@cyanheads/pubmed-mcp-server 2.2.6 → 2.3.1
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 +29 -5
- package/dist/index.js +4 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +25 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +75 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +25 -0
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +89 -0
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +3 -3
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/ncbi/api-client.d.ts +7 -0
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +49 -2
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +16 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +78 -32
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +48 -0
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/dist/services/ncbi/types.js +2 -0
- package/dist/services/ncbi/types.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/CLAUDE.md
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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:** 2.3.1
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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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parsing/ # XML parsers (article, esummary, PMC)
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formatting/ # Citation formatter (APA, MLA, BibTeX, RIS)
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mcp-server/
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tools/definitions/ #
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tools/definitions/ # 9 tool definitions (*.tool.ts)
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resources/definitions/ # database-info.resource.ts
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prompts/definitions/ # research-plan.prompt.ts
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```
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package/README.md
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<div align="center">
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<h1>@cyanheads/pubmed-mcp-server</h1>
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<p><b>MCP server for the NCBI E-utilities API. Search PubMed, fetch article metadata and full text, generate citations, explore MeSH terms, and discover related research. STDIO or Streamable HTTP.</b>
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<div>
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<div>9 Tools • 1 Resource • 1 Prompt</div>
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</p>
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</div>
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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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## Tools
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Nine tools for working with PubMed and NCBI data:
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| Tool | Description |
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|:---|:---|
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| `pubmed_find_related` | Find similar articles, citing articles, or references for a given PMID |
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| `pubmed_spell_check` | Spell-check biomedical queries using NCBI's ESpell service |
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| `pubmed_lookup_mesh` | Search and explore MeSH vocabulary — tree numbers, scope notes, entry terms |
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| `pubmed_lookup_citation` | Resolve partial bibliographic references to PubMed IDs via ECitMatch |
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| `pubmed_convert_ids` | Convert between DOI, PMID, and PMCID using the PMC ID Converter API |
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### `pubmed_search_articles`
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- Detailed records with tree numbers, scope notes, and entry terms by default
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- Useful for building precise PubMed queries with controlled vocabulary
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---
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### `pubmed_lookup_citation`
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Resolve partial bibliographic references to PubMed IDs via NCBI ECitMatch.
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- Match citations by journal, year, volume, first page, and/or author name
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- More fields = better match accuracy; at least one field required
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- Batch up to 25 citations per request
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- Deterministic matching — more reliable than free-text search for known references
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---
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### `pubmed_convert_ids`
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Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
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- Batch up to 50 IDs per request
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- Accepts DOIs, PMIDs, or PMCIDs (all IDs must be the same type)
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- Only resolves articles indexed in PubMed Central
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- Returns all available identifier mappings for each input ID
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## Resource and prompt
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| Type | Name | Description |
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PubMed-specific:
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- Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo)
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- Complete NCBI E-utilities integration (ESearch, EFetch, ESummary, ELink, ESpell, EInfo, ECitMatch) plus PMC ID Converter
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- Sequential request queue with configurable delay for NCBI rate limit compliance
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- NCBI-specific XML parser with `isArray` hints for PubMed's inconsistent XML structure
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- Hand-rolled citation formatters (APA, MLA, BibTeX, RIS) — zero deps, Workers-compatible
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| Directory | Purpose |
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|:---|:---|
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| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`).
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| `src/mcp-server/tools` | Tool definitions (`*.tool.ts`). Nine PubMed tools. |
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| `src/mcp-server/resources` | Resource definitions. Database info resource. |
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| `src/mcp-server/prompts` | Prompt definitions. Research plan prompt. |
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| `src/services/ncbi` | NCBI E-utilities service layer — API client, queue, parser, formatter. |
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package/dist/index.js
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import { createApp } from '@cyanheads/mcp-ts-core';
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import { researchPlanPrompt } from './mcp-server/prompts/definitions/research-plan.prompt.js';
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import { databaseInfoResource } from './mcp-server/resources/definitions/database-info.resource.js';
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import { convertIdsTool } from './mcp-server/tools/definitions/convert-ids.tool.js';
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import { fetchArticlesTool } from './mcp-server/tools/definitions/fetch-articles.tool.js';
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import { fetchFulltextTool } from './mcp-server/tools/definitions/fetch-fulltext.tool.js';
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import { findRelatedTool } from './mcp-server/tools/definitions/find-related.tool.js';
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import { formatCitationsTool } from './mcp-server/tools/definitions/format-citations.tool.js';
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import { lookupCitationTool } from './mcp-server/tools/definitions/lookup-citation.tool.js';
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import { lookupMeshTool } from './mcp-server/tools/definitions/lookup-mesh.tool.js';
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import { searchArticlesTool } from './mcp-server/tools/definitions/search-articles.tool.js';
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import { spellCheckTool } from './mcp-server/tools/definitions/spell-check.tool.js';
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findRelatedTool,
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spellCheckTool,
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lookupMeshTool,
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lookupCitationTool,
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convertIdsTool,
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],
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resources: [databaseInfoResource],
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prompts: [researchPlanPrompt],
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package/dist/index.js.map
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAElE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,mBAAmB;QACnB,eAAe;QACf,cAAc;QACd,cAAc;KACf;IACD,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,KAAK;QACH,eAAe,EAAE,CAAC;IACpB,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;GAGG;AAEH,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,0DAA0D,CAAC;AAC9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,iBAAiB,EAAE,MAAM,uDAAuD,CAAC;AAC1F,OAAO,EAAE,eAAe,EAAE,MAAM,qDAAqD,CAAC;AACtF,OAAO,EAAE,mBAAmB,EAAE,MAAM,yDAAyD,CAAC;AAC9F,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,kBAAkB,EAAE,MAAM,wDAAwD,CAAC;AAC5F,OAAO,EAAE,cAAc,EAAE,MAAM,oDAAoD,CAAC;AACpF,OAAO,EAAE,eAAe,EAAE,MAAM,iCAAiC,CAAC;AAElE,MAAM,SAAS,CAAC;IACd,KAAK,EAAE;QACL,kBAAkB;QAClB,iBAAiB;QACjB,iBAAiB;QACjB,mBAAmB;QACnB,eAAe;QACf,cAAc;QACd,cAAc;QACd,kBAAkB;QAClB,cAAc;KACf;IACD,SAAS,EAAE,CAAC,oBAAoB,CAAC;IACjC,OAAO,EAAE,CAAC,kBAAkB,CAAC;IAC7B,KAAK;QACH,eAAe,EAAE,CAAC;IACpB,CAAC;CACF,CAAC,CAAC"}
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/**
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* @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
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* using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
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* @module src/mcp-server/tools/definitions/convert-ids.tool
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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export declare const convertIdsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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ids: z.ZodArray<z.ZodString>;
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idtype: z.ZodEnum<{
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pmcid: "pmcid";
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pmid: "pmid";
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doi: "doi";
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}>;
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}, z.core.$strip>, z.ZodObject<{
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records: z.ZodArray<z.ZodObject<{
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requestedId: z.ZodString;
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pmid: z.ZodOptional<z.ZodString>;
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pmcid: z.ZodOptional<z.ZodString>;
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doi: z.ZodOptional<z.ZodString>;
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errmsg: z.ZodOptional<z.ZodString>;
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}, z.core.$strip>>;
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totalConverted: z.ZodNumber;
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totalSubmitted: z.ZodNumber;
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}, z.core.$strip>>;
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//# sourceMappingURL=convert-ids.tool.d.ts.map
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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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/**
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* @fileoverview Article ID conversion tool. Converts between DOI, PMID, and PMCID
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* using the NCBI PMC ID Converter API for deterministic, batch-friendly resolution.
