@cyanheads/pubmed-mcp-server 2.7.7 → 2.7.8
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 +365 -0
- package/CLAUDE.md +2 -2
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +1 -1
- 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 +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +4 -3
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +17 -9
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +3 -2
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +7 -8
- 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 +12 -11
- 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 +26 -13
- 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 +27 -26
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +51 -44
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/package.json +5 -4
- package/server.json +3 -3
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@@ -101,11 +101,15 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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})
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.describe('Matching MeSH descriptor record'))
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.describe('Matching MeSH records'),
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}),
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+
// Recovery guidance when no descriptor matched — agent-facing context, surfaced via
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// ctx.enrich.notice() to both structuredContent and content[]; absent on success.
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enrichment: {
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notice: z
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.string()
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.optional()
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.describe('Optional guidance when no descriptors matched — suggests spell-check or free-text search. Absent on successful results.'),
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}
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},
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async handler(input, ctx) {
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const { query, maxResults, includeDetails } = input;
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const ncbi = getNcbiService();
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@@ -127,11 +131,8 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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}
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ids.length = Math.min(ids.length, maxResults);
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if (ids.length === 0) {
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-
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-
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results: [],
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notice: `No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`,
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};
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ctx.enrich.notice(`No MeSH descriptors matched "${query}". Try \`pubmed_spell_check\` for a suggested correction, broaden the term, or use \`pubmed_search_articles\` for free-text discovery against article metadata.`);
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return { query, results: [] };
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}
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const summaryData = await ncbi.eSummary({ db: 'mesh', id: ids.join(',') }, callOpts);
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const results = parseSummaryRecords(summaryData, ids, includeDetails);
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@@ -148,8 +149,6 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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`# MeSH Lookup: "${result.query}"`,
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`Found **${result.results.length}** result(s).`,
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];
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-
if (result.notice)
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lines.push(`\n> ${result.notice}`);
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for (const r of result.results) {
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lines.push(`\n## ${r.name}`);
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lines.push(`- **MeSH ID:** ${r.meshId}`);
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@@ -1 +1 @@
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1
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-
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+
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,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;AAYxB,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,IAAI,GAAG;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IAC9B,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,mBAAmB,CAAC,IAAa,EAAE,GAAa,EAAE,cAAuB;IAChF,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC1F,MAAM,IAAI,GAAG,IAA+B,CAAC;IAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,cAAqD,CAAC;IACjF,MAAM,OAAO,GAAG,WAAW,CACzB,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,MAAiC,CAC1D,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,EAAE,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE7E,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,MAAM,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAC/B,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,IAAI,CAA8B,CAAC;QACjE,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,IAAI,MAAM,CAAC;QACpE,MAAM,MAAM,GAAe,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QAC5C,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YAC/D,IAAI,SAAS;gBAAE,MAAM,CAAC,SAAS,GAAG,SAAS,CAAC;YAC5C,MAAM,UAAU,GAAG,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YACjE,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC1D,MAAM,WAAW,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,WAAW,GAAG,WAAW,CAAC;QAC/D,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC,CAAC;AACL,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,2JAA2J;IAC7J,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC;QACjB,mBAAmB;QACnB,uBAAuB;QACvB,yBAAyB;QACzB,mBAAmB;KACpB,CAAC;IACF,SAAS,EACP,+GAA+G;IAEjH,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,cAAc,EAAE,CAAC;aACd,OAAO,EAAE;aACT,OAAO,CAAC,IAAI,CAAC;aACb,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnD,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mCAAmC,CAAC;YAChE,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;YACvD,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SAC9E,CAAC;aACD,QAAQ,CAAC,iCAAiC,CAAC,CAC/C;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,oFAAoF;IACpF,kFAAkF;IAClF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yHAAyH,CAC1H;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QACpD,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,cAAc,EAAE,CAAC,CAAC;QAE5E,MAAM,WAAW,GAAG,QAAQ,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC;QACzC,MAAM,QAAQ,GAAG,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;QACxC,MAAM,WAAW,GAAG,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5F,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,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