@cyanheads/pubmed-mcp-server 2.9.5 → 2.9.7
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.
- package/AGENTS.md +2 -2
- package/CLAUDE.md +2 -2
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +8 -2
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +28 -20
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +16 -5
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +12 -2
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +9 -4
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/text-helpers.d.ts +29 -0
- package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -0
- package/dist/services/ncbi/parsing/text-helpers.js +65 -0
- package/dist/services/ncbi/parsing/text-helpers.js.map +1 -0
- package/package.json +7 -7
- package/server.json +3 -3
package/AGENTS.md
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@@ -1,8 +1,8 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.9.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 2.9.7
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/CLAUDE.md
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.9.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.
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**Version:** 2.9.7
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/README.md
CHANGED
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@@ -9,7 +9,7 @@
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -25,7 +25,7 @@ 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. 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" (the "PMC" prefix is optional — bare digits like "3531190" are also accepted).'),
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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.'),
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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,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAC1D,MAAM,qBAAqB,GACzB,gIAAgI,CAAC;AAEnI,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,4NAA4N;IACzO,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,
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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,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,cAAc,EAAE,eAAe,EAAE,MAAM,gBAAgB,CAAC;AAE9E;;;;GAIG;AACH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAC1D,MAAM,qBAAqB,GACzB,gIAAgI,CAAC;AAEnI,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EAAE,4NAA4N;IACzO,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,eAAe,EAAE,cAAc,CAAC,CAAC;IACrD,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,GAAG,EAAE,CAAC;aACH,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC;aACxB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,oNAAoN,CACrN;QACH,MAAM,EAAE,CAAC;aACN,IAAI,CAAC,CAAC,OAAO,EAAE,MAAM,EAAE,KAAK,CAAC,CAAC;aAC9B,QAAQ,CACP,sFAAsF,CACvF;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;YAC7D,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACjF,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,0DAA0D,CAAC;YACvE,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yHAAyH,CAC1H;SACJ,CAAC;aACD,QAAQ,CAAC,0BAA0B,CAAC,CACxC;aACA,QAAQ,CAAC,sCAAsC,CAAC;QACnD,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QAC3E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;KAC/D,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,KAAK,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QAEH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,KAAK,CAAC,GAAG,EAAE,KAAK,CAAC,MAAM,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAE9F,0EAA0E;QAC1E,MAAM,OAAO,GAAG,GAAG,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC5B,MAAM,WAAW,GAAG,MAAM,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC;YAC9C,IAAI,MAA0B,CAAC;YAC/B,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC;gBAClC,IAAI,gBAAgB,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC;oBACpC,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,gCAAgC,EAAE,EAAE,WAAW,EAAE,QAAQ,EAAE,CAAC,CAAC;oBAC3E,MAAM,GAAG,qBAAqB,CAAC;gBACjC,CAAC;qBAAM,CAAC;oBACN,MAAM,GAAG,QAAQ,CAAC;gBACpB,CAAC;YACH,CAAC;YACD,OAAO;gBACL,WAAW;gBACX,GAAG,CAAC,CAAC,CAAC,IAAI,KAAK,SAAS,IAAI,EAAE,IAAI,EAAE,MAAM,CAAC,CAAC,CAAC,IAAI,CAAC,EAAE,CAAC;gBACrD,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,KAAK,EAAE,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC,EAAE,CAAC;gBACxD,GAAG,CAAC,CAAC,CAAC,GAAG,KAAK,SAAS,IAAI,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,GAAG,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,CAAC;aACxC,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,cAAc,GAAG,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,MAAM,CAAC;QAC/D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,8BAA8B,EAAE;YAC3C,cAAc;YACd,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,cAAc,EAAE,cAAc,EAAE,KAAK,CAAC,GAAG,CAAC,MAAM,EAAE,CAAC;IACvE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;YAClE,EAAE;YACF,+CAA+C;YAC/C,4BAA4B;SAC7B,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CACR,KAAK,CAAC,CAAC,WAAW,MAAM,CAAC,CAAC,IAAI,IAAI,GAAG,MAAM,CAAC,CAAC,KAAK,IAAI,GAAG,MAAM,CAAC,CAAC,GAAG,IAAI,GAAG,MAAM,CAAC,CAAC,MAAM,IAAI,GAAG,IAAI,CACrG,CAAC;QACJ,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgIzB,CAAC"}
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const structItems = ensureArray(struct.Item);
