@cyanheads/pubmed-mcp-server 2.4.1 → 2.5.1
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 +4 -2
- package/README.md +3 -2
- package/dist/config/server-config.d.ts +1 -0
- package/dist/config/server-config.d.ts.map +1 -1
- package/dist/config/server-config.js +8 -1
- package/dist/config/server-config.js.map +1 -1
- package/dist/index.js +22 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.js +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
- package/dist/mcp-server/tools/definitions/_concepts.d.ts +41 -0
- package/dist/mcp-server/tools/definitions/_concepts.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_concepts.js +74 -0
- package/dist/mcp-server/tools/definitions/_concepts.js.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +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 +12 -4
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.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 +5 -2
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/format-citations.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 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +12 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +5 -2
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +3 -0
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/ncbi/api-client.d.ts +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +12 -9
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +27 -14
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +102 -23
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +14 -0
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/package.json +4 -4
- package/server.json +3 -3
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{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAYjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;kBA0F9B,CAAC"}
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@@ -8,10 +8,13 @@ import { formatCitations, } from '../../../services/ncbi/formatting/citation-for
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
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import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
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import { pmidStringSchema } from './_schemas.js';
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export const formatCitationsTool = tool('pubmed_format_citations', {
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description: 'Get formatted citations for PubMed articles in APA, MLA, BibTeX, or RIS format.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',
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input: z.object({
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pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
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styles: z
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pmids: input.pmids,
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styles: input.styles,
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});
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const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25 });
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const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25, signal: ctx.signal });
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const xmlArticles = ensureArray(raw?.PubmedArticleSet?.PubmedArticle);
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if (xmlArticles.length === 0) {
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throw new Error(`No articles found for PMIDs: ${input.pmids.join(', ')}`);
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{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;
|
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1
|
+
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,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,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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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;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
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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;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;kBA2H7B,CAAC"}
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@@ -5,9 +5,12 @@
|
|
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5
5
|
*/
|
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6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
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7
7
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
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8
|
+
import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
|
|
8
9
|
export const lookupCitationTool = tool('pubmed_lookup_citation', {
|
|
9
10
|
description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID. Uses NCBI ECitMatch for deterministic matching — more reliable than searching by citation fields.`,
|
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10
11
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
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+
_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
|
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13
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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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11
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input: z.object({
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15
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citations: z
|
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|
.array(z.object({
|
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@@ -64,7 +67,7 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
|
