@cyanheads/pubmed-mcp-server 2.6.9 → 2.6.11
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/index.js +1 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +0 -12
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +26 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +7 -7
- 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:** 2.6.
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.
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**Version:** 2.6.11
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.9.0`
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**Engines:** Bun ≥1.3.2, Node ≥24.0.0
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/README.md
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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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package/dist/index.js
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],
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resources: [databaseInfoResource],
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prompts: [researchPlanPrompt],
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instructions: "PubMed/NCBI E-utilities wrapper. Typical research flow: `pubmed_search_articles` → `pubmed_fetch_articles` (metadata) → `pubmed_fetch_fulltext`. Prefer `pubmed_lookup_citation` over free-text search when you have a partial known reference — it's deterministic. Use `pubmed_lookup_mesh` and `pubmed_spell_check` to refine queries before searching, when needed.",
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landing: {
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tagline: 'Search PubMed, fetch articles, generate citations, explore MeSH terms, and discover related research.',
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repoRoot: 'https://github.com/cyanheads/pubmed-mcp-server',
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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,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;AAClE,OAAO,EAAE,oBAAoB,EAAE,MAAM,2CAA2C,CAAC;AAEjF,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,YAAY,EACV,yWAAyW;IAC3W,OAAO,EAAE;QACP,OAAO,EACL,uGAAuG;QACzG,QAAQ,EAAE,gDAAgD;QAC1D,KAAK,EAAE;YACL,EAAE,KAAK,EAAE,QAAQ,EAAE,IAAI,EAAE,kCAAkC,EAAE,QAAQ,EAAE,IAAI,EAAE;YAC7E;gBACE,KAAK,EAAE,kBAAkB;gBACzB,IAAI,EAAE,8CAA8C;gBACpD,QAAQ,EAAE,IAAI;aACf;YACD;gBACE,KAAK,EAAE,qBAAqB;gBAC5B,IAAI,EAAE,gDAAgD;gBACtD,QAAQ,EAAE,IAAI;aACf;YACD,EAAE,KAAK,EAAE,cAAc,EAAE,IAAI,EAAE,4BAA4B,EAAE,QAAQ,EAAE,IAAI,EAAE;SAC9E;QACD,UAAU,EAAE;YACV,YAAY,EAAE,mBAAmB;YACjC,gBAAgB,EAAE,iBAAiB;YACnC,eAAe,EAAE,iBAAiB;SACnC;KACF;IACD,KAAK;QACH,eAAe,EAAE,CAAC;QAClB,oBAAoB,EAAE,CAAC;IACzB,CAAC;CACF,CAAC,CAAC"}
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{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkN1B,CAAC"}
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const eLinkResult = (await ncbi.eLink(eLinkParams, { signal: ctx.signal }));
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const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
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const firstResult = eLinkResultsArray[0];
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// NCBI ELink stamps `<ERROR>` for invalid PMIDs alongside an absent or empty
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// LinkSet — the same observable shape as a valid PMID with no related links.
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// Fall through to the empty-LinkSet path below; the ESummary disambiguation
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// there distinguishes "unknown PMID" from "valid PMID, no relations" and
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// produces a notice in either case. Log the raw payload for telemetry.
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if (firstResult?.ERROR) {
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ctx.log.debug('NCBI ELink returned <ERROR>; disambiguating via ESummary', {
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pmid: input.pmid,
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relationship: input.relationship,
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ncbiError: firstResult.ERROR,
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});
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}
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const linkSet = firstResult?.LinkSet;
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let foundPmids = [];
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{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
|
|
1
|
+
{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAiMrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAED;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;;OAKG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;;IAsBjD;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA4BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE;IAsBtE,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC;CA0NL"}
|
|
@@ -6,6 +6,14 @@
|
|
|
6
6
|
*/
|
|
7
7
|
import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
8
|
import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
|
9
|
+
/**
|
|
10
|
+
* fast-xml-parser is pinned to `~5.7.3` in package.json. 5.8.0 deprecates
|
|
11
|
+
* `XMLValidator` in favor of a new sibling package `fast-xml-validator`
|
|
12
|
+
* (published days before the deprecation, 0 dependents, by the same author).
