@cyanheads/pubmed-mcp-server 2.6.4 → 2.6.5
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 +32 -12
- package/README.md +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts.map +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts +38 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js +42 -0
- package/dist/mcp-server/tools/definitions/_error-contracts.js.map +1 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +21 -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 +11 -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 +21 -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 +11 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +21 -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 +18 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +8 -3
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +9 -7
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +4 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +26 -15
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +14 -36
- 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 +24 -19
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +9 -9
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +2 -2
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +50 -29
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +22 -18
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +4 -3
- package/server.json +3 -3
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* @module src/mcp-server/tools/definitions/find-related.tool
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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pmid: z.ZodString;
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relationship: z.ZodDefault<z.ZodEnum<{
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@@ -29,5 +30,24 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
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}, z.core.$strip>>;
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totalFound: z.ZodNumber;
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notice: z.ZodOptional<z.ZodString>;
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}, z.core.$strip
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}, z.core.$strip>, readonly [{
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readonly reason: "queue_full";
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readonly code: JsonRpcErrorCode.RateLimited;
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readonly when: "Local NCBI request queue is at capacity.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_unreachable";
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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readonly retryable: true;
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}, {
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readonly reason: "ncbi_deadline_exceeded";
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readonly code: JsonRpcErrorCode.Timeout;
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readonly when: "Total request deadline expired before NCBI returned a response.";
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readonly retryable: true;
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}, {
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readonly reason: "elink_error";
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.";
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}]>;
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//# sourceMappingURL=find-related.tool.d.ts.map
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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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqCjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiN1B,CAAC"}
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* @module src/mcp-server/tools/definitions/find-related.tool
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
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import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
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import { NCBI_SERVICE_ERRORS } from './_error-contracts.js';
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import { pmidStringSchema } from './_schemas.js';
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function extractValue(field) {
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if (field === undefined || field === null)
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/find-related.tool.ts',
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errors: [
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...NCBI_SERVICE_ERRORS,
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{
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reason: 'elink_error',
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code: JsonRpcErrorCode.ServiceUnavailable,
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when: 'NCBI ELink returned an <ERROR> payload for this PMID/relationship pair.',
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},
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],
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input: z.object({
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pmid: pmidStringSchema.describe('Source PubMed ID'),
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relationship: z
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@@ -83,7 +93,14 @@ export const findRelatedTool = tool('pubmed_find_related', {
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const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
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const firstResult = eLinkResultsArray[0];
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if (firstResult?.ERROR) {
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const detail = typeof firstResult.ERROR === 'string'
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? firstResult.ERROR
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: 'NCBI returned a non-string ERROR payload';
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throw ctx.fail('elink_error', `ELink error: ${detail}`, {
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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,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,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,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,+IAA+I,CAChJ;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;QAExE,IAAI,WAAW,EAAE,KAAK,EAAE,CAAC;YACvB,MAAM,
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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,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AACrE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,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;QACN,GAAG,mBAAmB;QACtB;YACE,MAAM,EAAE,aAAa;YACrB,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,yEAAyE;SAChF;KACO;IAEV,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,+IAA+I,CAChJ;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;QAExE,IAAI,WAAW,EAAE,KAAK,EAAE,CAAC;YACvB,MAAM,MAAM,GACV,OAAO,WAAW,CAAC,KAAK,KAAK,QAAQ;gBACnC,CAAC,CAAC,WAAW,CAAC,KAAK;gBACnB,CAAC,CAAC,0CAA0C,CAAC;YACjD,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,gBAAgB,MAAM,EAAE,EAAE;gBACtD,IAAI,EAAE,KAAK,CAAC,IAAI;gBAChB,YAAY,EAAE,KAAK,CAAC,YAAY;gBAChC,SAAS,EAAE,WAAW,CAAC,KAAK;aAC7B,CAAC,CAAC;QACL,CAAC;QAED,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,oEAAoE;YACpE,uEAAuE;YACvE,qEAAqE;YACrE,kDAAkD;YAClD,IAAI,MAA0B,CAAC;YAC/B,IAAI,KAAK,CAAC,YAAY,KAAK,YAAY,EAAE,CAAC;gBACxC,IAAI,CAAC;oBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,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@@ -6,12 +6,17 @@
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import { z } from '@cyanheads/mcp-ts-core';
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export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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pmids: z.ZodArray<z.ZodString>;
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format: z.ZodDefault<z.ZodUnion<readonly [z.ZodEnum<{
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apa: "apa";
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mla: "mla";
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bibtex: "bibtex";
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ris: "ris";
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}
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}>, z.ZodArray<z.ZodEnum<{
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apa: "apa";
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mla: "mla";
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bibtex: "bibtex";
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ris: "ris";
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}>>]>>;
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}, z.core.$strip>, z.ZodObject<{
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citations: z.ZodArray<z.ZodObject<{
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pmid: z.ZodString;
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@@ -21,5 +26,5 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
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totalSubmitted: z.ZodNumber;
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totalFormatted: z.ZodNumber;
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unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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}, z.core.$strip
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}, z.core.$strip>, undefined>;
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//# sourceMappingURL=format-citations.tool.d.ts.map
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@@ -1 +1 @@
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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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1
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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;AAcjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;6BAiG9B,CAAC"}
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@@ -10,17 +10,18 @@ import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.
