@cyanheads/pubmed-mcp-server 2.6.7 → 2.6.9
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- package/CLAUDE.md +2 -2
- package/README.md +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +32 -2
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +12 -0
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts.map +1 -1
- 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 +18 -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 +6 -2
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +14 -8
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +46 -33
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts +31 -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 +2 -0
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts +31 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js +3 -1
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +31 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +2 -0
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +31 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +2 -0
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +31 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +2 -0
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +89 -0
- package/dist/services/error-contracts.d.ts.map +1 -0
- package/dist/services/error-contracts.js +97 -0
- package/dist/services/error-contracts.js.map +1 -0
- package/dist/services/ncbi/api-client.d.ts.map +1 -1
- package/dist/services/ncbi/api-client.js +3 -2
- package/dist/services/ncbi/api-client.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +3 -4
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +50 -6
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/request-queue.d.ts.map +1 -1
- package/dist/services/ncbi/request-queue.js +7 -1
- package/dist/services/ncbi/request-queue.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts +7 -2
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +57 -12
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.d.ts.map +1 -1
- package/dist/services/unpaywall/unpaywall-service.js +7 -2
- package/dist/services/unpaywall/unpaywall-service.js.map +1 -1
- package/package.json +3 -3
- package/server.json +3 -3
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts +0 -41
- package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map +0 -1
- package/dist/mcp-server/tools/definitions/_error-contracts.js +0 -45
- package/dist/mcp-server/tools/definitions/_error-contracts.js.map +0 -1
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{"version":3,"file":"find-related.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,QAAQ,EAAE,MAAM,+BAA+B,CAAC;AACzD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AACnF,OAAO,EAAE,WAAW,EAAE,MAAM,wCAAwC,CAAC;AAErE,OAAO,EAAE,WAAW,EAAE,mBAAmB,EAAE,wBAAwB,EAAE,MAAM,gBAAgB,CAAC;AAC5F,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAuBjD,SAAS,YAAY,CAAC,KAAkE;IACtF,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,IAAI;QAAE,OAAO,EAAE,CAAC;IACrD,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,KAAK,CAAC,OAAO,CAAC,KAAK,SAAS,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC;IACjG,OAAO,MAAM,CAAC,KAAK,CAAC,CAAC;AACvB,CAAC;AAED,gFAAgF;AAEhF,MAAM,CAAC,MAAM,eAAe,GAAG,IAAI,CAAC,qBAAqB,EAAE;IACzD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,CAAC,CAAC;IACnE,SAAS,EACP,gHAAgH;IAElH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,IAAI,EAAE,gBAAgB,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC;aACZ,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC;aAC3C,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,uHAAuH,CACxH;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,0BAA0B,CAAC;KAC7F,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;QACnD,YAAY,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC,SAAS,EAAE,UAAU,EAAE,YAAY,CAAC,CAAC,CAAC,QAAQ,CAAC,wBAAwB,CAAC;QAC9F,QAAQ,EAAE,CAAC;aACR,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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,eAAe,CAAC;YACxD,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,KAAK,EAAE,CAAC;iBACL,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,yFAAyF,CAC1F;SACJ,CAAC;aACD,QAAQ,CAAC,uCAAuC,CAAC,CACrD;aACA,QAAQ,CAAC,kBAAkB,CAAC;QAC/B,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QACjF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,uJAAuJ,CACxJ;KACJ,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0BAA0B,EAAE;YACxC,IAAI,EAAE,KAAK,CAAC,IAAI;YAChB,YAAY,EAAE,KAAK,CAAC,YAAY;SACjC,CAAC,CAAC;QAEH,MAAM,WAAW,GAA2B;YAC1C,MAAM,EAAE,QAAQ;YAChB,EAAE,EAAE,QAAQ;YACZ,EAAE,EAAE,KAAK,CAAC,IAAI;YACd,OAAO,EAAE,KAAK;SACf,CAAC;QACF,QAAQ,KAAK,CAAC,YAAY,EAAE,CAAC;YAC3B,KAAK,SAAS;gBACZ,WAAW,CAAC,GAAG,GAAG,gBAAgB,CAAC;gBACnC,MAAM;YACR,KAAK,UAAU;gBACb,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,uBAAuB,CAAC;gBAC/C,MAAM;YACR,KAAK,YAAY;gBACf,WAAW,CAAC,GAAG,GAAG,UAAU,CAAC;gBAC7B,WAAW,CAAC,QAAQ,GAAG,oBAAoB,CAAC;gBAC5C,MAAM;QACV,CAAC;QAED,MAAM,WAAW,GAAG,CAAC,MAAM,IAAI,CAAC,KAAK,CAAC,WAAW,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAkB,CAAC;QAC7F,MAAM,iBAAiB,GAAG,WAAW,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC;QAChE,MAAM,WAAW,GAAG,iBAAiB,CAAC,CAAC,CAAgC,CAAC;QAExE,6EAA6E;QAC7E,6EAA6E;QAC7E,4EAA4E;QAC5E,yEAAyE;QACzE,uEAAuE;QACvE,IAAI,WAAW,EAAE,KAAK,EAAE,CAAC;YACvB,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,0DAA0D,EAAE;gBACxE,IAAI,EAAE,KAAK,CAAC,IAAI;gBAChB,YAAY,EAAE,KAAK,CAAC,YAAY;gBAChC,SAAS,EAAE,WAAW,CAAC,KAAK;aAC7B,CAAC,CAAC;QACL,CAAC;QAED,MAAM,OAAO,GAAG,WAAW,EAAE,OAAO,CAAC;QACrC,IAAI,UAAU,GAAuC,EAAE,CAAC;QAExD,IAAI,OAAO,EAAE,SAAS,EAAE,CAAC;YACvB,MAAM,cAAc,GAAG,WAAW,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC;YACtD,MAAM,gBAAgB,GACpB,KAAK,CAAC,YAAY,KAAK,UAAU;gBAC/B,CAAC,CAAC,uBAAuB;gBACzB,CAAC,CAAC,KAAK,CAAC,YAAY,KAAK,YAAY;oBACnC,CAAC,CAAC,oBAAoB;oBACtB,CAAC,CAAC,eAAe,CAAC;YACxB,MAAM,QAAQ,GACZ,cAAc,CAAC,IAAI,CAAC,CAAC,EAAE,EAAE,EAAE,CAAC,EAAE,CAAC,QAAQ,KAAK,gBAAgB,CAAC,IAAI,cAAc,CAAC,CAAC,CAAC,CAAC;YAErF,IAAI,QAAQ,EAAE,IAAI,EAAE,CAAC;gBACnB,UAAU,GAAG,WAAW,CAAC,QAAQ,CAAC,IAAI,CAAC;qBACpC,GAAG,CAAC,CAAC,IAAkB,EAAE,EAAE,CAAC,CAAC;oBAC5B,IAAI,EAAE,YAAY,CAAC,IAAI,CAAC,EAAE,CAAC;oBAC3B,GAAG,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,KAAK,EAAE,MAAM,CAAC,YAAY,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC,EAAE,CAAC;iBACjF,CAAC,CAAC;qBACF,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,IAAI,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,KAAK,CAAC,IAAI,IAAI,IAAI,CAAC,IAAI,KAAK,GAAG,CAAC,CAAC;YAClF,CAAC;QACH,CAAC;QAED,MAAM,UAAU,GAAG,UAAU,CAAC,MAAM,CAAC;QACrC,IAAI,UAAU,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC5B,yEAAyE;YACzE,0EAA0E;YAC1E,yEAAyE;YACzE,yEAAyE;YACzE,wEAAwE;YACxE,IAAI,aAA6C,CAAC;YAClD,IAAI,sBAAsB,GAAG,KAAK,CAAC;YACnC,IAAI,CAAC;gBACH,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,KAAK,CAAC,IAAI,EAAE,EAChC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;gBACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;gBAC7D,aAAa,GAAG,SAAS,CAAC,CAAC,CAAC,CAAC;gBAC7B,uEAAuE;gBAC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@@ -26,5 +26,35 @@ export declare const formatCitationsTool: import("@cyanheads/mcp-ts-core").ToolD
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totalSubmitted: z.ZodNumber;
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totalFormatted: z.ZodNumber;
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unavailablePmids: z.ZodOptional<z.ZodArray<z.ZodString>>;
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}, z.core.$strip>,
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}, z.core.$strip>, readonly [{
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readonly reason: "queue_full";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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readonly when: "Local NCBI request queue is at capacity.";
|
|
33
|
+
readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
|
|
34
|
+
readonly retryable: true;
|
|
35
|
+
}, {
|
|
36
|
+
readonly reason: "ncbi_unreachable";
|
|
37
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
|
38
|
+
readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
|
|
39
|
+
readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
|
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40
|
+
readonly retryable: true;
|
|
41
|
+
}, {
|
|
42
|
+
readonly reason: "ncbi_deadline_exceeded";
|
|
43
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
|
|
44
|
+
readonly when: "Total request deadline expired before NCBI returned a response.";
|
|
45
|
+
readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
|
|
46
|
+
readonly retryable: true;
|
|
47
|
+
}, {
|
|
48
|
+
readonly reason: "ncbi_invalid_response";
|
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49
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
|
50
|
+
readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
|
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51
|
+
readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
|
|
52
|
+
readonly retryable: true;
|
|
53
|
+
}, {
|
|
54
|
+
readonly reason: "ncbi_resource_not_found";
|
|
55
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
56
|
+
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
|
57
|
+
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
|
58
|
+
readonly retryable: false;
|
|
59
|
+
}]>;
|
|
30
60
|
