@cyanheads/pubmed-mcp-server 2.10.0 → 2.10.2
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +1 -1
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.d.ts +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 +9 -2
- package/dist/mcp-server/prompts/definitions/research-plan.prompt.js.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js +26 -7
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js +4 -1
- package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +92 -20
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts +5 -3
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +17 -4
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +19 -2
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/text-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/text-helpers.js +15 -1
- package/dist/services/ncbi/parsing/text-helpers.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +1 -0
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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@@ -29,9 +29,11 @@ const epmcIdSchema = z
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.string()
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.regex(/^[A-Za-z0-9][A-Za-z0-9._-]*$/, 'epmcId must be a Europe PMC record identifier — letters, digits, dots, hyphens, or underscores only (e.g. "PPR1283828", "KR20120031038", "IND609436151"). Copy it verbatim from a pubmed_europepmc_search hit\'s `epmcId`.')
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.max(64);
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+
/** An `epmcId` in PMCID shape — `pubmed_fetch_fulltext` addresses these directly. */
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const PMCID_SHAPED_RE = /^PMC\d+$/i;
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const RecordRefSchema = z
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.object({
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source: SourceEnum.describe("Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`."),
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source: SourceEnum.describe("Europe PMC source corpus — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola). Copy it from the search hit's `source`. `PMC` paired with a PMCID resolves whether or not the article is also indexed in PubMed, and a PubMed-indexed one comes back as its canonical `MED` record carrying that PMCID in `pmcId`."),
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epmcId: epmcIdSchema.describe("Europe PMC's own record id within that source. Copy it from the search hit's `epmcId` — for `MED` records this is the PMID; for the other sources it is an EPMC-native accession."),
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})
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.describe('One record address: the Europe PMC source corpus plus its id within that corpus');
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@@ -46,7 +48,10 @@ const FetchedRecordSchema = z
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firstPublicationDate: z.string().optional().describe('First publication date (ISO YYYY-MM-DD)'),
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pmid: z.string().optional().describe('PMID when present in PubMed'),
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pmcId: z.string().optional().describe('PMC ID when present in PMC'),
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doi: z
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doi: z
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.string()
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.optional()
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.describe('DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch.'),
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isOpenAccess: z
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.boolean()
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.optional()
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@@ -135,20 +140,34 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
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// Europe PMC treats identifiers case-insensitively, so match the request
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// against the response on an upper-cased key rather than reporting a hit as
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// missing over a casing difference.
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const refKey = (
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const resolved = new Set(
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const
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const refKey = (source, id) => `${source}:${id.toUpperCase()}`;
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const resolved = new Set();
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for (const r of records) {
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resolved.add(refKey(r.source, r.epmcId));
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// A `PMC` request for a PubMed-indexed article resolves to that article's
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// canonical `MED` record, which reports the requested PMCID in `pmcId`
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// instead of as its own id. Without this alias the record comes back in
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// `records` and is reported missing in the same response.
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if (r.pmcId)
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resolved.add(refKey('PMC', r.pmcId));
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}
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const notFound = input.records.filter((ref) => !resolved.has(refKey(ref.source, ref.epmcId)));
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ctx.log.info('pubmed_europepmc_fetch completed', {
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requested: input.records.length,
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returned: records.length,
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});
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// An unresolved id shaped like a PMCID is reachable by another route:
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// pubmed_fetch_fulltext addresses PMCIDs directly, with no `source` pair.
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const pmcidHint = notFound.some((r) => PMCID_SHAPED_RE.test(r.epmcId))
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? ' An id shaped like a PMCID also resolves through pubmed_fetch_fulltext, whose `pmcids` input takes it on its own.'
