@cyanheads/pubmed-mcp-server 2.10.15 → 2.10.16
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/AGENTS.md +1 -1
- package/CLAUDE.md +1 -1
- package/README.md +22 -13
- package/changelog/2.10.x/2.10.16.md +26 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +11 -1
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +13 -1
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +3 -0
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +41 -9
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +3 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js +12 -4
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts +2 -0
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js +35 -12
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +7 -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 +38 -21
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +3 -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 +12 -4
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +11 -2
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +62 -41
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +3 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +3 -1
- 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 +5 -2
- 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 +19 -10
- 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 +9 -3
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +71 -11
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +5 -4
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +4 -3
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +2 -2
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +2 -2
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/europe-pmc/api-client.d.ts +14 -11
- package/dist/services/europe-pmc/api-client.d.ts.map +1 -1
- package/dist/services/europe-pmc/api-client.js +21 -18
- package/dist/services/europe-pmc/api-client.js.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.d.ts +2 -0
- package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
- package/dist/services/europe-pmc/europe-pmc-service.js +6 -2
- package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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+
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@@ -1,7 +1,7 @@
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1
1
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/**
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2
2
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* @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
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3
3
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* Searches the NCBI MeSH database with offset pagination and optionally
|
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4
|
-
* retrieves detailed records.
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4
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+
* retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
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5
5
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* @module src/mcp-server/tools/definitions/lookup-mesh.tool
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6
6
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*/
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7
7
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import { z } from '@cyanheads/mcp-ts-core';
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@@ -60,8 +60,8 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
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60
60
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}, {
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61
61
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readonly reason: 'blank_query';
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62
62
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
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63
|
-
readonly when: 'The query holds no search term once whitespace, and
|
|
64
|
-
readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
|
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63
|
+
readonly when: 'The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there.';
|
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64
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+
readonly recovery: 'Supply a nonblank search term — a bare field tag or empty parentheses carry none; NCBI cannot search a blank term and retrying the same input will not help.';
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65
65
|
readonly retryable: false;
|
|
66
66
|
}], {
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67
67
|
readonly totalCount: z.ZodNumber;
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@@ -1 +1 @@
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|
1
|
-
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;
|
|
1
|