//# sourceMappingURL=format-citations.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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;AAejD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyG9B,CAAC"}
|
|
@@ -4,6 +4,7 @@
|
|
|
4
4
|
* @module src/mcp-server/tools/definitions/format-citations.tool
|
|
5
5
|
*/
|
|
6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
|
+
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
7
8
|
import { formatCitations, } from '../../../services/ncbi/formatting/citation-formatter.js';
|
|
8
9
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
9
10
|
import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
|
|
@@ -16,6 +17,7 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
|
|
|
16
17
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
17
18
|
_meta: conceptMeta([SCHEMA_CREATIVE_WORK, EDAM_DATA_FORMATTING]),
|
|
18
19
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/format-citations.tool.ts',
|
|
20
|
+
errors: [...NCBI_SERVICE_ERRORS],
|
|
19
21
|
input: z.object({
|
|
20
22
|
pmids: z.array(pmidStringSchema).min(1).max(50).describe('PubMed IDs to cite'),
|
|
21
23
|
format: z
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,iBAAiB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;AAElE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,qJAAqJ;IACvJ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC;YACL,iBAAiB,CAAC,QAAQ,CAAC,uDAAuD,CAAC;YACnF,CAAC;iBACE,KAAK,CAAC,iBAAiB,CAAC;iBACxB,GAAG,CAAC,CAAC,CAAC;iBACN,QAAQ,CAAC,6EAA6E,CAAC;SAC3F,CAAC;aACD,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2HAA2H,CAC5H;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,OAAO,GAAoB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO;SACR,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,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,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,OAAO,CAAC;aAC5C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,IAAI,MAAM,CAAC,cAAc,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CACR,6NAA6N,CAC9N,CAAC;QACJ,CAAC;QACD,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"}
|
|
1
|
+
{"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,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,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;AAErE,OAAO,EAAE,WAAW,EAAE,oBAAoB,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AACzF,OAAO,EAAE,gBAAgB,EAAE,MAAM,eAAe,CAAC;AAEjD,MAAM,iBAAiB,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,QAAQ,EAAE,KAAK,CAAC,CAAC,CAAC;AAElE,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,qJAAqJ;IACvJ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,CAAC,CAAC;IAChE,SAAS,EACP,oHAAoH;IAEtH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC,CAAC,KAAK,CAAC,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC;QAC9E,MAAM,EAAE,CAAC;aACN,KAAK,CAAC;YACL,iBAAiB,CAAC,QAAQ,CAAC,uDAAuD,CAAC;YACnF,CAAC;iBACE,KAAK,CAAC,iBAAiB,CAAC;iBACxB,GAAG,CAAC,CAAC,CAAC;iBACN,QAAQ,CAAC,6EAA6E,CAAC;SAC3F,CAAC;aACD,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,2HAA2H,CAC5H;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,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;aACD,QAAQ,CAAC,gCAAgC,CAAC,CAC9C;aACA,QAAQ,CAAC,uBAAuB,CAAC;QACpC,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,mDAAmD,CAAC;QACxF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wCAAwC,CAAC;QAC7E,gBAAgB,EAAE,CAAC;aAChB,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,sDAAsD,CAAC;KACpE,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,OAAO,GAAoB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC;QAC7F,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,2CAA2C,EAAE;YACzD,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO;SACR,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,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAC1E,CAAC;QACF,MAAM,WAAW,GAAuB,WAAW,CAAC,GAAG,EAAE,gBAAgB,EAAE,aAAa,CAAC,CAAC;QAE1F,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,OAAO,CAAC;aAC5C,CAAC;QACJ,CAAC,CAAC,CAAC;QAEH,MAAM,aAAa,GAAG,IAAI,GAAG,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC;QACpE,MAAM,gBAAgB,GAAG,KAAK,CAAC,KAAK,CAAC,MAAM,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,CAAC,aAAa,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC,CAAC;QAEhF,OAAO;YACL,SAAS;YACT,cAAc,EAAE,KAAK,CAAC,KAAK,CAAC,MAAM;YAClC,cAAc,EAAE,SAAS,CAAC,MAAM;YAChC,GAAG,CAAC,gBAAgB,CAAC,MAAM,GAAG,CAAC,IAAI,EAAE,gBAAgB,EAAE,CAAC;SACzD,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,oBAAoB;YACpB,kBAAkB,MAAM,CAAC,cAAc,IAAI,MAAM,CAAC,cAAc,EAAE;SACnE,CAAC;QACF,IAAI,MAAM,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,0BAA0B,MAAM,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAC7E,CAAC;QACD,IAAI,MAAM,CAAC,cAAc,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CACR,6NAA6N,CAC9N,CAAC;QACJ,CAAC;QACD,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"}