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: '';
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if (records.length === 0) {
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ctx.enrich.notice(
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ctx.enrich.notice(`Europe PMC returned no record for any requested pair. Both fields must be copied verbatim from a pubmed_europepmc_search hit — \`epmcId\` is Europe PMC's own id (the PMID only for \`source: "MED"\`), and it must be paired with the same hit's \`source\`.${pmcidHint}`);
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}
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else if (notFound.length > 0) {
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ctx.enrich.notice(`Europe PMC returned no record for ${notFound.length} of ${input.records.length} requested pairs: ${notFound
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.map((r) => `${r.source}/${r.epmcId}`)
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.join(', ')}. Verify each against its pubmed_europepmc_search hit — a mismatched \`source\` is the usual cause
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.join(', ')}. Verify each against its pubmed_europepmc_search hit — a mismatched \`source\` is the usual cause.${pmcidHint}`);
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}
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return {
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records,
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@@ -1 +1 @@
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1
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-
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1
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+
{"version":3,"file":"pubmed-europepmc-fetch.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,+BAA+B,CAAC;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6CAA6C,CAAC;AAClF,OAAO,EAAE,qBAAqB,EAAE,MAAM,gCAAgC,CAAC;AACvE,OAAO,EAAE,aAAa,EAAE,MAAM,yCAAyC,CAAC;AACxE,OAAO,EACL,WAAW,EACX,cAAc,EACd,mBAAmB,EACnB,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;AAEjD;;;;;GAKG;AACH,MAAM,YAAY,GAAG,CAAC;KACnB,MAAM,EAAE;KACR,KAAK,CACJ,8BAA8B,EAC9B,4NAA4N,CAC7N;KACA,GAAG,CAAC,EAAE,CAAC,CAAC;AAEX,qFAAqF;AACrF,MAAM,eAAe,GAAG,WAAW,CAAC;AAEpC,MAAM,eAAe,GAAG,CAAC;KACtB,MAAM,CAAC;IACN,MAAM,EAAE,UAAU,CAAC,QAAQ,CACzB,2VAA2V,CAC5V;IACD,MAAM,EAAE,YAAY,CAAC,QAAQ,CAC3B,mLAAmL,CACpL;CACF,CAAC;KACD,QAAQ,CAAC,iFAAiF,CAAC,CAAC;AAE/F,MAAM,mBAAmB,GAAG,CAAC;KAC1B,MAAM,CAAC;IACN,MAAM,EAAE,UAAU,CAAC,QAAQ,CAAC,gDAAgD,CAAC;IAC7E,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IAC9D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;IACrD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IAClE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;IAC3D,oBAAoB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;IAC/F,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;IACnE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;IACnE,GAAG,EAAE,CAAC;SACH,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,qVAAqV,CACtV;IACH,YAAY,EAAE,CAAC;SACZ,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CAAC,sDAAsD,CAAC;IACnE,cAAc,EAAE,CAAC;SACd,OAAO,EAAE;SACT,QAAQ,EAAE;SACV,QAAQ,CACP,kJAAkJ,CACnJ;IACH,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,mLAAmL,CACpL;IACH,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;IACrF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;CACvD,CAAC;KACD,QAAQ,CAAC,4BAA4B,CAAC,CAAC;AAE1C,gFAAgF;AAEhF,MAAM,CAAC,MAAM,wBAAwB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IACrE,WAAW,EACT,kkBAAkkB;IACpkB,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,0HAA0H;IAE5H,MAAM,EAAE;QACN,GAAG,wBAAwB;QAC3B;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EAAE,mFAAmF;SAC9F;KACO;IAEV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,eAAe,CAAC;aACtB,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CACP,0JAA0J,CAC3J;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,mBAAmB,CAAC;aAC1B,QAAQ,CAAC,yDAAyD,CAAC;QACtE,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,eAAe,CAAC;aACtB,QAAQ,EAAE;aACV,QAAQ,CAAC,uEAAuE,CAAC;KACrF,CAAC;IAEF,0EAA0E;IAC1E,2EAA2E;IAC3E,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wGAAwG,CACzG;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,WAAW,EAAE,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,CAAC,CAAC;QACxF,MAAM,IAAI,GAAG,mBAAmB,EAAE,CAAC;QACnC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,GAAG,CAAC,IAAI,CACZ,oBAAoB,EACpB,mFAAmF,EACnF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC,EAAE,CAC7C,CAAC;QACJ,CAAC;QAED,MAAM,IAAI,GAAG,MAAM,IAAI,CAAC,YAAY,CAAC,KAAK,CAAC,OAAO,EAAE,GAAG,CAAC,MAAM,CAAC,CAAC;QAEhE,MAAM,OAAO,GAAG,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE;YAC7B,4EAA4E;YAC5E,wEAAwE;YACxE,2EAA2E;YAC3E,MAAM,QAAQ,GAAG,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;YACrE,OAAO;gBACL,MAAM,EAAE,CAAC,CAAC,MAAgD;gBAC1D,MAAM,EAAE,CAAC,CAAC,EAAE;gBACZ,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;gBAClC,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;gBAClD,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;gBAClD,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;gBACxC,GAAG,CAAC,CAAC,CAAC,oBAAoB,IAAI,EAAE,oBAAoB,EAAE,CAAC,CAAC,oBAAoB,EAAE,CAAC;gBAC/E,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC/B,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;gBAClC,GAAG,CAAC,CAAC,CAAC,GAAG,IAAI,EAAE,GAAG,EAAE,CAAC,CAAC,GAAG,EAAE,CAAC;gBAC5B,GAAG,CAAC,CAAC,CAAC,YAAY,KAAK,SAAS,IAAI,EAAE,YAAY,EAAE,CAAC,CAAC,YAAY,KAAK,GAAG,EAAE,CAAC;gBAC7E,GAAG,CAAC,CAAC,CAAC,KAAK,KAAK,SAAS,IAAI,EAAE,cAAc,EAAE,CAAC,CAAC,KAAK,KAAK,GAAG,EAAE,CAAC;gBACjE,GAAG,CAAC,QAAQ,IAAI,EAAE,QAAQ,EAAE,CAAC;gBAC7B,GAAG,CAAC,OAAO,CAAC,CAAC,YAAY,KAAK,QAAQ,IAAI,EAAE,YAAY,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;gBAC3E,OAAO,EAAE,iCAAiC,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,EAAE,EAAE;aAC7D,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,yEAAyE;QACzE,4EAA4E;QAC5E,oCAAoC;QACpC,MAAM,MAAM,GAAG,CAAC,MAAc,EAAE,EAAU,EAAE,EAAE,CAAC,GAAG,MAAM,IAAI,EAAE,CAAC,WAAW,EAAE,EAAE,CAAC;QAC/E,MAAM,QAAQ,GAAG,IAAI,GAAG,EAAU,CAAC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@@ -1 +1 @@