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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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const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris']);
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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
|
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description: 'Get formatted citations for PubMed articles in one or more styles (APA, MLA, BibTeX, RIS). Pass a single style as a string or multiple as an array.',
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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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-
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.
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.default(
|
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-
.describe('Citation
|
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21
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+
format: z
|
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22
|
+
.union([CitationStyleEnum, z.array(CitationStyleEnum).min(1)])
|
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23
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+
.default('apa')
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24
|
+
.describe('Citation format(s) to generate — single style as a string or multiple as an array. Allowed values: apa, mla, bibtex, ris.'),
|
|
24
25
|
}),
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25
26
|
output: z.object({
|
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26
27
|
citations: z
|
|
@@ -40,9 +41,10 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
|
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40
41
|
.describe('Requested PMIDs that did not return article metadata'),
|
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41
42
|
}),
|
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42
43
|
async handler(input, ctx) {
|
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44
|
+
const formats = Array.isArray(input.format) ? input.format : [input.format];
|
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43
45
|
ctx.log.debug('Fetching articles for citation generation', {
|
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44
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|
pmids: input.pmids,
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-
|
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47
|
+
formats,
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46
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|
});
|
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47
49
|
const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25, signal: ctx.signal });
|
|
48
50
|
const xmlArticles = ensureArray(raw?.PubmedArticleSet?.PubmedArticle);
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@@ -51,7 +53,7 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
|
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|
51
53
|
return {
|
|
52
54
|
pmid: parsed.pmid,
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53
55
|
title: parsed.title,
|
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54
|
-
citations: formatCitations(parsed,
|
|
56
|
+
citations: formatCitations(parsed, formats),
|
|
55
57
|
};
|
|
56
58
|
});
|
|
57
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|
const returnedPmids = new Set(citations.map((entry) => entry.pmid));
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@@ -1 +1 @@
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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,
|
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1
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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,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,iBAAiB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;AAElE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,qJAAqJ;IACvJ,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,iBAAiB,EAAE,CAAC,CAAC,KAAK,CAAC,iBAAiB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;aAC7D,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2HAA2H,CAC5H;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,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,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;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,MAAM,OAAO,GAAoB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO;SACR,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,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,OAAO,CAAC;aAC5C,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,IAAI,MAAM,CAAC,cAAc,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CACR,6NAA6N,CAC9N,CAAC;QACJ,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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@@ -39,5 +39,5 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
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totalMatched: z.ZodNumber;
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}, z.core.$strip
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}, z.core.$strip>, undefined>;
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//# sourceMappingURL=lookup-citation.tool.d.ts.map
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{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsR7B,CAAC"}
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*/
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import { z } from '@cyanheads/mcp-ts-core';
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export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
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query: z.ZodString;
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query: z.ZodString;
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results: z.ZodArray<z.ZodObject<{
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@@ -17,5 +17,6 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
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scopeNote: z.ZodOptional<z.ZodString>;
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entryTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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notice: z.ZodOptional<z.ZodString>;
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{"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
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{"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;;;;;;;;;;;;;;6BAwGzB,CAAC"}
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// ─── Tool Definition ─────────────────────────────────────────────────────────
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export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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description: 'Search and explore MeSH (Medical Subject Headings) vocabulary.
