@cyanheads/pubmed-mcp-server 2.6.9 → 2.6.10
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 +1 -1
- package/README.md +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 +18 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/CLAUDE.md
CHANGED
package/README.md
CHANGED
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@@ -7,7 +7,7 @@
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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":"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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@@ -85,18 +85,6 @@ export const findRelatedTool = tool('pubmed_find_related', {
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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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if (linkSet?.LinkSetDb) {
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@@ -1 +1 @@
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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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{"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;AAsBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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,eAAe,CAAC;YACxD,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,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yFAAyF,CAC1F;SACJ,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACjF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uJAAuJ,CACxJ;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0BAA0B,EAAE;YACxC,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,YAAY,EAAE,KAAK,CAAC,YAAY;SACjC,CAAC,CAAC;QAEH,MAAM,WAAW,GAA2B;YAC1C,MAAM,EAAE,QAAQ;YAChB,EAAE,EAAE,QAAQ;YACZ,EAAE,EAAE,KAAK,CAAC,IAAI;YACd,OAAO,EAAE,KAAK;SACf,CAAC;QACF,QAAQ,KAAK,CAAC,YAAY,EAAE,CAAC;YAC3B,KAAK,SAAS;gBACZ,WAAW,CAAC,GAAG,GAAG,gBAAgB,CAAC;gBACnC,MAAM;YACR,KAAK,UAAU;gBACb,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,uBAAuB,CAAC;gBAC/C,MAAM;YACR,KAAK,YAAY;gBACf,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,oBAAoB,CAAC;gBAC5C,MAAM;QACV,CAAC;QAED,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAkB,CAAC;QAC7F,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QAChE,MAAM,WAAW,GAAG,iBAAiB,CAAC,CAAC,CAAgC,CAAC;QACxE,MAAM,OAAO,GAAG,WAAW,EAAE,OAAO,CAAC;QACrC,IAAI,UAAU,GAAuC,EAAE,CAAC;QAExD,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;YACvB,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YACtD,MAAM,gBAAgB,GACpB,KAAK,CAAC,YAAY,KAAK,UAAU;gBAC/B,CAAC,CAAC,uBAAuB;gBACzB,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,YAAY;oBACnC,CAAC,CAAC,oBAAoB;oBACtB,CAAC,CAAC,eAAe,CAAC;YACxB,MAAM,QAAQ,GACZ,cAAc,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,gBAAgB,CAAC,IAAI,cAAc,CAAC,CAAC,CAAC,CAAC;YAErF,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;gBACnB,UAAU,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC;qBACpC,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE,CAAC,CAAC;oBAC5B,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;iBACjF,CAAC,CAAC;qBACF,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;QAED,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,yEAAyE;YACzE,0EAA0E;YAC1E,yEAAyE;YACzE,yEAAyE;YACzE,wEAAwE;YACxE,IAAI,aAA6C,CAAC;YAClD,IAAI,sBAAsB,GAAG,KAAK,CAAC;YACnC,IAAI,CAAC;gBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;gBACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;gBAC7D,aAAa,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;gBAC7B,uEAAuE;gBACvE,IAAI,CAAC,aAAa,EAAE,KAAK;oBAAE,sBAAsB,GAAG,IAAI,CAAC;YAC3D,CAAC;YAAC,OAAO,GAAG,EAAE,CAAC;gBACb,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,6BAA6B,EAAE,EAAE,GAAG,EAAE,CAAC,CAAC;gBACtD,yEAAyE;gBACzE,sEAAsE;gBACtE,wEAAwE;gBACxE,uBAAuB;gBACvB,MAAM,MAAM,GACV,GAAG,YAAY,QAAQ;oBACrB,CAAC,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{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,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;
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{"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAOH,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"}
|
|
@@ -315,6 +315,24 @@ export class NcbiResponseHandler {
|
|
|
315
315
|
}));
|
|
316
316
|
throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
|
|
317
317
|
}
|
|
318
|
+
// NCBI's eLink (and occasionally other endpoints) drops the root element
|
|
319
|
+
// when the upstream backend connection fails mid-response, yielding just
|
|
320
|
+
// `<?xml ... ?>` + DOCTYPE with no body. JSON retmode reveals the same
|
|
321
|
+
// failure as a TXCLIENT EOF in an `ERROR` field; XML just truncates.
|
|
322
|
+
// Reclassify as transient ServiceUnavailable so the retry chain recovers,
|
|
323
|
+
// rather than SerializationError which short-circuits retries.
|
|
324
|
+
const bodyMinusProlog = responseText
|
|
325
|
+
.replace(/<\?xml[^?]*\?>/gi, '')
|
|
326
|
+
.replace(/<!DOCTYPE[^>]*>/gi, '')
|
|
327
|
+
.trim();
|
|
328
|
+
if (bodyMinusProlog.length === 0) {
|
|
329
|
+
logger.warning('NCBI returned a prolog-only XML response (upstream backend failure).', requestContextService.createRequestContext({
|
|
330
|
+
operation: 'NcbiEmptyResponse',
|
|
331
|
+
endpoint,
|
|
332
|
+
responseLength: responseText.length,
|
|
333
|
+
}));
|
|
334
|
+
throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
|
|
335
|
+
}
|
|
318
336
|
const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
|
|
319
337
|
const validationResult = XMLValidator.validate(xmlForValidation);
|
|
320
338
|
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",
|
|
3
|
-
"version": "2.6.
|
|
3
|
+
"version": "2.6.10",
|
|
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",
|
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": "2.6.10",
|
|
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": "2.6.10",
|
|
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": "2.6.10",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|