;
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if (input.relationship === 'references') {
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try {
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+
const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: input.pmid }, { signal: ctx.signal });
|
|
117
|
+
const summaries = await extractBriefSummaries(summaryResult);
|
|
118
|
+
const sourcePmcId = summaries[0]?.pmcId;
|
|
119
|
+
notice = sourcePmcId
|
|
120
|
+
? `No reference list found in PMC for PMID ${input.pmid} (PMCID ${sourcePmcId}).`
|
|
121
|
+
: `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".`;
|
|
122
|
+
}
|
|
123
|
+
catch (err) {
|
|
124
|
+
ctx.log.debug('Failed to look up source PMCID for references hint', { err });
|
|
125
|
+
}
|
|
126
|
+
}
|
|
105
127
|
return {
|
|
106
128
|
sourcePmid: input.pmid,
|
|
107
129
|
relationship: input.relationship,
|
|
108
130
|
articles: [],
|
|
109
131
|
totalFound: 0,
|
|
132
|
+
...(notice && { notice }),
|
|
110
133
|
};
|
|
111
134
|
}
|
|
112
135
|
if (foundPmids.every((p) => p.score !== undefined)) {
|
|
@@ -137,8 +160,11 @@ export const findRelatedTool = tool('pubmed_find_related', {
|
|
|
137
160
|
`# Related Articles for PMID ${result.sourcePmid}`,
|
|
138
161
|
`**Relationship:** ${result.relationship} | **Found:** ${result.totalFound}`,
|
|
139
162
|
];
|
|
163
|
+
if (result.notice)
|
|
164
|
+
lines.push(`\n> ${result.notice}`);
|
|
140
165
|
if (result.articles.length === 0) {
|
|
141
|
-
|
|
166
|
+
if (!result.notice)
|
|
167
|
+
lines.push('No related articles found.');
|
|
142
168
|
}
|
|
143
169
|
else {
|
|
144
170
|
for (const a of result.articles) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yFAAyF,CAC1F;SACJ,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;
|
|
1
|
+
{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yFAAyF,CAC1F;SACJ,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACjF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,+IAA+I,CAChJ;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0BAA0B,EAAE;YACxC,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,YAAY,EAAE,KAAK,CAAC,YAAY;SACjC,CAAC,CAAC;QAEH,MAAM,WAAW,GAA2B;YAC1C,MAAM,EAAE,QAAQ;YAChB,EAAE,EAAE,QAAQ;YACZ,EAAE,EAAE,KAAK,CAAC,IAAI;YACd,OAAO,EAAE,KAAK;SACf,CAAC;QACF,QAAQ,KAAK,CAAC,YAAY,EAAE,CAAC;YAC3B,KAAK,SAAS;gBACZ,WAAW,CAAC,GAAG,GAAG,gBAAgB,CAAC;gBACnC,MAAM;YACR,KAAK,UAAU;gBACb,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,uBAAuB,CAAC;gBAC/C,MAAM;YACR,KAAK,YAAY;gBACf,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,oBAAoB,CAAC;gBAC5C,MAAM;QACV,CAAC;QAED,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAkB,CAAC;QAC7F,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QAChE,MAAM,WAAW,GAAG,iBAAiB,CAAC,CAAC,CAAgC,CAAC;QAExE,IAAI,WAAW,EAAE,KAAK,EAAE,CAAC;YACvB,MAAM,IAAI,KAAK,CACb,gBAAgB,OAAO,WAAW,CAAC,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,KAAK,CAAC,EAAE,CAChH,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,WAAW,EAAE,OAAO,CAAC;QACrC,IAAI,UAAU,GAAuC,EAAE,CAAC;QAExD,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;YACvB,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YACtD,MAAM,gBAAgB,GACpB,KAAK,CAAC,YAAY,KAAK,UAAU;gBAC/B,CAAC,CAAC,uBAAuB;gBACzB,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,YAAY;oBACnC,CAAC,CAAC,oBAAoB;oBACtB,CAAC,CAAC,eAAe,CAAC;YACxB,MAAM,QAAQ,GACZ,cAAc,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,gBAAgB,CAAC,IAAI,cAAc,CAAC,CAAC,CAAC,CAAC;YAErF,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;gBACnB,UAAU,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC;qBACpC,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE,CAAC,CAAC;oBAC5B,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;iBACjF,CAAC,CAAC;qBACF,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;QAED,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,oEAAoE;YACpE,uEAAuE;YACvE,qEAAqE;YACrE,kDAAkD;YAClD,IAAI,MAA0B,CAAC;YAC/B,IAAI,KAAK,CAAC,YAAY,KAAK,YAAY,EAAE,CAAC;gBACxC,IAAI,CAAC;oBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;oBACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;oBAC7D,MAAM,WAAW,GAAG,SAAS,CAAC,CAAC,CAAC,EAAE,KAAK,CAAC;oBACxC,MAAM,GAAG,WAAW;wBAClB,CAAC,CAAC,2CAA2C,KAAK,CAAC,IAAI,WAAW,WAAW,IAAI;wBACjF,CAAC,CAAC,yEAAyE,KAAK,CAAC,IAAI,+IAA+I,CAAC;gBACzO,CAAC;gBAAC,OAAO,GAAG,EAAE,CAAC;oBACb,GAAG,CAAC,GAAG,CAA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|
|
@@ -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;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
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;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAqT7B,CAAC"}
|
|
@@ -310,6 +310,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
310
310
|
if (result.pmids.length > 0)
|
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311
311
|
lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
|
|
312
312
|
if (result.summaries?.length) {
|
|
313
|
+
if (result.summaries.length < result.pmids.length) {
|
|
314
|
+
lines.push(`\n> Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs. Increase \`summaryCount\` (max 50) to fetch more.`);
|
|
315
|
+
}
|
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313
316
|
lines.push('\n### Summaries');
|
|
314
317
|
for (const s of result.summaries) {
|
|
315
318
|
lines.push(`\n#### ${s.title ?? s.pmid}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -5,6 +5,24 @@
|
|
|
5
5
|
* @module src/services/ncbi/response-handler
|
|
6
6
|
*/
|
|
7
7
|
import type { NcbiRequestOptions } from './types.js';
|
|
8
|
+
/**
|
|
9
|
+
* Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
|
|
10
|
+
* `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
|
|
11
|
+
* runs. The non-ordered parser used for EFetch responses doesn't preserve
|
|
12
|
+
* mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
|
|
13
|
+
* 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
|
|
14
|
+
* digit is silently dropped from abstracts and titles.
|
|
15
|
+
*
|
|
16
|
+
* Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
|
|
17
|
+
* falls back to a `^X` / `_X` ASCII prefix so the content survives in a
|
|
18
|
+
* recognizable form. Italic / bold / underline / small-caps tags are
|
|
19
|
+
* stripped (content kept) since they don't carry meaning in our text
|
|
20
|
+
* rendering. Only invoked on the regular parser path; the PMC JATS path
|
|
21
|
+
* already preserves inline markup via `preserveOrder: true`.
|
|
22
|
+
*
|
|
23
|
+
* @internal exported for direct unit tests
|
|
24
|
+
*/
|
|
25
|
+
export declare function flattenInlineMarkup(xml: string): string;
|
|
8
26
|
/**
|
|
9
27
|
* Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
|
|
10
28
|
* error structures embedded in response bodies.