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const treeItem = findItem(structItems, 'TreeNum');
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// Supplementary Concept Records (SCRs) surface a non-navigable mapped-heading
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// pointer (e.g. "@218176") in the same TreeNum field. Drop it so treeNumbers
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// holds only real, navigable MeSH tree numbers. (#76)
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.string()
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.describe('NCBI Entrez UID for this record — the join key for E-utilities (eSummary/eFetch db=mesh).'),
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name: z.string().describe('Descriptor name'),
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treeNumbers: z
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treeNumbers: z
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.array(z.string())
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.optional()
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.describe('Navigable MeSH tree numbers (e.g. "D02.078.370.141.450"). Omitted for supplementary concept records (SCRs), which map to a heading rather than occupying a tree position.'),
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scopeNote: z.string().optional().describe('Scope note'),
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entryTerms: z.array(z.string()).optional().describe('Synonyms / entry terms'),
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})
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{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAC9E,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,yBAAyB,EACzB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,gBAAgB,CAAC;AAaxB;;;;;;GAMG;AACH,MAAM,iBAAiB,GAA2B,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AAEtF,SAAS,sBAAsB,CAAC,SAAiB;IAC/C,IAAI,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,iBAAiB,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACxD,IAAI,MAAM;YAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;IACtD,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,IAAI,GAAG;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;
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{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAC9E,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,yBAAyB,EACzB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,gBAAgB,CAAC;AAaxB;;;;;;GAMG;AACH,MAAM,iBAAiB,GAA2B,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AAEtF,SAAS,sBAAsB,CAAC,SAAiB;IAC/C,IAAI,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,iBAAiB,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACxD,IAAI,MAAM;YAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;IACtD,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,8EAA8E;QAC9E,6EAA6E;QAC7E,sDAAsD;QACtD,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtD,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,mBAAmB,CAAC,IAAa,EAAE,GAAa,EAAE,cAAuB;IAChF,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QACnC,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC5F,MAAM,IAAI,GAAG,IAA+B,CAAC;IAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,cAAqD,CAAC;IACjF,MAAM,OAAO,GAAG,WAAW,CACzB,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,MAAiC,CAC1D,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QACtB,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE5F,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAClC,MAAM,MAAM,GAAG,sBAAsB,CAAC,SAAS,CAAC,CAAC;QACjD,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,IAAI,CAA8B,CAAC;QACjE,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,IAAI,MAAM,CAAC;QACpE,MAAM,MAAM,GAAe,EAAE,SAAS,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QACvD,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YAC/D,IAAI,SAAS;gBAAE,MAAM,CAAC,SAAS,GAAG,SAAS,CAAC;YAC5C,MAAM,UAAU,GAAG,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YACjE,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC1D,MAAM,WAAW,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,WAAW,GAAG,WAAW,CAAC;QAC/D,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC,CAAC;AACL,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,2JAA2J;IAC7J,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC;QACjB,mBAAmB;QACnB,uBAAuB;QACvB,yBAAyB;QACzB,mBAAmB;KACpB,CAAC;IACF,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACtF,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,iBAAiB,CAAC;QACnF,cAAc,EAAE,CAAC;aACd,OAAO,EAAE;aACT,OAAO,CAAC,IAAI,CAAC;aACb,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CACP,mKAAmK,CACpK;YACH,SAAS,EAAE,CAAC;iBACT,MAAM,EAAE;iBACR,QAAQ,CACP,2FAA2F,CAC5F;YACH,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC;iBACX,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;iBACjB,QAAQ,EAAE;iBACV,QAAQ,CACP,2KAA2K,CAC5K;YACH,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;YACvD,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SAC9E,CAAC;aACD,QAAQ,CAAC,iCAAiC,CAAC,CAC/C;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,oFAAoF;IACpF,iFAAiF;IACjF,yDAAyD;IACzD,UAAU,EAAE;QACV,