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64
67
|
authorName: c.authorName,
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65
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key: c.key ?? String(i + 1),
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|
}));
|
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67
|
-
const results = await getNcbiService().eCitMatch(citations);
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70
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+
const results = await getNcbiService().eCitMatch(citations, { signal: ctx.signal });
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|
const mapped = results.map((r) => ({
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key: r.key,
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matched: r.matched,
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;
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1
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+
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AAEjE,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,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,CAAC,MAAM,CAAC;YACP,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,CACH;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YACzD,MAAM,EAAE,CAAC;iBACN,IAAI,CAAC,CAAC,SAAS,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC;iBAC3C,QAAQ,CAAC,iDAAiD,CAAC;YAC9D,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,+DAA+D,CAAC;SAC7E,CAAC,CACH;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;KACrE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,KAAK,MAAM,CAAC,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;YAChC,IAAI,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,CAAC,UAAU,EAAE,CAAC;gBACxE,MAAM,IAAI,KAAK,CACb,gHAAgH,CACjH,CAAC;YACJ,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,OAAO,GAAG,MAAM,cAAc,EAAE,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACjC,GAAG,EAAE,CAAC,CAAC,GAAG;YACV,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,GAAG,CAAC,CAAC,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;SACtC,CAAC,CAAC,CAAC;QAEJ,MAAM,YAAY,GAAG,MAAM,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC;QAC5D,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE;YAC/C,YAAY;YACZ,cAAc,EAAE,SAAS,CAAC,MAAM;SACjC,CAAC,CAAC;QAEH,OAAO,EAAE,OAAO,EAAE,MAAM,EAAE,YAAY,EAAE,cAAc,EAAE,SAAS,CAAC,MAAM,EAAE,CAAC;IAC7E,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,4BAA4B;YAC5B,gBAAgB,MAAM,CAAC,YAAY,IAAI,MAAM,CAAC,cAAc,EAAE;SAC/D,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;YAC7B,IAAI,CAAC,CAAC,IAAI;gBAAE,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC9C,IAAI,CAAC,CAAC,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACpD,IAAI,CAAC,CAAC,MAAM,KAAK,SAAS,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,6EAA6E,CAAC,CAAC;gBAC1F,SAAS;YACX,CAAC;YAED,IAAI,CAAC,CAAC,MAAM,KAAK,WAAW,EAAE,CAAC;gBAC7B,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;gBACpC,KAAK,CAAC,IAAI,CACR,8GAA8G,CAC/G,CAAC;gBACF,SAAS;YACX,CAAC;YAED,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;YACnC,KAAK,CAAC,IAAI,CAAC,2EAA2E,CAAC,CAAC;QAC1F,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;kBAyFzB,CAAC"}
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@@ -6,6 +6,7 @@
|
|
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6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
7
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
8
8
|
import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
|
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9
|
+
import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
|
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9
10
|
function findItem(items, name) {
|
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11
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return items.find((it) => getText(it['@_Name']) === name);
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|
}
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@@ -70,6 +71,13 @@ function parseSummaryRecords(data, ids, includeDetails) {
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export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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71
72
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description: 'Search and explore MeSH (Medical Subject Headings) vocabulary. Essential for building precise PubMed queries.',
|
|
72
73
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annotations: { readOnlyHint: true, openWorldHint: true },
|
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74
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+
_meta: conceptMeta([
|
|
75
|
+
SCHEMA_DEFINED_TERM,
|
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+
SCHEMA_DEFINED_TERM_SET,
|
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+
EDAM_ONTOLOGY_TERMINOLOGY,
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|
+
EDAM_DATA_RETRIEVAL,
|
|
79
|
+
]),
|
|
80
|
+
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
|
|
73
81
|
input: z.object({
|
|
74
82
|
term: z.string().min(1).describe('MeSH term to look up'),
|
|
75
83
|
maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
|
|
@@ -95,10 +103,11 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
|
|
|
95
103
|
const ncbi = getNcbiService();
|
|
96
104
|
ctx.log.debug('MeSH lookup started', { term, maxResults, includeDetails });
|
|
97
105
|
const hasFieldTag = /\[.+\]/.test(term);
|
|
98
|
-
const
|
|
106
|
+
const callOpts = { signal: ctx.signal };
|
|
107
|
+
const broadSearch = ncbi.eSearch({ db: 'mesh', term, retmax: maxResults }, callOpts);
|
|
99
108
|
const exactSearch = hasFieldTag
|
|
100
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|
? undefined
|
|
101
|
-
: ncbi.eSearch({ db: 'mesh', term: `${term}[MH]`, retmax: 1 });
|
|
110
|
+