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1
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-
{"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;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;
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1
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+
{"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;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAyQjG,CAAC"}
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@@ -91,7 +91,10 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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91
91
|
.describe('First publication date (ISO YYYY-MM-DD)'),
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92
92
|
pmid: z.string().optional().describe('PMID when present in PubMed'),
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93
93
|
pmcId: z.string().optional().describe('PMC ID when present in PMC'),
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94
|
-
doi: z
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|
94
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+
doi: z
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95
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+
.string()
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96
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+
.optional()
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97
|
+
.describe('DOI when present, cased as Europe PMC reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so the same DOI can arrive in a different case from `pubmed_fetch_articles` (Europe PMC `10.1056/nejmoa2212948`, NCBI `10.1056/NEJMoa2212948`) — a byte-for-byte comparison across the two reports a false mismatch.'),
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95
98
|
isOpenAccess: z
|
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96
99
|
.boolean()
|
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97
100
|
.optional()
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@@ -1 +1 @@
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1
|
-
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@@ -1 +1 @@
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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;
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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;AA+IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgW7B,CAAC"}
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@@ -16,23 +16,67 @@ import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION
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16
16
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*/
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17
17
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const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
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18
18
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/**
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19
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-
*
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20
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-
*
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19
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+
* NCBI's eSearch serves `retstart` up to 9998 for PubMed and fails the whole
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20
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+
* request above it, so the ceiling is enforced at the edge where the caller can
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21
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+
* still act on it. The limit is db-specific — it does not apply to db=mesh.
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22
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+
*/
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23
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+
const OFFSET_MAX = 9998;
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24
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+
/** Upper bound on brief summaries fetched per call; shared by the schema and the format() cap message. */
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25
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+
const SUMMARY_COUNT_MAX = 50;
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26
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+
/** Renders a diagnostic list as a comma-separated set of backticked clauses. */
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27
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+
function quoteClauses(clauses) {
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28
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+
return clauses.map((clause) => `\`${clause}\``).join(', ');
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29
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+
}
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30
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+
/**
|
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31
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+
* Produces an optional human- and agent-readable hint for the cases where the
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32
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+
* returned PMIDs alone leave the caller without enough signal to recover.