,IAAI,GAAG,IAAI,GAAG,EAAU,CAAC;QAC/B,MAAM,GAAG,GAAa,EAAE,CAAC;QACzB,KAAK,MAAM,EAAE,IAAI,CAAC,GAAG,CAAC,WAAW,EAAE,MAAM,IAAI,EAAE,CAAC,EAAE,GAAG,WAAW,CAAC,MAAM,CAAC,EAAE,CAAC;YACzE,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,EAAE,CAAC;gBAClB,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;gBACb,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,CAAC;QACH,CAAC;QACD,GAAG,CAAC,MAAM,GAAG,IAAI,CAAC,GAAG,CAAC,GAAG,CAAC,MAAM,EAAE,UAAU,CAAC,CAAC;QAE9C,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,gCAAgC,KAAK,iKAAiK,CACvM,CAAC;YACF,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QAChC,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,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,CAAC;IAC5B,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,eAAe;SAChD,CAAC;QACF,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC7B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACzC,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACzF,IAAI,CAAC,CAAC,SAAS;gBAAE,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,UAAU,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACxF,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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@@ -30,7 +30,6 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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30
30
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}>>;
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31
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sort: z.ZodOptional<z.ZodString>;
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32
32
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}, z.core.$strip>, z.ZodObject<{
|
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33
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-
query: z.ZodString;
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34
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hits: z.ZodArray<z.ZodObject<{
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35
34
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source: z.ZodEnum<{
|
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36
35
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MED: "MED";
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@@ -54,18 +53,9 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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54
53
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citedByCount: z.ZodOptional<z.ZodNumber>;
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55
54
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epmcUrl: z.ZodString;
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56
55
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}, z.core.$strip>>;
|
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57
|
-
hitCount: z.ZodNumber;
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58
56
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cursorMark: z.ZodString;
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59
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nextCursorMark: z.ZodOptional<z.ZodString>;
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60
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-
appliedSources: z.ZodArray<z.ZodEnum<{
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61
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-
MED: "MED";
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62
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-
PMC: "PMC";
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63
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-
PPR: "PPR";
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64
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-
PAT: "PAT";
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65
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-
AGR: "AGR";
|
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-
}>>;
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67
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searchUrl: z.ZodString;
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68
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-
notice: z.ZodOptional<z.ZodString>;
|
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69
59
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}, z.core.$strip>, readonly [{
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70
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|
readonly reason: "europepmc_unreachable";
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71
61
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readonly code: JsonRpcErrorCode.ServiceUnavailable;
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@@ -89,5 +79,16 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
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89
79
|
readonly code: JsonRpcErrorCode.ConfigurationError;
|
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90
80
|
readonly when: "Europe PMC service is disabled via EUROPEPMC_ENABLED=false.";
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91
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|
readonly recovery: "Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.";
|
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92
|
-
}]
|
|
82
|
+
}], {
|
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83
|
+
readonly query: z.ZodString;
|
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84
|
+
readonly hitCount: z.ZodNumber;
|
|
85
|
+
readonly appliedSources: z.ZodArray<z.ZodEnum<{
|
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86
|
+
MED: "MED";
|
|
87
|
+
PMC: "PMC";
|
|
88
|
+
PPR: "PPR";
|
|
89
|
+
PAT: "PAT";
|
|
90
|
+
AGR: "AGR";
|
|
91
|
+
}>>;
|
|
92
|
+
readonly notice: z.ZodOptional<z.ZodString>;
|
|
93
|
+
}>;
|
|
93
94
|
//# sourceMappingURL=pubmed-europepmc-search.tool.d.ts.map
|
|
@@ -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;AAmBjE,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;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8OpC,CAAC"}
|
|
@@ -64,7 +64,6 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
|
|
|
64
64
|
.describe('Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC.'),
|
|
65
65
|
}),
|
|
66
66
|
output: z.object({
|
|
67
|
-
query: z.string().describe('Effective query string echoed by Europe PMC'),
|
|
68
67
|
hits: z
|
|
69
68
|
.array(z
|
|
70
69
|
.object({
|
|
@@ -100,21 +99,36 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
|
|
|
100
99
|
})
|
|
101
100
|
.describe('Single Europe PMC record returned by the search'))
|
|
102
101
|
.describe('Matching Europe PMC records, in the order EPMC returned them'),
|
|
103
|
-
hitCount: z.number().describe('Total matching records across all pages'),
|
|
104
102
|
cursorMark: z.string().describe('Cursor used for this response (echoed from the request)'),
|
|
105
103
|
nextCursorMark: z
|
|
106
104
|
.string()
|
|
107
105
|
.optional()
|
|
108
106
|
.describe('Cursor to pass back as `cursorMark` for the next page. Absent on the final page.'),
|
|
107
|
+
searchUrl: z.string().describe("Europe PMC's website search URL for this query"),
|
|
108
|
+
}),
|
|
109
|
+
// Result-set context the agent reasons with — the query as EPMC echoed it, the total
|
|
110
|
+
// match count, the sources actually queried, and recovery guidance for empty pages.