: ncbi.eSearch({ db: 'mesh', term: `${term}[MH]`, retmax: 1 }, callOpts);
|
|
102
111
|
const [broadResult, exactResult] = await Promise.all([broadSearch, exactSearch]);
|
|
103
112
|
const seen = new Set();
|
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104
113
|
const ids = [];
|
|
@@ -111,7 +120,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
|
|
|
111
120
|
ids.length = Math.min(ids.length, maxResults);
|
|
112
121
|
if (ids.length === 0)
|
|
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|
return { term, results: [] };
|
|
114
|
-
const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') });
|
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123
|
+
const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
|
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|
const results = parseSummaryRecords(summaryData, ids, includeDetails);
|
|
116
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|
const termLower = term.toLowerCase();
|
|
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|
results.sort((a, b) => {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;
|
|
1
|
+
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAC9E,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,yBAAyB,EACzB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,gBAAgB,CAAC;AAYxB,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,IAAI,GAAG;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IAC9B,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,mBAAmB,CAAC,IAAa,EAAE,GAAa,EAAE,cAAuB;IAChF,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1F,MAAM,IAAI,GAAG,IAA+B,CAAC;IAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,cAAqD,CAAC;IACjF,MAAM,OAAO,GAAG,WAAW,CACzB,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,MAAiC,CAC1D,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE7E,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAC/B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,IAAI,CAA8B,CAAC;QACjE,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,IAAI,MAAM,CAAC;QACpE,MAAM,MAAM,GAAe,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QAC5C,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YAC/D,IAAI,SAAS;gBAAE,MAAM,CAAC,SAAS,GAAG,SAAS,CAAC;YAC5C,MAAM,UAAU,GAAG,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YACjE,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC1D,MAAM,WAAW,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,WAAW,GAAG,WAAW,CAAC;QAC/D,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC,CAAC;AACL,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,+GAA+G;IACjH,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC;QACjB,mBAAmB;QACnB,uBAAuB;QACvB,yBAAyB;QACzB,mBAAmB;KACpB,CAAC;IACF,SAAS,EACP,+GAA+G;IAEjH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACxD,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,iBAAiB,CAAC;QACnF,cAAc,EAAE,CAAC;aACd,OAAO,EAAE;aACT,OAAO,CAAC,IAAI,CAAC;aACb,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QACjD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;YAChE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;YACvD,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SAC9E,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,IAAI,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QACnD,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,IAAI,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE3E,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC;QACxC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;QACxC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,UAAU,EAAE,EAAE,QAAQ,CAAC,CAAC;QACrF,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,IAAI,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC3E,MAAM,CAAC,WAAW,EAAE,WAAW,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC;QAEjF,MAAM,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;QAC/B,MAAM,GAAG,GAAa,EAAE,CAAC;QACzB,KAAK,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,MAAM,IAAI,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;YACzE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAClB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;gBACb,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,CAAC;QACH,CAAC;QACD,GAAG,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;QAE9C,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC;YAAE,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QAEnD,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QACrF,MAAM,OAAO,GAAG,mBAAmB,CAAC,WAAW,EAAE,GAAG,EAAE,cAAc,CAAC,CAAC;QAEtE,MAAM,SAAS,GAAG,IAAI,CAAC,WAAW,EAAE,CAAC;QACrC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpB,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC1D,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC1D,OAAO,MAAM,GAAG,MAAM,CAAC;QACzB,CAAC,CAAC,CAAC;QAEH,OAAO,EAAE,IAAI,EAAE,OAAO,EAAE,CAAC;IAC3B,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,mBAAmB,MAAM,CAAC,IAAI,GAAG;YACjC,WAAW,MAAM,CAAC,OAAO,CAAC,MAAM,eAAe;SAChD,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC7B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACzC,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACzF,IAAI,CAAC,CAAC,SAAS;gBAAE,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,UAAU,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACxF,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA4EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBA8S7B,CAAC"}
|
|
@@ -7,6 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
|
7
7
|
import { sanitization } from '@cyanheads/mcp-ts-core/utils';
|
|
8
8
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
9
9
|
import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
|
|
10
|
+
import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
|
|
10
11
|
/**
|
|
11
12
|
* Accepts empty strings (treated as "no filter" by the handler) or dates in
|
|
12
13
|
* YYYY, YYYY/MM, or YYYY/MM/DD form with `/`, `-`, or `.` separators.