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;QAClE,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yHAAyH,CAC1H;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QACpD,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE5E,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACzC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;QACxC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5F,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5E,MAAM,CAAC,WAAW,EAAE,WAAW,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC;QAEjF,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;QAC/B,MAAM,GAAG,GAAa,EAAE,CAAC;QACzB,KAAK,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,MAAM,IAAI,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;YACzE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAClB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;gBACb,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,CAAC;QACH,CAAC;QACD,GAAG,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;QAE9C,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC;YACpB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,gCAAgC,KAAK,iKAAiK,CACvM,CAAC;YACF,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QAChC,CAAC;QAED,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QACrF,MAAM,OAAO,GAAG,mBAAmB,CAAC,WAAW,EAAE,GAAG,EAAE,cAAc,CAAC,CAAC;QAEtE,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;QACvC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpB,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,OAAO,MAAM,GAAG,MAAM,CAAC;QACzB,CAAC,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC;QACjC,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC;IAC5B,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,mBAAmB,MAAM,CAAC,KAAK,GAAG;YAClC,WAAW,MAAM,CAAC,OAAO,CAAC,MAAM,eAAe;SAChD,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC7B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACzC,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC/C,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACzF,IAAI,CAAC,CAAC,SAAS;gBAAE,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,UAAU,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACxF,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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@@ -1 +1 @@
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1
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-
{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;
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1
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+
{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA+PpC,CAAC"}
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@@ -16,6 +16,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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16
16
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import { EUROPEPMC_SERVICE_ERRORS } from '../../../services/error-contracts.js';
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17
17
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import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
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18
18
|
import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
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19
|
+
import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
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19
20
|
import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
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20
21
|
const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
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21
22
|
// ─── Tool Definition ─────────────────────────────────────────────────────────
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@@ -93,7 +94,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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93
94
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abstractSnippet: z
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94
95
|
.string()
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95
96
|
.optional()
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96
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-
.describe('First few hundred characters of the abstract when `resultType: "core"` is requested'),
|
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97
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+
.describe('First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: "core"` is requested'),
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97
98
|
citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
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98
99
|
epmcUrl: z.string().describe('Europe PMC article URL'),
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99
100
|
})
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@@ -145,25 +146,32 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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145
146
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...(input.sort && { sort: input.sort }),
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146
147
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...(ctx.signal && { signal: ctx.signal }),
