@cyanheads/pubmed-mcp-server 2.3.0 → 2.3.2
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/CLAUDE.md +1 -1
- package/README.md +2 -2
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +1 -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 +1 -13
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +4 -4
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts +11 -0
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +60 -3
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/package.json +6 -5
- package/server.json +3 -3
package/CLAUDE.md
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@@ -1,7 +1,7 @@
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# Agent Protocol
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**Server:** @cyanheads/pubmed-mcp-server
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**Version:** 2.3.
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**Version:** 2.3.2
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**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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> **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
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package/README.md
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<div align="center">
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[](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](./CHANGELOG.md) [](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [](https://modelcontextprotocol.io/)
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[](./LICENSE) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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@@ -56,7 +56,7 @@ Search PubMed with full NCBI query syntax and filters.
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Fetch full article metadata by PubMed IDs.
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- Batch fetch up to 200 articles at once (auto-switches to POST for
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- Batch fetch up to 200 articles at once (auto-switches to POST for batches >= 100)
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- Returns structured data: title, abstract, authors with deduplicated affiliations, journal info, DOI
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- Direct links to PubMed and PubMed Central (when available)
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- Optional MeSH terms, grant information, and publication types
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@@ -110,7 +110,7 @@ export const fetchArticlesTool = tool('pubmed_fetch_articles', {
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}),
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async handler(input, ctx) {
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ctx.log.info('Executing pubmed_fetch', { pmidCount: input.pmids.length });
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const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length
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const xmlData = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 100 });
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if (!xmlData || !('PubmedArticleSet' in xmlData)) {
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throw new Error('Invalid EFetch response from NCBI: missing PubmedArticleSet');
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}
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-
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+
{"version":3,"file":"fetch-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,iBAAiB,GAAG,IAAI,CAAC,uBAAuB,EAAE;IAC7D,WAAW,EACT,mIAAmI;IACrI,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,GAAG,CAAC,CAAC,QAAQ,CAAC,qBAAqB,CAAC;QACzF,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,IAAI,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACrE,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,OAAO,CAAC,KAAK,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACjD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YAC7D,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;YACzF,OAAO,EAAE,CAAC;iBACP,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;gBACrD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;gBAC7D,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBAC3D,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8BAA8B,CAAC;gBAC9E,kBAAkB,EAAE,CAAC;qBAClB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;qBACjB,QAAQ,EAAE;qBACV,QAAQ,CAAC,+CAA+C,CAAC;gBAC5D,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;aAC1D,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,aAAa,CAAC;YAC1B,WAAW,EAAE,CAAC;iBACX,MAAM,CAAC;gBACN,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;gBAC3D,eAAe,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;gBAC3E,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;gBAClD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;gBACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;gBACvD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,cAAc,CAAC;gBACrD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;gBAClE,eAAe,EAAE,CAAC;qBACf,MAAM,CAAC;oBACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;oBACxD,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;oBAC1D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;oBACtD,WAAW,EAAE,CAAC;yBACX,MAAM,EAAE;yBACR,QAAQ,EAAE;yBACV,QAAQ,CAAC,+CAA+C,CAAC;iBAC7D,CAAC;qBACD,QAAQ,EAAE;qBACV,QAAQ,CAAC,0BAA0B,CAAC;aACxC,CAAC;iBACD,QAAQ,EAAE;iBACV,QAAQ,CAAC,qBAAqB,CAAC;YAClC,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;YAC1C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC;YAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;YAC/D,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC3D,gBAAgB,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9E,QAAQ,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,UAAU,CAAC;YAC7D,SAAS,EAAE,CAAC;iBACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;gBACtE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;gBACzE,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;gBAClF,UAAU,EAAE,CAAC;qBACV,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;oBACP,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2BAA2B,CAAC;oBAC/D,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qBAAqB,CAAC;oBAClE,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;iBAC9E,CAAC,CACH;qBACA,QAAQ,EAAE;qBACV,QAAQ,CAAC,6BAA6B,CAAC;aAC3C,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,YAAY,CAAC;YACzB,SAAS,EAAE,CAAC;iBACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;gBAC3D,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;gBACxD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;gBACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;aAC1D,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,mBAAmB,CAAC;YAChC,YAAY,EAAE,CAAC;iBACZ,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;gBACP,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;gBACrD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC;gBAC5C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,OAAO,CAAC;gBAC9C,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;aAC3C,CAAC,CACH;iBACA,QAAQ,EAAE;iBACV,QAAQ,CAAC,eAAe,CAAC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AAM,EAAE,CAAC,CAAC,OAAO,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,CAAC;oBAC/D,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;gBACvC,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
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|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8FjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"fetch-fulltext.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/fetch-fulltext.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8FjD,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;kBAkO5B,CAAC"}
|
|
@@ -170,19 +170,7 @@ export const fetchFulltextTool = tool('pubmed_fetch_fulltext', {
|
|
|
170
170
|
else {
|
|
171
171
|
pmcIds = (input.pmcids ?? []).map(normalizePmcId);
|
|
172
172
|
}
|
|
173
|
-
|
|
174
|
-
try {
|
|
175
|
-
xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: pmcIds.length > 5 });
|
|
176
|
-
}
|
|
177
|
-
catch {
|
|
178
|
-
const ids = pmcIds.map((id) => `PMC${id}`);
|
|
179
|
-
return {
|
|
180
|
-
articles: [],
|
|
181
|
-
totalReturned: 0,
|
|
182
|
-
...(unavailablePmids && { unavailablePmids }),
|
|
183
|
-
...(!input.pmids && { unavailablePmcIds: ids }),
|
|
184
|
-
};
|
|
185
|
-
}
|
|
173
|
+
const xmlData = await getNcbiService().eFetch({ db: 'pmc', id: pmcIds.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: pmcIds.length > 5 });
|
|
186
174
|
if (!xmlData || !('pmc-articleset' in xmlData)) {
|
|
187
175
|
throw new Error('Invalid PMC EFetch response: missing pmc-articleset');
|
|
188
176
|
}
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;
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1
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+
{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAUjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;kBAmE9B,CAAC"}
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@@ -32,7 +32,7 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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32
32
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pmids: input.pmids,
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33
33
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styles: input.styles,
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34
34
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});
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35
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-
const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(',') });
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35
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+
const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25 });
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36
36
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const xmlArticles = ensureArray(raw?.PubmedArticleSet?.PubmedArticle);