+
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA6GjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyMzB,CAAC"}
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@@ -1,7 +1,7 @@
|
|
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1
1
|
/**
|
|
2
2
|
* @fileoverview MeSH (Medical Subject Headings) vocabulary lookup tool.
|
|
3
3
|
* Searches the NCBI MeSH database with offset pagination and optionally
|
|
4
|
-
* retrieves detailed records.
|
|
4
|
+
* retrieves detailed records. `limit` is accepted as an alias for `maxResults`.
|
|
5
5
|
* @module src/mcp-server/tools/definitions/lookup-mesh.tool
|
|
6
6
|
*/
|
|
7
7
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
@@ -101,6 +101,8 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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|
101
101
|
]),
|
|
102
102
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
|
|
103
103
|
errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
|
|
104
|
+
// Never advertised; rewritten to the canonical key before the schema parses. (#156)
|
|
105
|
+
inputAliases: { limit: 'maxResults' },
|
|
104
106
|
input: z.object({
|
|
105
107
|
query: z
|
|
106
108
|
.string()
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
|
+
{"version":3,"file":"lookup-mesh.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,uBAAuB,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AAC7F,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAC9E,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,yBAAyB,EACzB,mBAAmB,EACnB,uBAAuB,GACxB,MAAM,gBAAgB,CAAC;AAaxB;;;;;;GAMG;AACH,MAAM,iBAAiB,GAA2B,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,IAAI,EAAE,GAAG,EAAE,CAAC;AAEtF,SAAS,sBAAsB,CAAC,SAAiB;IAC/C,IAAI,SAAS,CAAC,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,iBAAiB,CAAC,SAAS,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,CAAC;QACxD,IAAI,MAAM;YAAE,OAAO,GAAG,MAAM,GAAG,SAAS,CAAC,KAAK,CAAC,CAAC,CAAC,EAAE,CAAC;IACtD,CAAC;IACD,OAAO,SAAS,CAAC;AACnB,CAAC;AAED,SAAS,QAAQ,CACf,KAAgC,EAChC,IAAY;IAEZ,OAAO,KAAK,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,QAAQ,CAAC,CAAC,KAAK,IAAI,CAAC,CAAC;AAC5D,CAAC;AAED,SAAS,WAAW,CAAC,IAAyC;IAC5D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,MAAM,GAAG,OAAO,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC;IACjC,IAAI,MAAM;QAAE,OAAO,MAAM,CAAC;IAC1B,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;AACzD,CAAC;AAED,SAAS,YAAY,CAAC,IAAyC;IAC7D,IAAI,CAAC,IAAI;QAAE,OAAO,EAAE,CAAC;IACrB,MAAM,QAAQ,GAAG,WAAW,CAAC,IAAI,CAAC,IAAI,CAA8B,CAAC;IACrE,OAAO,QAAQ,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC;AACvE,CAAC;AAED,SAAS,kBAAkB,CAAC,KAAgC;IAC1D,MAAM,QAAQ,GAAG,QAAQ,CAAC,KAAK,EAAE,aAAa,CAAC,CAAC;IAChD,IAAI,CAAC,QAAQ;QAAE,OAAO,EAAE,CAAC;IACzB,MAAM,cAAc,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAA8B,CAAC;IAC/E,MAAM,QAAQ,GAAa,EAAE,CAAC;IAC9B,KAAK,MAAM,MAAM,IAAI,cAAc,EAAE,CAAC;QACpC,MAAM,WAAW,GAAG,WAAW,CAAC,MAAM,CAAC,IAAI,CAA8B,CAAC;QAC1E,MAAM,QAAQ,GAAG,QAAQ,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;QAClD,MAAM,GAAG,GAAG,QAAQ,CAAC,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;QAC9C,8EAA8E;QAC9E,6EAA6E;QAC7E,sDAAsD;QACtD,IAAI,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,GAAG,CAAC;YAAE,QAAQ,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC;IACtD,CAAC;IACD,OAAO,QAAQ,CAAC;AAClB,CAAC;AAED,SAAS,mBAAmB,CAAC,IAAa,EAAE,GAAa,EAAE,cAAuB;IAChF,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QACnC,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAC5F,MAAM,IAAI,GAAG,IAA+B,CAAC;IAC7C,MAAM,aAAa,GAAG,IAAI,CAAC,cAAqD,CAAC;IACjF,MAAM,OAAO,GAAG,WAAW,CACzB,CAAC,aAAa,IAAI,IAAI,CAAC,CAAC,MAAiC,CAC1D,CAAC;IACF,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;QACtB,OAAO,GAAG,CAAC,GAAG,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,SAAS,EAAE,EAAE,EAAE,MAAM,EAAE,sBAAsB,CAAC,EAAE,CAAC,EAAE,IAAI,EAAE,EAAE,EAAE,CAAC,CAAC,CAAC;IAE5F,OAAO,OAAO,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE;QACzB,MAAM,SAAS,GAAG,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC;QAClC,MAAM,MAAM,GAAG,sBAAsB,CAAC,SAAS,CAAC,CAAC;QACjD,MAAM,KAAK,GAAG,WAAW,CAAC,GAAG,CAAC,IAAI,CAA8B,CAAC;QACjE,MAAM,IAAI,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,IAAI,MAAM,CAAC;QACpE,MAAM,MAAM,GAAe,EAAE,SAAS,EAAE,MAAM,EAAE,IAAI,EAAE,CAAC;QACvD,IAAI,cAAc,EAAE,CAAC;YACnB,MAAM,SAAS,GAAG,WAAW,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YAC/D,IAAI,SAAS;gBAAE,MAAM,CAAC,SAAS,GAAG,SAAS,CAAC;YAC5C,MAAM,UAAU,GAAG,YAAY,CAAC,QAAQ,CAAC,KAAK,EAAE,cAAc,CAAC,CAAC,CAAC;YACjE,IAAI,UAAU,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,UAAU,GAAG,UAAU,CAAC;YAC1D,MAAM,WAAW,GAAG,kBAAkB,CAAC,KAAK,CAAC,CAAC;YAC9C,IAAI,WAAW,CAAC,MAAM,GAAG,CAAC;gBAAE,MAAM,CAAC,WAAW,GAAG,WAAW,CAAC;QAC/D,CAAC;QACD,OAAO,MAAM,CAAC;IAChB,CAAC,CAAC,CAAC;AACL,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,0NAA0N;IAC5N,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC;QACjB,mBAAmB;QACnB,uBAAuB;QACvB,yBAAyB;QACzB,mBAAmB;KACpB,CAAC;IACF,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,EAAE,GAAG,uBAAuB,CAAU;IAErE,oFAAoF;IACpF,YAAY,EAAE,EAAE,KAAK,EAAE,YAAY,EAAE;IAErC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,0IAA0I,CAC3I;QACH,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,OAAO,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,iBAAiB,CAAC;QACnF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,OAAO,CAAC,CAAC,CAAC;aACV,QAAQ,CACP,kLAAkL,CACnL;QACH,cAAc,EAAE,CAAC;aACd,OAAO,EAAE;aACT,OAAO,CAAC,IAAI,CAAC;aACb,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QACnD,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QACpE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uHAAuH,CACxH;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CACP,mKAAmK,CACpK;YACH,SAAS,EAAE,CAAC;iBACT,MAAM,EAAE;iBACR,QAAQ,CACP,2FAA2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|
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@@ -3,7 +3,10 @@
|
|
|
3
3
|
* can't reach: preprints (source `PPR`), Agricola (`AGR`), patents (`PAT`),
|
|
4
4
|
* and EPMC-only OA articles. Uses EPMC's cursor-based pagination
|
|
5
5
|
* (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
|
|
6
|
-
* because EPMC's search API doesn't support offset.
|
|
6
|
+
* because EPMC's search API doesn't support offset. `max_results` and `limit`
|
|
7
|
+
* are accepted as aliases for `pageSize`. The total hit count rides in
|
|
8
|
+
* `output` so `format()` can state it in the header, and `searchUrl` opens the
|
|
9
|
+
* source-filtered query Europe PMC actually ran.
|
|
7
10
|
*
|
|
8
11
|
* Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
|
|
9
12
|
* fails fast with a configuration error if the service is unset, since the
|
|
@@ -57,6 +60,7 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
|
|
|
57
60
|
cursorMark: z.ZodString;
|
|
58
61
|
nextCursorMark: z.ZodOptional<z.ZodString>;
|
|
59
62
|
searchUrl: z.ZodString;
|
|
63
|
+
totalCount: z.ZodNumber;
|
|
60
64
|
}, z.core.$strip>, readonly [{
|
|
61
65
|
readonly reason: 'europepmc_unreachable';
|
|
62
66
|
readonly code: JsonRpcErrorCode.ServiceUnavailable;
|
|
@@ -85,7 +89,6 @@ export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core")
|
|
|
85
89
|
readonly recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.';
|
|
86
90
|
}], {
|
|
87
91
|
readonly query: z.ZodString;
|
|
88
|
-
readonly totalCount: z.ZodNumber;
|
|
89
92
|
readonly appliedSources: z.ZodArray<z.ZodEnum<{
|
|
90
93
|
AGR: "AGR";
|
|
91
94
|
MED: "MED";
|
|
@@ -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
|
|
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;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;EAwSjG,CAAC"}
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@@ -3,7 +3,10 @@
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3
3
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* can't reach: preprints (source `PPR`), Agricola (`AGR`), patents (`PAT`),
|
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4
4
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* and EPMC-only OA articles. Uses EPMC's cursor-based pagination
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5
5
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* (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
|
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6
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-
* because EPMC's search API doesn't support offset.
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6
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+
* because EPMC's search API doesn't support offset. `max_results` and `limit`
|
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7
|
+
* are accepted as aliases for `pageSize`. The total hit count rides in
|
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8
|
+
* `output` so `format()` can state it in the header, and `searchUrl` opens the
|
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9
|
+
* source-filtered query Europe PMC actually ran.
|
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7
10
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*
|
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8
11
|
* Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
|
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9
12
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* fails fast with a configuration error if the service is unset, since the
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@@ -43,11 +46,14 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
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43
46
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recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.',
|
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44
47
|
},
|
|
45
48
|
],
|
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49
|
+
// Never advertised; rewritten to the canonical key before the schema parses.