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* @module src/mcp-server/tools/definitions/convert-ids.tool
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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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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input: z.object({
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ids: z
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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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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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}),
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output: z.object({
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records: z
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.array(z.object({
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requestedId: z.string().describe('The ID that was submitted'),
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pmid: z.string().optional().describe('PubMed ID'),
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pmcid: z.string().optional().describe('PubMed Central ID'),
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doi: z.string().optional().describe('Digital Object Identifier'),
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errmsg: z.string().optional().describe('Error message if conversion failed'),
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}))
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.describe('Conversion results, one per input ID'),
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totalConverted: z.number().describe('Number of IDs successfully converted'),
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totalSubmitted: z.number().describe('Number of IDs submitted'),
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}),
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async handler(input, ctx) {
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ctx.log.info('Executing pubmed_convert_ids', {
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count: input.ids.length,
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idtype: input.idtype,
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});
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const raw = await getNcbiService().idConvert(input.ids, input.idtype);
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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: String(r['requested-id']),
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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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...(r.errmsg !== undefined && { errmsg: String(r.errmsg) }),
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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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totalSubmitted: input.ids.length,
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});
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return { records, totalConverted, totalSubmitted: input.ids.length };
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},
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format: (result) => {
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const lines = [
|
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`## ID Conversion Results`,
|
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+
`**Converted:** ${result.totalConverted}/${result.totalSubmitted}`,
|
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'',
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'| Requested ID | PMID | PMCID | DOI |',
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'|:---|:---|:---|:---|',
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];
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for (const r of result.records) {
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if (r.errmsg) {
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lines.push(`| ${r.requestedId} | - | - | Error: ${r.errmsg} |`);
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}
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else {
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lines.push(`| ${r.requestedId} | ${r.pmid ?? '-'} | ${r.pmcid ?? '-'} | ${r.doi ?? '-'} |`);
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}
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}
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return [{ type: 'text', text: lines.join('\n') }];
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},
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});
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//# sourceMappingURL=convert-ids.tool.js.map
|
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@@ -0,0 +1 @@
|
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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,iEAAiE;YAC/D,uEAAuE,CAC1E;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"}
|
|
@@ -0,0 +1,25 @@
|
|
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1
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+
/**
|
|
2
|
+
* @fileoverview Citation lookup tool. Resolves partial bibliographic references
|
|
3
|
+
* to PubMed IDs using NCBI's ECitMatch service.
|
|
4
|
+
* @module src/mcp-server/tools/definitions/lookup-citation.tool
|
|
5
|
+
*/
|
|
6
|
+
import { z } from '@cyanheads/mcp-ts-core';
|
|
7
|
+
export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
|
|
8
|
+
citations: z.ZodArray<z.ZodObject<{
|
|
9
|
+
journal: z.ZodOptional<z.ZodString>;
|
|
10
|
+
year: z.ZodOptional<z.ZodString>;
|
|
11
|
+
volume: z.ZodOptional<z.ZodString>;
|
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12
|
+
firstPage: z.ZodOptional<z.ZodString>;
|
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13
|
+
authorName: z.ZodOptional<z.ZodString>;
|
|
14
|
+
key: z.ZodOptional<z.ZodString>;
|
|
15
|
+
}, z.core.$strip>>;
|
|
16
|
+
}, z.core.$strip>, z.ZodObject<{
|
|
17
|
+
results: z.ZodArray<z.ZodObject<{
|
|
18
|
+
key: z.ZodString;
|
|
19
|
+
pmid: z.ZodOptional<z.ZodString>;
|
|
20
|
+
matched: z.ZodBoolean;
|
|
21
|
+
}, z.core.$strip>>;
|
|
22
|
+
totalMatched: z.ZodNumber;
|
|
23
|
+
totalSubmitted: z.ZodNumber;
|
|
24
|
+
}, z.core.$strip>>;
|
|
25
|
+
//# sourceMappingURL=lookup-citation.tool.d.ts.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;kBAkG7B,CAAC"}
|
|
@@ -0,0 +1,89 @@
|
|
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1
|
+
/**
|
|
2
|
+
* @fileoverview Citation lookup tool. Resolves partial bibliographic references
|
|
3
|
+
* to PubMed IDs using NCBI's ECitMatch service.
|
|
4
|
+
* @module src/mcp-server/tools/definitions/lookup-citation.tool
|
|
5
|
+
*/
|
|
6
|
+
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
|
+
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
8
|
+
export const lookupCitationTool = tool('pubmed_lookup_citation', {
|
|
9
|
+
description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.`,
|
|
10
|
+
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
11
|
+
input: z.object({
|
|
12
|
+
citations: z
|
|
13
|
+
.array(z.object({
|
|
14
|
+
journal: z
|
|
15
|
+
.string()
|
|
16
|
+
.optional()
|
|
17
|
+
.describe('Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a")'),
|
|
18
|
+
year: z.string().optional().describe('Publication year (e.g., "1991")'),
|
|
19
|
+
volume: z.string().optional().describe('Volume number'),
|
|
20
|
+
firstPage: z.string().optional().describe('First page number'),
|
|
21
|
+
authorName: z
|
|
22
|
+
.string()
|
|
23
|
+
.optional()
|
|
24
|
+
.describe('Author name, typically "lastname initials" (e.g., "mann bj")'),
|
|
25
|
+
key: z
|
|
26
|
+
.string()
|
|
27
|
+
.optional()
|
|
28
|
+
.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