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147
148
|
});
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148
|
-
const hits = result.hits.map((h) =>
|
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149
|
-
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150
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-
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151
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152
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153
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154
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160
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165
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166
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-
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149
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+
const hits = result.hits.map((h) => {
|
|
150
|
+
// EPMC returns abstractText as a raw JSON string carrying JATS/HTML markup,
|
|
151
|
+
// un-decoded entities, and soft hyphens (no XML parser runs on it). Clean it
|
|
152
|
+
// to display-ready plain text before truncating, so the snippet budget is
|
|
153
|
+
// spent on text and soft hyphens don't corrupt downstream token matching. (#74)
|
|
154
|
+
const snippet = h.abstractText ? toDisplayText(h.abstractText) : '';
|
|
155
|
+
return {
|
|
156
|
+
source: h.source,
|
|
157
|
+
epmcId: h.id,
|
|
158
|
+
...(h.title && { title: h.title }),
|
|
159
|
+
...(h.authorString && { authors: h.authorString }),
|
|
160
|
+
...(h.journalTitle && { journal: h.journalTitle }),
|
|
161
|
+
...(h.pubYear && { pubYear: h.pubYear }),
|
|
162
|
+
...(h.firstPublicationDate && { firstPublicationDate: h.firstPublicationDate }),
|
|
163
|
+
...(h.pmid && { pmid: h.pmid }),
|
|
164
|
+
...(h.pmcid && { pmcId: h.pmcid }),
|
|
165
|
+
...(h.doi && { doi: h.doi }),
|
|
166
|
+
...(h.isOpenAccess !== undefined && { isOpenAccess: h.isOpenAccess === 'Y' }),
|
|
167
|
+
...(h.inPMC !== undefined && { hasFullTextXml: h.inPMC === 'Y' }),
|
|
168
|
+
...(snippet && {
|
|
169
|
+
abstractSnippet: snippet.length > 400 ? `${snippet.slice(0, 400)}…` : snippet,
|
|
170
|
+
}),
|
|
171
|
+
...(typeof h.citedByCount === 'number' && { citedByCount: h.citedByCount }),
|
|
172
|
+
epmcUrl: `https://europepmc.org/article/${h.source}/${h.id}`,
|
|
173
|
+
};
|
|
174
|
+
});
|
|
167
175
|
// Europe PMC accepts a `P_PDATE_D` sort but silently ignores it for
|
|
168
176
|
// preprint-only (PPR) result sets — preprints have no populated publication
|
|
169
177
|
// date, so results come back relevance-ranked, not date-ordered. Signal it so
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAGvB,sBAAsB,EAEtB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2BpB;;;;;;;GAOG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;gBAG1B,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM;IAmBrC;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC;
|
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1
|
+
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAGvB,sBAAsB,EAEtB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2BpB;;;;;;;GAOG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;gBAG1B,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM;IAmBrC;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC;IA+F3E;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC;IAkBnC;;;;;;;;;OASG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC;IAUlC;;;;;;;;;OASG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC;IAUlC;;;OAGG;YACW,iBAAiB;IA6C/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS;IAgCnD;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
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@@ -119,15 +119,26 @@ export class EuropePmcService {
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119
119
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if (parsed.hitCount === undefined &&
|
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120
120
|
parsed.request === undefined &&
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121
121
|
parsed.resultList === undefined) {
|
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122
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-
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123
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-
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|
124
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-
|
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125
|
-
|
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122
|
+
// Split the diagnosis (message) from the actionable next step (recovery
|
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123
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+
// hint). The framework mirrors data.recovery.hint into content[], so
|
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124
|
+
// passing one string as both renders byte-identical Error:/Recovery:
|
|
125
|
+
// blocks — the same distinct message-vs-hint shape as the errMsg throw
|
|
126
|
+
// ~20 lines up. (#75)
|
|
127
|
+
const { message, hint } = params.sort
|
|
128
|