|
|
111
|
+
// Surfaced via ctx.enrich(...) to structuredContent and content[]; out of the return.
|
|
112
|
+
enrichment: {
|
|
113
|
+
query: z.string().describe('Effective query string echoed by Europe PMC'),
|
|
114
|
+
hitCount: z.number().describe('Total matching records across all pages'),
|
|
109
115
|
appliedSources: z
|
|
110
116
|
.array(SourceEnum)
|
|
111
117
|
.describe('Sources the query was filtered against (defaults applied)'),
|
|
112
|
-
searchUrl: z.string().describe("Europe PMC's website search URL for this query"),
|
|
113
118
|
notice: z
|
|
114
119
|
.string()
|
|
115
120
|
.optional()
|
|
116
121
|
.describe('Optional guidance when results are empty or paging overshot'),
|
|
117
|
-
}
|
|
122
|
+
},
|
|
123
|
+
// content[] trailer presentation for the enrichment block. structuredContent always
|
|
124
|
+
// carries the full structured value; this only shapes the human-facing trailer line.
|
|
125
|
+
enrichmentTrailer: {
|
|
126
|
+
query: { label: 'Effective Query' },
|
|
127
|
+
hitCount: { label: 'Total Hits' },
|
|
128
|
+
appliedSources: {
|
|
129
|
+
render: (sources) => `**Sources:** ${sources.join(', ')}`,
|
|
130
|
+
},
|
|
131
|
+
},
|
|
118
132
|
async handler(input, ctx) {
|
|
119
133
|
ctx.log.info('Executing pubmed_europepmc_search', { query: input.query });
|
|
120
134
|
const epmc = getEuropePmcService();
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@@ -158,28 +172,27 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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158
172
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returnedHits: hits.length,
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159
173
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hasNextPage: !!result.nextCursorMark,
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160
174
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});
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161
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-
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175
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+
ctx.enrich({
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162
176
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query: result.query,
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163
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-
hits,
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164
177
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hitCount: result.hitCount,
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178
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+
appliedSources: [...sources],
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179
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+
});
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180
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+
if (notice)
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181
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+
ctx.enrich.notice(notice);
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182
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+
return {
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183
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+
hits,
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165
184
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cursorMark: result.cursorMark ?? '*',
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166
185
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...(result.nextCursorMark && { nextCursorMark: result.nextCursorMark }),
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167
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-
appliedSources: [...sources],
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168
186
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searchUrl: `https://europepmc.org/search?query=${encodeURIComponent(input.query)}`,
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169
|
-
...(notice && { notice }),
|
|
170
187
|
};
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|
171
188
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},
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|
172
189
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format: (result) => {
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173
190
|
const lines = [
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174
191
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'## Europe PMC Search Results',
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175
|
-
`**
|
|
176
|
-
`**Total Hits:** ${result.hitCount} | **Returned:** ${result.hits.length}`,
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177
|
-
`**Sources:** ${result.appliedSources.join(', ')}`,
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192
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+
`**Returned:** ${result.hits.length}`,
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|
178
193
|
`**Cursor:** ${result.cursorMark}${result.nextCursorMark ? ` → \`${result.nextCursorMark}\` (next page)` : ' (final page)'}`,
|
|
179
194
|
`**Search URL:** ${result.searchUrl}`,
|
|
180
195
|
];
|
|
181
|
-
if (result.notice)
|
|
182
|
-
lines.push(`\n> ${result.notice}`);
|
|
183
196
|
if (result.hits.length > 0) {
|
|
184
197
|
lines.push('\n### Hits');
|
|
185
198
|
for (const h of result.hits) {
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|
@@ -1 +1 @@
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|
|
1
|
-
{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.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,EACL,qBAAqB,EACrB,yBAAyB,GAE1B,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,WAAW,EACX,oBAAoB,EACpB,cAAc,EACd,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC;AAE/D,gFAAgF;AAEhF,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACvE,WAAW,EACT,4YAA4Y;IAC9Y,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,EAAE,cAAc,CAAC,CAAC;IAChF,SAAS,EACP,2HAA2H;IAE7H,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,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,kPAAkP,CACnP;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,yCAAyC,CAAC;QACtD,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,8HAA8H,CAC/H;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,UAAU,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,gDAAgD,yBAAyB,CAAC,IAAI,CAAC,IAAI,CAAC,mGAAmG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAC3N;QACH,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;aACtB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,qGAAqG,CACtG;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6VAA6V,CAC9V;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,
|
|
1
|
+