|
|
29
|
+
}))
|
|
30
|
+
.min(1)
|
|
31
|
+
.max(25)
|
|
32
|
+
.describe('Citations to look up. More fields = better match accuracy.'),
|
|
33
|
+
}),
|
|
34
|
+
output: z.object({
|
|
35
|
+
results: z
|
|
36
|
+
.array(z.object({
|
|
37
|
+
key: z.string().describe('Citation tracking key'),
|
|
38
|
+
pmid: z.string().optional().describe('Matched PubMed ID'),
|
|
39
|
+
matched: z.boolean().describe('Whether a PMID was found'),
|
|
40
|
+
}))
|
|
41
|
+
.describe('Match results, one per input citation'),
|
|
42
|
+
totalMatched: z.number().describe('Number of citations with PMID matches'),
|
|
43
|
+
totalSubmitted: z.number().describe('Number of citations submitted'),
|
|
44
|
+
}),
|
|
45
|
+
async handler(input, ctx) {
|
|
46
|
+
ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
|
|
47
|
+
for (const c of input.citations) {
|
|
48
|
+
if (!c.journal && !c.year && !c.volume && !c.firstPage && !c.authorName) {
|
|
49
|
+
throw new Error('Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).');
|
|
50
|
+
}
|
|
51
|
+
}
|
|
52
|
+
const citations = input.citations.map((c, i) => ({
|
|
53
|
+
journal: c.journal,
|
|
54
|
+
year: c.year,
|
|
55
|
+
volume: c.volume,
|
|
56
|
+
firstPage: c.firstPage,
|
|
57
|
+
authorName: c.authorName,
|
|
58
|
+
key: c.key ?? String(i + 1),
|
|
59
|
+
}));
|
|
60
|
+
const results = await getNcbiService().eCitMatch(citations);
|
|
61
|
+
const mapped = results.map((r) => ({
|
|
62
|
+
key: r.key,
|
|
63
|
+
matched: r.matched,
|
|
64
|
+
...(r.pmid && { pmid: r.pmid }),
|
|
65
|
+
}));
|
|
66
|
+
const totalMatched = mapped.filter((r) => r.matched).length;
|
|
67
|
+
ctx.log.info('pubmed_lookup_citation completed', {
|
|
68
|
+
totalMatched,
|
|
69
|
+
totalSubmitted: citations.length,
|
|
70
|
+
});
|
|
71
|
+
return { results: mapped, totalMatched, totalSubmitted: citations.length };
|
|
72
|
+
},
|
|
73
|
+
format: (result) => {
|
|
74
|
+
const lines = [
|
|
75
|
+
`## Citation Lookup Results`,
|
|
76
|
+
`**Matched:** ${result.totalMatched}/${result.totalSubmitted}`,
|
|
77
|
+
'',
|
|
78
|
+
'| Key | PMID | Status |',
|
|
79
|
+
'|:---|:---|:---|',
|
|
80
|
+
];
|
|
81
|
+
for (const r of result.results) {
|
|
82
|
+
const pmid = r.pmid ?? '-';
|
|
83
|
+
const status = r.matched ? 'Matched' : 'No match';
|
|
84
|
+
lines.push(`| ${r.key} | ${pmid} | ${status} |`);
|
|
85
|
+
}
|
|
86
|
+
return [{ type: 'text', text: lines.join('\n') }];
|
|
87
|
+
},
|
|
88
|
+
});
|
|
89
|
+
//# sourceMappingURL=lookup-citation.tool.js.map
|
|
@@ -0,0 +1 @@
|
|
|
1
|
+
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAGjE,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,sPAAsP;IACnQ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;YACvE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACvD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8EAA8E,CAC/E;SACJ,CAAC,CACH;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SAC1D,CAAC,CACH;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YAChC,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;gBACxE,MAAM,IAAI,KAAK,CACb,gHAAgH,CACjH,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,OAAO,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,SAAS,CAAC,CAAC;QAE5D,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjC,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;SAChC,CAAC,CAAC,CAAC;QAEJ,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAC5D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE;YAC/C,YAAY;YACZ,cAAc,EAAE,SAAS,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,cAAc,EAAE,SAAS,CAAC,MAAM,EAAE,CAAC;IAC7E,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,4BAA4B;YAC5B,gBAAgB,MAAM,CAAC,YAAY,IAAI,MAAM,CAAC,cAAc,EAAE;YAC9D,EAAE;YACF,yBAAyB;YACzB,kBAAkB;SACnB,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,MAAM,IAAI,GAAG,CAAC,CAAC,IAAI,IAAI,GAAG,CAAC;YAC3B,MAAM,MAAM,GAAG,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,UAAU,CAAC;YAClD,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,GAAG,MAAM,IAAI,MAAM,MAAM,IAAI,CAAC,CAAC;QACnD,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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|
@@ -22,8 +22,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
22
22
|
.describe('Sort order: relevance (default), pub_date (newest first), author, or journal'),
|
|
23
23
|
dateRange: z
|
|
24
24
|
.object({
|
|
25
|
-
minDate: z.string().describe('Start date (YYYY
|
|
26
|
-
maxDate: z.string().describe('End date (YYYY
|
|
25
|
+
minDate: z.string().describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
|
|
26
|
+
maxDate: z.string().describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
|
|
27
27
|
dateType: z
|
|
28
28
|
.enum(['pdat', 'mdat', 'edat'])
|
|
29
29
|
.default('pdat')
|
|
@@ -74,7 +74,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
74
74
|
ctx.log.info('Executing pubmed_search', { query: input.query });
|
|
75
75
|
const ncbi = getNcbiService();
|
|
76
76
|
let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
|
|
77
|
-
if (input.dateRange) {
|
|
77
|
+
if (input.dateRange?.minDate && input.dateRange?.maxDate) {
|
|
78
78
|
const minDate = input.dateRange.minDate.replace(/-/g, '/');
|
|
79
79
|
const maxDate = input.dateRange.maxDate.replace(/-/g, '/');
|
|
80
80
|
effectiveQuery += ` AND (${minDate}[${input.dateRange.dateType}] : ${maxDate}[${input.dateRange.dateType}])`;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"search-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EACT,8GAA8G;QAC9G,qHAAqH;QACrH,iEAAiE;IACnE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;QACpF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC/F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;aACpD,OAAO,CAAC,WAAW,CAAC;aACpB,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,
|
|
1
|
+
{"version":3,"file":"search-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EACT,8GAA8G;QAC9G,qHAAqH;QACrH,iEAAiE;IACnE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;QACpF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC/F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;aACpD,OAAO,CAAC,WAAW,CAAC;aACpB,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACzE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;YACvE,QAAQ,EAAE,CAAC;iBACR,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;iBAC9B,OAAO,CAAC,MAAM,CAAC;iBACf,QAAQ,CAAC,mEAAmE,CAAC;SACjF,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CAAC,sBAAsB,CAAC;QACnC,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAChF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACjE,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAC1E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC/E,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QACpF,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QACrF,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC/E,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CAAC,0DAA0D,CAAC;KACxE,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC5C,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAC1D,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACjD,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC;QACjD,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;YAClE,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,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;YAC1C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC;YAC/C,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC;YACjD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;SACxD,CAAC,CACH;aACA,QAAQ,CAAC,sDAAsD,CAAC;QACnE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;KACpD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,yBAAyB,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAE9B,IAAI,cAAc,GAAG,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC;QAEzF,IAAI,KAAK,CAAC,SAAS,EAAE,OAAO,IAAI,KAAK,CAAC,SAAS,EAAE,OAAO,EAAE,CAAC;YACzD,MAAM,OAAO,GAAG,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YAC3D,MAAM,OAAO,GAAG,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YAC3D,cAAc,IAAI,SAAS,OAAO,IAAI,KAAK,CAAC,SAAS,CAAC,QAAQ,OAAO,OAAO,IAAI,KAAK,CAAC,SAAS,CAAC,QAAQ,IAAI,CAAC;QAC/G,CAAC;QACD,IAAI,KAAK,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACnC,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,YAAY,CAAC,cAAc,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC,CACzF,CAAC;YACF,MAAM,OAAO,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE,qBAAqB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACnF,cAAc,IAAI,SAAS,OAAO,GAAG,CAAC;QACxC,CAAC;QACD,IAAI,KAAK,CAAC,MAAM;YACd,cAAc,IAAI,QAAQ,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC;QAC3G,IAAI,KAAK,CAAC,OAAO;YACf,cAAc,IAAI,SAAS,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,YAAY,CAAC;QAC/G,IAAI,KAAK,CAAC,SAAS,EAAE,MAAM,EAAE,CAAC;YAC5B,MAAM,cAAc,GAAG,MAAM,OAAO,CAAC,GAAG,CACtC,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,YAAY,CAAC,cAAc,CAAC,IAAI,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC,CACtF,CAAC;YACF,MAAM,SAAS,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,IAAI,eAAe,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,CAAC;YACtF,cAAc,IAAI,SAAS,SAAS,GAAG,CAAC;QAC1C,CAAC;QACD,IAAI,KAAK,CAAC,QAAQ;YAChB,cAAc,IAAI,QAAQ,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,QAAQ,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,YAAY,CAAC;QAC/G,IAAI,KAAK,CAAC,WAAW;YAAE,cAAc,IAAI,6BAA6B,CAAC;QACvE,IAAI,KAAK,CAAC,YAAY;YAAE,cAAc,IAAI,6BAA6B,CAAC;QACxE,IAAI,KAAK,CAAC,OAAO;YAAE,cAAc,IAAI,QAAQ,KAAK,CAAC,OAAO,cAAc,CAAC;QAEzE,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,OAAO,CAAC;YAClC,EAAE,EAAE,QAAQ;YACZ,IAAI,EAAE,cAAc;YACpB,MAAM,EAAE,KAAK,CAAC,UAAU;YACxB,QAAQ,EAAE,KAAK,CAAC,MAAM;YACtB,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,UAAU,EAAE,KAAK,CAAC,YAAY,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,SAAS;SACrD,CAAC,CAAC;QAEH,MAAM,KAAK,GAAG,QAAQ,CAAC,MAAM,CAAC;QAC9B,IAAI,SAAS,GAUP,EAAE,CAAC;QAET,IAAI,KAAK,CAAC,YAAY,GAAG,CAAC,IAAI,KAAK,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC/C,MAAM,cAAc,GAAgD;gBAClE,EAAE,EAAE,QAAQ;gBACZ,OAAO,EAAE,KAAK;gBACd,OAAO,EAAE,KAAK;aACf,CAAC;YACF,IAAI,QAAQ,CAAC,MAAM,IAAI,QAAQ,CAAC,QAAQ,EAAE,CAAC;gBACzC,cAAc,CAAC,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;gBACxC,cAAc,CAAC,SAAS,GAAG,QAAQ,CAAC,QAAQ,CAAC;gBAC7C,cAAc,CAAC,MAAM,GAAG,KAAK,CAAC,YAAY,CAAC;gBAC3C,cAAc,CAAC,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC;YACzC,CAAC;iBAAM,CAAC;gBACN,cAAc,CAAC,EAAE,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACnE,CAAC;YAED,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,cAAc,CAAC,CAAC;YAC3D,IAAI,cAAc,EAAE,CAAC;gBACnB,MAAM,cAAc,GAAG,MAAM,qBAAqB,CAAC,cAAc,CAAC,CAAC;gBACnE,SAAS,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;oBACrC,IAAI,EAAE,CAAC,CAAC,IAAI;oBACZ,KAAK,EAAE,CAAC,CAAC,KAAK;oBACd,OAAO,EAAE,CAAC,CAAC,OAAO;oBAClB,MAAM,EAAE,CAAC,CAAC,MAAM;oBAChB,OAAO,EAAE,CAAC,CAAC,OAAO;oBAClB,GAAG,EAAE,CAAC,CAAC,GAAG;oBACV,KAAK,EAAE,CAAC,CAAC,KAAK;oBACd,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,MAAM,EAAE,6CAA6C,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnF,SAAS,EAAE,mCAAmC,CAAC,CAAC,IAAI,GAAG;iBACxD,CAAC,CAAC,CAAC;YACN,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAG,yCAAyC,kBAAkB,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,yBAAyB,EAAE;YACtC,UAAU,EAAE,QAAQ,CAAC,KAAK;YAC1B,SAAS,EAAE,KAAK,CAAC,MAAM;SACxB,CAAC,CAAC;QACH,OAAO;YACL,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,UAAU,EAAE,QAAQ,CAAC,KAAK;YAC1B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,KAAK;YACL,SAAS;YACT,SAAS;SACV,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,cAAc,MAAM,CAAC,KAAK,EAAE;YAC5B,oBAAoB,MAAM,CAAC,UAAU,oBAAoB,MAAM,CAAC,KAAK,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,EAAE;YAC7G,mBAAmB,MAAM,CAAC,SAAS,EAAE;SACtC,CAAC;QACF,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACnF,IAAI,MAAM,CAAC,SAAS,EAAE,MAAM,EAAE,CAAC;YAC7B,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;YAC9B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;gBACjC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAC1C,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAClC,IAAI,CAAC,CAAC,OAAO;oBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;gBACvD,IAAI,CAAC,CAAC,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;gBACpD,IAAI,CAAC,CAAC,OAAO;oBAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;gBACzD,IAAI,CAAC,CAAC,GAAG;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;gBAC3C,IAAI,CAAC,CAAC,SAAS;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;gBAC1D,IAAI,CAAC,CAAC,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACnD,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"}
|
|
@@ -20,6 +20,13 @@ export declare class NcbiApiClient {
|
|
|
20
20
|
private readonly config;
|
|
21
21
|
constructor(config: NcbiApiClientConfig);
|
|
22
22
|
makeRequest(endpoint: string, params: NcbiRequestParams, options?: NcbiRequestOptions): Promise<string>;
|
|
23
|
+
/**
|
|
24
|
+
* Make a GET request to a non-eutils NCBI endpoint (e.g., PMC ID Converter).
|
|
25
|
+
* Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
|
|
26
|
+
* error status codes — fetchWithTimeout throws before the body can be read.
|
|
27
|
+
* Injects tool and email params but not api_key (eutils-specific).
|
|
28
|
+
*/
|
|
29
|
+
makeExternalRequest(url: string, params: NcbiRequestParams): Promise<string>;
|
|
23
30
|
private buildParams;
|
|
24
31
|
private shouldPost;
|
|
25
32
|
private getRequest;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;
|
|
1
|
+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,OAAO,EAAwB,KAAK,kBAAkB,EAAE,KAAK,iBAAiB,EAAE,MAAM,YAAY,CAAC;AAKnG,MAAM,WAAW,mBAAmB;IAClC,UAAU,CAAC,EAAE,MAAM,CAAC;IACpB,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,SAAS,EAAE,MAAM,CAAC;IAClB,cAAc,EAAE,MAAM,CAAC;CACxB;AAED;;;;GAIG;AACH,qBAAa,aAAa;IACZ,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,mBAAmB;IAElD,WAAW,CACf,QAAQ,EAAE,MAAM,EAChB,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,OAAO,CAAC,MAAM,CAAC;IAqClB;;;;;OAKG;IACG,mBAAmB,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,MAAM,CAAC;IA0ClF,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAOlB,OAAO,CAAC,WAAW;CASpB"}
|
|
@@ -22,7 +22,8 @@ export class NcbiApiClient {
|
|
|
22
22
|
async makeRequest(endpoint, params, options) {
|
|
23
23
|
const finalParams = this.buildParams(params);
|
|
24
24
|
const usePost = this.shouldPost(finalParams, options);
|
|
25
|
-
const
|
|
25
|
+
const suffix = endpoint.includes('.') ? '' : '.fcgi';
|
|
26
|
+
const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
|
|
26
27
|
try {
|
|
27
28
|
logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
|
|
28
29
|
endpoint,
|
|
@@ -31,7 +32,13 @@ export class NcbiApiClient {
|
|
|
31
32
|
? await this.postRequest(url, finalParams)
|
|
32
33
|
: await this.getRequest(url, finalParams);
|
|
33
34
|
if (!response.ok) {
|
|
34
|
-
|
|
35
|
+
const code = response.status >= 400 && response.status < 500
|
|
36
|
+
? JsonRpcErrorCode.InvalidRequest
|
|
37
|
+
: JsonRpcErrorCode.ServiceUnavailable;
|
|
38
|
+
throw new McpError(code, `NCBI API returned HTTP ${response.status}.`, {
|
|
39
|
+
endpoint,
|
|
40
|
+
status: response.status,
|
|
41
|
+
});
|
|
35
42
|
}
|
|
36
43
|
return await response.text();
|
|
37
44
|
}
|
|
@@ -44,6 +51,46 @@ export class NcbiApiClient {
|
|
|
44
51
|
});
|
|
45
52
|
}
|
|
46
53
|
}
|
|
54
|
+
/**
|
|
55
|
+
* Make a GET request to a non-eutils NCBI endpoint (e.g., PMC ID Converter).
|
|
56
|
+
* Uses plain fetch (not fetchWithTimeout) so we can capture response bodies on
|
|
57
|
+
* error status codes — fetchWithTimeout throws before the body can be read.
|
|
58
|
+
* Injects tool and email params but not api_key (eutils-specific).
