@cyanheads/pubmed-mcp-server 2.9.7 → 2.9.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +30 -8
- package/CLAUDE.md +30 -8
- package/Dockerfile +13 -7
- package/README.md +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +17 -17
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +18 -18
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +43 -41
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +79 -11
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +33 -33
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +17 -17
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +1 -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 +16 -16
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +9 -12
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +20 -16
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +73 -22
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts +18 -18
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +22 -22
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +15 -15
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +2 -2
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +33 -33
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.js +1 -0
- package/dist/services/europe-pmc/api-client.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/europe-pmc/request-queue.d.ts.map +1 -1
- package/dist/services/europe-pmc/request-queue.js.map +1 -1
- package/dist/services/europe-pmc/types.d.ts +2 -2
- package/dist/services/europe-pmc/types.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +3 -0
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/xml-helpers.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/types.d.ts +6 -0
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/dist/services/openalex/api-client.d.ts.map +1 -1
- package/dist/services/openalex/api-client.js +1 -0
- package/dist/services/openalex/api-client.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +1 -0
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +24 -17
- package/server.json +3 -3
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@@ -21,9 +21,9 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
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pmid: z.ZodOptional<z.ZodString>;
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matched: z.ZodBoolean;
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status: z.ZodEnum<{
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ambiguous: "ambiguous";
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matched: "matched";
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not_found: "not_found";
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ambiguous: "ambiguous";
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}>;
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detail: z.ZodOptional<z.ZodString>;
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candidatePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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@@ -40,34 +40,34 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
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totalSubmitted: z.ZodNumber;
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totalWarnings: z.ZodNumber;
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}, z.core.$strip>, readonly [{
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readonly reason:
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readonly reason: 'queue_full';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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readonly when:
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readonly recovery:
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readonly when: 'Local NCBI request queue is at capacity.';
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readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
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readonly retryable: true;
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}, {
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readonly reason:
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readonly reason: 'ncbi_unreachable';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
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readonly when:
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readonly recovery:
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readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
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readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
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readonly retryable: true;
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}, {
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readonly reason:
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readonly reason: 'ncbi_deadline_exceeded';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
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readonly when:
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readonly recovery:
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readonly when: 'Total request deadline expired before NCBI returned a response.';
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readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
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readonly retryable: true;
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}, {
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readonly reason:
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readonly reason: 'ncbi_invalid_response';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
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readonly when:
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readonly recovery:
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readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
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readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
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readonly retryable: true;
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}, {
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readonly reason:
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readonly reason: 'ncbi_resource_not_found';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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readonly when:
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readonly recovery:
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readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
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readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
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readonly retryable: false;
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}], undefined>;
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//# sourceMappingURL=lookup-citation.tool.d.ts.map
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@@ -1 +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;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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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;AAiBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA+R7B,CAAC"}
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@@ -14,13 +14,6 @@ import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTI
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function surname(name) {
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return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
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}
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/** Split a formatted authors string ("Lastname FI, Lastname FI, et al.") into surnames. */
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function authorSurnames(authors) {
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return authors
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.split(', ')
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.map((a) => surname(a))
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.filter((s) => s.length > 0 && s !== 'et');
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}
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export const lookupCitationTool = tool('pubmed_lookup_citation', {
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description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
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annotations: { readOnlyHint: true, openWorldHint: true },
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@@ -125,6 +118,7 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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for (const s of summaries) {
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summaryByPmid.set(s.pmid, {
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...(s.authors && { authors: s.authors }),
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...(s.authorNames?.length && { authorNames: s.authorNames }),
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...(s.pubDate && { pubDate: s.pubDate }),
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});
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}
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@@ -144,25 +138,28 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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if (!summary)
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return base;
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const warnings = [];
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const { authors, pubDate } = summary;
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const { authors, authorNames, pubDate } = summary;
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if (authors) {
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const firstAuthor = authors.split(', ')[0]?.trim();
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if (firstAuthor && firstAuthor !== 'et al.')