|
|
50
|
+
// `pageSize` is this tool's only count parameter, so both map to it. (#156)
|
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51
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+
inputAliases: { max_results: 'pageSize', limit: 'pageSize' },
|
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46
52
|
input: z.object({
|
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47
53
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query: z
|
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48
54
|
.string()
|
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49
55
|
.min(1)
|
|
50
|
-
.describe('Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens
|
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56
|
+
.describe('Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:<pmid> AND SRC:MED`, `PMCID:PMC<digits>`. Identifier tokens may be quoted or unquoted — this tool wraps every query with its `sources` filter, and Europe PMC honors a quoted identifier inside that wrapper. A PubMed-indexed article resolves under `SRC:MED`, not `SRC:PMC`, whichever identifier is used. Free text is matched broadly across abstract/title/keywords.'),
|
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51
57
|
pageSize: z
|
|
52
58
|
.number()
|
|
53
59
|
.int()
|
|
@@ -131,13 +137,15 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
|
|
|
131
137
|
.optional()
|
|
132
138
|
.describe('Cursor to pass back as `cursorMark` for the next page. Absent on the final page.'),
|
|
133
139
|
searchUrl: z.string().describe("Europe PMC's website search URL for this query"),
|
|
140
|
+
// A domain field, not enrichment: format() sees only this payload, and the
|
|
141
|
+
// header states the total beside the returned count. (#147)
|
|
142
|
+
totalCount: z.number().describe('Total matching records across all pages'),
|
|
134
143
|
}),
|
|
135
|
-
// Result-set context the agent reasons with — the query as EPMC echoed it, the
|
|
136
|
-
//
|
|
137
|
-
//
|
|
144
|
+
// Result-set context the agent reasons with — the query as EPMC echoed it, the
|
|
145
|
+
// sources actually queried, and recovery guidance for empty pages. Surfaced via
|
|
146
|
+
// ctx.enrich(...) to structuredContent and content[]; out of the return.
|
|
138
147
|
enrichment: {
|
|
139
148
|
query: z.string().describe('Effective query string echoed by Europe PMC'),
|
|
140
|
-
totalCount: z.number().describe('Total matching records across all pages'),
|
|
141
149
|
appliedSources: z
|
|
142
150
|
.array(SourceEnum)
|
|
143
151
|
.describe('Sources the query was filtered against (defaults applied)'),
|
|
@@ -150,7 +158,6 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
|
|
|
150
158
|
// carries the full structured value; this only shapes the human-facing trailer line.
|
|
151
159
|
enrichmentTrailer: {
|
|
152
160
|
query: { label: 'Effective Query' },
|
|
153
|
-
totalCount: { label: 'Total Hits' },
|
|
154
161
|
appliedSources: {
|
|
155
162
|
render: (sources) => `**Sources:** ${sources.join(', ')}`,
|
|
156
163
|
},
|
|
@@ -233,20 +240,22 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
|
|
|
233
240
|
query: result.query,
|
|
234
241
|
appliedSources: [...sources],
|
|
235
242
|
});
|
|
236
|
-
ctx.enrich.total(result.hitCount);
|
|
237
243
|
if (notice)
|
|
238
244
|
ctx.enrich.notice(notice);
|
|
239
245
|
return {
|
|
240
246
|
hits,
|
|
241
247
|
cursorMark: result.cursorMark ?? '*',
|
|
242
248
|
...(result.nextCursorMark && { nextCursorMark: result.nextCursorMark }),
|
|
243
|
-
|
|
249
|
+
// The query Europe PMC ran, source wrapper included — `input.query` alone
|
|
250
|
+
// opens an unfiltered search with a different hit count. (#150)
|
|
251
|
+
searchUrl: `https://europepmc.org/search?query=${encodeURIComponent(result.query)}`,
|
|
252
|
+
totalCount: result.hitCount,
|
|
244
253
|
};
|
|
245
254
|
},
|
|
246
255
|
format: (result) => {
|
|
247
256
|
const lines = [
|
|
248
257
|
'## Europe PMC Search Results',
|
|
249
|
-
`**Returned:** ${result.hits.length}`,
|
|
258
|
+
`**Returned:** ${result.hits.length} of ${result.totalCount}`,
|
|
250
259
|
`**Cursor:** ${result.cursorMark}${result.nextCursorMark ? ` → \`${result.nextCursorMark}\` (next page)` : ' (final page)'}`,
|
|
251
260
|
`**Search URL:** ${result.searchUrl}`,
|
|
252
261
|
];
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA
|
|
1
|
+
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@@ -1,6 +1,12 @@
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1
1
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/**
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2
2
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* @fileoverview PubMed search tool. Searches PubMed with full query syntax,
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3
3
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* field-specific filters, date ranges, pagination, and optional brief summaries.