{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.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,EACL,qBAAqB,EACrB,yBAAyB,GAE1B,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,WAAW,EACX,oBAAoB,EACpB,cAAc,EACd,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC;AAE/D,gFAAgF;AAEhF,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACvE,WAAW,EACT,4YAA4Y;IAC9Y,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,EAAE,cAAc,CAAC,CAAC;IAChF,SAAS,EACP,2HAA2H;IAE7H,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,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,kPAAkP,CACnP;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,yCAAyC,CAAC;QACtD,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,8HAA8H,CAC/H;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,UAAU,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,gDAAgD,yBAAyB,CAAC,IAAI,CAAC,IAAI,CAAC,mGAAmG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAC3N;QACH,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;aACtB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,qGAAqG,CACtG;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,6VAA6V,CAC9V;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,IAAI,EAAE,CAAC;aACJ,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,UAAU,CAAC,QAAQ,CACzB,gHAAgH,CACjH;YACD,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CAAC,+DAA+D,CAAC;YAC5E,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;YAClE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,oBAAoB,EAAE,CAAC;iBACpB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,yCAAyC,CAAC;YACtD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YACnE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;YACnE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YACvD,YAAY,EAAE,CAAC;iBACZ,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CAAC,gDAAgD,CAAC;YAC7D,cAAc,EAAE,CAAC;iBACd,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CACP,iMAAiM,CAClM;YACH,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,qFAAqF,CACtF;YACH,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;YACrF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SACvD,CAAC;aACD,QAAQ,CAAC,iDAAiD,CAAC,CAC/D;aACA,QAAQ,CAAC,8DAA8D,CAAC;QAC3E,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;QAC1F,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kFAAkF,CAAC;QAC/F,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;KACjF,CAAC;IAEF,qFAAqF;IACrF,oFAAoF;IACpF,sFAAsF;IACtF,UAAU,EAAE;QACV,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QACzE,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACxE,cAAc,EAAE,CAAC;aACd,KAAK,CAAC,UAAU,CAAC;aACjB,QAAQ,CAAC,2DAA2D,CAAC;QACxE,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6DAA6D,CAAC;KAC3E;IAED,oFAAoF;IACpF,qFAAqF;IACrF,iBAAiB,EAAE;QACjB,KAAK,EAAE,EAAE,KAAK,EAAE,iBAAiB,EAAE;QACnC,QAAQ,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE;QACjC,cAAc,EAAE;YACd,MAAM,EAAE,CAAC,OAAO,EAAE,EAAE,CAAC,gBAAgB,OAAO,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE;SAC1D;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,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,OAAO,GAAG,CAAC,KAAK,CAAC,OAAO,IAAI,yBAAyB,CAA+B,CAAC;QAC3F,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC;YAC/B,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,QAAQ,EAAE,KAAK,CAAC,QAAQ;YACxB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,OAAO;YACP,GAAG,CAAC,KAAK,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC;YACvC,GAAG,CAAC,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;SAC1C,CAAC,CAAC;QAEH,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACnC,MAAM,EAAE,CAAC,CAAC,MAA+C;YACzD,MAAM,EAAE,CAAC,CAAC,EAAE;YACZ,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;YAClC,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,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@@ -37,30 +37,6 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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37
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summaryCount: z.ZodDefault<z.ZodNumber>;
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38
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}, z.core.$strip>, z.ZodObject<{
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query: z.ZodString;
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-
effectiveQuery: z.ZodString;
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appliedFilters: z.ZodObject<{
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dateRange: z.ZodOptional<z.ZodObject<{
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minDate: z.ZodString;
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maxDate: z.ZodString;
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dateType: z.ZodEnum<{
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pdat: "pdat";
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-
mdat: "mdat";
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edat: "edat";
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-
}>;
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-
}, z.core.$strip>>;
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-
publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
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author: z.ZodOptional<z.ZodString>;
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journal: z.ZodOptional<z.ZodString>;
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meshTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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language: z.ZodOptional<z.ZodString>;
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hasAbstract: z.ZodOptional<z.ZodBoolean>;
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freeFullText: z.ZodOptional<z.ZodBoolean>;
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species: z.ZodOptional<z.ZodEnum<{
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humans: "humans";
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animals: "animals";
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-
}>>;
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-
}, z.core.$strip>;
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-
totalFound: z.ZodNumber;
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40
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offset: z.ZodNumber;
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65
41
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pmids: z.ZodArray<z.ZodString>;
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66
42
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summaries: z.ZodArray<z.ZodObject<{
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@@ -75,7 +51,6 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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75
51
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pubmedUrl: z.ZodOptional<z.ZodString>;
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76
52
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}, z.core.$strip>>;
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53
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searchUrl: z.ZodString;
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-
notice: z.ZodOptional<z.ZodString>;