+
? {
|
|
129
|
+
message: `Europe PMC silently rejected the request — most likely the invalid sort field "${params.sort}".`,
|
|
130
|
+
hint: 'Use a documented sort (`P_PDATE_D desc`, `CITED desc`, `AUTH_FIRST asc`, or `PUB_YEAR desc`), or omit `sort` for relevance ranking.',
|
|
131
|
+
}
|
|
132
|
+
: {
|
|
133
|
+
message: 'Europe PMC silently rejected the request — empty envelope with no hitCount.',
|
|
134
|
+
hint: 'Verify the query syntax, sort field, and cursorMark, then retry.',
|
|
135
|
+
};
|
|
136
|
+
throw validationError(message, {
|
|
126
137
|
reason: 'europepmc_invalid_input',
|
|
127
138
|
...(params.sort && { sort: params.sort }),
|
|
128
139
|
...(params.cursorMark && params.cursorMark !== '*' && { cursorMark: params.cursorMark }),
|
|
129
140
|
responseSnippet: text.substring(0, 200),
|
|
130
|
-
recovery: { hint
|
|
141
|
+
recovery: { hint },
|
|
131
142
|
});
|
|
132
143
|
}
|
|
133
144
|
const hits = ensureArray(parsed.resultList?.result);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
|
1
|
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+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,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,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;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;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,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,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAoE7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAmE7B,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -20,7 +20,7 @@ import { NCBI_PMC_IDCONV_URL, } from './types.js';
|
|
|
20
20
|
*/
|
|
21
21
|
const ID_CONVERT_FORMAT_HINTS = {
|
|
22
22
|
pmid: 'numeric digits, e.g. "23193287"',
|
|
23
|
-
pmcid: '"PMC" + digits, e.g. "PMC3531190"',
|
|
23
|
+
pmcid: '"PMC" + digits or bare digits, e.g. "PMC3531190" or "3531190"',
|
|
24
24
|
doi: 'starts with "10.", e.g. "10.1093/nar/gks1195"',
|
|
25
25
|
};
|
|
26
26
|
/** Sentinel reason used when the service-level deadline expires. */
|
|
@@ -190,8 +190,18 @@ export class NcbiService {
|
|
|
190
190
|
* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
|
|
191
191
|
*/
|
|
192
192
|
async idConvert(ids, idtype, options) {
|
|
193
|
+
// The PMC ID Converter rejects an entire batch (HTTP 400) when PMC-prefixed
|
|
194
|
+
// and bare-digit PMCIDs are mixed, even though it accepts each form on its
|
|
195
|
+
// own. Canonicalize bare digits to "PMC"+digits so every pmcid batch is
|
|
196
|
+
// homogeneous and resolves like a same-format one. (#73)
|
|
197
|
+
const normalizedIds = idtype === 'pmcid'
|
|
198
|
+
? ids.map((id) => {
|
|
199
|
+
const trimmed = id.trim();
|
|
200
|
+
return /^\d+$/.test(trimmed) ? `PMC${trimmed}` : trimmed;
|
|
201
|
+
})
|
|
202
|
+
: ids;
|
|
193
203
|
const params = {
|
|
194
|
-
ids:
|
|
204
|
+
ids: normalizedIds.join(','),
|
|
195
205
|
format: 'json',
|
|
196
206
|
...(idtype && { idtype }),
|
|
197
207
|
};
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EAEb,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAElB,sBAAsB,EACtB,gBAAgB,EACjB,MAAM,aAAa,CAAC;
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1
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+
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EACjB,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EAEb,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAElB,sBAAsB,EACtB,gBAAgB,EACjB,MAAM,aAAa,CAAC;AAIrB;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,mBAAmB,EAAE,CAAC;CAChC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,aAAa,CAAC,EAAE,aAAa,GAAG,gBAAgB,CAqD9E;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAChC,UAAU,CAAC,EAAE,UAAU,EACvB,UAAU,CAAC,EAAE,UAAU,GACtB,iBAAiB,GAAG,SAAS,CAgC/B;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,cAAc,EAAE,CA8B1F;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,EAAE,CAmBxE;AAED;;;;;;;GAOG;AACH,wBAAgB,UAAU,CACxB,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAyCpB;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAsBpB;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,sBAAsB,CAAC,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAIjG;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,eAAe,CAAC,EAAE,cAAc,EAAE,GAAG,cAAc,GAAG,MAAM,EAAE,CAa7F;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,SAAS,CAyB5F;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,MAAM,GAAG,SAAS,CAGvF;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,UAAU,CAAC,EAAE,UAAU,GAAG,iBAAiB,EAAE,CAShF;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,aAAa,CAiCf"}
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@@ -3,6 +3,7 @@
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3
3
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* typically from EFetch results.
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4
4
|
* @module src/services/ncbi/parsing/article-parser
|
|
5
5
|
*/
|
|
6
|
+
import { decodeHtmlEntities } from './text-helpers.js';
|
|
6
7
|
import { ensureArray, getAttribute, getText } from './xml-helpers.js';
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|
7
8
|
/**
|
|
8
9
|
* Extracts and formats author information from XML, deduplicating affiliations.