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description: 'Search and explore the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms.',
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annotations: { readOnlyHint: true, openWorldHint: true },
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_meta: conceptMeta([
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SCHEMA_DEFINED_TERM,
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@@ -79,7 +79,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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]),
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
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input: z.object({
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query: z.string().min(1).describe('MeSH descriptor name or free-text term to look up'),
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includeDetails: z
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.boolean()
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@@ -87,7 +87,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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.describe('Fetch full MeSH records (scope notes, tree numbers, entry terms)'),
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output: z.object({
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query: z.string().describe('Original search query'),
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results: z
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.array(z
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.object({
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@@ -99,17 +99,21 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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})
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.describe('Matching MeSH descriptor record'))
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.describe('Matching MeSH records'),
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notice: z
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.string()
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.optional()
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.describe('Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results.'),
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}),
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async handler(input, ctx) {
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const {
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const { query, maxResults, includeDetails } = input;
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const ncbi = getNcbiService();
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ctx.log.debug('MeSH lookup started', {
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const hasFieldTag = /\[.+\]/.test(
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ctx.log.debug('MeSH lookup started', { query, maxResults, includeDetails });
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const hasFieldTag = /\[.+\]/.test(query);
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const callOpts = { signal: ctx.signal };
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const broadSearch = ncbi.eSearch({ db: 'mesh', term, retmax: maxResults }, callOpts);
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const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults }, callOpts);
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const exactSearch = hasFieldTag
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? undefined
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: ncbi.eSearch({ db: 'mesh', term: `${
|
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: ncbi.eSearch({ db: 'mesh', term: `${query}[MH]`, retmax: 1 }, callOpts);
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const [broadResult, exactResult] = await Promise.all([broadSearch, exactSearch]);
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const seen = new Set();
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const ids = [];
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@@ -120,23 +124,30 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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}
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}
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ids.length = Math.min(ids.length, maxResults);
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if (ids.length === 0)
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return {
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if (ids.length === 0) {
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return {
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query,
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results: [],
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notice: `No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`,
|
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};
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}
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|
const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
|
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const results = parseSummaryRecords(summaryData, ids, includeDetails);
|
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|
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const
|
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|
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const queryLower = query.toLowerCase();
|
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|
results.sort((a, b) => {
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|
-
const aExact = a.name.toLowerCase() ===
|
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const bExact = b.name.toLowerCase() ===
|
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const aExact = a.name.toLowerCase() === queryLower ? 0 : 1;
|
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|
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const bExact = b.name.toLowerCase() === queryLower ? 0 : 1;
|
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|
return aExact - bExact;
|
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|
});
|
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|
-
return {
|
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|
+
return { query, results };
|
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|
},
|
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|
format: (result) => {
|
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|
const lines = [
|
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|
-
`# MeSH Lookup: "${result.
|
|
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|
+
`# MeSH Lookup: "${result.query}"`,
|
|
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147
|
`Found **${result.results.length}** result(s).`,
|
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|
];
|
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|
+
if (result.notice)
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|
+
lines.push(`\n> ${result.notice}`);
|
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|
for (const r of result.results) {
|
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|
lines.push(`\n## ${r.name}`);
|
|
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|
lines.push(`- **MeSH ID:** ${r.meshId}`);
|
|
@@ -1 +1 @@
|
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1
|
-
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|
|
1
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+
{"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,2JAA2J;IAC7J,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,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACtF,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,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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;aACD,QAAQ,CAAC,iCAAiC,CAAC,CAC/C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yHAAyH,CAC1H;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QACpD,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE5E,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACzC,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,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5F,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,KAA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@@ -76,5 +76,5 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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76
76
|
}, z.core.$strip>>;
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77
77
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searchUrl: z.ZodString;
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78
78
|
notice: z.ZodOptional<z.ZodString>;
|
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79
|
-
}, z.core.$strip
|
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79
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+
}, z.core.$strip>, undefined>;
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80
80
|
//# sourceMappingURL=search-articles.tool.d.ts.map
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@@ -1 +1 @@
|
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|
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
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1
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+
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAuT7B,CAAC"}
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@@ -10,5 +10,5 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
|
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10
10
|
original: z.ZodString;
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11
11
|
corrected: z.ZodString;
|
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12
12
|
hasSuggestion: z.ZodBoolean;
|
|
13
|
-
}, z.core.$strip
|
|
13
|
+
}, z.core.$strip>, undefined>;
|
|
14
14
|
//# sourceMappingURL=spell-check.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;;;;;;
|
|
1
|
+
{"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;;;;;;6BA4CzB,CAAC"}
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
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1
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+
{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAUH,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;IAgClB;;;;;OAKG;IACG,mBAAmB,CACvB,GAAG,EAAE,MAAM,EACX,MAAM,EAAE,iBAAiB,EACzB,cAAc,CAAC,EAAE,WAAW,GAC3B,OAAO,CAAC,MAAM,CAAC;IA0ClB,OAAO,CAAC,WAAW;IAiBnB,OAAO,CAAC,UAAU;IAMlB,OAAO,CAAC,UAAU;IAWlB,OAAO,CAAC,WAAW;CAcpB"}
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@@ -4,8 +4,8 @@
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4
4
|
* retry logic lives in NcbiService.performRequest to cover both HTTP and XML-level errors.
