@cyanheads/pubmed-mcp-server 2.6.1 → 2.6.3
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CLAUDE.md +2 -2
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +7 -7
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +4 -6
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/package.json +3 -3
- package/server.json +3 -3
package/CLAUDE.md
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@@ -1,7 +1,7 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.6.
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**Version:** 2.6.3
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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@@ -301,7 +301,7 @@ import { getNcbiService } from '@/services/ncbi/ncbi-service.js';
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## Checklist
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- [ ] Zod schemas: all fields have `.describe()`, only JSON-Schema-serializable types (no `z.custom()`, `z.date()`, `z.transform()`, `z.bigint()`, `z.symbol()`, `z.void()`, `z.map()`, `z.set()`, `z.function()`, `z.nan()`)
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- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`)
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- [ ] Optional nested objects: handler guards for empty inner values from form-based clients (`if (input.obj?.field && ...)`, not just `if (input.obj)`). When regex/length constraints matter, use `z.union([z.literal(''), z.string().regex(...).describe(...)])` — literal variants are exempt from `describe-on-fields`.
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- [ ] JSDoc `@fileoverview` + `@module` on every file
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- [ ] `ctx.log` for logging, `ctx.state` for storage
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- [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
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package/README.md
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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@@ -1 +1 @@
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{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgL/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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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;;;;;;;GAOG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgL/D,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAkO5B,CAAC"}
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@@ -148,19 +148,20 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/fetch-fulltext.tool.ts',
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input: z
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input: z
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.object({
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pmcids: z
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.array(z.string())
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.min(1)
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.max(10)
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.optional()
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.describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide
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.describe('PMC IDs to fetch (e.g. ["PMC9575052"]). Provide exactly one of `pmcids` or `pmids`.'),
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pmids: z
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.array(pmidStringSchema)
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.min(1)
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.max(10)
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.optional()
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.describe('PubMed IDs. Articles in PMC are returned as structured JATS
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.describe('PubMed IDs. Provide exactly one of `pmcids` or `pmids`. Articles in PMC are returned as structured JATS; articles not in PMC are retrieved from Unpaywall when UNPAYWALL_EMAIL is set and a DOI is available.'),
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includeReferences: z
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.boolean()
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.default(false)
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.array(z.string())
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.optional()
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.describe('Filter to specific sections by title, case-insensitive (e.g. ["Introduction", "Methods", "Results", "Discussion"]). Applies to `source=pmc` results only.'),
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})
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.refine((v) => (v.pmcids === undefined) !== (v.pmids === undefined), {
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message: 'Provide exactly one of `pmcids` or `pmids` (not both, not neither).',
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}),
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output: z.object({
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articles: z.array(ArticleSchema).describe('Full-text articles'),
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hasPmids: !!input.pmids,
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idCount: (input.pmcids ?? input.pmids)?.length,
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});
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if (!input.pmcids && !input.pmids)
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throw new Error('Either pmcids or pmids must be provided');
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if (input.pmcids && input.pmids)
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throw new Error('Provide pmcids or pmids, not both');
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// ── PMID path: resolve to PMC + collect unresolved PMIDs for Unpaywall fallback ──
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let pmcIds = [];
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let fallbackCandidates = [];
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1
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+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAsR7B,CAAC"}
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@@ -45,7 +45,10 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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45
45
|
.optional()
|
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46
46
|
.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
|
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47
47
|
})
|
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48
|
-
.describe('Citation to match against PubMed')
|
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48
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+
.describe('Citation to match against PubMed. Must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).')
|
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49
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+
.refine((c) => !!(c.journal || c.year || c.volume || c.firstPage || c.authorName), {
|
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50
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+
message: 'Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).',
|
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51
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+
}))
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49
52
|
.min(1)
|
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50
53
|
.max(25)
|
|
51
54
|
.describe('Citations to look up. More fields = better match accuracy.'),
|
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@@ -94,11 +97,6 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
|
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94
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}),
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95
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|
async handler(input, ctx) {
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96
99
|
ctx.log.info('Executing pubmed_lookup_citation', { count: input.citations.length });
|
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97
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-
for (const c of input.citations) {
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98
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-
if (!c.journal && !c.year && !c.volume && !c.firstPage && !c.authorName) {
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99
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-
throw new Error('Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName).');
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100
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-
}
|
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101
|
-
}
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102
100
|
const citations = input.citations.map((c, i) => ({
|
|
103
101
|
journal: c.journal,
|
|
104
102
|
year: c.year,
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@@ -1 +1 @@
|
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1
|
-
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,2FAA2F;AAC3F,SAAS,cAAc,CAAC,OAAe;IACrC,OAAO,OAAO;SACX,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;SACtB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC;AAC/C,CAAC;AAED,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;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,EAAE,cAAc,CAAC,CAAC;IACnF,SAAS,EACP,mHAAmH;IAErH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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;aACD,QAAQ,CAAC,
|
|
1
|
+
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.6.
|
|
3
|
+
"version": "2.6.3",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
|
|
6
6
|
"type": "module",
|
|
@@ -71,9 +71,9 @@
|
|
|
71
71
|
"access": "public"
|
|
72
72
|
},
|
|
73
73
|
"dependencies": {
|
|
74
|
-
"@cyanheads/mcp-ts-core": "^0.7.
|
|
74
|
+
"@cyanheads/mcp-ts-core": "^0.7.5",
|
|
75
75
|
"defuddle": "^0.18.1",
|
|
76
|
-
"fast-xml-parser": "^5.7.
|
|
76
|
+
"fast-xml-parser": "^5.7.2",
|
|
77
77
|
"linkedom": "^0.18.12",
|
|
78
78
|
"pino-pretty": "^13.1.3",
|
|
79
79
|
"sanitize-html": "^2.17.3",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.6.
|
|
9
|
+
"version": "2.6.3",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "2.6.
|
|
22
|
+
"version": "2.6.3",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -66,7 +66,7 @@
|
|
|
66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.6.
|
|
69
|
+
"version": "2.6.3",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|