@cyanheads/pubmed-mcp-server 2.3.7 → 2.3.8

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (7) hide show
  1. package/CLAUDE.md +1 -1
  2. package/README.md +1 -1
  3. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
  4. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +5 -31
  5. package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
  6. package/package.json +2 -2
  7. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** @cyanheads/pubmed-mcp-server
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- **Version:** 2.3.7
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+ **Version:** 2.3.8
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.3.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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+ [![npm](https://img.shields.io/npm/v/@cyanheads/pubmed-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [![Version](https://img.shields.io/badge/Version-2.3.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.27.1-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
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  [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.2-blueviolet.svg?style=flat-square)](https://bun.sh/)
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package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map CHANGED
@@ -1 +1 @@
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- {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8FjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAiO5B,CAAC"}
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+ {"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgDjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAiO5B,CAAC"}
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js CHANGED
@@ -7,41 +7,15 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
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  import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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  import { parsePmcArticle } from '../../../services/ncbi/parsing/pmc-article-parser.js';
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  import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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- function extractLinkId(field) {
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- if (field === undefined || field === null)
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- return '';
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- if (typeof field === 'object')
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- return field['#text'] !== undefined ? String(field['#text']) : '';
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- return String(field);
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- }
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  function normalizePmcId(id) {
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  return id.replace(/^PMC/i, '');
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  }
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  async function resolvePmidsToPmcIds(pmids) {
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- const eLinkResult = (await getNcbiService().eLink({
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- cmd: 'neighbor',
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- db: 'pmc',
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- dbfrom: 'pubmed',
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- id: pmids.join(','),
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- linkname: 'pubmed_pmc',
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- retmode: 'xml',
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- }));
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+ const records = await getNcbiService().idConvert(pmids, 'pmid');
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  const resolved = new Map();
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- for (const result of ensureArray(eLinkResult?.eLinkResult)) {
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- if (result?.ERROR)
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- continue;
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- const linkSet = result?.LinkSet;
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- if (!linkSet?.LinkSetDb)
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- continue;
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- const linkSetDbArray = ensureArray(linkSet.LinkSetDb);
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- const pmcLinkSet = linkSetDbArray.find((db) => db.LinkName === 'pubmed_pmc') ?? linkSetDbArray[0];
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- if (pmcLinkSet?.Link) {
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- const sourcePmid = extractLinkId(linkSet.IdList?.Id);
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- for (const link of ensureArray(pmcLinkSet.Link)) {
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- const pmcId = extractLinkId(link.Id);
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- if (pmcId && sourcePmid)
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- resolved.set(sourcePmid, pmcId);
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- }
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+ for (const record of records) {
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+ if (record.pmid !== undefined && record.pmcid) {
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+ resolved.set(String(record.pmid), normalizePmcId(String(record.pmcid)));
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  }
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  }
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  return { resolved, unavailable: pmids.filter((pmid) => !resolved.has(pmid)) };
@@ -63,7 +37,7 @@ const SectionSchema = z.object({
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  subsections: z.array(SubsectionSchema).optional().describe('Nested subsections'),
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  });
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  export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
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- description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via ELink).',
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+ description: 'Fetch full-text articles from PubMed Central (PMC). Returns complete article body text, sections, and references for open-access articles. Accepts PMC IDs directly or PubMed IDs (auto-resolved via the PMC ID Converter).',
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  annotations: { readOnlyHint: true, openWorldHint: true },
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  input: z.object({
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  pmcids: z
package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED
@@ -1 +1 @@
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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.3.7",
3
+ "version": "2.3.8",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
6
6
  "type": "module",
@@ -67,7 +67,7 @@
67
67
  "access": "public"
68
68
  },
69
69
  "dependencies": {
70
- "@cyanheads/mcp-ts-core": "^0.3.7",
70
+ "@cyanheads/mcp-ts-core": "^0.4.1",
71
71
  "fast-xml-parser": "^5.7.1",
72
72
  "pino-pretty": "^13.1.3",
73
73
  "sanitize-html": "^2.17.3"
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.3.7",
9
+ "version": "2.3.8",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.3.7",
22
+ "version": "2.3.8",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -60,7 +60,7 @@
60
60
  "registryBaseUrl": "https://registry.npmjs.org",
61
61
  "identifier": "@cyanheads/pubmed-mcp-server",
62
62
  "runtimeHint": "bun",
63
- "version": "2.3.7",
63
+ "version": "2.3.8",
64
64
  "packageArguments": [
65
65
  {
66
66
  "type": "positional",