|
|
59
|
+
*/
|
|
60
|
+
async makeExternalRequest(url, params) {
|
|
61
|
+
const finalParams = {
|
|
62
|
+
tool: this.config.toolIdentifier,
|
|
63
|
+
...(this.config.adminEmail && { email: this.config.adminEmail }),
|
|
64
|
+
};
|
|
65
|
+
for (const [key, value] of Object.entries(params)) {
|
|
66
|
+
if (value != null)
|
|
67
|
+
finalParams[key] = String(value);
|
|
68
|
+
}
|
|
69
|
+
const qs = new URLSearchParams(finalParams).toString();
|
|
70
|
+
const fullUrl = qs ? `${url}?${qs}` : url;
|
|
71
|
+
try {
|
|
72
|
+
logger.debug(`NCBI external request: GET ${fullUrl}`, { url });
|
|
73
|
+
const response = await fetch(fullUrl, {
|
|
74
|
+
signal: AbortSignal.timeout(this.config.timeoutMs),
|
|
75
|
+
});
|
|
76
|
+
const body = await response.text();
|
|
77
|
+
if (!response.ok) {
|
|
78
|
+
const code = response.status >= 400 && response.status < 500
|
|
79
|
+
? JsonRpcErrorCode.InvalidRequest
|
|
80
|
+
: JsonRpcErrorCode.ServiceUnavailable;
|
|
81
|
+
throw new McpError(code, `NCBI API returned HTTP ${response.status}: ${body.substring(0, 300)}`, { url, status: response.status, body: body.substring(0, 500) });
|
|
82
|
+
}
|
|
83
|
+
return body;
|
|
84
|
+
}
|
|
85
|
+
catch (error) {
|
|
86
|
+
if (error instanceof McpError)
|
|
87
|
+
throw error;
|
|
88
|
+
const msg = error instanceof Error ? error.message : String(error);
|
|
89
|
+
throw new McpError(JsonRpcErrorCode.ServiceUnavailable, `NCBI request failed: ${msg}`, {
|
|
90
|
+
url,
|
|
91
|
+
});
|
|
92
|
+
}
|
|
93
|
+
}
|
|
47
94
|
buildParams(params) {
|
|
48
95
|
const raw = {
|
|
49
96
|
tool: this.config.toolIdentifier,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,
|
|
1
|
+
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,GAAG,MAAM,EAAE,CAAC;QAE3D,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EAAE;gBACpE,QAAQ;aACA,CAAC,CAAC;YAEZ,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,CAAC;gBAC1C,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,WAAW,CAAC,CAAC;YAE5C,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,IAAI,GACR,QAAQ,CAAC,MAAM,IAAI,GAAG,IAAI,QAAQ,CAAC,MAAM,GAAG,GAAG;oBAC7C,CAAC,CAAC,gBAAgB,CAAC,cAAc;oBACjC,CAAC,CAAC,gBAAgB,CAAC,kBAAkB,CAAC;gBAC1C,MAAM,IAAI,QAAQ,CAAC,IAAI,EAAE,0BAA0B,QAAQ,CAAC,MAAM,GAAG,EAAE;oBACrE,QAAQ;oBACR,MAAM,EAAE,QAAQ,CAAC,MAAM;iBACxB,CAAC,CAAC;YACL,CAAC;YAED,OAAO,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAE3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,QAAQ;aACT,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,mBAAmB,CAAC,GAAW,EAAE,MAAyB;QAC9D,MAAM,WAAW,GAA2B;YAC1C,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,CAAC;SACjE,CAAC;QACF,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;YAClD,IAAI,KAAK,IAAI,IAAI;gBAAE,WAAW,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;QACtD,CAAC;QAED,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC;QACvD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAE1C,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,8BAA8B,OAAO,EAAE,EAAE,EAAE,GAAG,EAAW,CAAC,CAAC;YACxE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,EAAE;gBACpC,MAAM,EAAE,WAAW,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC;aACnD,CAAC,CAAC;YAEH,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAEnC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,MAAM,IAAI,GACR,QAAQ,CAAC,MAAM,IAAI,GAAG,IAAI,QAAQ,CAAC,MAAM,GAAG,GAAG;oBAC7C,CAAC,CAAC,gBAAgB,CAAC,cAAc;oBACjC,CAAC,CAAC,gBAAgB,CAAC,kBAAkB,CAAC;gBAC1C,MAAM,IAAI,QAAQ,CAChB,IAAI,EACJ,0BAA0B,QAAQ,CAAC,MAAM,KAAK,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EACtE,EAAE,GAAG,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC/D,CAAC;YACJ,CAAC;YAED,OAAO,IAAI,CAAC;QACd,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAC3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,GAAG;aACJ,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAEO,WAAW,CAAC,MAAyB;QAC3C,MAAM,GAAG,GAAgD;YACvD,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU;YAC7B,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM;YAC3B,GAAG,MAAM;SACV,CAAC;QAEF,MAAM,MAAM,GAA2B,EAAE,CAAC;QAC1C,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;gBAClB,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEO,UAAU,CAAC,MAA8B,EAAE,OAA4B;QAC7E,IAAI,OAAO,EAAE,OAAO;YAAE,OAAO,IAAI,CAAC;QAClC,MAAM,WAAW,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAC3D,OAAO,WAAW,CAAC,MAAM,GAAG,cAAc,CAAC;IAC7C,CAAC;IAEO,UAAU,CAAC,GAAW,EAAE,MAA8B;QAC5D,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAClD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAC1C,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC;QAC/F,OAAO,gBAAgB,CAAC,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,CAAC,CAAC;IAC/D,CAAC;IAEO,WAAW,CAAC,GAAW,EAAE,MAA8B;QAC7D,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QACpD,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,CAAC;QACvF,OAAO,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE;YACvD,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;SACL,CAAC,CAAC;IACL,CAAC;CACF"}
|
|
@@ -7,7 +7,7 @@
|
|
|
7
7
|
import { NcbiApiClient } from './api-client.js';
|
|
8
8
|
import { NcbiRequestQueue } from './request-queue.js';
|
|
9
9
|
import { NcbiResponseHandler } from './response-handler.js';
|
|
10
|
-
import type
|
|
10
|
+
import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
|
|
11
11
|
/**
|
|
12
12
|
* Facade over NCBI's E-utility suite. Each public method corresponds to a
|
|
13
13
|
* single E-utility endpoint.
|
|
@@ -26,6 +26,21 @@ export declare class NcbiService {
|
|
|
26
26
|
eLink<T = Record<string, unknown>>(params: NcbiRequestParams): Promise<T>;
|
|
27
27
|
eSpell(params: NcbiRequestParams): Promise<ESpellResult>;
|
|
28
28
|
eInfo(params: NcbiRequestParams): Promise<unknown>;
|
|
29
|
+
/**
|
|
30
|
+
* Look up PMIDs from partial citation strings via NCBI ECitMatch.
|
|
31
|
+
* Each citation can include journal, year, volume, first page, and author name.
|
|
32
|
+
*/
|
|
33
|
+
eCitMatch(citations: ECitMatchCitation[]): Promise<ECitMatchResult[]>;
|
|
34
|
+
/**
|
|
35
|
+
* Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
|
|
36
|
+
* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
|
|
37
|
+
*/
|
|
38
|
+
idConvert(ids: string[], idtype?: string): Promise<IdConvertRecord[]>;
|
|
39
|
+
/**
|
|
40
|
+
* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
|
|
41
|
+
* Non-transient errors (validation, serialization) fail immediately.
|
|
42
|
+
*/
|
|
43
|
+
private withRetry;
|
|
29
44
|
/**
|
|
30
45
|
* Enqueues a request with retry logic that covers both HTTP-level failures
|
|
31
46
|
* (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,KAAK,
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAEpB,KAAK,aAAa,EAElB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;gBAHV,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM;IAG/B,OAAO,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,aAAa,CAAC;IAmB1D,QAAQ,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,cAAc,CAAC;IAQlE,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC;IAMb,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAAE,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,CAAC,CAAC;IAInE,MAAM,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,YAAY,CAAC;IAsB9D,KAAK,CAAC,MAAM,EAAE,iBAAiB,GAAG,OAAO,CAAC,OAAO,CAAC;IAIlD;;;OAGG;IACG,SAAS,CAAC,SAAS,EAAE,iBAAiB,EAAE,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA6B3E;;;OAGG;IACG,SAAS,CAAC,GAAG,EAAE,MAAM,EAAE,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,OAAO,CAAC,eAAe,EAAE,CAAC;IA+B3E;;;OAGG;YACW,SAAS;IAuCvB;;;;;OAKG;IACH,OAAO,CAAC,cAAc;CAevB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAgBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
|
@@ -10,6 +10,7 @@ import { getServerConfig } from '../../config/server-config.js';
|
|
|
10
10
|
import { NcbiApiClient } from './api-client.js';
|
|
11
11
|
import { NcbiRequestQueue } from './request-queue.js';
|
|
12
12
|
import { NcbiResponseHandler } from './response-handler.js';
|
|
13
|
+
import { NCBI_PMC_IDCONV_URL, } from './types.js';
|
|
13
14
|
/**
|
|
14
15
|
* Facade over NCBI's E-utility suite. Each public method corresponds to a
|
|
15
16
|
* single E-utility endpoint.
|
|
@@ -77,6 +78,79 @@ export class NcbiService {
|
|
|
77
78
|
eInfo(params) {
|
|
78
79
|
return this.performRequest('einfo', params, { retmode: 'xml' });
|
|
79
80
|
}
|
|
81
|
+
/**
|
|
82
|
+
* Look up PMIDs from partial citation strings via NCBI ECitMatch.
|
|
83
|
+
* Each citation can include journal, year, volume, first page, and author name.