|
|
@@ -67,6 +68,8 @@ const AppliedFiltersSchema = z.object({
|
|
|
67
68
|
export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
68
69
|
description: 'Search PubMed with full query syntax, filters, and date ranges. Returns PMIDs and optional brief summaries. Supports field-specific filters (author, journal, MeSH terms), common filters (language, species, free full text), and pagination via offset for paging through large result sets.',
|
|
69
70
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
71
|
+
_meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
|
|
72
|
+
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
|
|
70
73
|
input: z.object({
|
|
71
74
|
query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
|
|
72
75
|
maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
|
|
@@ -194,7 +197,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
194
197
|
retstart: input.offset,
|
|
195
198
|
sort: input.sort,
|
|
196
199
|
usehistory: input.summaryCount > 0 ? 'y' : undefined,
|
|
197
|
-
});
|
|
200
|
+
}, { signal: ctx.signal });
|
|
198
201
|
const pmids = esResult.idList;
|
|
199
202
|
let summaries = [];
|
|
200
203
|
if (input.summaryCount > 0 && pmids.length > 0) {
|
|
@@ -212,7 +215,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
212
215
|
else {
|
|
213
216
|
eSummaryParams.id = pmids.slice(0, input.summaryCount).join(',');
|
|
214
217
|
}
|
|
215
|
-
const eSummaryResult = await ncbi.eSummary(eSummaryParams);
|
|
218
|
+
const eSummaryResult = await ncbi.eSummary(eSummaryParams, { signal: ctx.signal });
|
|
216
219
|
if (eSummaryResult) {
|
|
217
220
|
const briefSummaries = await extractBriefSummaries(eSummaryResult);
|
|
218
221
|
summaries = briefSummaries.map((s) => ({
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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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":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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1
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+
{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAIjD,eAAO,MAAM,cAAc;;;;;;kBA4CzB,CAAC"}
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@@ -5,9 +5,12 @@
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5
5
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*/
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6
6
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import { tool, z } from '@cyanheads/mcp-ts-core';
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7
7
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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8
|
+
import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
|
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8
9
|
export const spellCheckTool = tool('pubmed_spell_check', {
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9
10
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description: "Spell-check a query and get NCBI's suggested correction. Useful for refining search queries.",
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10
11
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annotations: { readOnlyHint: true, openWorldHint: true },
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12
|
+
_meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
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13
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+
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
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11
14
|
input: z.object({
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12
15
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query: z.string().min(2).describe('PubMed search query to spell-check'),
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13
16
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}),
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;
|
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1
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+
{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;KACxE,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,6BAA6B,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QACpE,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAClF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -26,7 +26,7 @@ export declare class NcbiApiClient {
|
|
|
26
26
|
* error status codes — fetchWithTimeout throws before the body can be read.
|
|
27
27
|
* Injects tool and email params but not api_key (eutils-specific).
|
|
28
28
|
*/
|
|
29
|
-
makeExternalRequest(url: string, params: NcbiRequestParams): Promise<string>;
|
|
29
|
+
makeExternalRequest(url: string, params: NcbiRequestParams, externalSignal?: AbortSignal): Promise<string>;
|
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|
private buildParams;
|
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private shouldPost;
|
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|
private getRequest;
|
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@@ -1 +1 @@
|
|
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1
|
-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,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,
|
|
1
|
+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAKH,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;IAiDlB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}
|
|
@@ -29,8 +29,8 @@ export class NcbiApiClient {
|
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|
29
29
|
endpoint,
|
|
30
30
|
});
|
|
31
31
|
const response = usePost
|
|
32
|
-
? await this.postRequest(url, finalParams)
|
|
33
|
-
: await this.getRequest(url, finalParams);
|
|
32
|
+
? await this.postRequest(url, finalParams, options?.signal)
|
|
33
|
+
: await this.getRequest(url, finalParams, options?.signal);
|
|
34
34
|
if (!response.ok) {
|
|
35
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|
let code;
|
|
36
36
|
if (response.status === 429) {
|
|
@@ -64,7 +64,7 @@ export class NcbiApiClient {
|
|
|
64
64
|
* error status codes — fetchWithTimeout throws before the body can be read.
|
|
65
65
|
* Injects tool and email params but not api_key (eutils-specific).