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4
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+
* A query with no search term — blank, markup only, a bare field tag, or empty
|
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5
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+
* parentheses — is rejected before NCBI is called. `limit` is accepted as an
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6
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+
* alias for `maxResults`. The total match count rides in `output` so `format()`
|
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7
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+
* can state it in the header beside the returned count, and a summary's
|
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8
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+
* `docType` is rendered only when it marks something other than an ordinary
|
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9
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+
* journal article (`citation`).
|
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4
10
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* @module src/mcp-server/tools/definitions/search-articles.tool
|
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5
11
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*/
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6
12
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import { z } from '@cyanheads/mcp-ts-core';
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@@ -55,6 +61,7 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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55
61
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pubmedUrl: z.ZodOptional<z.ZodString>;
|
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56
62
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}, z.core.$strip>>;
|
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57
63
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searchUrl: z.ZodString;
|
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64
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+
totalCount: z.ZodNumber;
|
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58
65
|
}, z.core.$strip>, readonly [{
|
|
59
66
|
readonly reason: 'queue_full';
|
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60
67
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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@@ -93,12 +100,11 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
|
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93
100
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}, {
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94
101
|
readonly reason: 'blank_query';
|
|
95
102
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
96
|
-
readonly when: 'The query holds no search term once whitespace, and
|
|
97
|
-
readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
|
|
103
|
+
readonly when: 'The query holds no search term once whitespace, and anything the tool strips before searching, are removed — so NCBI would receive a blank term. pubmed_search_articles strips markup, bracketed field tags, and parentheses, so a bare field tag such as `[pdat]` or empty parentheses `()` count as blank there.';
|
|
104
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+
readonly recovery: 'Supply a nonblank search term — a bare field tag or empty parentheses carry none; NCBI cannot search a blank term and retrying the same input will not help.';
|
|
98
105
|
readonly retryable: false;
|
|
99
106
|
}], {
|
|
100
107
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readonly effectiveQuery: z.ZodString;
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readonly totalCount: z.ZodNumber;
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readonly appliedFilters: z.ZodObject<{
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dateRange: z.ZodOptional<z.ZodObject<{
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minDate: z.ZodString;
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@@ -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
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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;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA8LjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmb7B,CAAC"}
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/**
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* @fileoverview PubMed search tool. Searches PubMed with full query syntax,
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* field-specific filters, date ranges, pagination, and optional brief summaries.
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* A query with no search term — blank, markup only, a bare field tag, or empty
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5
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* parentheses — is rejected before NCBI is called. `limit` is accepted as an
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6
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* alias for `maxResults`. The total match count rides in `output` so `format()`
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7
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* can state it in the header beside the returned count, and a summary's
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* `docType` is rendered only when it marks something other than an ordinary
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9
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* journal article (`citation`).
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* @module src/mcp-server/tools/definitions/search-articles.tool
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*/
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12
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import { tool, z } from '@cyanheads/mcp-ts-core';
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@@ -22,6 +28,48 @@ const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
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* still act on it. The limit is db-specific — it does not apply to db=mesh.
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*/
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const OFFSET_MAX = 9998;
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/**
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* PubMed search field tags, lowercased: the tags in PubMed's search-field help,
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* their full names, and ESearch's own field names, each confirmed live to be
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* read as a field tag — a bare `[pdat]` returns "No items found." PubMed searches
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* the content of any other bracket as text (`[18F]`, `[cancer]`, `[smith j]`, and
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* `[ab]` all return matches), so the blank-term check treats only these as
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* carrying no term. A tag missing here fails safe: its bare form is sent and
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* answered as an ordinary zero-hit search.