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base.matchedFirstAuthor = firstAuthor;
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const queried = queriedAuthorByKey.get(r.key);
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// Verified against the full roster, not `authors` — that display string
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// collapses to three names plus "et al.", so matching on it flags a
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// genuine fourth-or-later author as a mismatch. (#87)
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if (queried && authorNames?.length) {
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const querySurname = surname(queried);
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const articleSurnames =
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const articleSurnames = authorNames.map(surname);
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if (querySurname && !articleSurnames.includes(querySurname)) {
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warnings.push({
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code: 'author_mismatch',
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message: `Queried author "${queried}" not found in matched article
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message: `Queried author "${queried}" not found in the matched article's ${authorNames.length}-author roster (${authors}). ECitMatch weights journal+volume+page and may return a PMID whose authors disagree with the query — verify before using this PMID.`,
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});
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ctx.log.warning('Citation match returned PMID with author mismatch', {
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key: r.key,
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pmid: r.pmid,
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queriedAuthor: queried,
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matchedAuthorCount: authorNames.length,
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});
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}
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}
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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;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,
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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;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,qbAAqb;IAClc,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,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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;aACD,QAAQ,CACP,mLAAmL,CACpL;aACA,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,EAAE;YACtC,OAAO,EACL,uKAAuK;SAC1K,CAAC,CACL;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;aACE,MAAM,CAAC;YACN,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;YAC5E,cAAc,EAAE,CAAC;iBACd,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;iBAClC,QAAQ,EAAE;iBACV,QAAQ,CACP,sMAAsM,CACvM;YACH,kBAAkB,EAAE,CAAC;iBAClB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,sGAAsG,CACvG;YACH,QAAQ,EAAE,CAAC;iBACR,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,IAAI,CAAC,CAAC,iBAAiB,EAAE,eAAe,CAAC,CAAC;qBAC1C,QAAQ,CAAC,+BAA+B,CAAC;gBAC5C,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;aAC1E,CAAC;iBACD,QAAQ,CAAC,mCAAmC,CAAC,CACjD;iBACA,QAAQ,EAAE;iBACV,QAAQ,CACP,yLAAyL,CAC1L;SACJ,CAAC;aACD,QAAQ,CAAC,2BAA2B,CAAC,CACzC;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;QACpE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CAAC,6DAA6D,CAAC;KAC3E,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,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,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAExE,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACrD,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACnD,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;YAC1B,IAAI,CAAC,CAAC,UAAU;gBAAE,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC;YAC9D,IAAI,CAAC,CAAC,IAAI;gBAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC;QAClD,CAAC;QAED,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAC7B,IAAI,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAc,CAAC,CAAC,CACjF,CAAC;QAEF,MAAM,aAAa,GAAG,IAAI,GAAG,EAG1B,CAAC;QACJ,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAC5C,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;YACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;YAC7D,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE;oBACxB,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;oBACxC,GAAG,CAAC,CAAC,CAAC,WAAW,EAAE,MAAM,IAAI,EAAE,WAAW,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;oBAC5D,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;iBACzC,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAkBD,MAAM,MAAM,GAAmB,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC/C,MAAM,IAAI,GAAiB;gBACzB,GAAG,EAAE,CAAC,CAAC,GAAG;gBACV,OAAO,EAAE,CAAC,CAAC,OAAO;gBAClB,MAAM,EAAE,CAAC,CAAC,MAAM;gBAChB,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@@ -1,15 +1,19 @@
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1
1
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/**
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* @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
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-
* Searches the NCBI MeSH database
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3
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* Searches the NCBI MeSH database with offset pagination and optionally
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* retrieves detailed records.