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79
54
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}, z.core.$strip>, readonly [{
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80
55
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readonly reason: "queue_full";
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81
56
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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@@ -106,5 +81,31 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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106
81
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readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
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107
82
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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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108
83
|
readonly retryable: false;
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109
|
-
}]
|
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84
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+
}], {
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85
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+
readonly effectiveQuery: z.ZodString;
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86
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+
readonly totalFound: z.ZodNumber;
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87
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+
readonly appliedFilters: z.ZodObject<{
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88
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+
dateRange: z.ZodOptional<z.ZodObject<{
|
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89
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+
minDate: z.ZodString;
|
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90
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+
maxDate: z.ZodString;
|
|
91
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+
dateType: z.ZodEnum<{
|
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92
|
+
pdat: "pdat";
|
|
93
|
+
mdat: "mdat";
|
|
94
|
+
edat: "edat";
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|
95
|
+
}>;
|
|
96
|
+
}, z.core.$strip>>;
|
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97
|
+
publicationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
98
|
+
author: z.ZodOptional<z.ZodString>;
|
|
99
|
+
journal: z.ZodOptional<z.ZodString>;
|
|
100
|
+
meshTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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101
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+
language: z.ZodOptional<z.ZodString>;
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102
|
+
hasAbstract: z.ZodOptional<z.ZodBoolean>;
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103
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+
freeFullText: z.ZodOptional<z.ZodBoolean>;
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104
|
+
species: z.ZodOptional<z.ZodEnum<{
|
|
105
|
+
humans: "humans";
|
|
106
|
+
animals: "animals";
|
|
107
|
+
}>>;
|
|
108
|
+
}, z.core.$strip>;
|
|
109
|
+
readonly notice: z.ZodOptional<z.ZodString>;
|
|
110
|
+
}>;
|
|
110
111
|
//# sourceMappingURL=search-articles.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
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;AA6EjD,eAAO,MAAM,kBAAkB
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1
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{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6EjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA6T7B,CAAC"}
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@@ -121,11 +121,6 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
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}),
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output: z.object({
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query: z.string().describe('Original query'),
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effectiveQuery: z
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.string()
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.describe('Sanitized query sent to PubMed after applying all active filters'),
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appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
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totalFound: z.number().describe('Total matching articles'),
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offset: z.number().describe('Result offset used'),
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pmids: z.array(z.string()).describe('PubMed IDs'),
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summaries: z
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.describe('Brief article summary'))
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.describe('Brief summaries (empty array when summaryCount is 0)'),
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searchUrl: z.string().describe('PubMed search URL'),
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}),
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// Result-set context the agent reasons with — the query as PubMed parsed it, the
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// total match count, the normalized filters, and recovery guidance for empty or
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// overshot pages. Populated via ctx.enrich(...) so it reaches structuredContent and
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// content[] alike; kept out of the domain return.
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enrichment: {
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effectiveQuery: z
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.string()
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.describe('Sanitized query sent to PubMed after applying all active filters'),
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totalFound: z.number().describe('Total matching articles'),
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appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
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notice: z
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.string()
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.optional()
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.describe('Optional guidance when results are empty or paging overshot — e.g. how to broaden filters or reset offset. Absent on successful result pages.'),
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}
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},
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// content[] trailer presentation for the enrichment block. structuredContent always
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// carries the full structured value; this only shapes the human-facing trailer line.
