@cyanheads/pubmed-mcp-server 2.7.9 → 2.7.10
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/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +4 -4
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +6 -1
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +11 -1
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/AGENTS.md
CHANGED
package/CLAUDE.md
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package/README.md
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@@ -9,7 +9,7 @@
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[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -22,7 +22,7 @@ function authorSurnames(authors) {
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.filter((s) => s.length > 0 && s !== 'et');
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}
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export const lookupCitationTool = tool('pubmed_lookup_citation', {
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description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least
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description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
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@@ -47,9 +47,9 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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.optional()
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.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
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})
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.describe('Citation to match against PubMed. Must include at least
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.refine((c) => !!(c.journal || c.year
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message: 'Each citation must include at least
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.describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
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.refine((c) => !!(c.journal || c.year), {
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message: 'Each citation must include at least a journal or year field — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.',
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}))
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.min(1)
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.max(25)
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@@ -1 +1 @@
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+
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@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,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;AAWH,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;IAyClB;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC;IA8ClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}
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@@ -4,7 +4,7 @@
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|
4
4
|
* retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
|
|
5
5
|
* @module src/services/ncbi/api-client
|
|
6
6
|
*/
|
|
7
|
-
import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
7
|
+
import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
|
8
8
|
import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
|
|
9
9
|
import { recoveryFor } from '../../services/error-contracts.js';
|
|
10
10
|
import { NCBI_EUTILS_BASE_URL } from './types.js';
|
|
@@ -33,6 +33,11 @@ export class NcbiApiClient {
|
|
|
33
33
|
if (!response.ok) {
|
|
34
34
|
throw await httpErrorFromResponse(response, {
|
|
35
35
|
service: 'NCBI',
|
|
36
|
+
// NCBI's eutils proxy returns HTTP 500 for transient mesh-layer failures
|
|
37
|
+
// that are safe to retry. Reclassify as ServiceUnavailable so the retry
|
|
38
|
+
// loop in NcbiService.withRetry picks it up — 501 (Not Implemented) is
|
|
39
|
+
// left as InternalError since those are not transient.
|
|
40
|
+
codeOverride: (s) => (s === 500 ? JsonRpcErrorCode.ServiceUnavailable : undefined),
|
|
36
41
|
data: { endpoint },
|
|
37
42
|
});
|
|
38
43
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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AAG,EAAE;YACvD,MAAM,EAAE,MAAM;YACd,OAAO,EAAE,EAAE,cAAc,EAAE,mCAAmC,EAAE;YAChE,IAAI;YACJ,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC,CAAC;IACL,CAAC;CACF"}
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,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,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;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;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,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,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;
|
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1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,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,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AA0CpB;;;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;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;gBAJf,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM;IAGpC,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC;IAoBrF,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC;IAS7F,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,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC;IAOP,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC;IA2BzF,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC;IAO7E;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAoE7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAwD7B,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|
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@@ -139,7 +139,7 @@ export class NcbiService {
|
|
|
139
139
|
.map((c) => `${c.journal ?? ''}|${c.year ?? ''}|${c.volume ?? ''}|${c.firstPage ?? ''}|${c.authorName ?? ''}|${c.key}|`)
|
|
140
140
|
.join('\r');
|
|
141
141
|
const text = await this.performRequest('ecitmatch.cgi', { db: 'pubmed', retmode: 'xml', bdata }, { retmode: 'text', ...(options?.signal && { signal: options.signal }) });
|
|
142
|
-
|
|
142
|
+
const parsed = text
|
|
143
143
|
.split(/[\r\n]+/)
|
|
144
144
|
.filter((line) => line.trim().length > 0)
|
|
145
145
|
.map((line) => {
|
|
@@ -174,6 +174,16 @@ export class NcbiService {
|
|
|
174
174
|
...(rawOutcome && { detail: rawOutcome }),
|
|
175
175
|
};
|
|
176
176
|
});
|
|
177
|
+
// ECitMatch omits lines for citations it cannot classify. Reconcile against
|
|
178
|
+
// the submitted citations so every input gets a result row — callers can rely
|
|
179
|
+
// on results.length === citations.length and correlate by key.
|
|
180
|
+
const parsedByKey = new Map(parsed.map((r) => [r.key, r]));
|
|
181
|
+
return citations.map((c) => parsedByKey.get(c.key) ?? {
|
|
182
|
+
key: c.key,
|
|
183
|
+
matched: false,
|
|
184
|
+
pmid: null,
|
|
185
|
+
status: 'not_found',
|
|
186
|
+
});
|
|
177
187
|
}
|
|
178
188
|
/**
|
|
179
189
|
* Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
|
|
@@ -1 +1 @@
|
|
|
1
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-
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1
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.7.
|
|
3
|
+
"version": "2.7.10",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
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": "2.7.
|
|
9
|
+
"version": "2.7.10",
|
|
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": "2.7.
|
|
22
|
+
"version": "2.7.10",
|
|
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": "2.7.
|
|
69
|
+
"version": "2.7.10",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|