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37
37
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if (xmlArticles.length === 0) {
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38
38
|
throw new Error(`No articles found for PMIDs: ${input.pmids.join(', ')}`);
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACvF,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,
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1
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+
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAEL,eAAe,GAChB,MAAM,kDAAkD,CAAC;AAC1D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,gBAAgB,EAAE,MAAM,2CAA2C,CAAC;AAC7E,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAGrE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EAAE,iFAAiF;IAC9F,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACvF,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;aAC9C,OAAO,CAAC,CAAC,KAAK,CAAC,CAAC;aAChB,QAAQ,CAAC,6BAA6B,CAAC;KAC3C,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,SAAS,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,0BAA0B,CAAC;SACjF,CAAC,CACH;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,MAAM,EAAE,KAAK,CAAC,MAAM;SACrB,CAAC,CAAC;QACH,MAAM,GAAG,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,OAAO,EAAE,KAAK,EAAE,EAC3D,EAAE,OAAO,EAAE,KAAK,EAAE,OAAO,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM,IAAI,EAAE,EAAE,CACtD,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,IAAI,WAAW,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC7B,MAAM,IAAI,KAAK,CAAC,gCAAgC,KAAK,CAAC,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC5E,CAAC;QAED,MAAM,SAAS,GAAG,WAAW,CAAC,GAAG,CAAC,CAAC,UAAU,EAAE,EAAE;YAC/C,MAAM,MAAM,GAAG,gBAAgB,CAAC,UAAU,CAAC,CAAC;YAC5C,OAAO;gBACL,IAAI,EAAE,MAAM,CAAC,IAAI;gBACjB,KAAK,EAAE,MAAM,CAAC,KAAK;gBACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,KAAK,CAAC,MAAyB,CAAC;aACpE,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,OAAO,EAAE,SAAS,EAAE,CAAC;IACvB,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG,CAAC,oBAAoB,CAAC,CAAC;QACrC,KAAK,MAAM,KAAK,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrC,KAAK,CAAC,IAAI,CAAC,aAAa,KAAK,CAAC,IAAI,EAAE,CAAC,CAAC;YACtC,IAAI,KAAK,CAAC,KAAK;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,KAAK,IAAI,CAAC,CAAC;YAClD,KAAK,MAAM,CAAC,KAAK,EAAE,QAAQ,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAK,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChE,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,CAAC,WAAW,EAAE,EAAE,CAAC,CAAC;gBAC3C,IAAI,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,KAAK,EAAE,CAAC;oBAC1C,KAAK,CAAC,IAAI,CAAC,SAAS,KAAK,KAAK,QAAQ,UAAU,CAAC,CAAC;gBACpD,CAAC;qBAAM,CAAC;oBACN,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC;gBACvB,CAAC;YACH,CAAC;QACH,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -22,8 +22,8 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
22
22
|
.describe('Sort order: relevance (default), pub_date (newest first), author, or journal'),
|
|
23
23
|
dateRange: z
|
|
24
24
|
.object({
|
|
25
|
-
minDate: z.string().describe('Start date (YYYY
|
|
26
|
-
maxDate: z.string().describe('End date (YYYY
|
|
25
|
+
minDate: z.string().describe('Start date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
|
|
26
|
+
maxDate: z.string().describe('End date (YYYY/MM/DD, YYYY/MM, or YYYY)'),
|
|
27
27
|
dateType: z
|
|
28
28
|
.enum(['pdat', 'mdat', 'edat'])
|
|
29
29
|
.default('pdat')
|
|
@@ -74,7 +74,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
74
74
|
ctx.log.info('Executing pubmed_search', { query: input.query });
|
|
75
75
|
const ncbi = getNcbiService();
|
|
76
76
|
let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
|
|
77
|
-
if (input.dateRange) {
|
|
77
|
+
if (input.dateRange?.minDate && input.dateRange?.maxDate) {
|
|
78
78
|
const minDate = input.dateRange.minDate.replace(/-/g, '/');
|
|
79
79
|
const maxDate = input.dateRange.maxDate.replace(/-/g, '/');
|
|
80
80
|
effectiveQuery += ` AND (${minDate}[${input.dateRange.dateType}] : ${maxDate}[${input.dateRange.dateType}])`;
|
|
@@ -142,7 +142,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
142
142
|
}));
|
|
143
143
|
}
|
|
144
144
|
}
|
|
145
|
-
const searchUrl = `https://pubmed.ncbi.nlm.nih.gov/?term=${encodeURIComponent(
|
|
145
|
+
const searchUrl = `https://pubmed.ncbi.nlm.nih.gov/?term=${encodeURIComponent(effectiveQuery)}`;
|
|
146
146
|
ctx.log.info('pubmed_search completed', {
|
|
147
147
|
totalFound: esResult.count,
|
|
148
148
|
pmidCount: pmids.length,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"search-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EACT,8GAA8G;QAC9G,qHAAqH;QACrH,iEAAiE;IACnE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;QACpF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC/F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;aACpD,OAAO,CAAC,WAAW,CAAC;aACpB,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,
|
|
1
|
+