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* @module src/mcp-server/tools/definitions/lookup-mesh.tool
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*/
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7
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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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9
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maxResults: z.ZodDefault<z.ZodNumber>;
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offset: z.ZodDefault<z.ZodNumber>;
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includeDetails: z.ZodDefault<z.ZodBoolean>;
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}, z.core.$strip>, z.ZodObject<{
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query: z.ZodString;
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15
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+
offset: z.ZodNumber;
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nextOffset: z.ZodOptional<z.ZodNumber>;
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results: z.ZodArray<z.ZodObject<{
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meshId: z.ZodString;
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15
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entrezUid: z.ZodString;
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@@ -19,34 +23,34 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
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19
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entryTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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20
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}, z.core.$strip>>;
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}, z.core.$strip>, readonly [{
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-
readonly reason:
|
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26
|
+
readonly reason: 'queue_full';
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23
27
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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|
24
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-
readonly when:
|
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25
|
-
readonly recovery:
|
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28
|
+
readonly when: 'Local NCBI request queue is at capacity.';
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29
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+
readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
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|
26
30
|
readonly retryable: true;
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27
31
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}, {
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|
28
|
-
readonly reason:
|
|
32
|
+
readonly reason: 'ncbi_unreachable';
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29
33
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
|
30
|
-
readonly when:
|
|
31
|
-
readonly recovery:
|
|
34
|
+
readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
|
|
35
|
+
readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
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|
32
36
|
readonly retryable: true;
|
|
33
37
|
}, {
|
|
34
|
-
readonly reason:
|
|
38
|
+
readonly reason: 'ncbi_deadline_exceeded';
|
|
35
39
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
|
|
36
|
-
readonly when:
|
|
37
|
-
readonly recovery:
|
|
40
|
+
readonly when: 'Total request deadline expired before NCBI returned a response.';
|
|
41
|
+
readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
|
|
38
42
|
readonly retryable: true;
|
|
39
43
|
}, {
|
|
40
|
-
readonly reason:
|
|
44
|
+
readonly reason: 'ncbi_invalid_response';
|
|
41
45
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
|
42
|
-
readonly when:
|
|
43
|
-
readonly recovery:
|
|
46
|
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readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
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readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
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readonly retryable: true;
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}, {
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readonly reason:
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readonly reason: 'ncbi_resource_not_found';
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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readonly when:
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readonly recovery:
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readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
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readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
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readonly retryable: false;
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}], {
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readonly totalCount: z.ZodNumber;
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@@ -1 +1 @@
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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
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1
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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;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwLzB,CAAC"}
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@@ -1,6 +1,7 @@
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/**
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* @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
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* Searches the NCBI MeSH database
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* Searches the NCBI MeSH database with offset pagination and optionally
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* retrieves detailed records.
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* @module src/mcp-server/tools/definitions/lookup-mesh.tool
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*/
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import { tool, z } from '@cyanheads/mcp-ts-core';
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@@ -90,7 +91,7 @@ function parseSummaryRecords(data, ids, includeDetails) {
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}
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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 the MeSH (Medical Subject Headings) controlled vocabulary. Returns descriptor records with tree numbers, scope notes, and entry terms.',
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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, plus pagination via offset for paging past the maxResults cap.',
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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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@@ -103,6 +104,12 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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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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maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
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offset: z
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.number()
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.int()
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.min(0)
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.default(0)
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.describe('Result offset for pagination (0-based). Pass the `nextOffset` from the previous response to get the following page; the exact-descriptor match is pinned to the first page only.'),
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includeDetails: z
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.boolean()
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.default(true)
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@@ -110,6 +117,11 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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}),
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output: z.object({
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query: z.string().describe('Original search query'),
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offset: z.number().describe('Result offset this page was read from'),
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nextOffset: z
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.number()
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.optional()
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.describe('Offset to request for the next page. Omitted when this is the last page, so its absence is the end-of-results signal.'),
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results: z
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.array(z
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.object({
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@@ -130,40 +142,70 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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.describe('Matching MeSH descriptor record'))
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.describe('Matching MeSH records'),
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}),
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// Result-set context —
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// and recovery guidance when no descriptor matched
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// to structuredContent and content[]
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// Result-set context — the upstream match count for disclosure against the maxResults
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// cap, and recovery guidance when no descriptor matched or the offset overshot.
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// Surfaced via ctx.enrich(...) to structuredContent and content[] alike.
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enrichment: {
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totalCount: z
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totalCount: z
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.number()
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.describe('Total MeSH descriptors matching the query upstream, before the maxResults cap'),
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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
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.describe('Optional guidance when no descriptors matched or the offset overshot the result set — suggests spell-check, free-text search, or resetting the offset. Absent on successful result pages.'),
|
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},
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async handler(input, ctx) {
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-
const { query, maxResults, includeDetails } = input;
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+
const { query, maxResults, offset, includeDetails } = input;
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const ncbi = getNcbiService();
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-
ctx.log.debug('MeSH lookup started', { query, maxResults, includeDetails });
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ctx.log.debug('MeSH lookup started', { query, maxResults, offset, 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: query, retmax: maxResults }, callOpts);
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const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults, retstart: offset }, callOpts);
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+
// The exact-descriptor match is resolved on every page, not just the first: it is
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+
// normally a member of the ranked list too, so every page has to know which UID to
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+
// hold back. The first page leads with it; later pages skip it where it ranks.