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33
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+
*
|
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34
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+
* The signals are independent and can co-occur, so every applicable one is
|
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35
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+
* collected and joined rather than the first match being returned:
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36
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+
* - A `dateRange` with one bound filled, which drops the date filter entirely
|
|
37
|
+
* - Field tags PubMed did not recognize (results silently unrestricted)
|
|
38
|
+
* - Phrases PubMed matched nothing for
|
|
21
39
|
* - No matches at all (suggest spell-check / removing filters)
|
|
22
|
-
* - Filters applied but nothing matched (suggest relaxing filters)
|
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23
40
|
* - Pagination overshoot (offset ≥ totalCount)
|
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41
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+
*
|
|
42
|
+
* The one precedence rule: an unmatched phrase names the exact clause that
|
|
43
|
+
* returned nothing, so it replaces the generic empty-result guidance, which
|
|
44
|
+
* would only guess across every filter the request might have set.
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24
45
|
*/
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|
25
46
|
function buildNotice(args) {
|
|
26
|
-
const { totalCount, pmidCount, offset, hasFilters } = args;
|
|
47
|
+
const { totalCount, pmidCount, offset, hasFilters, partialDateBound, errorList, warningList } = args;
|
|
48
|
+
const notices = [];
|
|
49
|
+
if (partialDateBound) {
|
|
50
|
+
const missing = partialDateBound.name === 'minDate' ? 'maxDate' : 'minDate';
|
|
51
|
+
const sentinel = missing === 'maxDate' ? '3000' : '1800';
|
|
52
|
+
notices.push(`No date filter was applied: dateRange needs both bounds and only \`${partialDateBound.name}\` ("${partialDateBound.value}") was supplied. Set \`${missing}\` as well — for an open-ended range pass a wide sentinel (e.g. \`${missing}: "${sentinel}"\`).`);
|
|
53
|
+
}
|
|
54
|
+
const ignoredFields = [
|
|
55
|
+
...(errorList?.FieldNotFound ?? []),
|
|
56
|
+
...(warningList?.FieldNotFound ?? []),
|
|
57
|
+
];
|
|
58
|
+
if (ignoredFields.length > 0) {
|
|
59
|
+
notices.push(`PubMed did not recognize the field tag(s) ${quoteClauses(ignoredFields)} and searched those terms as free text, so these results are not restricted by that field. Correct the tag or drop it.`);
|
|
60
|
+
}
|
|
61
|
+
const unmatchedPhrases = [
|
|
62
|
+
...(errorList?.PhraseNotFound ?? []),
|
|
63
|
+
...(warningList?.PhraseNotFound ?? []),
|
|
64
|
+
...(warningList?.QuotedPhraseNotFound ?? []),
|
|
65
|
+
];
|
|
66
|
+
if (unmatchedPhrases.length > 0) {
|
|
67
|
+
notices.push(`PubMed matched nothing for ${quoteClauses(unmatchedPhrases)}, so that clause contributed no results. Check the spelling, or resolve the term with pubmed_lookup_mesh before filtering on it.`);
|
|
68
|
+
}
|
|
27
69
|
if (totalCount === 0) {
|
|
28
|
-
|
|
29
|
-
|
|
30
|
-
|
|
70
|
+
if (unmatchedPhrases.length === 0) {
|
|
71
|
+
notices.push(hasFilters
|
|
72
|
+
? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
|
|
73
|
+
: 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.');
|
|
74
|
+
}
|
|
31
75
|
}
|
|
32
|
-
if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
|
|
33
|
-
|
|
76
|
+
else if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
|
|
77
|
+
notices.push(`Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
|
|
34
78
|
}
|
|
35
|
-
return;
|
|
79
|
+
return notices.length > 0 ? notices.join(' ') : undefined;
|
|
36
80
|
}
|
|
37
81
|
const AppliedFiltersSchema = z.object({
|
|
38
82
|
dateRange: z
|
|
@@ -75,7 +119,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
75
119
|
input: z.object({
|
|
76
120
|
query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
|
|
77
121
|
maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
|
|
78
|
-
offset: z
|
|
122
|
+
offset: z
|
|
123
|
+
.number()
|
|
124
|
+
.int()
|
|
125
|
+
.min(0)
|
|
126
|
+
.max(OFFSET_MAX)
|
|
127
|
+
.default(0)
|
|
128
|
+
.describe(`Result offset for pagination (0-based). PubMed serves at most the first ${OFFSET_MAX + 1} records of a result set, so this caps at ${OFFSET_MAX}; narrow the query or add filters to reach anything beyond it.`),
|
|
79
129
|
sort: z
|
|
80
130
|
.enum(['relevance', 'pub_date', 'author', 'journal'])