{"version":3,"file":"search-articles.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EACT,8GAA8G;QAC9G,qHAAqH;QACrH,iEAAiE;IACnE,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IAExD,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;QACpF,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,2BAA2B,CAAC;QAC/F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7F,IAAI,EAAE,CAAC;aACJ,IAAI,CAAC,CAAC,WAAW,EAAE,UAAU,EAAE,QAAQ,EAAE,SAAS,CAAC,CAAC;aACpD,OAAO,CAAC,WAAW,CAAC;aACpB,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,SAAS,EAAE,CAAC;aACT,MAAM,CAAC;YACN,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;YACzE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;YACvE,QAAQ,EAAE,CAAC;iBACR,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,CAAC;iBAC9B,OAAO,CAAC,MAAM,CAAC;iBACf,QAAQ,CAAC,mEAAmE,CAAC;SACjF,CAAC;aACD,QAAQ,EAAE;aACV,QAAQ,CAAC,sBAAsB,CAAC;QACnC,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAChF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QACjE,SAAS,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;QAC1E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QAC/E,WAAW,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QACpF,YAAY,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;QACrF,OAAO,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,QAAQ,EAAE,SAAS,CAAC,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;QAC/E,YAAY,EAAE,CAAC;aACZ,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CAAC,0DAA0D,CAAC;KACxE,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC5C,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;QAC1D,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QACjD,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,CAAC,YAAY,CAAC;QACjD,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC,CAAC,MAAM,CAAC;YACP,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,WAAW,CAAC;YACtC,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;YAClE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,KAAK,CAAC;YAC1C,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,QAAQ,CAAC;YAC/C,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,SAAS,CAAC;YACjD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;SACxD,CAAC,CACH;aACA,QAAQ,CAAC,sDAAsD,CAAC;QACnE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;KACpD,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,yBAAyB,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAChE,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAE9B,IAAI,cAAc,GAAG,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,KAAK,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC;QAEzF,IAAI,KAAK,CAAC,SAAS,EAAE,OAAO,IAAI,KAAK,CAAC,SAAS,EAAE,OAAO,EAAE,CAAC;YACzD,MAAM,OAAO,GAAG,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YAC3D,MAAM,OAAO,GAAG,KAAK,CAAC,SAAS,CAAC,OAAO,CAAC,OAAO,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;YAC3D,cAAc,IAAI,SAAS,OAAO,IAAI,KAAK,CAAC,SAAS,CAAC,QAAQ,OAAO,OAAO,IAAI,KAAK,CAAC,SAAS,CAAC,QAAQ,IAAI,CAAC;QAC/G,CAAC;QACD,IAAI,KAAK,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACnC,MAAM,YAAY,GAAG,MAAM,OAAO,CAAC,GAAG,CACpC,KAAK,CAAC,gBAAgB,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,YAAY,CAAC,cAAc,CAAC,EAAE,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC,CACzF,CAAC;YACF,MAAM,OAAO,GAAG,YAAY,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,IAAI,EAAE,qBAAqB,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC;YACnF,cAAc,IAAI,SAAS,OAAO,GAAG,CAAC;QACxC,CAAC;QACD,IAAI,KAAK,CAAC,MAAM;YACd,cAAc,IAAI,QAAQ,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,MAAM,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,UAAU,CAAC;QAC3G,IAAI,KAAK,CAAC,OAAO;YACf,cAAc,IAAI,SAAS,MAAM,YAAY,CAAC,cAAc,CAAC,KAAK,CAAC,OAAO,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,YAAY,CAAC;QAC/G,IAAI,KAAK,CAAC,SAAS,EAAE,MAAM,EAAE,CAAC;YAC5B,MAAM,cAAc,GAAG,MAAM,OAAO,CAAC,GAAG,CACtC,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,YAAY,CAAC,cAAc,CAAC,IAAI,EAAE,EAAE,OAAO,EAAE,MAAM,EAAE,CAAC,CAAC,CACtF,CAAC;YACF,MAAM,SAAS,GAAG,cAAc,CAAC,GAAG,CAAC,CA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|
|
@@ -11,8 +11,19 @@ import type { ESummaryResult, ParsedBriefSummary, ESummaryAuthor as XmlESummaryA
|
|
|
11
11
|
* Limits to the first 3 authors and adds 'et al.' if more exist.
|
|
12
12
|
*/
|
|
13
13
|
export declare function formatESummaryAuthors(authors?: XmlESummaryAuthor[]): string;
|
|
14
|
+
/**
|
|
15
|
+
* Parses NCBI ESummary date strings into YYYY-MM-DD (or YYYY-MM-01 / YYYY-01-01
|
|
16
|
+
* for partial dates). Returns undefined for unrecognized formats.
|
|
17
|
+
*
|
|
18
|
+
* NCBI's ESummary API returns a small set of predictable date formats. chrono-node
|
|
19
|
+
* (used by the framework's dateParser) mishandles most of them — its `forwardDate`
|
|
20
|
+
* option causes "2023 Dec" to resolve to a future December, ignoring the year.
|
|
21
|
+
*/
|
|
22
|
+
export declare function parseNcbiDate(dateStr: string): string | undefined;
|
|
14
23
|
/**
|
|
15
24
|
* Standardizes date strings from ESummary to 'YYYY-MM-DD' format.
|
|
25
|
+
* Uses a dedicated NCBI date parser for known formats, falling back to
|
|
26
|
+
* chrono-node via the framework's dateParser for anything unexpected.