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enrichmentTrailer: {
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effectiveQuery: { label: 'Effective Query' },
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totalFound: { label: 'Total Found' },
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appliedFilters: {
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render: (filters) => {
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const lines = [];
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if (filters.dateRange) {
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lines.push(`- **Date range:** ${filters.dateRange.minDate} – ${filters.dateRange.maxDate} (${filters.dateRange.dateType})`);
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}
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if (filters.publicationTypes?.length) {
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lines.push(`- **Publication types:** ${filters.publicationTypes.join(', ')}`);
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}
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if (filters.author)
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lines.push(`- **Author:** ${filters.author}`);
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if (filters.journal)
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lines.push(`- **Journal:** ${filters.journal}`);
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if (filters.meshTerms?.length) {
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lines.push(`- **MeSH terms:** ${filters.meshTerms.join(', ')}`);
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}
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if (filters.language)
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lines.push(`- **Language:** ${filters.language}`);
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if (filters.hasAbstract)
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lines.push('- **Has abstract:** yes');
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if (filters.freeFullText)
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lines.push('- **Free full text:** yes');
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if (filters.species)
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lines.push(`- **Species:** ${filters.species}`);
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return lines.length > 0
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? `**Applied Filters:**\n${lines.join('\n')}`
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: '**Applied Filters:** none';
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},
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},
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},
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async handler(input, ctx) {
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ctx.log.info('Executing pubmed_search', { query: input.query });
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const ncbi = getNcbiService();
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@@ -257,58 +298,24 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
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offset: input.offset,
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hasFilters: Object.keys(appliedFilters).length > 0,
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});
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ctx.enrich({ effectiveQuery, totalFound: esResult.count, appliedFilters });
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if (notice)
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ctx.enrich.notice(notice);
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return {
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query: input.query,
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effectiveQuery,
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appliedFilters,
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totalFound: esResult.count,
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offset: input.offset,
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pmids,
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summaries,
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searchUrl,
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...(notice && { notice }),
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};
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},
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format: (result) => {
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|
const lines = [
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`## PubMed Search Results`,
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|
`**Query:** ${result.query}`,
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`**
|
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|
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`**Total Found:** ${result.totalFound} | **Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
|
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|
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`**Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
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|
`**Search URL:** ${result.searchUrl}`,
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];
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if (Object.keys(result.appliedFilters).length > 0) {
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lines.push('\n### Applied Filters');
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if (result.appliedFilters.dateRange) {
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lines.push(`- **Date Range (${result.appliedFilters.dateRange.dateType}):** ${result.appliedFilters.dateRange.minDate} to ${result.appliedFilters.dateRange.maxDate}`);
|
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}
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if (result.appliedFilters.publicationTypes?.length) {
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lines.push(`- **Publication Types:** ${result.appliedFilters.publicationTypes.join(', ')}`);
|
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}
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if (result.appliedFilters.author) {
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|
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lines.push(`- **Author:** ${result.appliedFilters.author}`);