|
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5
5
|
* @module src/services/ncbi/api-client
|
|
6
6
|
*/
|
|
7
|
-
import {
|
|
8
|
-
import { fetchWithTimeout, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
|
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7
|
+
import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
|
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8
|
+
import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
|
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9
9
|
import { NCBI_EUTILS_BASE_URL } from './types.js';
|
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10
10
|
/** Maximum encoded query-string length before automatically switching to POST. */
|
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11
11
|
const POST_THRESHOLD = 2000;
|
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@@ -25,26 +25,14 @@ export class NcbiApiClient {
|
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25
25
|
const suffix = endpoint.includes('.') ? '' : '.fcgi';
|
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26
26
|
const url = `${NCBI_EUTILS_BASE_URL}/${endpoint}${suffix}`;
|
|
27
27
|
try {
|
|
28
|
-
logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, {
|
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29
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-
endpoint,
|
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30
|
-
});
|
|
28
|
+
logger.debug(`NCBI HTTP request: ${usePost ? 'POST' : 'GET'} ${url}`, requestContextService.createRequestContext({ operation: 'NcbiHttpRequest', endpoint }));
|
|
31
29
|
const response = usePost
|
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32
30
|
? await this.postRequest(url, finalParams, options?.signal)
|
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33
31
|
: await this.getRequest(url, finalParams, options?.signal);
|
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34
32
|
if (!response.ok) {
|
|
35
|
-
|
|
36
|
-
|
|
37
|
-
|
|
38
|
-
}
|
|
39
|
-
else if (response.status >= 500) {
|
|
40
|
-
code = JsonRpcErrorCode.ServiceUnavailable;
|
|
41
|
-
}
|
|
42
|
-
else {
|
|
43
|
-
code = JsonRpcErrorCode.InvalidRequest;
|
|
44
|
-
}
|
|
45
|
-
throw new McpError(code, `NCBI API returned HTTP ${response.status}.`, {
|
|
46
|
-
endpoint,
|
|
47
|
-
status: response.status,
|
|
33
|
+
throw await httpErrorFromResponse(response, {
|
|
34
|
+
service: 'NCBI',
|
|
35
|
+
data: { endpoint },
|
|
48
36
|
});
|
|
49
37
|
}
|
|
50
38
|
return await response.text();
|
|
@@ -53,9 +41,7 @@ export class NcbiApiClient {
|
|
|
53
41
|
if (error instanceof McpError)
|
|
54
42
|
throw error;
|
|
55
43
|
const msg = error instanceof Error ? error.message : String(error);
|
|
56
|
-
throw
|
|
57
|
-
endpoint,
|
|
58
|
-
});
|
|
44
|
+
throw serviceUnavailable(`NCBI request failed: ${msg}`, { endpoint }, { cause: error });
|
|
59
45
|
}
|
|
60
46
|
}
|
|
61
47
|
/**
|
|
@@ -80,21 +66,15 @@ export class NcbiApiClient {
|
|
|
80
66
|
? AbortSignal.any([timeoutSignal, externalSignal])
|
|
81
67
|
: timeoutSignal;
|
|
82
68
|
try {
|
|
83
|
-
logger.debug(`NCBI external request: GET ${fullUrl}`, { url });
|
|
69
|
+