|
|
84
|
+
*/
|
|
85
|
+
async eCitMatch(citations) {
|
|
86
|
+
const bdata = citations
|
|
87
|
+
.map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
|
|
88
|
+
.join('\r');
|
|
89
|
+
const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text' });
|
|
90
|
+
return text
|
|
91
|
+
.split(/[\r\n]+/)
|
|
92
|
+
.filter((line) => line.trim().length > 0)
|
|
93
|
+
.map((line) => {
|
|
94
|
+
const parts = line.split('|');
|
|
95
|
+
const key = parts[5]?.trim() ?? '';
|
|
96
|
+
const pmidField = parts[6]?.trim() ?? '';
|
|
97
|
+
const pmid = pmidField && !pmidField.startsWith('NOT_FOUND') && !pmidField.startsWith('AMBIGUOUS')
|
|
98
|
+
? pmidField
|
|
99
|
+
: null;
|
|
100
|
+
return { key, matched: pmid !== null, pmid };
|
|
101
|
+
});
|
|
102
|
+
}
|
|
103
|
+
/**
|
|
104
|
+
* Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
|
|
105
|
+
* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
|
|
106
|
+
*/
|
|
107
|
+
async idConvert(ids, idtype) {
|
|
108
|
+
const params = {
|
|
109
|
+
ids: ids.join(','),
|
|
110
|
+
format: 'json',
|
|
111
|
+
...(idtype && { idtype }),
|
|
112
|
+
};
|
|
113
|
+
const text = await this.queue.enqueue(() => this.withRetry(() => this.apiClient.makeExternalRequest(NCBI_PMC_IDCONV_URL, params), 'idconv'), 'idconv', params);
|
|
114
|
+
let parsed;
|
|
115
|
+
try {
|
|
116
|
+
parsed = JSON.parse(text);
|
|
117
|
+
}
|
|
118
|
+
catch {
|
|
119
|
+
throw new McpError(JsonRpcErrorCode.SerializationError, 'Failed to parse ID Converter JSON response.', { responseSnippet: text.substring(0, 200) });
|
|
120
|
+
}
|
|
121
|
+
return parsed.records ?? [];
|
|
122
|
+
}
|
|
123
|
+
/**
|
|
124
|
+
* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout).
|
|
125
|
+
* Non-transient errors (validation, serialization) fail immediately.
|
|
126
|
+
*/
|
|
127
|
+
async withRetry(execute, label) {
|
|
128
|
+
for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
|
|
129
|
+
try {
|
|
130
|
+
return await execute();
|
|
131
|
+
}
|
|
132
|
+
catch (error) {
|
|
133
|
+
if (error instanceof McpError) {
|
|
134
|
+
if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
|
|
135
|
+
error.code !== JsonRpcErrorCode.Timeout) {
|
|
136
|
+
throw error;
|
|
137
|
+
}
|
|
138
|
+
}
|
|
139
|
+
if (attempt < this.maxRetries) {
|
|
140
|
+
const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
|
|
141
|
+
logger.warning(`NCBI request to ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint: label, attempt: attempt + 1, retryDelay });
|
|
142
|
+
await new Promise((r) => setTimeout(r, retryDelay));
|
|
143
|
+
continue;
|
|
144
|
+
}
|
|
145
|
+
const attempts = this.maxRetries + 1;
|
|
146
|
+
const msg = error instanceof Error ? error.message : String(error);
|
|
147
|
+
throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint: label, attempts });
|
|
148
|
+
}
|
|
149
|
+
}
|
|
150
|
+
throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
|
|
151
|
+
endpoint: label,
|
|
152
|
+
});
|
|
153
|
+
}
|
|
80
154
|
/**
|
|
81
155
|
* Enqueues a request with retry logic that covers both HTTP-level failures
|
|
82
156
|
* (network errors, timeouts) and XML-level errors (NCBI returning 200 OK
|
|
@@ -84,38 +158,10 @@ export class NcbiService {
|
|
|
84
158
|
* surfaced as C++ exception traces).
|
|
85
159
|
*/
|
|
86
160
|
performRequest(endpoint, params, options) {
|
|
87
|
-
return this.queue.enqueue(async () => {
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
|
|
92
|
-
}
|
|
93
|
-
catch (error) {
|
|
94
|
-
// Only retry transient errors (ServiceUnavailable, Timeout).
|
|
95
|
-
// Validation, serialization, and other errors fail immediately.
|
|
96
|
-
if (error instanceof McpError) {
|
|
97
|
-
if (error.code !== JsonRpcErrorCode.ServiceUnavailable &&
|
|
98
|
-
error.code !== JsonRpcErrorCode.Timeout) {
|
|
99
|
-
throw error;
|
|
100
|
-
}
|
|
101
|
-
}
|
|
102
|
-
if (attempt < this.maxRetries) {
|
|
103
|
-
const retryDelay = 1000 * 2 ** attempt; // 1s, 2s, 4s
|
|
104
|
-
logger.warning(`NCBI request to ${endpoint} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, { endpoint, attempt: attempt + 1, retryDelay });
|
|
105
|
-
await new Promise((r) => setTimeout(r, retryDelay));
|
|
106
|
-
continue;
|
|
107
|
-
}
|
|
108
|
-
// Final attempt exhausted — surface retry context so the caller
|
|
109
|
-
// knows this wasn't a single failed request.
|
|
110
|
-
const attempts = this.maxRetries + 1;
|
|
111
|
-
const msg = error instanceof Error ? error.message : String(error);
|
|
112
|
-
throw new McpError(error instanceof McpError ? error.code : JsonRpcErrorCode.ServiceUnavailable, `${msg} (failed after ${attempts} attempts)`, { endpoint, attempts });
|
|
113
|
-
}
|
|
114
|
-
}
|
|
115
|
-
throw new McpError(JsonRpcErrorCode.InternalError, 'Request failed after all retries.', {
|
|
116
|
-
endpoint,
|
|
117
|
-
});
|
|
118
|
-
}, endpoint, params);
|
|
161
|
+
return this.queue.enqueue(() => this.withRetry(async () => {
|
|
162
|
+
const text = await this.apiClient.makeRequest(endpoint, params, options);
|
|
163
|
+
return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
|
|
164
|
+
}, endpoint), endpoint, params);
|
|
119
165
|
}
|
|
120
166
|
}
|
|
121
167
|
// ─── Init / Accessor ────────────────────────────────────────────────────────
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.js","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;
|
|
1
|
+
{"version":3,"file":"ncbi-service.js","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,MAAM,EAAE,MAAM,8BAA8B,CAAC;AAEtD,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,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,EAWL,mBAAmB,GAIpB,MAAM,YAAY,CAAC;AAEpB;;;GAGG;AACH,MAAM,OAAO,WAAW;IAEH;IACA;IACA;IACA;IAJnB,YACmB,SAAwB,EACxB,KAAuB,EACvB,eAAoC,EACpC,UAAkB;QAHlB,cAAS,GAAT,SAAS,CAAe;QACxB,UAAK,GAAL,KAAK,CAAkB;QACvB,oBAAe,GAAf,eAAe,CAAqB;QACpC,eAAU,GAAV,UAAU,CAAQ;IAClC,CAAC;IAEJ,KAAK,CAAC,OAAO,CAAC,MAAyB;QACrC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA2B,SAAS,EAAE,MAAM,EAAE;YACtF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,QAAQ,GAAG,QAAQ,CAAC,aAAa,CAAC;QACxC,OAAO;YACL,KAAK,EAAE,QAAQ,CAAC,QAAQ,CAAC,KAAK,EAAE,EAAE,CAAC,IAAI,CAAC;YACxC,MAAM,EAAE,QAAQ,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,IAAI,CAAC;YAC1C,QAAQ,EAAE,QAAQ,CAAC,QAAQ,CAAC,QAAQ,EAAE,EAAE,CAAC,IAAI,CAAC;YAC9C,GAAG,CAAC,QAAQ,CAAC,QAAQ,KAAK,SAAS,IAAI,EAAE,QAAQ,EAAE,QAAQ,CAAC,QAAQ,EAAE,CAAC;YACvE,GAAG,CAAC,QAAQ,CAAC,MAAM,KAAK,SAAS,IAAI,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,CAAC;YACjE,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,EAAE,EAAE,IAAI,EAAE,CAAC,CAAC,GAAG,CAAC,MAAM,CAAC;YAC/C,gBAAgB,EAAE,QAAQ,CAAC,gBAAgB;YAC3C,GAAG,CAAC,QAAQ,CAAC,SAAS,KAAK,SAAS,IAAI,EAAE,SAAS,EAAE,QAAQ,CAAC,SAAS,EAAE,CAAC;YAC1E,GAAG,CAAC,QAAQ,CAAC,WAAW,KAAK,SAAS,IAAI,EAAE,WAAW,EAAE,QAAQ,CAAC,WAAW,EAAE,CAAC;SACjF,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,QAAQ,CAAC,MAAyB;QACtC,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,KAAK,KAAK,IAAI,MAAM,CAAC,OAAO,KAAK,MAAM,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,CAAC;QACvF,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA4B,UAAU,EAAE,MAAM,EAAE;YACxF,OAAO;SACR,CAAC,CAAC;QACH,OAAO,QAAQ,CAAC,cAAc,CAAC;IACjC,CAAC;IAED,MAAM,CACJ,MAAyB,EACzB,UAA8B,EAAE,OAAO,EAAE,KAAK,EAAE;QAEhD,MAAM,OAAO,GACX,OAAO,CAAC,OAAO,IAAI,CAAC,OAAO,MAAM,CAAC,EAAE,KAAK,QAAQ,IAAI,MAAM,CAAC,EAAE,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,MAAM,GAAG,GAAG,CAAC,CAAC;QAC1F,OAAO,IAAI,CAAC,cAAc,CAAI,QAAQ,EAAE,MAAM,EAAE,EAAE,GAAG,OAAO,EAAE,OAAO,EAAE,CAAC,CAAC;IAC3E,CAAC;IAED,KAAK,CAA8B,MAAyB;QAC1D,OAAO,IAAI,CAAC,cAAc,CAAI,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IACrE,CAAC;IAED,KAAK,CAAC,MAAM,CAAC,MAAyB;