|
|
81
131
|
.default('relevance')
|
|
@@ -115,9 +165,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
115
165
|
.number()
|
|
116
166
|
.int()
|
|
117
167
|
.min(0)
|
|
118
|
-
.max(
|
|
168
|
+
.max(SUMMARY_COUNT_MAX)
|
|
119
169
|
.default(0)
|
|
120
|
-
.describe(
|
|
170
|
+
.describe(`Fetch brief summaries for top N results (0 = PMIDs only). Above the ${SUMMARY_COUNT_MAX} cap, pass the remaining PMIDs to pubmed_fetch_articles.`),
|
|
121
171
|
}),
|
|
122
172
|
output: z.object({
|
|
123
173
|
query: z.string().describe('Original query'),
|
|
@@ -131,7 +181,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
131
181
|
authors: z.string().optional().describe('Formatted author string'),
|
|
132
182
|
source: z.string().optional().describe('Journal source'),
|
|
133
183
|
pubDate: z.string().optional().describe('Publication date'),
|
|
134
|
-
doi: z
|
|
184
|
+
doi: z
|
|
185
|
+
.string()
|
|
186
|
+
.optional()
|
|
187
|
+
.describe('DOI, cased as NCBI reports it. DOIs are case-insensitive by spec and no case normalization is applied here, so casing can differ from a Europe PMC-sourced `doi` — compare the two case-insensitively.'),
|
|
135
188
|
pmcId: z.string().optional().describe('PMC ID'),
|
|
136
189
|
pmcUrl: z.string().optional().describe('PMC URL'),
|
|
137
190
|
pubmedUrl: z.string().optional().describe('PubMed URL'),
|
|
@@ -153,7 +206,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
153
206
|
notice: z
|
|
154
207
|
.string()
|
|
155
208
|
.optional()
|
|
156
|
-
.describe('Optional guidance when
|
|
209
|
+
.describe('Optional guidance when the result set does not reflect what was asked for — a field tag PubMed ignored, a phrase it matched nothing for, a dateRange dropped for having one bound, no matches at all, or paging past the end. Absent when nothing applies.'),
|
|
157
210
|
},
|
|
158
211
|
// content[] trailer presentation for the enrichment block. structuredContent always
|
|
159
212
|
// carries the full structured value; this only shapes the human-facing trailer line.
|
|
@@ -196,14 +249,24 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
196
249
|
let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
|
|
197
250
|
// Build filters — capture normalized values for both query construction and appliedFilters
|
|
198
251
|
let normalizedDateRange;
|
|
199
|
-
|
|
252
|
+
const { dateRange } = input;
|
|
253
|
+
const minDate = dateRange?.minDate.trim() ?? '';
|
|
254
|
+
const maxDate = dateRange?.maxDate.trim() ?? '';
|
|
255
|
+
if (dateRange && minDate && maxDate) {
|
|
200
256
|
normalizedDateRange = {
|
|
201
|
-
minDate:
|
|
202
|
-
maxDate:
|
|
203
|
-
dateType:
|
|
257
|
+
minDate: minDate.replace(/[-.]/g, '/'),
|
|
258
|
+
maxDate: maxDate.replace(/[-.]/g, '/'),
|
|
259
|
+
dateType: dateRange.dateType,
|
|
204
260
|
};
|
|
205
261
|
effectiveQuery += ` AND (${normalizedDateRange.minDate}[${normalizedDateRange.dateType}] : ${normalizedDateRange.maxDate}[${normalizedDateRange.dateType}])`;
|
|
206
262
|
}
|
|
263
|
+
// Both bounds are required for the filter to apply, so one filled bound is a
|
|
264
|
+
// dropped date range the caller gets no other signal about.
|
|
265
|
+
const partialDateBound = minDate && !maxDate
|
|
266
|
+
? { name: 'minDate', value: minDate }
|
|
267
|
+
: maxDate && !minDate
|
|
268
|
+
? { name: 'maxDate', value: maxDate }
|
|
269
|
+
: undefined;
|
|
207
270
|
let sanitizedPubTypes;
|
|
208
271
|
if (input.publicationTypes?.length) {
|
|
209
272
|
sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
|
|
@@ -297,6 +360,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
297
360
|
pmidCount: pmids.length,
|
|
298
361
|
offset: input.offset,
|
|
299
362
|
hasFilters: Object.keys(appliedFilters).length > 0,
|
|
363
|
+
...(partialDateBound && { partialDateBound }),
|
|
364
|
+
...(esResult.errorList && { errorList: esResult.errorList }),
|
|
365
|
+
...(esResult.warningList && { warningList: esResult.warningList }),
|
|
300
366
|
});
|
|
301
367
|
ctx.enrich({ effectiveQuery, appliedFilters });
|
|
302
368
|
ctx.enrich.total(esResult.count);
|
|
@@ -321,7 +387,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
321
387
|
lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
|
|
322
388
|
if (result.summaries?.length) {
|
|
323
389
|
if (result.summaries.length < result.pmids.length) {
|
|
324
|
-
|
|
390
|
+
const shown = `Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs`;
|
|
391
|
+
lines.push(
|
|
392
|
+
// At the cap there is no knob left to raise, so point at the tool that
|
|
393
|
+
// can read the rest instead of at `summaryCount`.