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|
const exactSearch = hasFieldTag
|
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168
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? undefined
|
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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
|
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|
+
const totalCount = broadResult.count;
|
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+
const pinnedUid = exactResult?.idList[0];
|
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173
|
const ids = [];
|
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|
-
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|
-
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-
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-
|
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|
+
if (pinnedUid !== undefined && offset === 0)
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+
ids.push(pinnedUid);
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+
// Count the ranked records this page consumed rather than assuming maxResults:
|
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|
+
// a pinned exact match outside the ranked window displaces one, and the next
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+
// offset has to resume exactly where this page stopped or that record is lost.
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+
let consumed = 0;
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+
for (const id of broadResult.idList) {
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+
// The pinned descriptor is served once, on the first page. Count its rank slot
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+
// as consumed wherever it lands so no later page hands it back a second time.
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|
+
if (id === pinnedUid) {
|
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+
consumed++;
|
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185
|
+
continue;
|
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|
}
|
|
187
|
+
if (ids.length >= maxResults)
|
|
188
|
+
break;
|
|
189
|
+
consumed++;
|
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|
+
ids.push(id);
|
|
161
191
|
}
|
|
162
|
-
|
|
192
|
+
const nextOffset = offset + consumed;
|
|
193
|
+
const hasMore = consumed > 0 && nextOffset < totalCount;
|
|
163
194
|
if (ids.length === 0) {
|
|
164
|
-
ctx.enrich.total(
|
|
165
|
-
|
|
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|
-
|
|
195
|
+
ctx.enrich.total(totalCount);
|
|
196
|
+
let notice;
|
|
197
|
+
if (totalCount === 0) {
|
|
198
|
+
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.`;
|
|
199
|
+
}
|
|
200
|
+
else if (consumed > 0) {
|
|
201
|
+
// The window held nothing but the pinned descriptor, already served at offset 0.
|
|
202
|
+
notice = `Offset ${offset} held only the exact-descriptor match for "${query}", which was returned on the first page.${hasMore ? ` Continue with offset ${nextOffset}.` : ''}`;
|
|
203
|
+
}
|
|
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|
+
else {
|
|
205
|
+
notice = `Offset ${offset} returned no records — "${query}" matches ${totalCount} MeSH descriptor(s). Reset offset to 0 or lower it below ${totalCount}.`;
|
|
206
|
+
}
|
|
207
|
+
ctx.enrich.notice(notice);
|
|
208
|
+
return { query, offset, ...(hasMore && { nextOffset }), results: [] };
|
|
167
209
|
}
|
|
168
210
|
const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
|
|
169
211
|
const results = parseSummaryRecords(summaryData, ids, includeDetails);
|
|
@@ -173,14 +215,23 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
|
|
|
173
215
|
const bExact = b.name.toLowerCase() === queryLower ? 0 : 1;
|
|
174
216
|
return aExact - bExact;
|
|
175
217
|
});
|
|
176
|
-
ctx.enrich.total(
|
|
177
|
-
|
|
218
|
+
ctx.enrich.total(totalCount);
|
|
219
|
+
// A page filled entirely by the pinned exact match consumed no ranked record,
|
|
220
|
+
// so there is no offset that advances — say so instead of emitting one that
|
|
221
|
+
// would replay this page.
|
|
222
|
+
if (consumed === 0 && totalCount > 0) {
|
|
223
|
+
ctx.enrich.notice(`The exact-descriptor match filled this page of ${maxResults}. Raise maxResults to see the ${totalCount} ranked match(es) for "${query}".`);
|
|
224
|
+
}
|
|
225
|
+
return { query, offset, ...(hasMore && { nextOffset }), results };
|
|
178
226
|
},
|
|
179
227
|
format: (result) => {
|
|
180
228
|
const lines = [
|
|
181
229
|
`# MeSH Lookup: "${result.query}"`,
|
|
182
|
-
`Found **${result.results.length}** result(s)
|
|
230
|
+
`Found **${result.results.length}** result(s) at offset **${result.offset}**.`,
|
|
183
231
|
];
|
|
232
|
+
if (result.nextOffset !== undefined) {
|
|
233
|
+
lines.push(`More available — call again with \`offset: ${result.nextOffset}\`.`);
|
|
234
|
+
}
|
|
184
235
|
for (const r of result.results) {
|
|
185
236
|
lines.push(`\n## ${r.name}`);
|
|
186
237
|