|
|
@@ -39,5 +39,35 @@ export declare const lookupCitationTool: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
39
39
|
totalMatched: z.ZodNumber;
|
|
40
40
|
totalSubmitted: z.ZodNumber;
|
|
41
41
|
totalWarnings: z.ZodNumber;
|
|
42
|
-
}, z.core.$strip>,
|
|
42
|
+
}, z.core.$strip>, readonly [{
|
|
43
|
+
readonly reason: "queue_full";
|
|
44
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
|
|
45
|
+
readonly when: "Local NCBI request queue is at capacity.";
|
|
46
|
+
readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
|
|
47
|
+
readonly retryable: true;
|
|
48
|
+
}, {
|
|
49
|
+
readonly reason: "ncbi_unreachable";
|
|
50
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
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readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
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readonly retryable: true;
|
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}, {
|
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|
+
readonly reason: "ncbi_deadline_exceeded";
|
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
|
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|
+
readonly when: "Total request deadline expired before NCBI returned a response.";
|
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readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
|
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readonly retryable: true;
|
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}, {
|
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|
+
readonly reason: "ncbi_invalid_response";
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
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readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
|
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readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
|
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+
readonly retryable: true;
|
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}, {
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+
readonly reason: "ncbi_resource_not_found";
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|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
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|
+
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
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+
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
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71
|
+
readonly retryable: false;
|
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|
+
}]>;
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|
//# sourceMappingURL=lookup-citation.tool.d.ts.map
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
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1
|
+
{"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAyBjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAwR7B,CAAC"}
|
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@@ -6,6 +6,7 @@
|
|
|
6
6
|
* @module src/mcp-server/tools/definitions/lookup-citation.tool
|
|
7
7
|
*/
|
|
8
8
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
9
|
+
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
9
10
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
10
11
|
import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
|
|
11
12
|
import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
|
|
@@ -21,10 +22,11 @@ function authorSurnames(authors) {
|
|
|
21
22
|
.filter((s) => s.length > 0 && s !== 'et');
|
|
22
23
|
}
|
|
23
24
|
export const lookupCitationTool = tool('pubmed_lookup_citation', {
|
|
24
|
-
description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID
|
|
25
|
+
description: `Look up PubMed IDs from partial bibliographic citations. Useful when you have a reference (journal, year, volume, page, author) and need the PMID — deterministic citation matching, more reliable than free-text search for structured references. Each citation must include at least one bibliographic field (journal, year, volume, firstPage, or authorName); more fields = better match accuracy.`,
|
|
25
26
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
26
27
|
_meta: conceptMeta([SCHEMA_SCHOLARLY_ARTICLE, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID]),
|
|
27
28
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-citation.tool.ts',
|
|
29
|
+
errors: [...NCBI_SERVICE_ERRORS],
|
|
28
30
|
input: z.object({
|
|
29
31
|
citations: z
|
|
30
32
|
.array(z