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*/
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const PUBMED_FIELD_TAGS = new Set([
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'1au|ad|aid|all|au|auid|book|cn|cois|crdt|dcom|doi|dp|ed|edat|fau|filter|fir|gr|ip|ir',
|
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42
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'isbn|jid|la|lastau|lid|lr|majr|mh|mhda|nm|ot|pa|pg|pl|pmid|ps|pt|pubn|rn|sb|sh|si|so',
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'ta|ti|tiab|tt|tw|vi|affl|aucl|auth|cdat|cnty|coln|ecno|eid|epdat|epdt|faut|filt|finv',
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'full|grnt|iss|jour|lang|laut|mdat|mesh|otrm|page|papx|pdat|pid|ppdat|ppdt|ptyp|subh',
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45
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'subs|titl|vol|word|author|editor|issue|subset|title|volume',
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'keyword|affiliation|all fields|author - corporate|author - first|author - identifier',
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'author - last|author cluster id|completion date|conflict of interest statements',
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48
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'corporate author|create date|date - completion|date - create|date - entry|date - mesh',
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'date - modification|date - publication|ec/rn number|electronic publication date',
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'entry date|extended pmid|first author name|full author name|full investigator name',
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'grants and funding|investigator|journal|language|last author name|location id',
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'mesh date|mesh major topic|mesh subheading|mesh terms|modification date|other term',
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'pagination|personal name as subject|pharmacological action|place of publication',
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'print publication date|publication date|publication type|publisher|publisher id',
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'secondary source id|subheading|subject - personal name|supplementary concept|text word',
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+
'title/abstract|transliterated title',
|
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+
]
|
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+
.join('|')
|
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+
.split('|'));
|
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|
+
/**
|
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|
+
* The query with every parenthesis and every bracketed field tag removed — what
|
|
62
|
+
* the blank-term check tests. A tag's search modifier (`[mh:noexp]`,
|
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63
|
+
* `[tiab:~3]`) does not change what it is; an empty bracket carries no term.
|
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|
+
*/
|
|
65
|
+
function withoutTermlessMarkup(query) {
|
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|
+
return query
|
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67
|
+
.replace(/\[([^\]]*)\]/g, (bracket, content) => {
|
|
68
|
+
const tag = content.trim().toLowerCase();
|
|
69
|
+
return tag === '' || PUBMED_FIELD_TAGS.has(tag.replace(/\s*:.*$/, '')) ? '' : bracket;
|
|
70
|
+
})
|
|
71
|
+
.replace(/[()]/g, '');
|
|
72
|
+
}
|
|
25
73
|
/** Upper bound on brief summaries fetched per call; shared by the schema and the format() cap message. */
|
|
26
74
|
const SUMMARY_COUNT_MAX = 50;
|
|
27
75
|
/** Renders a diagnostic list as a comma-separated set of backticked clauses. */
|
|
@@ -117,11 +165,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
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|
117
165
|
_meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
|
|
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166
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
|
|
119
167
|
errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
|
|
168
|
+
// Never advertised; rewritten to the canonical key before the schema parses.
|
|
169
|
+
// `max_results` needs no entry — the framework's case-style repair maps it. (#156)
|
|
170
|
+
inputAliases: { limit: 'maxResults' },
|
|
120
171
|
input: z.object({
|
|
121
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|
query: z
|
|
122
173
|
.string()
|
|
123
174
|
.min(1)
|
|
124
|
-
.describe('PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup
|
|
175
|
+
.describe('PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup, bracketed field tags (`[pdat]`), and parentheses are removed is rejected rather than sent to PubMed as an empty term.'),
|
|
125
176
|
maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
|
|
126
177
|
offset: z
|
|
127
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|
.number()
|
|
@@ -218,16 +269,18 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
218
269
|
.describe('Brief article summary'))
|
|
219
270
|
.describe('Brief summaries (empty array when summaryCount is 0)'),
|
|
220
271
|
searchUrl: z.string().describe('PubMed search URL'),
|
|
272
|
+
// A domain field, not enrichment: format() sees only this payload, and the
|
|
273
|
+
// header states the total beside the returned count. (#147)
|
|
274
|
+
totalCount: z.number().describe('Total matching articles'),
|
|
221
275
|
}),
|
|
222
276
|
// Result-set context the agent reasons with — the query as PubMed parsed it, the
|
|
223
|
-
//
|
|
224
|
-
//
|
|
225
|
-
//
|
|
277
|
+
// normalized filters, and recovery guidance for empty or overshot pages.
|
|
278
|
+
// Populated via ctx.enrich(...) so it reaches structuredContent and content[]
|
|
279
|
+
// alike; kept out of the domain return.