|
|
16
27
|
*/
|
|
17
28
|
export declare function standardizeESummaryDate(dateStr?: string, parentContext?: RequestContext): Promise<string | undefined>;
|
|
18
29
|
/**
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AAED
|
|
1
|
+
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAKV,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CAkC7B;AAiPD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAiD/B"}
|
|
@@ -18,13 +18,70 @@ export function formatESummaryAuthors(authors) {
|
|
|
18
18
|
.map((author) => author.name)
|
|
19
19
|
.join(', ') + (authors.length > 3 ? ', et al.' : ''));
|
|
20
20
|
}
|
|
21
|
+
/** 3-letter month abbreviations used by NCBI ESummary PubDate/EPubDate fields. */
|
|
22
|
+
const MONTH_ABBREV = {
|
|
23
|
+
Jan: '01',
|
|
24
|
+
Feb: '02',
|
|
25
|
+
Mar: '03',
|
|
26
|
+
Apr: '04',
|
|
27
|
+
May: '05',
|
|
28
|
+
Jun: '06',
|
|
29
|
+
Jul: '07',
|
|
30
|
+
Aug: '08',
|
|
31
|
+
Sep: '09',
|
|
32
|
+
Oct: '10',
|
|
33
|
+
Nov: '11',
|
|
34
|
+
Dec: '12',
|
|
35
|
+
};
|
|
36
|
+
/**
|
|
37
|
+
* Matches NCBI ESummary date formats:
|
|
38
|
+
* - "2024" → year only
|
|
39
|
+
* - "2024 Jan" → year + month
|
|
40
|
+
* - "2024 Jan 15" → year + month + day
|
|
41
|
+
* - "2018 Jul-Aug" → year + month range (dash)
|
|
42
|
+
* - "2018 Jan/Feb" → year + month range (slash)
|
|
43
|
+
*
|
|
44
|
+
* Groups: 1=year, 2=firstMonth?, 3=day? (second month in range is non-capturing)
|
|
45
|
+
*/
|
|
46
|
+
const NCBI_DATE_RE = /^(\d{4})(?:\s+([A-Za-z]{3})(?:[/-][A-Za-z]{3})?(?:\s+(\d{1,2}))?)?$/;
|
|
47
|
+
/**
|
|
48
|
+
* Parses NCBI ESummary date strings into YYYY-MM-DD (or YYYY-MM-01 / YYYY-01-01
|
|
49
|
+
* for partial dates). Returns undefined for unrecognized formats.
|
|
50
|
+
*
|
|
51
|
+
* NCBI's ESummary API returns a small set of predictable date formats. chrono-node
|
|
52
|
+
* (used by the framework's dateParser) mishandles most of them — its `forwardDate`
|
|
53
|
+
* option causes "2023 Dec" to resolve to a future December, ignoring the year.
|
|
54
|
+
*/
|
|
55
|
+
export function parseNcbiDate(dateStr) {
|
|
56
|
+
const m = NCBI_DATE_RE.exec(dateStr.trim());
|
|
57
|
+
if (!m)
|
|
58
|
+
return;
|
|
59
|
+
const [, year, monthAbbrev, day] = m;
|
|
60
|
+
if (!year)
|
|
61
|
+
return;
|
|
62
|
+
const month = monthAbbrev ? MONTH_ABBREV[monthAbbrev] : undefined;
|
|
63
|
+
if (monthAbbrev && !month)
|
|
64
|
+
return; // unrecognized month abbreviation
|
|
65
|
+
if (month && day)
|
|
66
|
+
return `${year}-${month}-${day.padStart(2, '0')}`;
|
|
67
|
+
if (month)
|
|
68
|
+
return `${year}-${month}-01`;
|
|
69
|
+
return `${year}-01-01`;
|
|
70
|
+
}
|
|
21
71
|
/**
|
|
22
72
|
* Standardizes date strings from ESummary to 'YYYY-MM-DD' format.
|
|
73
|
+
* Uses a dedicated NCBI date parser for known formats, falling back to
|
|
74
|
+
* chrono-node via the framework's dateParser for anything unexpected.