|
|
@@ -142,10 +143,14 @@ export function extractGrants(grantListXml) {
|
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142
143
|
return [];
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|
143
144
|
const grants = ensureArray(grantListXml.Grant);
|
|
144
145
|
return grants.map((g) => {
|
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145
|
-
|
|
146
|
-
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|
147
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-
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|
148
|
-
|
|
146
|
+
// NCBI double-encodes ampersands in grant identifiers and agencies
|
|
147
|
+
// (`CSR&amp;D`), so the XML parser's single entity-decode pass still
|
|
148
|
+
// leaves a literal `&`. Decode once more here to surface display-ready
|
|
149
|
+
// text (`CSR&D`) rather than making every caller re-sanitize. (#74)
|
|
150
|
+
const grantId = decodeHtmlEntities(getText(g.GrantID));
|
|
151
|
+
const acronym = decodeHtmlEntities(getText(g.Acronym));
|
|
152
|
+
const agency = decodeHtmlEntities(getText(g.Agency));
|
|
153
|
+
const country = decodeHtmlEntities(getText(g.Country));
|
|
149
154
|
return {
|
|
150
155
|
...(grantId && { grantId }),
|
|
151
156
|
...(acronym && { acronym }),
|
|
@@ -1 +1 @@
|
|
|
1
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-
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@@ -0,0 +1,29 @@
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1
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+
/**
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2
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+
* @fileoverview Plain-text normalization for upstream biomedical strings.
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3
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+
* Europe PMC search snippets and NCBI grant identifiers arrive carrying
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4
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+
* structural JATS/HTML markup, un-decoded HTML character references, and soft
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5
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+
* hyphens. These helpers turn such strings into clean, display-ready plain text
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6
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+
* so callers — often a smaller model pre-screening hits — don't have to
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7
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+
* re-sanitize upstream markup.
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8
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+
* @module src/services/ncbi/parsing/text-helpers
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9
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+
*/
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10
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+
/**
|
|
11
|
+
* Decode well-formed named and numeric HTML/XML character references in a plain
|
|
12
|
+
* string. A bare `&` (e.g. `AT&T`) is left untouched — only `&name;` / `&#NN;` /
|
|
13
|
+
* `&#xHH;` forms are decoded — so this is safe to run on text an XML parser
|
|
14
|
+
* already decoded once: a surviving double-encoding (`&amp;`) collapses to
|
|
15
|
+
* `&`, while a genuine ampersand stays put. Unknown named entities and
|
|
16
|
+
* out-of-range code points are left verbatim rather than dropped.
|
|
17
|
+
*/
|
|
18
|
+
export declare function decodeHtmlEntities(text: string): string;
|
|
19
|
+
/**
|
|
20
|
+
* Turn an upstream string that may carry JATS/HTML markup into display-ready
|
|
21
|
+
* plain text: strip structural tags, decode character references, drop soft
|
|
22
|
+
* hyphens (U+00AD — invisible, and it corrupts token matching mid-word), and
|
|
23
|
+
* collapse the resulting whitespace. Tags are stripped before decoding so a
|
|
24
|
+
* structural `<bold>` is removed while an entity-escaped `<gene>` survives
|
|
25
|
+
* as literal text. Used for Europe PMC abstract snippets before truncation, so
|
|
26
|
+
* the character budget is spent on text rather than markup.
|
|
27
|
+
*/
|
|
28
|
+
export declare function toDisplayText(text: string): string;
|
|
29
|
+
//# sourceMappingURL=text-helpers.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"text-helpers.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAmBH;;;;;;;GAOG;AACH,wBAAgB,kBAAkB,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAcvD;AAED;;;;;;;;GAQG;AACH,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,GAAG,MAAM,CAKlD"}
|
|
@@ -0,0 +1,65 @@
|
|
|
1
|
+
/**
|
|
2
|
+
* @fileoverview Plain-text normalization for upstream biomedical strings.
|
|
3
|
+
* Europe PMC search snippets and NCBI grant identifiers arrive carrying
|
|
4
|
+
* structural JATS/HTML markup, un-decoded HTML character references, and soft
|
|
5
|
+
* hyphens. These helpers turn such strings into clean, display-ready plain text
|
|
6
|
+
* so callers — often a smaller model pre-screening hits — don't have to
|
|
7
|
+
* re-sanitize upstream markup.