|
|
394
|
+
result.summaries.length >= SUMMARY_COUNT_MAX
|
|
395
|
+
? `\n> ${shown} — \`summaryCount\` is at its maximum (${SUMMARY_COUNT_MAX}). Fetch the remaining ${result.pmids.length - result.summaries.length} with \`pubmed_fetch_articles\` using the PMIDs above.`
|
|
396
|
+
: `\n> ${shown}. Increase \`summaryCount\` (max ${SUMMARY_COUNT_MAX}) to fetch more.`);
|
|
325
397
|
}
|
|
326
398
|
lines.push('\n### Summaries');
|
|
327
399
|
for (const s of result.summaries) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -40,12 +40,14 @@ export declare class EuropePmcService {
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40
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search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
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41
41
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/**
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* Look up specific records by `source` + EPMC id. One search request covers
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43
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-
* the whole batch: each ref becomes
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44
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-
*
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43
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+
* the whole batch: each ref becomes a `recordLookupQuery` clause, OR-joined
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44
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+
* into a single query.
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*
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* Returns the hits Europe PMC resolved, in the order it returned them.
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* Unmatched refs are simply absent — callers diff against their own request
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48
|
-
* to report misses rather than getting a padded array back.
|
|
48
|
+
* to report misses rather than getting a padded array back. A `PMC` ref can
|
|
49
|
+
* resolve to a `MED`-source hit that reports the requested PMCID in `pmcid`
|
|
50
|
+
* rather than as its `id`, so that diff matches on the PMCID too.
|
|
49
51
|
*/
|
|
50
52
|
fetchRecords(refs: readonly EuropePmcRecordRef[], signal?: AbortSignal): Promise<EuropePmcSearchHit[]>;
|
|
51
53
|
/**
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;
|
|
1
|
+
{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAkDpB;;;;;;;;;GASG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM,EAiBpC;IAED;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA6F1E;IAED;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CAgBlC;IAED;;;;;;;;;OASG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;OASG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;OAGG;YACW,iBAAiB;IA6C/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}
|
|
@@ -53,9 +53,20 @@ function abortableSleep(ms, signal) {
|
|
|
53
53
|
* `EXT_ID:"<id>" AND SRC:<source>` — quotes survive on an identifier token only
|
|
54
54
|
* while no `AND SRC:` clause follows it. Callers pass ids through a schema that
|
|
55
55
|
* restricts them to identifier characters, so no escaping is applied here.
|
|
56
|
+
*
|
|
57
|
+
* `SRC:PMC` alone under-resolves: the PMC corpus holds only articles Europe PMC
|
|
58
|
+
* has no PubMed record for. Once an article is indexed in PubMed its canonical
|
|
59
|
+
* record moves to `MED` and carries the PMCID as a field, so `EXT_ID:PMC8371605
|
|
60
|
+
* AND SRC:PMC` matches nothing while `PMCID:PMC8371605` resolves it. OR the two
|
|
61
|
+
* together for `PMC` so both corpus placements resolve from one request. The
|
|
62
|
+
* same asymmetry drove the PMCID branch of `pubmed_fetch_fulltext` (#85); that
|
|
63
|
+
* path can drop the `SRC:PMC` clause outright because it never takes a
|
|
64
|
+
* caller-supplied source, whereas this one must still serve genuine PMC-only
|
|
65
|
+
* records. (#94)
|
|
56
66
|
*/
|
|
57
67
|
function recordLookupQuery({ epmcId, source }) {
|
|
58
|
-
|
|
68
|
+
const extIdClause = `(EXT_ID:${epmcId} AND SRC:${source})`;
|
|
69
|
+
return source === 'PMC' ? `${extIdClause} OR (PMCID:${epmcId})` : extIdClause;
|
|
59
70
|
}
|
|
60
71
|
/**
|
|
61
72
|
* Facade over the Europe PMC REST API:
|
|
@@ -176,12 +187,14 @@ export class EuropePmcService {
|
|
|
176
187
|
}
|
|
177
188
|
/**
|
|
178
189
|
* Look up specific records by `source` + EPMC id. One search request covers
|
|
179
|
-
* the whole batch: each ref becomes
|
|
180
|
-
*
|
|
190
|
+
* the whole batch: each ref becomes a `recordLookupQuery` clause, OR-joined
|
|
191
|
+
* into a single query.