|
|
66
66
|
*/
|
|
67
|
-
async makeExternalRequest(url, params) {
|
|
67
|
+
async makeExternalRequest(url, params, externalSignal) {
|
|
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68
|
const finalParams = {
|
|
69
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|
tool: this.config.toolIdentifier,
|
|
70
70
|
...(this.config.adminEmail && { email: this.config.adminEmail }),
|
|
@@ -75,11 +75,13 @@ export class NcbiApiClient {
|
|
|
75
75
|
}
|
|
76
76
|
const qs = new URLSearchParams(finalParams).toString();
|
|
77
77
|
const fullUrl = qs ? `${url}?${qs}` : url;
|
|
78
|
+
const timeoutSignal = AbortSignal.timeout(this.config.timeoutMs);
|
|
79
|
+
const signal = externalSignal
|
|
80
|
+
? AbortSignal.any([timeoutSignal, externalSignal])
|
|
81
|
+
: timeoutSignal;
|
|
78
82
|
try {
|
|
79
83
|
logger.debug(`NCBI external request: GET ${fullUrl}`, { url });
|
|
80
|
-
const response = await fetch(fullUrl, {
|
|
81
|
-
signal: AbortSignal.timeout(this.config.timeoutMs),
|
|
82
|
-
});
|
|
84
|
+
const response = await fetch(fullUrl, { signal });
|
|
83
85
|
const body = await response.text();
|
|
84
86
|
if (!response.ok) {
|
|
85
87
|
let code;
|
|
@@ -126,19 +128,20 @@ export class NcbiApiClient {
|
|
|
126
128
|
const queryString = new URLSearchParams(params).toString();
|
|
127
129
|
return queryString.length > POST_THRESHOLD;
|
|
128
130
|
}
|
|
129
|
-
getRequest(url, params) {
|
|
131
|
+
getRequest(url, params, signal) {
|
|
130
132
|
const qs = new URLSearchParams(params).toString();
|
|
131
133
|
const fullUrl = qs ? `${url}?${qs}` : url;
|
|
132
134
|
const ctx = requestContextService.createRequestContext({ operation: 'NcbiGet', url: fullUrl });
|
|
133
|
-
return fetchWithTimeout(fullUrl, this.config.timeoutMs, ctx);
|
|
135
|
+
return fetchWithTimeout(fullUrl, this.config.timeoutMs, ctx, signal ? { signal } : undefined);
|
|
134
136
|
}
|
|
135
|
-
postRequest(url, params) {
|
|
137
|
+
postRequest(url, params, signal) {
|
|
136
138
|
const body = new URLSearchParams(params).toString();
|
|
137
139
|
const ctx = requestContextService.createRequestContext({ operation: 'NcbiPost', url });
|
|
138
140
|
return fetchWithTimeout(url, this.config.timeoutMs, ctx, {
|
|
139
141
|
method: 'POST',
|
|
140
142
|
headers: { 'Content-Type': 'application/x-www-form-urlencoded' },
|
|
141
143
|
body,
|
|
144
|
+
...(signal && { signal }),
|
|
142
145
|
});
|
|
143
146
|
}
|
|
144
147
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,GAAG,MAAM,EAAE,CAAC;QAE3D,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EAAE;gBACpE,QAAQ;aACA,CAAC,CAAC;YAEZ,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,CAAC;
|
|
1
|
+
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,gBAAgB,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AAC3E,OAAO,EAAE,gBAAgB,EAAE,MAAM,EAAE,qBAAqB,EAAE,MAAM,8BAA8B,CAAC;AAE/F,OAAO,EAAE,oBAAoB,EAAmD,MAAM,YAAY,CAAC;AAEnG,kFAAkF;AAClF,MAAM,cAAc,GAAG,IAAI,CAAC;AAS5B;;;;GAIG;AACH,MAAM,OAAO,aAAa;IACK;IAA7B,YAA6B,MAA2B;QAA3B,WAAM,GAAN,MAAM,CAAqB;IAAG,CAAC;IAE5D,KAAK,CAAC,WAAW,CACf,QAAgB,EAChB,MAAyB,EACzB,OAA4B;QAE5B,MAAM,WAAW,GAAG,IAAI,CAAC,WAAW,CAAC,MAAM,CAAC,CAAC;QAC7C,MAAM,OAAO,GAAG,IAAI,CAAC,UAAU,CAAC,WAAW,EAAE,OAAO,CAAC,CAAC;QACtD,MAAM,MAAM,GAAG,QAAQ,CAAC,QAAQ,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,OAAO,CAAC;QACrD,MAAM,GAAG,GAAG,GAAG,oBAAoB,IAAI,QAAQ,GAAG,MAAM,EAAE,CAAC;QAE3D,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EAAE;gBACpE,QAAQ;aACA,CAAC,CAAC;YAEZ,MAAM,QAAQ,GAAG,OAAO;gBACtB,CAAC,CAAC,MAAM,IAAI,CAAC,WAAW,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,CAAC;gBAC3D,CAAC,CAAC,MAAM,IAAI,CAAC,UAAU,CAAC,GAAG,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,CAAC,CAAC;YAE7D,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,IAAI,IAAY,CAAC;gBACjB,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;oBAC5B,IAAI,GAAG,gBAAgB,CAAC,WAAW,CAAC;gBACtC,CAAC;qBAAM,IAAI,QAAQ,CAAC,MAAM,IAAI,GAAG,EAAE,CAAC;oBAClC,IAAI,GAAG,gBAAgB,CAAC,kBAAkB,CAAC;gBAC7C,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,gBAAgB,CAAC,cAAc,CAAC;gBACzC,CAAC;gBACD,MAAM,IAAI,QAAQ,CAAC,IAAI,EAAE,0BAA0B,QAAQ,CAAC,MAAM,GAAG,EAAE;oBACrE,QAAQ;oBACR,MAAM,EAAE,QAAQ,CAAC,MAAM;iBACxB,CAAC,CAAC;YACL,CAAC;YAED,OAAO,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;QAC/B,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAE3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,QAAQ;aACT,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAED;;;;;OAKG;IACH,KAAK,CAAC,mBAAmB,CACvB,GAAW,EACX,MAAyB,EACzB,cAA4B;QAE5B,MAAM,WAAW,GAA2B;YAC1C,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,GAAG,CAAC,IAAI,CAAC,MAAM,CAAC,UAAU,IAAI,EAAE,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU,EAAE,CAAC;SACjE,CAAC;QACF,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;YAClD,IAAI,KAAK,IAAI,IAAI;gBAAE,WAAW,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;QACtD,CAAC;QAED,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC;QACvD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAE1C,MAAM,aAAa,GAAG,WAAW,CAAC,OAAO,CAAC,IAAI,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC;QACjE,MAAM,MAAM,GAAG,cAAc;YAC3B,CAAC,CAAC,WAAW,CAAC,GAAG,CAAC,CAAC,aAAa,EAAE,cAAc,CAAC,CAAC;YAClD,CAAC,CAAC,aAAa,CAAC;QAElB,IAAI,CAAC;YACH,MAAM,CAAC,KAAK,CAAC,8BAA8B,OAAO,EAAE,EAAE,EAAE,GAAG,EAAW,CAAC,CAAC;YACxE,MAAM,QAAQ,GAAG,MAAM,KAAK,CAAC,OAAO,EAAE,EAAE,MAAM,EAAE,CAAC,CAAC;YAElD,MAAM,IAAI,GAAG,MAAM,QAAQ,CAAC,IAAI,EAAE,CAAC;YAEnC,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,CAAC;gBACjB,IAAI,IAAY,CAAC;gBACjB,IAAI,QAAQ,CAAC,MAAM,KAAK,GAAG,EAAE,CAAC;oBAC5B,IAAI,GAAG,gBAAgB,CAAC,WAAW,CAAC;gBACtC,CAAC;qBAAM,IAAI,QAAQ,CAAC,MAAM,IAAI,GAAG,EAAE,CAAC;oBAClC,IAAI,GAAG,gBAAgB,CAAC,kBAAkB,CAAC;gBAC7C,CAAC;qBAAM,CAAC;oBACN,IAAI,GAAG,gBAAgB,CAAC,cAAc,CAAC;gBACzC,CAAC;gBACD,MAAM,IAAI,QAAQ,CAChB,IAAI,EACJ,0BAA0B,QAAQ,CAAC,MAAM,KAAK,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,EACtE,EAAE,GAAG,EAAE,MAAM,EAAE,QAAQ,CAAC,MAAM,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE,CAC/D,CAAC;YACJ,CAAC;YAED,OAAO,IAAI,CAAC;QACd,CAAC;QAAC,OAAO,KAAc,EAAE,CAAC;YACxB,IAAI,KAAK,YAAY,QAAQ;gBAAE,MAAM,KAAK,CAAC;YAC3C,MAAM,GAAG,GAAG,KAAK,YAAY,KAAK,CAAC,CAAC,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;YACnE,MAAM,IAAI,QAAQ,CAAC,gBAAgB,CAAC,kBAAkB,EAAE,wBAAwB,GAAG,EAAE,EAAE;gBACrF,GAAG;aACJ,CAAC,CAAC;QACL,CAAC;IACH,CAAC;IAEO,WAAW,CAAC,MAAyB;QAC3C,MAAM,GAAG,GAAgD;YACvD,IAAI,EAAE,IAAI,CAAC,MAAM,CAAC,cAAc;YAChC,KAAK,EAAE,IAAI,CAAC,MAAM,CAAC,UAAU;YAC7B,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,MAAM;YAC3B,GAAG,MAAM;SACV,CAAC;QAEF,MAAM,MAAM,GAA2B,EAAE,CAAC;QAC1C,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;YAC/C,IAAI,KAAK,IAAI,IAAI,EAAE,CAAC;gBAClB,MAAM,CAAC,GAAG,CAAC,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;YAC9B,CAAC;QACH,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC;IAEO,UAAU,CAAC,MAA8B,EAAE,OAA4B;QAC7E,IAAI,OAAO,EAAE,OAAO;YAAE,OAAO,IAAI,CAAC;QAClC,MAAM,WAAW,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAC3D,OAAO,WAAW,CAAC,MAAM,GAAG,cAAc,CAAC;IAC7C,CAAC;IAEO,UAAU,CAChB,GAAW,EACX,MAA8B,EAC9B,MAAoB;QAEpB,MAAM,EAAE,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QAClD,MAAM,OAAO,GAAG,EAAE,CAAC,CAAC,CAAC,GAAG,GAAG,IAAI,EAAE,EAAE,CAAC,CAAC,CAAC,GAAG,CAAC;QAC1C,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,SAAS,EAAE,GAAG,EAAE,OAAO,EAAE,CAAC,CAAC;QAC/F,OAAO,gBAAgB,CAAC,OAAO,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC;IAChG,CAAC;IAEO,WAAW,CACjB,GAAW,EACX,MAA8B,EAC9B,MAAoB;QAEpB,MAAM,IAAI,GAAG,IAAI,eAAe,CAAC,MAAM,CAAC,CAAC,QAAQ,EAAE,CAAC;QACpD,MAAM,GAAG,GAAG,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,UAAU,EAAE,GAAG,EAAE,CAAC,CAAC;QACvF,OAAO,gBAAgB,CAAC,GAAG,EAAE,IAAI,CAAC,MAAM,CAAC,SAAS,EAAE,GAAG,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"}
|
|
@@ -7,7 +7,7 @@
|
|
|
7
7
|
import { NcbiApiClient } from './api-client.js';
|
|
8
8
|
import { NcbiRequestQueue } from './request-queue.js';
|
|
9
9
|
import { NcbiResponseHandler } from './response-handler.js';
|
|
10
|
-
import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
|
|
10
|
+
import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiCallOptions, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
|
|
11
11
|
/**
|
|
12
12
|
* Facade over NCBI's E-utility suite. Each public method corresponds to a
|
|
13
13
|
* single E-utility endpoint.
|
|
@@ -17,40 +17,53 @@ export declare class NcbiService {
|
|
|
17
17
|
private readonly queue;
|
|
18
18
|
private readonly responseHandler;
|
|
19
19
|
private readonly maxRetries;
|
|
20
|
-
|
|
21
|
-
|
|
22
|
-
|
|
20
|
+
private readonly totalDeadlineMs;
|
|
21
|
+
constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler, maxRetries: number, totalDeadlineMs: number);
|
|
22
|
+
eSearch(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESearchResult>;
|
|
23
|
+
eSummary(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESummaryResult>;
|
|
23
24
|
eFetch<T = {
|
|
24
25
|
PubmedArticleSet?: XmlPubmedArticleSet;
|
|
25
26
|
}>(params: NcbiRequestParams, options?: NcbiRequestOptions): Promise<T>;
|
|
26
|
-
eLink<T = Record<string, unknown>>(params: NcbiRequestParams): Promise<T>;
|
|
27
|
-
eSpell(params: NcbiRequestParams): Promise<ESpellResult>;
|
|
28
|
-
eInfo(params: NcbiRequestParams): Promise<unknown>;
|
|
27
|
+
eLink<T = Record<string, unknown>>(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<T>;
|
|
28
|
+
eSpell(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESpellResult>;
|
|
29
|
+
eInfo(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<unknown>;
|
|
29
30
|
/**
|
|
30
31
|
* Look up PMIDs from partial citation strings via NCBI ECitMatch.