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;
|
|
1
|
+
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAsLrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;OAGG;IACH,OAAO,CAAC,cAAc;IAatB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA6HL"}
|
|
@@ -117,6 +117,88 @@ function sanitizeNcbiError(message) {
|
|
|
117
117
|
* to the caller which reports it via `unavailablePmcIds`.
|
|
118
118
|
*/
|
|
119
119
|
const ERROR_TAG_REGEX = /<ERROR(?:\s[^>]*)?>/;
|
|
120
|
+
/**
|
|
121
|
+
* Unicode superscript map. Covers digits, common operators, and the few
|
|
122
|
+
* letters that have superscript codepoints (n, i). `−` (U+2212, the proper
|
|
123
|
+
* minus) is normalized to U+207B alongside ASCII `-`.
|
|
124
|
+
*/
|
|
125
|
+
const SUPERSCRIPT_MAP = {
|
|
126
|
+
'0': '⁰',
|
|
127
|
+
'1': '¹',
|
|
128
|
+
'2': '²',
|
|
129
|
+
'3': '³',
|
|
130
|
+
'4': '⁴',
|
|
131
|
+
'5': '⁵',
|
|
132
|
+
'6': '⁶',
|
|
133
|
+
'7': '⁷',
|
|
134
|
+
'8': '⁸',
|
|
135
|
+
'9': '⁹',
|
|
136
|
+
'+': '⁺',
|
|
137
|
+
'-': '⁻',
|
|
138
|
+
'−': '⁻',
|
|
139
|
+
'=': '⁼',
|
|
140
|
+
'(': '⁽',
|
|
141
|
+
')': '⁾',
|
|
142
|
+
n: 'ⁿ',
|
|
143
|
+
i: 'ⁱ',
|
|
144
|
+
};
|
|
145
|
+
/**
|
|
146
|
+
* Unicode subscript map. Covers digits and operators; alphabetic subscripts
|
|
147
|
+
* are limited in Unicode and rarely appear in MEDLINE so they fall through
|
|
148
|
+
* to the `_X` ASCII fallback.
|
|
149
|
+
*/
|
|
150
|
+
const SUBSCRIPT_MAP = {
|
|
151
|
+
'0': '₀',
|
|
152
|
+
'1': '₁',
|
|
153
|
+
'2': '₂',
|
|
154
|
+
'3': '₃',
|
|
155
|
+
'4': '₄',
|
|
156
|
+
'5': '₅',
|
|
157
|
+
'6': '₆',
|
|
158
|
+
'7': '₇',
|
|
159
|
+
'8': '₈',
|
|
160
|
+
'9': '₉',
|
|
161
|
+
'+': '₊',
|
|
162
|
+
'-': '₋',
|
|
163
|
+
'−': '₋',
|
|
164
|
+
'=': '₌',
|
|
165
|
+
'(': '₍',
|
|
166
|
+
')': '₎',
|
|
167
|
+
};
|
|
168
|
+
function mapInlineContent(content, table, asciiPrefix) {
|
|
169
|
+
let out = '';
|
|
170
|
+
for (const ch of content) {
|
|
171
|
+
const mapped = table[ch];
|
|
172
|
+
if (mapped === undefined)
|
|
173
|
+
return `${asciiPrefix}${content}`;
|
|
174
|
+
out += mapped;
|
|
175
|
+
}
|
|
176
|
+
return out;
|
|
177
|
+
}
|
|
178
|
+
/**
|
|
179
|
+
* Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
|
|
180
|
+
* `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
|
|
181
|
+
* runs. The non-ordered parser used for EFetch responses doesn't preserve
|
|
182
|
+
* mixed content — `1.73 m<sup>2</sup>` parses to `{ '#text': '1.73 m', sup:
|
|
183
|
+
* 2 }`, and `extractAbstractText` only reads `#text`, so the superscript
|
|
184
|
+
* digit is silently dropped from abstracts and titles.
|
|
185
|
+
*
|
|
186
|
+
* Numeric and operator characters map to Unicode (²/³/⁻²/₂…); anything else
|
|
187
|
+
* falls back to a `^X` / `_X` ASCII prefix so the content survives in a
|
|
188
|
+
* recognizable form. Italic / bold / underline / small-caps tags are
|
|
189
|
+
* stripped (content kept) since they don't carry meaning in our text
|
|
190
|
+
* rendering. Only invoked on the regular parser path; the PMC JATS path
|
|
191
|
+
* already preserves inline markup via `preserveOrder: true`.