|
|
181
192
|
*
|
|
182
193
|
* Returns the hits Europe PMC resolved, in the order it returned them.
|
|
183
194
|
* Unmatched refs are simply absent — callers diff against their own request
|
|
184
|
-
* to report misses rather than getting a padded array back.
|
|
195
|
+
* to report misses rather than getting a padded array back. A `PMC` ref can
|
|
196
|
+
* resolve to a `MED`-source hit that reports the requested PMCID in `pmcid`
|
|
197
|
+
* rather than as its `id`, so that diff matches on the PMCID too.
|
|
185
198
|
*/
|
|
186
199
|
async fetchRecords(refs, signal) {
|
|
187
200
|
const result = await this.search({
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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@@ -1 +1 @@
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1
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{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,
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1
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+
{"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgEpB;;;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;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,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,CAIZ;IAED,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,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CAyBxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;OAGG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAkE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAiE5B;IAED,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA4BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
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@@ -23,6 +23,21 @@ const ID_CONVERT_FORMAT_HINTS = {
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23
23
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pmcid: '"PMC" + digits or bare digits, e.g. "PMC3531190" or "3531190"',
|
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24
24
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doi: 'starts with "10.", e.g. "10.1093/nar/gks1195"',
|
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25
25
|
};
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26
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+
/**
|
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27
|
+
* NCBI collapses a single-entry `ErrorList`/`WarningList` member to a scalar and
|
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28
|
+
* leaves multi-entry members as arrays, and `parseTagValue` coerces a numeric-looking
|
|
29
|
+
* phrase to a number. Normalize every member to `string[]` so `ESearchErrorList` /
|
|
30
|
+
* `ESearchWarningList` describe what callers actually receive.
|
|
31
|
+
*/
|
|
32
|
+
function normalizeDiagnosticList(list) {
|
|
33
|
+
if (!list)
|
|
34
|
+
return;
|
|
35
|
+
const normalized = {};
|
|
36
|
+
for (const [key, value] of Object.entries(list)) {
|
|
37
|
+
normalized[key] = (Array.isArray(value) ? value : [value]).map(String);
|
|
38
|
+
}
|
|
39
|
+
return normalized;
|
|
40
|
+
}
|
|
26
41
|
/** Sentinel reason used when the service-level deadline expires. */
|
|
27
42
|
class NcbiDeadlineExceeded extends Error {
|
|
28
43
|
constructor(deadlineMs) {
|
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@@ -74,6 +89,8 @@ export class NcbiService {
|
|
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74
89
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...(options?.signal && { signal: options.signal }),
|
|
75
90
|
});
|
|
76
91
|
const esResult = response.eSearchResult;
|
|
92
|
+
const errorList = normalizeDiagnosticList(esResult.ErrorList);
|
|
93
|
+
const warningList = normalizeDiagnosticList(esResult.WarningList);
|
|
77
94
|
return {
|
|
78
95
|
count: parseInt(esResult.Count, 10) || 0,
|
|
79
96
|
retmax: parseInt(esResult.RetMax, 10) || 0,
|
|
@@ -82,8 +99,8 @@ export class NcbiService {
|
|
|
82
99
|
...(esResult.WebEnv !== undefined && { webEnv: esResult.WebEnv }),
|
|
83
100
|
idList: (esResult.IdList?.Id ?? []).map(String),
|
|
84
101
|
queryTranslation: esResult.QueryTranslation,
|
|
85
|
-
...(
|
|
86
|
-
...(
|
|
102
|
+
...(errorList !== undefined && { errorList }),
|
|
103
|
+
...(warningList !== undefined && { warningList }),
|
|
87
104
|
};
|
|
88
105
|
}
|
|
89
106
|
async eSummary(params, options) {
|