|
|
13
|
+
* 5.8.0 carries no security fix or feature we need, so we stay on 5.7.x until
|
|
14
|
+
* `fast-xml-validator` has time in the wild. Re-evaluate during a future
|
|
15
|
+
* `maintenance` pass — if `bun update --latest` bumps this, restore the pin.
|
|
16
|
+
*/
|
|
9
17
|
import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
|
|
10
18
|
import { recoveryFor } from '../../services/error-contracts.js';
|
|
11
19
|
/**
|
|
@@ -315,6 +323,24 @@ export class NcbiResponseHandler {
|
|
|
315
323
|
}));
|
|
316
324
|
throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
|
|
317
325
|
}
|
|
326
|
+
// NCBI's eLink (and occasionally other endpoints) drops the root element
|
|
327
|
+
// when the upstream backend connection fails mid-response, yielding just
|
|
328
|
+
// `<?xml ... ?>` + DOCTYPE with no body. JSON retmode reveals the same
|
|
329
|
+
// failure as a TXCLIENT EOF in an `ERROR` field; XML just truncates.
|
|
330
|
+
// Reclassify as transient ServiceUnavailable so the retry chain recovers,
|
|
331
|
+
// rather than SerializationError which short-circuits retries.
|
|
332
|
+
const bodyMinusProlog = responseText
|
|
333
|
+
.replace(/<\?xml[^?]*\?>/gi, '')
|
|
334
|
+
.replace(/<!DOCTYPE[^>]*>/gi, '')
|
|
335
|
+
.trim();
|
|
336
|
+
if (bodyMinusProlog.length === 0) {
|
|
337
|
+
logger.warning('NCBI returned a prolog-only XML response (upstream backend failure).', requestContextService.createRequestContext({
|
|
338
|
+
operation: 'NcbiEmptyResponse',
|
|
339
|
+
endpoint,
|
|
340
|
+
responseLength: responseText.length,
|
|
341
|
+
}));
|
|
342
|
+
throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
|
|
343
|
+
}
|
|
318
344
|
const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
|
|
319
345
|
const validationResult = XMLValidator.validate(xmlForValidation);
|
|
320
346
|
if (validationResult !== true) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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package/package.json
CHANGED
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@@ -1,6 +1,6 @@
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1
1
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{
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|
2
2
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"name": "@cyanheads/pubmed-mcp-server",
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|
3
|
-
"version": "2.6.
|
|
3
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+
"version": "2.6.11",
|
|
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.",
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|
6
6
|
"type": "module",
|
|
@@ -71,9 +71,9 @@
|
|
|
71
71
|
"access": "public"
|
|
72
72
|
},
|
|
73
73
|
"dependencies": {
|
|
74
|
-
"@cyanheads/mcp-ts-core": "^0.
|
|
74
|
+
"@cyanheads/mcp-ts-core": "^0.9.0",
|
|
75
75
|
"defuddle": "^0.18.1",
|
|
76
|
-
"fast-xml-parser": "
|
|
76
|
+
"fast-xml-parser": "~5.7.3",
|
|
77
77
|
"linkedom": "^0.18.12",
|
|
78
78
|
"pino-pretty": "^13.1.3",
|
|
79
79
|
"sanitize-html": "^2.17.3",
|
|
@@ -81,14 +81,14 @@
|
|
|
81
81
|
},
|
|
82
82
|
"devDependencies": {
|
|
83
83
|
"@biomejs/biome": "^2.4.15",
|
|
84
|
-
"@types/node": "^25.
|
|
84
|
+
"@types/node": "^25.7.0",
|
|
85
85
|
"@types/sanitize-html": "^2.16.1",
|
|
86
|
-
"@vitest/coverage-istanbul": "^4.1.
|
|
86
|
+
"@vitest/coverage-istanbul": "^4.1.6",
|
|
87
87
|
"depcheck": "^1.4.7",
|
|
88
|
-
"fast-check": "^4.
|
|
88
|
+
"fast-check": "^4.8.0",
|
|
89
89
|
"ignore": "^7.0.5",
|
|
90
90
|
"tsc-alias": "^1.8.17",
|
|
91
91
|
"typescript": "^6.0.3",
|
|
92
|
-
"vitest": "^4.1.
|
|
92
|
+
"vitest": "^4.1.6"
|
|
93
93
|
}
|
|
94
94
|
}
|
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": "2.6.11",
|
|
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": "2.6.11",
|
|
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": "2.6.11",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|