|
|
8
|
+
* @module src/services/ncbi/parsing/text-helpers
|
|
9
|
+
*/
|
|
10
|
+
/** Named HTML/XML character references that appear in PubMed / Europe PMC text. */
|
|
11
|
+
const NAMED_ENTITIES = {
|
|
12
|
+
amp: '&',
|
|
13
|
+
lt: '<',
|
|
14
|
+
gt: '>',
|
|
15
|
+
quot: '"',
|
|
16
|
+
apos: "'",
|
|
17
|
+
nbsp: ' ',
|
|
18
|
+
shy: '',
|
|
19
|
+
};
|
|
20
|
+
/** A well-formed numeric (`­`, `­`) or named (`&`) character reference. */
|
|
21
|
+
const ENTITY_RE = /&(#x[0-9a-f]+|#\d+|[a-z][a-z0-9]*);/gi;
|
|
22
|
+
const MARKUP_TAG_RE = /<[^>]+>/g;
|
|
23
|
+
const SOFT_HYPHEN_RE = //g;
|
|
24
|
+
const WHITESPACE_RE = /\s+/g;
|
|
25
|
+
/**
|
|
26
|
+
* Decode well-formed named and numeric HTML/XML character references in a plain
|
|
27
|
+
* string. A bare `&` (e.g. `AT&T`) is left untouched — only `&name;` / `&#NN;` /
|
|
28
|
+
* `&#xHH;` forms are decoded — so this is safe to run on text an XML parser
|
|
29
|
+
* already decoded once: a surviving double-encoding (`&amp;`) collapses to
|
|
30
|
+
* `&`, while a genuine ampersand stays put. Unknown named entities and
|
|
31
|
+
* out-of-range code points are left verbatim rather than dropped.
|
|
32
|
+
*/
|
|
33
|
+
export function decodeHtmlEntities(text) {
|
|
34
|
+
return text.replace(ENTITY_RE, (match, body) => {
|
|
35
|
+
if (body.charCodeAt(0) === 35 /* '#' */) {
|
|
36
|
+
const isHex = body.charCodeAt(1) === 120 || body.charCodeAt(1) === 88; /* 'x' | 'X' */
|
|
37
|
+
const codePoint = isHex ? parseInt(body.slice(2), 16) : parseInt(body.slice(1), 10);
|
|
38
|
+
if (!Number.isFinite(codePoint) || codePoint < 0 || codePoint > 0x10ffff)
|
|
39
|
+
return match;
|
|
40
|
+
try {
|
|
41
|
+
return String.fromCodePoint(codePoint);
|
|
42
|
+
}
|
|
43
|
+
catch {
|
|
44
|
+
return match;
|
|
45
|
+
}
|
|
46
|
+
}
|
|
47
|
+
return NAMED_ENTITIES[body.toLowerCase()] ?? match;
|
|
48
|
+
});
|
|
49
|
+
}
|
|
50
|
+
/**
|
|
51
|
+
* Turn an upstream string that may carry JATS/HTML markup into display-ready
|
|
52
|
+
* plain text: strip structural tags, decode character references, drop soft
|
|
53
|
+
* hyphens (U+00AD — invisible, and it corrupts token matching mid-word), and
|
|
54
|
+
* collapse the resulting whitespace. Tags are stripped before decoding so a
|
|
55
|
+
* structural `<bold>` is removed while an entity-escaped `<gene>` survives
|
|
56
|
+
* as literal text. Used for Europe PMC abstract snippets before truncation, so
|
|
57
|
+
* the character budget is spent on text rather than markup.