|
|
31
32
|
* Each citation can include journal, year, volume, first page, and author name.
|
|
32
33
|
*/
|
|
33
|
-
eCitMatch(citations: ECitMatchCitation[]): Promise<ECitMatchResult[]>;
|
|
34
|
+
eCitMatch(citations: ECitMatchCitation[], options?: NcbiCallOptions): Promise<ECitMatchResult[]>;
|
|
34
35
|
/**
|
|
35
36
|
* Convert between article identifiers (DOI, PMID, PMCID) using the PMC ID Converter API.
|
|
36
37
|
* Accepts up to 200 IDs in a single request. Only works for articles in PMC.
|
|
37
38
|
*/
|
|
38
|
-
idConvert(ids: string[], idtype?: string): Promise<IdConvertRecord[]>;
|
|
39
|
+
idConvert(ids: string[], idtype?: string, options?: NcbiCallOptions): Promise<IdConvertRecord[]>;
|
|
39
40
|
/** Error codes that are transient and worth retrying with backoff. */
|
|
40
41
|
private static readonly RETRYABLE_CODES;
|
|
41
42
|
/** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
|
|
42
43
|
private static readonly MAX_BACKOFF_MS;
|
|
44
|
+
/**
|
|
45
|
+
* Wraps a task with a service-level deadline. Returns a combined AbortSignal
|
|
46
|
+
* (internal deadline OR'd with the caller's `ctx.signal`, if any) that the
|
|
47
|
+
* task must forward to both the HTTP call and any backoff sleep so cancellation
|
|
48
|
+
* interrupts the full retry chain — not just the next attempt.
|
|
49
|
+
*/
|
|
50
|
+
private runWithDeadline;
|
|
43
51
|
/**
|
|
44
52
|
* Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
|
|
45
53
|
* Non-transient McpErrors and unexpected plain Errors fail immediately.
|
|
46
|
-
* Uses capped exponential backoff with jitter.
|
|
54
|
+
* Uses capped exponential backoff with jitter. Backoff sleep is abortable via
|
|
55
|
+
* `signal`, so deadline expiration or caller cancel short-circuits the chain.
|
|
47
56
|
*/
|
|
48
57
|
private withRetry;
|
|
49
58
|
/**
|
|
50
|
-
* Enqueues a request with retry logic that covers
|
|
51
|
-
* (network errors, timeouts) and XML-level errors
|
|
52
|
-
* with an error structure in the response body, e.g.
|
|
53
|
-
* surfaced as C++ exception traces).
|
|
59
|
+
* Enqueues a request with a service-level deadline and retry logic that covers
|
|
60
|
+
* both HTTP-level failures (network errors, timeouts) and XML-level errors
|
|
61
|
+
* (NCBI returning 200 OK with an error structure in the response body, e.g.
|
|
62
|
+
* connection resets surfaced as C++ exception traces).
|
|
63
|
+
*
|
|
64
|
+
* The combined deadline+caller signal is threaded into both the HTTP fetch
|
|
65
|
+
* (cancels wedged requests) and the backoff sleep (cancels pending retries),
|
|
66
|
+
* bounding the total time to `totalDeadlineMs` regardless of retry count.
|
|
54
67
|
*/
|
|
55
68
|
private performRequest;
|
|
56
69
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAMH,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;AA8BpB;;;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;IAuBzF,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;IA8C7B;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC;IAoC7B,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;IA4B7B;;;;;OAKG;YACW,SAAS;IA+CvB;;;;;;;;;OASG;IACH,OAAO,CAAC,cAAc;CA0BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CAuBtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|