QACpC,MAAM,QAAQ,GAAG,MAAM,IAAI,CAAC,cAAc,CAA0B,QAAQ,EAAE,MAAM,EAAE;YACpF,OAAO,EAAE,KAAK;SACf,CAAC,CAAC;QAEH,MAAM,WAAW,GAAG,QAAQ,CAAC,YAAY,CAAC;QAC1C,MAAM,QAAQ,GAAG,WAAW,CAAC,KAAK,IAAK,MAAM,CAAC,IAAe,IAAI,EAAE,CAAC;QACpE,MAAM,SAAS,GAAG,WAAW,CAAC,cAAc,IAAI,EAAE,CAAC;QAEnD,MAAM,CAAC,KAAK,CAAC,uBAAuB,EAAE;YACpC,QAAQ;YACR,SAAS;YACT,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SACrD,CAAC,CAAC;QAEZ,OAAO;YACL,QAAQ;YACR,SAAS,EAAE,SAAS,IAAI,QAAQ;YAChC,aAAa,EAAE,SAAS,CAAC,MAAM,GAAG,CAAC,IAAI,SAAS,KAAK,QAAQ;SAC9D,CAAC;IACJ,CAAC;IAED,KAAK,CAAC,MAAyB;QAC7B,OAAO,IAAI,CAAC,cAAc,CAAC,OAAO,EAAE,MAAM,EAAE,EAAE,OAAO,EAAE,KAAK,EAAE,CAAC,CAAC;IAClE,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,SAA8B;QAC5C,MAAM,KAAK,GAAG,SAAS;aACpB,GAAG,CACF,CAAC,CAAC,EAAE,EAAE,CACJ,GAAG,CAAC,CAAC,OAAO,IAAI,EAAE,IAAI,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,CAAC,CAAC,MAAM,IAAI,EAAE,IAAI,CAAC,CAAC,SAAS,IAAI,EAAE,IAAI,CAAC,CAAC,UAAU,IAAI,EAAE,IAAI,CAAC,CAAC,GAAG,GAAG,CAC9G;aACA,IAAI,CAAC,IAAI,CAAC,CAAC;QAEd,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,cAAc,CACpC,eAAe,EACf,EAAE,EAAE,EAAE,QAAQ,EAAE,OAAO,EAAE,KAAK,EAAE,KAAK,EAAE,EACvC,EAAE,OAAO,EAAE,MAAM,EAAE,CACpB,CAAC;QAEF,OAAO,IAAI;aACR,KAAK,CAAC,SAAS,CAAC;aAChB,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC;aACxC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE;YACZ,MAAM,KAAK,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YAC9B,MAAM,GAAG,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YACnC,MAAM,SAAS,GAAG,KAAK,CAAC,CAAC,CAAC,EAAE,IAAI,EAAE,IAAI,EAAE,CAAC;YACzC,MAAM,IAAI,GACR,SAAS,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,WAAW,CAAC,IAAI,CAAC,SAAS,CAAC,UAAU,CAAC,WAAW,CAAC;gBACnF,CAAC,CAAC,SAAS;gBACX,CAAC,CAAC,IAAI,CAAC;YACX,OAAO,EAAE,GAAG,EAAE,OAAO,EAAE,IAAI,KAAK,IAAI,EAAE,IAAI,EAAE,CAAC;QAC/C,CAAC,CAAC,CAAC;IACP,CAAC;IAED;;;OAGG;IACH,KAAK,CAAC,SAAS,CAAC,GAAa,EAAE,MAAe;QAC5C,MAAM,MAAM,GAAsB;YAChC,GAAG,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC;YAClB,MAAM,EAAE,MAAM;YACd,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC;QAEF,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,KAAK,CAAC,OAAO,CACnC,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CACZ,GAAG,EAAE,CAAC,IAAI,CAAC,SAAS,CAAC,mBAAmB,CAAC,mBAAmB,EAAE,MAAM,CAAC,EACrE,QAAQ,CACT,EACH,QAAQ,EACR,MAAM,CACP,CAAC;QAEF,IAAI,MAAe,CAAC;QACpB,IAAI,CAAC;YACH,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC;QAC5B,CAAC;QAAC,MAAM,CAAC;YACP,MAAM,IAAI,QAAQ,CAChB,gBAAgB,CAAC,kBAAkB,EACnC,6CAA6C,EAC7C,EAAE,eAAe,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC5C,CAAC;QACJ,CAAC;QAED,OAAQ,MAA4B,CAAC,OAAO,IAAI,EAAE,CAAC;IACrD,CAAC;IAED;;;OAGG;IACK,KAAK,CAAC,SAAS,CAAI,OAAyB,EAAE,KAAa;QACjE,KAAK,IAAI,OAAO,GAAG,CAAC,EAAE,OAAO,IAAI,IAAI,CAAC,UAAU,EAAE,OAAO,EAAE,EAAE,CAAC;YAC5D,IAAI,CAAC;gBACH,OAAO,MAAM,OAAO,EAAE,CAAC;YACzB,CAAC;YAAC,OAAO,KAAc,EAAE,CAAC;gBACxB,IAAI,KAAK,YAAY,QAAQ,EAAE,CAAC;oBAC9B,IACE,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,kBAAkB;wBAClD,KAAK,CAAC,IAAI,KAAK,gBAAgB,CAAC,OAAO,EACvC,CAAC;wBACD,MAAM,KAAK,CAAC;oBACd,CAAC;gBACH,CAAC;gBAED,IAAI,OAAO,GAAG,IAAI,CAAC,UAAU,EAAE,CAAC;oBAC9B,MAAM,UAAU,GAAG,IAAI,GAAG,CAAC,IAAI,OAAO,CAAC,CAAC,aAAa;oBACrD,MAAM,CAAC,OAAO,CACZ,mBAAmB,KAAK,sBAAsB,OAAO,GAAG,CAAC,IAAI,IAAI,CAAC,UAAU,QAAQ,UAAU,KAAK,EACnG,EAAE,QAAQ,EAAE,KAAK,EAAE,OAAO,EAAE,OAAO,GAAG,CAAC,EAAE,UAAU,EAAW,CAC/D,CAAC;oBACF,MAAM,IAAI,OAAO,CAAO,CAAC,CAAC,EAAE,EAAE,CAAC,UAAU,CAAC,CAAC,EAAE,UAAU,CAAC,CAAC,CAAC;oBAC1D,SAAS;gBACX,CAAC;gBAED,MAAM,QAAQ,GAAG,IAAI,CAAC,UAAU,GAAG,CAAC,CAAC;gBACrC,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;gBACnE,MAAM,IAAI,QAAQ,CAChB,KAAK,YAAY,QAAQ,CAAC,CAAC,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,gBAAgB,CAAC,kBAAkB,EAC5E,GAAG,GAAG,kBAAkB,QAAQ,YAAY,EAC5C,EAAE,QAAQ,EAAE,KAAK,EAAE,QAAQ,EAAE,CAC9B,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,aAAa,EAAE,mCAAmC,EAAE;YACtF,QAAQ,EAAE,KAAK;SAChB,CAAC,CAAC;IACL,CAAC;IAED;;;;;OAKG;IACK,cAAc,CACpB,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,OAAO,IAAI,CAAC,KAAK,CAAC,OAAO,CACvB,GAAG,EAAE,CACH,IAAI,CAAC,SAAS,CAAC,KAAK,IAAI,EAAE;YACxB,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,WAAW,CAAC,QAAQ,EAAE,MAAM,EAAE,OAAO,CAAC,CAAC;YACzE,OAAO,IAAI,CAAC,eAAe,CAAC,sBAAsB,CAAI,IAAI,EAAE,QAAQ,EAAE,OAAO,CAAC,CAAC;QACjF,CAAC,EAAE,QAAQ,CAAC,EACd,QAAQ,EACR,MAAM,CACP,CAAC;IACJ,CAAC;CACF;AAED,+EAA+E;AAE/E,IAAI,QAAiC,CAAC;AAEtC,qEAAqE;AACrE,MAAM,UAAU,eAAe;IAC7B,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;IACjC,MAAM,SAAS,GAAG,IAAI,aAAa,CAAC;QAClC,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,SAAS,EAAE,MAAM,CAAC,SAAS;QAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC;QAC/C,GAAG,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,UAAU,EAAE,MAAM,CAAC,UAAU,EAAE,CAAC;KAC5D,CAAC,CAAC;IACH,MAAM,KAAK,GAAG,IAAI,gBAAgB,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC;IAC1D,MAAM,eAAe,GAAG,IAAI,mBAAmB,EAAE,CAAC;IAClD,QAAQ,GAAG,IAAI,WAAW,CAAC,SAAS,EAAE,KAAK,EAAE,eAAe,EAAE,MAAM,CAAC,UAAU,CAAC,CAAC;IACjF,MAAM,CAAC,IAAI,CAAC,2BAA2B,EAAE;QACvC,cAAc,EAAE,MAAM,CAAC,cAAc;QACrC,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,MAAM;QAC1B,cAAc,EAAE,MAAM,CAAC,cAAc;KAC7B,CAAC,CAAC;AACd,CAAC;AAED,mEAAmE;AACnE,MAAM,UAAU,cAAc;IAC5B,IAAI,CAAC,QAAQ;QAAE,MAAM,IAAI,KAAK,CAAC,6DAA6D,CAAC,CAAC;IAC9F,OAAO,QAAQ,CAAC;AAClB,CAAC"}
|
|
@@ -5,6 +5,8 @@
|
|
|
5
5
|
*/
|
|
6
6
|
/** Base URL for all NCBI E-utility endpoints. */
|
|
7
7
|
export declare const NCBI_EUTILS_BASE_URL = "https://eutils.ncbi.nlm.nih.gov/entrez/eutils";
|
|
8
|
+
/** Base URL for the PMC ID Converter API (separate from E-utilities). */
|
|
9
|
+
export declare const NCBI_PMC_IDCONV_URL = "https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/";
|
|
8
10
|
/**
|
|
9
11
|
* Common NCBI E-utility request parameters.
|
|
10
12
|
* Specific endpoints extend this with their own fields via the index signature.
|
|
@@ -593,4 +595,50 @@ export interface ParsedPmcReference {
|
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593
595
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id?: string;
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594
596
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label?: string;
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595
597
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}
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598
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+
/** Single citation for ECitMatch lookup. */
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599
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+
export interface ECitMatchCitation {
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600
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+
/** Author name (e.g., "mann bj") */
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601
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+
authorName?: string | undefined;
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602
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+
/** First page number */
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603
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+
firstPage?: string | undefined;
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604
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+
/** Journal title or ISO abbreviation */
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605
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+
journal?: string | undefined;
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606
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+
/** Arbitrary key for tracking this citation in results */
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607
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+