|
|
58
|
+
*/
|
|
59
|
+
export function toDisplayText(text) {
|
|
60
|
+
return decodeHtmlEntities(text.replace(MARKUP_TAG_RE, ' '))
|
|
61
|
+
.replace(SOFT_HYPHEN_RE, '')
|
|
62
|
+
.replace(WHITESPACE_RE, ' ')
|
|
63
|
+
.trim();
|
|
64
|
+
}
|
|
65
|
+
//# sourceMappingURL=text-helpers.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"text-helpers.js","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/text-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,mFAAmF;AACnF,MAAM,cAAc,GAAqC;IACvD,GAAG,EAAE,GAAG;IACR,EAAE,EAAE,GAAG;IACP,EAAE,EAAE,GAAG;IACP,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,IAAI,EAAE,GAAG;IACT,GAAG,EAAE,GAAG;CACT,CAAC;AAEF,yFAAyF;AACzF,MAAM,SAAS,GAAG,uCAAuC,CAAC;AAC1D,MAAM,aAAa,GAAG,UAAU,CAAC;AACjC,MAAM,cAAc,GAAG,IAAI,CAAC;AAC5B,MAAM,aAAa,GAAG,MAAM,CAAC;AAE7B;;;;;;;GAOG;AACH,MAAM,UAAU,kBAAkB,CAAC,IAAY;IAC7C,OAAO,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,CAAC,KAAK,EAAE,IAAY,EAAE,EAAE;QACrD,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,SAAS,EAAE,CAAC;YACxC,MAAM,KAAK,GAAG,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,GAAG,IAAI,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC,eAAe;YACtF,MAAM,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACpF,IAAI,CAAC,MAAM,CAAC,QAAQ,CAAC,SAAS,CAAC,IAAI,SAAS,GAAG,CAAC,IAAI,SAAS,GAAG,QAAQ;gBAAE,OAAO,KAAK,CAAC;YACvF,IAAI,CAAC;gBACH,OAAO,MAAM,CAAC,aAAa,CAAC,SAAS,CAAC,CAAC;YACzC,CAAC;YAAC,MAAM,CAAC;gBACP,OAAO,KAAK,CAAC;YACf,CAAC;QACH,CAAC;QACD,OAAO,cAAc,CAAC,IAAI,CAAC,WAAW,EAAE,CAAC,IAAI,KAAK,CAAC;IACrD,CAAC,CAAC,CAAC;AACL,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,aAAa,CAAC,IAAY;IACxC,OAAO,kBAAkB,CAAC,IAAI,CAAC,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC,CAAC;SACxD,OAAO,CAAC,cAAc,EAAE,EAAE,CAAC;SAC3B,OAAO,CAAC,aAAa,EAAE,GAAG,CAAC;SAC3B,IAAI,EAAE,CAAC;AACZ,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.9.
|
|
3
|
+
"version": "2.9.7",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -81,9 +81,9 @@
|
|
|
81
81
|
"access": "public"
|
|
82
82
|
},
|
|
83
83
|
"dependencies": {
|
|
84
|
-
"@cyanheads/mcp-ts-core": "^0.10.
|
|
85
|
-
"defuddle": "^0.
|
|
86
|
-
"fast-xml-parser": "^5.
|
|
84
|
+
"@cyanheads/mcp-ts-core": "^0.10.9",
|
|
85
|
+
"defuddle": "^0.19.0",
|
|
86
|
+
"fast-xml-parser": "^5.9.3",
|
|
87
87
|
"linkedom": "^0.18.12",
|
|
88
88
|
"pino-pretty": "^13.1.3",
|
|
89
89
|
"sanitize-html": "^2.17.5",
|
|
@@ -92,14 +92,14 @@
|
|
|
92
92
|
},
|
|
93
93
|
"devDependencies": {
|
|
94
94
|
"@biomejs/biome": "^2.5.0",
|
|
95
|
-
"@types/node": "^
|
|
95
|
+
"@types/node": "^26.0.0",
|
|
96
96
|
"@types/sanitize-html": "^2.16.1",
|
|
97
|
-
"@vitest/coverage-istanbul": "^4.1.
|
|
97
|
+
"@vitest/coverage-istanbul": "^4.1.9",
|
|
98
98
|
"depcheck": "^1.4.7",
|
|
99
99
|
"fast-check": "^4.8.0",
|
|
100
100
|
"ignore": "^7.0.5",
|
|
101
101
|
"tsc-alias": "^1.8.17",
|
|
102
102
|
"typescript": "^6.0.3",
|
|
103
|
-
"vitest": "^4.1.
|
|
103
|
+
"vitest": "^4.1.9"
|
|
104
104
|
}
|
|
105
105
|
}
|
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": "2.9.
|
|
9
|
+
"version": "2.9.7",
|
|
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": "2.9.
|
|
22
|
+
"version": "2.9.7",
|
|
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": "2.9.
|
|
69
|
+
"version": "2.9.7",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|