lines.push(`- **MeSH ID:** ${r.meshId}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,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;AAaxB;;;;;;GAMG;AACH,MAAM,iBAAiB,GAA2B,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AAEtF,SAAS,sBAAsB,CAAC,SAAiB;IAC/C,IAAI,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,iBAAiB,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACxD,IAAI,MAAM;YAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;IACtD,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,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,8EAA8E;QAC9E,6EAA6E;QAC7E,sDAAsD;QACtD,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtD,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;QACnC,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC5F,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;QACtB,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE5F,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAClC,MAAM,MAAM,GAAG,sBAAsB,CAAC,SAAS,CAAC,CAAC;QACjD,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,SAAS,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QACvD,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,0NAA0N;IAC5N,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,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,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,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,kLAAkL,CACnL;QACH,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,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QACpE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uHAAuH,CACxH;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CACP,mKAAmK,CACpK;YACH,SAAS,EAAE,CAAC;iBACT,MAAM,EAAE;iBACR,QAAQ,CACP,2FAA2F,CAC5F;YACH,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC;iBACX,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;iBACjB,QAAQ,EAAE;iBACV,QAAQ,CACP,2KAA2K,CAC5K;YACH,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;KACrC,CAAC;IAEF,sFAAsF;IACtF,gFAAgF;IAChF,yEAAyE;IACzE,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,2LAA2L,CAC5L;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QAC5D,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,cAAc,EAAE,CAAC,CAAC;QAEpF,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,CAC9B,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,EAAE,EACjE,QAAQ,CACT,CAAC;QACF,kFAAkF;QAClF,mFAAmF;QACnF,+EAA+E;QAC/E,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5E,MAAM,CAAC,WAAW,EAAE,WAAW,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC;QAEjF,MAAM,UAAU,GAAG,WAAW,CAAC,KAAK,CAAC;QACrC,MAAM,SAAS,GAAG,WAAW,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC;QACzC,MAAM,GAAG,GAAa,EAAE,CAAC;QACzB,IAAI,SAAS,KAAK,SAAS,IAAI,MAAM,KAAK,CAAC;YAAE,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QACjE,+EAA+E;QAC/E,6EAA6E;QAC7E,+EAA+E;QAC/E,IAAI,QAAQ,GAAG,CAAC,CAAC;QACjB,KAAK,MAAM,EAAE,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;YACpC,+EAA+E;YAC/E,8EAA8E;YAC9E,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;gBACrB,QAAQ,EAAE,CAAC;gBACX,SAAS;YACX,CAAC;YACD,IAAI,GAAG,CAAC,MAAM,IAAI,UAAU;gBAAE,MAAM;YACpC,QAAQ,EAAE,CAAC;YACX,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,GAAG,QAAQ,CAAC;QACrC,MAAM,OAAO,GAAG,QAAQ,GAAG,CAAC,IAAI,UAAU,GAAG,UAAU,CAAC;QAExD,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YAC7B,IAAI,MAAc,CAAC;YACnB,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;gBACrB,MAAM,GAAG,gCAAgC,KAAK,iKAAiK,CAAC;YAClN,CAAC;iBAAM,IAAI,QAAQ,GAAG,CAAC,EAAE,CAAC;gBACxB,iFAAiF;gBACjF,MAAM,GAAG,UAAU,MAAM,8CAA8C,KAAK,2CAC1E,OAAO,CAAC,CAAC,CAAC,yBAAyB,UAAU,GAAG,CAAC,CAAC,CAAC,EACrD,EAAE,CAAC;YACL,CAAC;iBAAM,CAAC;gBACN,MAAM,GAAG,UAAU,MAAM,2BAA2B,KAAK,aAAa,UAAU,4DAA4D,UAAU,GAAG,CAAC;YAC5J,CAAC;YACD,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;YAC1B,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,OAAO,IAAI,EAAE,UAAU,EAAE,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACxE,CAAC;QAED,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,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;QACvC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpB,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,OAAO,MAAM,GAAG,MAAM,CAAC;QACzB,CAAC,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAC7B,8EAA8E;QAC9E,4EAA4E;QAC5E,0BAA0B;QAC1B,IAAI,QAAQ,KAAK,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACrC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,kDAAkD,UAAU,iCAAiC,UAAU,0BAA0B,KAAK,IAAI,CAC3I,CAAC;QACJ,CAAC;QACD,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,OAAO,IAAI,EAAE,UAAU,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC;IACpE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,mBAAmB,MAAM,CAAC,KAAK,GAAG;YAClC,WAAW,MAAM,CAAC,OAAO,CAAC,MAAM,4BAA4B,MAAM,CAAC,MAAM,KAAK;SAC/E,CAAC;QACF,IAAI,MAAM,CAAC,UAAU,KAAK,SAAS,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,8CAA8C,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC;QACnF,CAAC;QACD,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,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC/C,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"}
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@@ -18,11 +18,11 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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18
18
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pageSize: z.ZodDefault<z.ZodNumber>;
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19
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cursorMark: z.ZodDefault<z.ZodString>;
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20
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sources: z.ZodOptional<z.ZodArray<z.ZodEnum<{
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21