|
|
192
|
+
*
|
|
193
|
+
* @internal exported for direct unit tests
|
|
194
|
+
*/
|
|
195
|
+
export function flattenInlineMarkup(xml) {
|
|
196
|
+
return xml
|
|
197
|
+
.replace(/<sup>([^<]*)<\/sup>/g, (_, c) => mapInlineContent(c, SUPERSCRIPT_MAP, '^'))
|
|
198
|
+
.replace(/<sub>([^<]*)<\/sub>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
|
|
199
|
+
.replace(/<inf>([^<]*)<\/inf>/g, (_, c) => mapInlineContent(c, SUBSCRIPT_MAP, '_'))
|
|
200
|
+
.replace(/<\/?(?:i|b|u|sc)>/g, '');
|
|
201
|
+
}
|
|
120
202
|
/**
|
|
121
203
|
* Parses NCBI E-utility responses (XML, JSON, text) and checks for NCBI-specific
|
|
122
204
|
* error structures embedded in response bodies.
|
|
@@ -215,9 +297,13 @@ export class NcbiResponseHandler {
|
|
|
215
297
|
this.throwNcbiError(errorParsed, endpoint);
|
|
216
298
|
}
|
|
217
299
|
const parser = useOrdered ? this.orderedXmlParser : this.xmlParser;
|
|
300
|
+
// Pre-flatten <sup>/<sub>/<inf>/<i>/<b>/<u>/<sc> on the regular parser
|
|
301
|
+
// path. The ordered parser walks mixed content correctly via
|
|
302
|
+
// preserveOrder; the regular parser does not.
|
|
303
|
+
const xmlForParse = useOrdered ? responseText : flattenInlineMarkup(responseText);
|
|
218
304
|
let parsedXml;
|
|
219
305
|
try {
|
|
220
|
-
parsedXml = parser.parse(
|
|
306
|
+
parsedXml = parser.parse(xmlForParse);
|
|
221
307
|
}
|
|
222
308
|
catch (error) {
|
|
223
309
|
const parserError = error instanceof Error ? error.message : String(error);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,8 +1,8 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.6.
|
|
3
|
+
"version": "2.6.2",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
|
-
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
|
|
5
|
+
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
|
|
6
6
|
"type": "module",
|
|
7
7
|
"main": "dist/index.js",
|
|
8
8
|
"types": "dist/index.d.ts",
|
|
@@ -37,7 +37,10 @@
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|
|
37
37
|
"mcp-server",
|
|
38
38
|
"typescript",
|
|
39
39
|
"ai-agent",
|
|
40
|
-
"e-utilities"
|
|
40
|
+
"e-utilities",
|
|
41
|
+
"open-access",
|
|
42
|
+
"full-text",
|
|
43
|
+
"unpaywall"
|
|
41
44
|
],
|
|
42
45
|
"repository": {
|
|
43
46
|
"type": "git",
|
|
@@ -68,9 +71,9 @@
|
|
|
68
71
|
"access": "public"
|
|
69
72
|
},
|
|
70
73
|
"dependencies": {
|
|
71
|
-
"@cyanheads/mcp-ts-core": "^0.7.
|
|
74
|
+
"@cyanheads/mcp-ts-core": "^0.7.5",
|
|
72
75
|
"defuddle": "^0.18.1",
|
|
73
|
-
"fast-xml-parser": "^5.7.
|
|
76
|
+
"fast-xml-parser": "^5.7.2",
|
|
74
77
|
"linkedom": "^0.18.12",
|
|
75
78
|
"pino-pretty": "^13.1.3",
|
|
76
79
|
"sanitize-html": "^2.17.3",
|
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": "2.6.
|
|
9
|
+
"version": "2.6.2",
|
|
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": "2.6.
|
|
22
|
+
"version": "2.6.2",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.6.
|
|
69
|
+
"version": "2.6.2",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|