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,2FAA2F;AAC3F,SAAS,cAAc,CAAC,OAAe;IACrC,OAAO,OAAO;SACX,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;SACtB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC;AAC/C,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,
|
|
1
|
+
{"version":3,"file":"lookup-citation.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;AACpE,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,qBAAqB,EAAE,MAAM,4CAA4C,CAAC;AAEnF,OAAO,EACL,WAAW,EACX,mBAAmB,EACnB,cAAc,EACd,wBAAwB,GACzB,MAAM,gBAAgB,CAAC;AAExB,yFAAyF;AACzF,SAAS,OAAO,CAAC,IAAY;IAC3B,OAAO,IAAI,CAAC,IAAI,EAAE,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,EAAE,WAAW,EAAE,IAAI,EAAE,CAAC;AAC1D,CAAC;AAED,2FAA2F;AAC3F,SAAS,cAAc,CAAC,OAAe;IACrC,OAAO,OAAO;SACX,KAAK,CAAC,IAAI,CAAC;SACX,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC;SACtB,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,MAAM,GAAG,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,CAAC;AAC/C,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,yYAAyY;IACtZ,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,wBAAwB,EAAE,mBAAmB,EAAE,cAAc,CAAC,CAAC;IACnF,SAAS,EACP,mHAAmH;IAErH,MAAM,EAAE,CAAC,GAAG,mBAAmB,CAAU;IAEzC,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,SAAS,EAAE,CAAC;aACT,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,OAAO,EAAE,CAAC;iBACP,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,sEAAsE,CAAC;YACnF,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;YACvE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACvD,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YAC9D,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,8DAA8D,CAAC;YAC3E,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,8EAA8E,CAC/E;SACJ,CAAC;aACD,QAAQ,CACP,oIAAoI,CACrI;aACA,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,IAAI,CAAC,CAAC,MAAM,IAAI,CAAC,CAAC,SAAS,IAAI,CAAC,CAAC,UAAU,CAAC,EAAE;YACjF,OAAO,EACL,gHAAgH;SACnH,CAAC,CACL;aACA,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,EAAE,CAAC;aACP,QAAQ,CAAC,4DAA4D,CAAC;KAC1E,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,OAAO,EAAE,CAAC;aACP,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;YACjD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;YACzD,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC;YACzD,MAAM,EAAE,CAAC;iBACN,IAAI,CAAC,CAAC,SAAS,EAAE,WAAW,EAAE,WAAW,CAAC,CAAC;iBAC3C,QAAQ,CAAC,iDAAiD,CAAC;YAC9D,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,+DAA+D,CAAC;YAC5E,cAAc,EAAE,CAAC;iBACd,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,MAAM,CAAC,CAAC;iBAClC,QAAQ,EAAE;iBACV,QAAQ,CACP,sMAAsM,CACvM;YACH,kBAAkB,EAAE,CAAC;iBAClB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,sGAAsG,CACvG;YACH,QAAQ,EAAE,CAAC;iBACR,KAAK,CACJ,CAAC;iBACE,MAAM,CAAC;gBACN,IAAI,EAAE,CAAC;qBACJ,IAAI,CAAC,CAAC,iBAAiB,EAAE,eAAe,CAAC,CAAC;qBAC1C,QAAQ,CAAC,+BAA+B,CAAC;gBAC5C,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,2CAA2C,CAAC;aAC1E,CAAC;iBACD,QAAQ,CAAC,mCAAmC,CAAC,CACjD;iBACA,QAAQ,EAAE;iBACV,QAAQ,CACP,yLAAyL,CAC1L;SACJ,CAAC;aACD,QAAQ,CAAC,2BAA2B,CAAC,CACzC;aACA,QAAQ,CAAC,uCAAuC,CAAC;QACpD,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC1E,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;QACpE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,QAAQ,CAAC,6DAA6D,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,kCAAkC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,SAAS,CAAC,MAAM,EAAE,CAAC,CAAC;QAEpF,MAAM,SAAS,GAAwB,KAAK,CAAC,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC;YACpE,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,IAAI,EAAE,CAAC,CAAC,IAAI;YACZ,MAAM,EAAE,CAAC,CAAC,MAAM;YAChB,SAAS,EAAE,CAAC,CAAC,SAAS;YACtB,UAAU,EAAE,CAAC,CAAC,UAAU;YACxB,GAAG,EAAE,CAAC,CAAC,GAAG,IAAI,MAAM,CAAC,CAAC,GAAG,CAAC,CAAC;SAC5B,CAAC,CAAC,CAAC;QAEJ,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAExE,MAAM,kBAAkB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACrD,MAAM,gBAAgB,GAAG,IAAI,GAAG,EAAkB,CAAC;QACnD,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;YAC1B,IAAI,CAAC,CAAC,UAAU;gBAAE,kBAAkB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,UAAU,CAAC,CAAC;YAC9D,IAAI,CAAC,CAAC,IAAI;gBAAE,gBAAgB,CAAC,GAAG,CAAC,CAAC,CAAC,GAAG,EAAE,CAAC,CAAC,IAAI,CAAC,CAAC;QAClD,CAAC;QAED,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAC7B,IAAI,GAAG,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,IAAc,CAAC,CAAC,CACjF,CAAC;QAEF,MAAM,aAAa,GAAG,IAAI,GAAG,EAAkD,CAAC;QAChF,IAAI,YAAY,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC5B,MAAM,aAAa,GAAG,MAAM,IAAI,CAAC,QAAQ,CACvC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,YAAY,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAC5C,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;YACF,MAAM,SAAS,GAAG,MAAM,qBAAqB,CAAC,aAAa,CAAC,CAAC;YAC7D,KAAK,MAAM,CAAC,IAAI,SAAS,EAAE,CAAC;gBAC1B,aAAa,CAAC,GAAG,CAAC,CAAC,CAAC,IAAI,EAAE;oBACxB,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;oBACxC,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAA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@@ -18,5 +18,35 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