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}
|
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if (result.appliedFilters.journal) {
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|
-
lines.push(`- **Journal:** ${result.appliedFilters.journal}`);
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}
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-
if (result.appliedFilters.meshTerms?.length) {
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|
-
lines.push(`- **MeSH Terms:** ${result.appliedFilters.meshTerms.join(', ')}`);
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|
-
}
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if (result.appliedFilters.language) {
|
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|
-
lines.push(`- **Language:** ${result.appliedFilters.language}`);
|
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|
-
}
|
|
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|
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if (result.appliedFilters.hasAbstract) {
|
|
301
|
-
lines.push(`- **Has Abstract:** Yes`);
|
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302
|
-
}
|
|
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|
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if (result.appliedFilters.freeFullText) {
|
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304
|
-
lines.push(`- **Free Full Text:** Yes`);
|
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|
-
}
|
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|
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if (result.appliedFilters.species) {
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307
|
-
lines.push(`- **Species:** ${result.appliedFilters.species}`);
|
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308
|
-
}
|
|
309
|
-
}
|
|
310
|
-
if (result.notice)
|
|
311
|
-
lines.push(`\n> ${result.notice}`);
|
|
312
319
|
if (result.pmids.length > 0)
|
|
313
320
|
lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
|
|
314
321
|
if (result.summaries?.length) {
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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AAC,CAAC;gBACnE,cAAc,CAAC,QAAQ,GAAG,KAAK,CAAC,MAAM,CAAC;YACzC,CAAC;iBAAM,CAAC;gBACN,cAAc,CAAC,EAAE,GAAG,KAAK,CAAC,KAAK,CAAC,CAAC,EAAE,KAAK,CAAC,YAAY,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;YACnE,CAAC;YAED,MAAM,cAAc,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,cAAc,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;YACnF,IAAI,cAAc,EAAE,CAAC;gBACnB,MAAM,cAAc,GAAG,MAAM,qBAAqB,CAAC,cAAc,CAAC,CAAC;gBACnE,SAAS,GAAG,cAAc,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;oBACrC,IAAI,EAAE,CAAC,CAAC,IAAI;oBACZ,KAAK,EAAE,CAAC,CAAC,KAAK;oBACd,OAAO,EAAE,CAAC,CAAC,OAAO;oBAClB,MAAM,EAAE,CAAC,CAAC,MAAM;oBAChB,OAAO,EAAE,CAAC,CAAC,OAAO;oBAClB,GAAG,EAAE,CAAC,CAAC,GAAG;oBACV,KAAK,EAAE,CAAC,CAAC,KAAK;oBACd,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,MAAM,EAAE,6CAA6C,CAAC,CAAC,KAAK,GAAG,EAAE,CAAC;oBACnF,SAAS,EAAE,mCAAmC,CAAC,CAAC,IAAI,GAAG;iBACxD,CAAC,CAAC,CAAC;YACN,CAAC;QACH,CAAC;QAED,MAAM,SAAS,GAAG,yCAAyC,kBAAkB,CAAC,cAAc,CAAC,EAAE,CAAC;QAChG,MAAM,cAAc,GAAG;YACrB,GAAG,CAAC,mBAAmB,IAAI,EAAE,SAAS,EAAE,mBAAmB,EAAE,CAAC;YAC9D,GAAG,CAAC,iBAAiB,EAAE,MAAM,IAAI,EAAE,gBAAgB,EAAE,iBAAiB,EAAE,CAAC;YACzE,GAAG,CAAC,eAAe,IAAI,EAAE,MAAM,EAAE,eAAe,EAAE,CAAC;YACnD,GAAG,CAAC,gBAAgB,IAAI,EAAE,OAAO,EAAE,gBAAgB,EAAE,CAAC;YACtD,GAAG,CAAC,kBAAkB,EAAE,MAAM,IAAI,EAAE,SAAS,EAAE,kBAAkB,EAAE,CAAC;YACpE,GAAG,CAAC,iBAAiB,IAAI,EAAE,QAAQ,EAAE,iBAAiB,EAAE,CAAC;YACzD,GAAG,CAAC,KAAK,CAAC,WAAW,IAAI,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;YAC/C,GAAG,CAAC,KAAK,CAAC,YAAY,IAAI,EAAE,YAAY,EAAE,IAAI,EAAE,CAAC;YACjD,GAAG,CAAC,KAAK,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,KAAK,CAAC,OAAO,EAAE,CAAC;SACjD,CAAC;QACF,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,yBAAyB,EAAE;YACtC,UAAU,EAAE,QAAQ,CAAC,KAAK;YAC1B,SAAS,EAAE,KAAK,CAAC,MAAM;SACxB,CAAC,CAAC;QAEH,MAAM,MAAM,GAAG,WAAW,CAAC;YACzB,UAAU,EAAE,QAAQ,CAAC,KAAK;YAC1B,SAAS,EAAE,KAAK,CAAC,MAAM;YACvB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,UAAU,EAAE,MAAM,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,MAAM,GAAG,CAAC;SACnD,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,EAAE,cAAc,EAAE,UAAU,EAAE,QAAQ,CAAC,KAAK,EAAE,cAAc,EAAE,CAAC,CAAC;QAC3E,IAAI,MAAM;YAAE,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;QAEtC,OAAO;YACL,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,KAAK;YACL,SAAS;YACT,SAAS;SACV,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,cAAc,MAAM,CAAC,KAAK,EAAE;YAC5B,iBAAiB,MAAM,CAAC,KAAK,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,EAAE;YACrE,mBAAmB,MAAM,CAAC,SAAS,EAAE;SACtC,CAAC;QACF,IAAI,MAAM,CAAC,KAAK,CAAC,MAAM,GAAG,CAAC;YAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,MAAM,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACnF,IAAI,MAAM,CAAC,SAAS,EAAE,MAAM,EAAE,CAAC;YAC7B,IAAI,MAAM,CAAC,SAAS,CAAC,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,MAAM,EAAE,CAAC;gBAClD,KAAK,CAAC,IAAI,CACR,+BAA+B,MAAM,CAAC,SAAS,CAAC,MAAM,OAAO,MAAM,CAAC,KAAK,CAAC,MAAM,2DAA2D,CAC5I,CAAC;YACJ,CAAC;YACD,KAAK,CAAC,IAAI,CAAC,iBAAiB,CAAC,CAAC;YAC9B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;gBACjC,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAC1C,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;gBAClC,IAAI,CAAC,CAAC,OAAO;oBAAE,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;gBACvD,IAAI,CAAC,CAAC,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;gBACpD,IAAI,CAAC,CAAC,OAAO;oBAAE,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;gBACzD,IAAI,CAAC,CAAC,GAAG;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC;gBAC3C,IAAI,CAAC,CAAC,KAAK;oBAAE,KAAK,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC,KAAK,EAAE,CAAC,CAAC;gBACjD,IAAI,CAAC,CAAC,SAAS;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;gBAC1D,IAAI,CAAC,CAAC,MAAM;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACnD,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -40,5 +40,5 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
|
|
|
40
40
|
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
|
41
41
|
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
|
42
42
|
readonly retryable: false;
|
|
43
|
-
}]>;
|
|
43
|
+
}], undefined>;
|
|
44
44
|
//# sourceMappingURL=spell-check.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"spell-check.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAKjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8CzB,CAAC"}
|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.7.