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+
AGR: "AGR";
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MED: "MED";
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23
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+
PAT: "PAT";
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PMC: "PMC";
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23
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PPR: "PPR";
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24
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-
PAT: "PAT";
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25
|
-
AGR: "AGR";
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26
26
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}>>>;
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27
27
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resultType: z.ZodDefault<z.ZodEnum<{
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core: "core";
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@@ -32,11 +32,11 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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32
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}, z.core.$strip>, z.ZodObject<{
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hits: z.ZodArray<z.ZodObject<{
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34
34
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source: z.ZodEnum<{
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35
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+
AGR: "AGR";
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35
36
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MED: "MED";
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37
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+
PAT: "PAT";
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36
38
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PMC: "PMC";
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37
39
|
PPR: "PPR";
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|
38
|
-
PAT: "PAT";
|
|
39
|
-
AGR: "AGR";
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40
40
|
}>;
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41
41
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epmcId: z.ZodString;
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42
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title: z.ZodOptional<z.ZodString>;
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@@ -57,37 +57,37 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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57
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nextCursorMark: z.ZodOptional<z.ZodString>;
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58
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searchUrl: z.ZodString;
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59
59
|
}, z.core.$strip>, readonly [{
|
|
60
|
-
readonly reason:
|
|
60
|
+
readonly reason: 'europepmc_unreachable';
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61
61
|
readonly code: JsonRpcErrorCode.ServiceUnavailable;
|
|
62
|
-
readonly when:
|
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63
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-
readonly recovery:
|
|
62
|
+
readonly when: 'Europe PMC was unreachable after all retry attempts.';
|
|
63
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+
readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
|
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64
64
|
readonly retryable: true;
|
|
65
65
|
}, {
|
|
66
|
-
readonly reason:
|
|
66
|
+
readonly reason: 'europepmc_invalid_response';
|
|
67
67
|
readonly code: JsonRpcErrorCode.SerializationError;
|
|
68
|
-
readonly when:
|
|
69
|
-
readonly recovery:
|
|
68
|
+
readonly when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).';
|
|
69
|
+
readonly recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.';
|
|
70
70
|
readonly retryable: true;
|
|
71
71
|
}, {
|
|
72
|
-
readonly reason:
|
|
72
|
+
readonly reason: 'europepmc_invalid_input';
|
|
73
73
|
readonly code: JsonRpcErrorCode.ValidationError;
|
|
74
|
-
readonly when:
|
|
75
|
-
readonly recovery:
|
|
74
|
+
readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
|
|
75
|
+
readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
|
|
76
76
|
readonly retryable: false;
|
|
77
77
|
}, {
|
|
78
|
-
readonly reason:
|
|
78
|
+
readonly reason: 'europepmc_disabled';
|
|
79
79
|
readonly code: JsonRpcErrorCode.ConfigurationError;
|
|
80
|
-
readonly when:
|
|
81
|
-
readonly recovery:
|
|
80
|
+
readonly when: 'Europe PMC service is disabled via EUROPEPMC_ENABLED=false.';
|
|
81
|
+
readonly recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.';
|
|
82
82
|
}], {
|
|
83
83
|
readonly query: z.ZodString;
|
|
84
84
|
readonly totalCount: z.ZodNumber;
|
|
85
85
|
readonly appliedSources: z.ZodArray<z.ZodEnum<{
|
|
86
|
+
AGR: "AGR";
|
|
86
87
|
MED: "MED";
|
|
88
|
+
PAT: "PAT";
|
|
87
89
|
PMC: "PMC";
|
|
88
90
|
PPR: "PPR";
|
|
89
|
-
PAT: "PAT";
|
|
90
|
-
AGR: "AGR";
|
|
91
91
|
}>>;
|
|
92
92
|
readonly notice: z.ZodOptional<z.ZodString>;
|
|
93
93
|
}>;
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,yBAAyB
|
|
1
|
+
{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAiPjG,CAAC"}
|