logger.debug(`NCBI external request: GET ${fullUrl}`, requestContextService.createRequestContext({ operation: 'NcbiExternalRequest', url }));
|
|
84
70
|
const response = await fetch(fullUrl, { signal });
|
|
85
71
|
const body = await response.text();
|
|
86
72
|
if (!response.ok) {
|
|
87
|
-
|
|
88
|
-
|
|
89
|
-
|
|
90
|
-
|
|
91
|
-
|
|
92
|
-
code = JsonRpcErrorCode.ServiceUnavailable;
|
|
93
|
-
}
|
|
94
|
-
else {
|
|
95
|
-
code = JsonRpcErrorCode.InvalidRequest;
|
|
96
|
-
}
|
|
97
|
-
throw new McpError(code, `NCBI API returned HTTP ${response.status}: ${body.substring(0, 300)}`, { url, status: response.status, body: body.substring(0, 500) });
|
|
73
|
+
throw await httpErrorFromResponse(response, {
|
|
74
|
+
service: 'NCBI',
|
|
75
|
+
captureBody: false,
|
|
76
|
+
data: { url, body: body.substring(0, 500) },
|
|
77
|
+
});
|
|
98
78
|
}
|
|
99
79
|
return body;
|
|
100
80
|
}
|
|
@@ -102,9 +82,7 @@ export class NcbiApiClient {
|
|
|
102
82
|
if (error instanceof McpError)
|
|
103
83
|
throw error;
|
|
104
84
|
const msg = error instanceof Error ? error.message : String(error);
|
|
105
|
-
throw
|
|
106
|
-
url,
|
|
107
|
-
});
|
|
85
|
+
throw serviceUnavailable(`NCBI request failed: ${msg}`, { url }, { cause: error });
|
|
108
86
|
}
|
|
109
87
|
}
|
|
110
88
|
buildParams(params) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,
|
|
1
|
+
{"version":3,"file":"api-client.js","sourceRoot":"","sources":["../../../src/services/ncbi/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,QAAQ,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AAC7E,OAAO,EACL,gBAAgB,EAChB,qBAAqB,EACrB,MAAM,EACN,qBAAqB,GACtB,MAAM,8BAA8B,CAAC;AAEtC,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,CACV,sBAAsB,OAAO,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,KAAK,IAAI,GAAG,EAAE,EACvD,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,iBAAiB,EAAE,QAAQ,EAAE,CAAC,CACvF,CAAC;YAEF,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,MAAM,MAAM,qBAAqB,CAAC,QAAQ,EAAE;oBAC1C,OAAO,EAAE,MAAM;oBACf,IAAI,EAAE,EAAE,QAAQ,EAAE;iBACnB,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,kBAAkB,CAAC,wBAAwB,GAAG,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;QAC1F,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,CACV,8BAA8B,OAAO,EAAE,EACvC,qBAAqB,CAAC,oBAAoB,CAAC,EAAE,SAAS,EAAE,qBAAqB,EAAE,GAAG,EAAE,CAAC,CACtF,CAAC;YACF,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,MAAM,MAAM,qBAAqB,CAAC,QAAQ,EAAE;oBAC1C,OAAO,EAAE,MAAM;oBACf,WAAW,EAAE,KAAK;oBAClB,IAAI,EAAE,EAAE,GAAG,EAAE,IAAI,EAAE,IAAI,CAAC,SAAS,CAAC,CAAC,EAAE,GAAG,CAAC,EAAE;iBAC5C,CAAC,CAAC;YACL,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,kBAAkB,CAAC,wBAAwB,GAAG,EAAE,EAAE,EAAE,GAAG,EAAE,EAAE,EAAE,KAAK,EAAE,KAAK,EAAE,CAAC,CAAC;QACrF,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"}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;
|
|
1
|
+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAYH,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;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;IAsD7B;;;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;IA8B7B;;;;;OAKG;YACW,SAAS;IA0DvB;;;;;;;;;OASG;IACH,OAAO,CAAC,cAAc;CA0BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA2BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
|