|
|
3
|
+
"version": "2.7.8",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
|
|
6
6
|
"type": "module",
|
|
@@ -9,14 +9,15 @@
|
|
|
9
9
|
"bin": {
|
|
10
10
|
"pubmed-mcp-server": "dist/index.js"
|
|
11
11
|
},
|
|
12
|
-
"files": ["dist/", "README.md", "LICENSE", "CLAUDE.md", "Dockerfile", "server.json"],
|
|
12
|
+
"files": ["dist/", "README.md", "LICENSE", "CLAUDE.md", "AGENTS.md", "Dockerfile", "server.json"],
|
|
13
13
|
"scripts": {
|
|
14
14
|
"build": "bun run scripts/build.ts",
|
|
15
15
|
"rebuild": "bun run scripts/clean.ts && bun run build",
|
|
16
16
|
"clean": "bun run scripts/clean.ts",
|
|
17
17
|
"devcheck": "bun run scripts/devcheck.ts",
|
|
18
18
|
"tree": "bun run scripts/tree.ts",
|
|
19
|
-
"format": "biome check --write
|
|
19
|
+
"format": "biome check --write .",
|
|
20
|
+
"format:unsafe": "biome check --write --unsafe .",
|
|
20
21
|
"test": "bunx vitest run",
|
|
21
22
|
"audit:refresh": "rm -f bun.lock && bun install && bun audit",
|
|
22
23
|
"list-skills": "bun run scripts/list-skills.ts",
|
|
@@ -79,7 +80,7 @@
|
|
|
79
80
|
"access": "public"
|
|
80
81
|
},
|
|
81
82
|
"dependencies": {
|
|
82
|
-
"@cyanheads/mcp-ts-core": "^0.9.
|
|
83
|
+
"@cyanheads/mcp-ts-core": "^0.9.16",
|
|
83
84
|
"defuddle": "^0.18.1",
|
|
84
85
|
"fast-xml-parser": "^5.8.0",
|
|
85
86
|
"linkedom": "^0.18.12",
|
package/server.json
CHANGED
|
@@ -6,7 +6,7 @@
|
|
|
6
6
|
"url": "https://github.com/cyanheads/pubmed-mcp-server",
|
|
7
7
|
"source": "github"
|
|
8
8
|
},
|
|
9
|
-
"version": "2.7.
|
|
9
|
+
"version": "2.7.8",
|
|
10
10
|
"remotes": [
|
|
11
11
|
{
|
|
12
12
|
"type": "streamable-http",
|
|
@@ -19,7 +19,7 @@
|
|
|
19
19
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
20
20
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
21
21
|
"runtimeHint": "bun",
|
|
22
|
-
"version": "2.7.
|
|
22
|
+
"version": "2.7.8",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
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|
25
25
|
"type": "positional",
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|
@@ -66,7 +66,7 @@
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66
66
|
"registryBaseUrl": "https://registry.npmjs.org",
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|
67
67
|
"identifier": "@cyanheads/pubmed-mcp-server",
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|
68
68
|
"runtimeHint": "bun",
|
|
69
|
-
"version": "2.7.
|
|
69
|
+
"version": "2.7.8",
|
|
70
70
|
"packageArguments": [
|
|
71
71
|
{
|
|
72
72
|
"type": "positional",
|