|
|
23
75
|
*/
|
|
24
76
|
export async function standardizeESummaryDate(dateStr, parentContext) {
|
|
25
77
|
if (dateStr == null)
|
|
26
78
|
return;
|
|
27
|
-
const dateInputString = String(dateStr);
|
|
79
|
+
const dateInputString = String(dateStr).trim();
|
|
80
|
+
if (!dateInputString)
|
|
81
|
+
return;
|
|
82
|
+
const ncbiResult = parseNcbiDate(dateInputString);
|
|
83
|
+
if (ncbiResult)
|
|
84
|
+
return ncbiResult;
|
|
28
85
|
const currentContext = parentContext ||
|
|
29
86
|
requestContextService.createRequestContext({
|
|
30
87
|
operation: 'standardizeESummaryDateInternal',
|
|
@@ -35,10 +92,10 @@ export async function standardizeESummaryDate(dateStr, parentContext) {
|
|
|
35
92
|
if (parsedDate) {
|
|
36
93
|
return parsedDate.toISOString().split('T')[0];
|
|
37
94
|
}
|
|
38
|
-
logger.debug(`standardizeESummaryDate:
|
|
95
|
+
logger.debug(`standardizeESummaryDate: could not parse "${dateInputString}", returning undefined.`, currentContext);
|
|
39
96
|
}
|
|
40
97
|
catch (e) {
|
|
41
|
-
logger.warning(`standardizeESummaryDate:
|
|
98
|
+
logger.warning(`standardizeESummaryDate: dateParser.parseDate error for "${dateInputString}", returning undefined.`, {
|
|
42
99
|
...currentContext,
|
|
43
100
|
error: e instanceof Error ? e.message : String(e),
|
|
44
101
|
});
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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|
package/package.json
CHANGED
|
@@ -1,6 +1,6 @@
|
|
|
1
1
|
{
|
|
2
2
|
"name": "@cyanheads/pubmed-mcp-server",
|
|
3
|
-
"version": "2.3.
|
|
3
|
+
"version": "2.3.2",
|
|
4
4
|
"mcpName": "io.github.cyanheads/pubmed-mcp-server",
|
|
5
5
|
"description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata, generate citations, explore MeSH terms, and discover related research.",
|
|
6
6
|
"type": "module",
|
|
@@ -72,17 +72,18 @@
|
|
|
72
72
|
"hono": ">=4.12.7",
|
|
73
73
|
"path-to-regexp": ">=8.4.0",
|
|
74
74
|
"picomatch": ">=4.0.4",
|
|
75
|
-
"yaml": ">=2.8.3"
|
|
75
|
+
"yaml": ">=2.8.3",
|
|
76
|
+
"lodash": ">=4.17.24"
|
|
76
77
|
},
|
|
77
78
|
"dependencies": {
|
|
78
|
-
"@cyanheads/mcp-ts-core": "^0.2.
|
|
79
|
-
"fast-xml-parser": "^5.5.
|
|
79
|
+
"@cyanheads/mcp-ts-core": "^0.2.12",
|
|
80
|
+
"fast-xml-parser": "^5.5.10",
|
|
80
81
|
"pino-pretty": "^13.1.3",
|
|
81
82
|
"sanitize-html": "^2.17.2"
|
|
82
83
|
},
|
|
83
84
|
"devDependencies": {
|
|
84
85
|
"@biomejs/biome": "^2.4.10",
|
|
85
|
-
"@types/node": "^25.5.
|
|
86
|
+
"@types/node": "^25.5.2",
|
|
86
87
|
"@types/sanitize-html": "^2.16.1",
|
|
87
88
|
"depcheck": "^1.4.7",
|
|
88
89
|
"ignore": "^7.0.5",
|
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": "2.3.
|
|
9
|
+
"version": "2.3.2",
|
|
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": "2.3.
|
|
22
|
+
"version": "2.3.2",
|
|
23
23
|
"packageArguments": [
|
|
24
24
|
{
|
|
25
25
|
"type": "positional",
|
|
@@ -60,7 +60,7 @@
|
|
|
60
60
|
"registryBaseUrl": "https://registry.npmjs.org",
|
|
61
61
|
"identifier": "@cyanheads/pubmed-mcp-server",
|
|
62
62
|
"runtimeHint": "bun",
|
|
63
|
-
"version": "2.3.
|
|
63
|
+
"version": "2.3.2",
|
|
64
64
|
"packageArguments": [
|
|
65
65
|
{
|
|
66
66
|
"type": "positional",
|