key: string;
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608
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+
/** Volume number */
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609
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+
volume?: string | undefined;
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610
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+
/** Publication year */
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611
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+
year?: string | undefined;
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612
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+
}
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613
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+
/** Single result from ECitMatch lookup. */
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614
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+
export interface ECitMatchResult {
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615
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+
/** The tracking key from the input citation */
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616
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+
key: string;
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617
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+
/** Whether a PMID was found */
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618
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+
matched: boolean;
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619
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+
/** Matched PubMed ID, or null if no match */
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620
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pmid: string | null;
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621
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+
}
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622
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+
/** Single record from the PMC ID Converter API response. */
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623
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+
export interface IdConvertRecord {
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624
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+
/** Digital Object Identifier */
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625
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+
doi?: string;
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626
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+
/** Error message if conversion failed for this ID */
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627
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+
errmsg?: string;
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628
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+
/** PubMed Central ID (e.g., "PMC1234567") */
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629
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+
pmcid?: string;
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630
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+
/** PubMed ID (numeric string) */
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631
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+
pmid?: string;
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632
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+
/** The ID that was originally requested */
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633
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+
'requested-id': string;
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634
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+
/** Record-level status: present only on error records */
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635
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+
status?: string;
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636
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+
}
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637
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+
/** JSON response from the PMC ID Converter API. */
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638
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+
export interface IdConvertResponse {
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639
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+
records: IdConvertRecord[];
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640
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+
request: Record<string, unknown>;
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641
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+
'response-date': string;
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642
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+
status: string;
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643
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+
}
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596
644
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//# sourceMappingURL=types.d.ts.map
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@@ -1 +1 @@
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1
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-
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1
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+
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@@ -6,4 +6,6 @@
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6
6
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// ─── NCBI API Constants & Request Types ─────────────────────────────────────
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7
7
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/** Base URL for all NCBI E-utility endpoints. */
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8
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export const NCBI_EUTILS_BASE_URL = 'https://eutils.ncbi.nlm.nih.gov/entrez/eutils';
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9
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+
/** Base URL for the PMC ID Converter API (separate from E-utilities). */
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10
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+
export const NCBI_PMC_IDCONV_URL = 'https://pmc.ncbi.nlm.nih.gov/tools/idconv/api/v1/articles/';
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9
11
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//# sourceMappingURL=types.js.map
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@@ -1 +1 @@
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1
|
-
{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/ncbi/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,+EAA+E;AAE/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,oBAAoB,GAAG,+CAA+C,CAAC"}
|
|
1
|
+
{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/ncbi/types.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,+EAA+E;AAE/E,iDAAiD;AACjD,MAAM,CAAC,MAAM,oBAAoB,GAAG,+CAA+C,CAAC;AAEpF,yEAAyE;AACzE,MAAM,CAAC,MAAM,mBAAmB,GAAG,4DAA4D,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.
|
|
3
|
+
"version": "2.3.1",
|
|
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",
|
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
|
+
"version": "2.3.1",
|
|
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.
|
|
22
|
+
"version": "2.3.1",
|
|
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.
|
|
63
|
+
"version": "2.3.1",
|
|
64
64
|
"packageArguments": [
|
|
65
65
|
{
|
|
66
66
|
"type": "positional",
|