|
|
226
280
|
enrichment: {
|
|
227
281
|
effectiveQuery: z
|
|
228
282
|
.string()
|
|
229
283
|
.describe('Sanitized query sent to PubMed after applying all active filters'),
|
|
230
|
-
totalCount: z.number().describe('Total matching articles'),
|
|
231
284
|
appliedFilters: AppliedFiltersSchema.describe('Normalized filter values that were applied to the PubMed query'),
|
|
232
285
|
notice: z
|
|
233
286
|
.string()
|
|
@@ -238,7 +291,6 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
238
291
|
// carries the full structured value; this only shapes the human-facing trailer line.
|
|
239
292
|
enrichmentTrailer: {
|
|
240
293
|
effectiveQuery: { label: 'Effective Query' },
|
|
241
|
-
totalCount: { label: 'Total Found' },
|
|
242
294
|
appliedFilters: {
|
|
243
295
|
render: (filters) => {
|
|
244
296
|
const lines = [];
|
|
@@ -279,8 +331,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
279
331
|
// "Search is temporarily unavailable", which classifies as a retryable
|
|
280
332
|
// outage — the caller would spend the whole retry deadline on a
|
|
281
333
|
// deterministic input mistake. Reject before the call instead. (#122)
|
|
282
|
-
|
|
283
|
-
|
|
334
|
+
//
|
|
335
|
+
// A bare field tag (`[pdat]`) or empty parentheses carry no term either, so
|
|
336
|
+
// the check runs on a copy with those removed; `effectiveQuery` itself is
|
|
337
|
+
// sent as written. A bracket that is not a field tag (`[18F]`) is a term, and
|
|
338
|
+
// boolean operators are kept: NCBI reads an operand-less `NOT[ti]` as
|
|
339
|
+
// literal text and returns real matches. (#145)
|
|
340
|
+
if (withoutTermlessMarkup(effectiveQuery).trim().length === 0) {
|
|
341
|
+
throw ctx.fail('blank_query', 'The `query` carries no search term — it is blank once markup, bracketed field tags, and parentheses are removed.', { ...ctx.recoveryFor('blank_query') });
|
|
284
342
|
}
|
|
285
343
|
// Build filters — capture normalized values for both query construction and appliedFilters
|
|
286
344
|
let normalizedDateRange;
|
|
@@ -404,7 +462,6 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
404
462
|
...(esResult.warningList && { warningList: esResult.warningList }),
|
|
405
463
|
});
|
|
406
464
|
ctx.enrich({ effectiveQuery, appliedFilters });
|
|
407
|
-
ctx.enrich.total(esResult.count);
|
|
408
465
|
if (notice)
|
|
409
466
|
ctx.enrich.notice(notice);
|
|
410
467
|
return {
|
|
@@ -413,13 +470,14 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
413
470
|
pmids,
|
|
414
471
|
summaries,
|
|
415
472
|
searchUrl,
|
|
473
|
+
totalCount: esResult.count,
|
|
416
474
|
};
|
|
417
475
|
},
|
|
418
476
|
format: (result) => {
|
|
419
477
|
const lines = [
|
|
420
478
|
`## PubMed Search Results`,
|
|
421
479
|
`**Query:** ${result.query}`,
|
|
422
|
-
`**Returned:** ${result.pmids.length} | **Offset:** ${result.offset}`,
|
|
480
|
+
`**Returned:** ${result.pmids.length} of ${result.totalCount} | **Offset:** ${result.offset}`,
|
|
423
481
|
`**Search URL:** ${result.searchUrl}`,
|
|
424
482
|
];
|
|
425
483
|
if (result.pmids.length > 0)
|
|
@@ -451,7 +509,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
451
509
|
if (s.bookTitle || s.publisherName) {
|
|
452
510
|
lines.push(`**Book:** ${[s.bookTitle, s.publisherName].filter(Boolean).join(' — ')}`);
|
|
453
511
|
}
|
|
454
|
-
|
|
512
|
+
// `citation` is every ordinary journal article; the line earns its
|
|
513
|
+
// place only when it flags a Bookshelf chapter or book. (#146)
|
|
514
|
+
if (s.docType && s.docType !== 'citation')
|
|
455
515
|
lines.push(`**Doc Type:** ${s.docType}`);
|
|
456
516
|
if (s.pubDate)
|
|
457
517
|
lines.push(`**Published:** ${s.pubDate}`);
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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