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|
|
18
18
|
entryTerms: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
19
19
|
}, z.core.$strip>>;
|
|
20
20
|
notice: z.ZodOptional<z.ZodString>;
|
|
21
|
-
}, z.core.$strip>,
|
|
21
|
+
}, z.core.$strip>, readonly [{
|
|
22
|
+
readonly reason: "queue_full";
|
|
23
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
|
|
24
|
+
readonly when: "Local NCBI request queue is at capacity.";
|
|
25
|
+
readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
|
|
26
|
+
readonly retryable: true;
|
|
27
|
+
}, {
|
|
28
|
+
readonly reason: "ncbi_unreachable";
|
|
29
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
|
30
|
+
readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
|
|
31
|
+
readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
|
|
32
|
+
readonly retryable: true;
|
|
33
|
+
}, {
|
|
34
|
+
readonly reason: "ncbi_deadline_exceeded";
|
|
35
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
|
|
36
|
+
readonly when: "Total request deadline expired before NCBI returned a response.";
|
|
37
|
+
readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
|
|
38
|
+
readonly retryable: true;
|
|
39
|
+
}, {
|
|
40
|
+
readonly reason: "ncbi_invalid_response";
|
|
41
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
|
42
|
+
readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
|
|
43
|
+
readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
|
|
44
|
+
readonly retryable: true;
|
|
45
|
+
}, {
|
|
46
|
+
readonly reason: "ncbi_resource_not_found";
|
|
47
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
48
|
+
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
|
49
|
+
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
|
50
|
+
readonly retryable: false;
|
|
51
|
+
}]>;
|
|
22
52
|
//# sourceMappingURL=lookup-mesh.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
|
|
1
|
+
{"version":3,"file":"lookup-mesh.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-mesh.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqFjD,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0GzB,CAAC"}
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|
@@ -4,6 +4,7 @@
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|
|
4
4
|
* @module src/mcp-server/tools/definitions/lookup-mesh.tool
|
|
5
5
|
*/
|
|
6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
|
+
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
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|
7
8
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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8
9
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import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
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9
10
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import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
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@@ -78,6 +79,7 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
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78
79
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EDAM_DATA_RETRIEVAL,
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79
80
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]),
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80
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sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
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82
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+
errors: [...NCBI_SERVICE_ERRORS],
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81
83
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input: z.object({
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82
84
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query: z.string().min(1).describe('MeSH descriptor name or free-text term to look up'),
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83
85
|
maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
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@@ -1 +1 @@
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1
|
-
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|
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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;;;;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;QACpC,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,yHAAyH,CAC1H;KACJ,CAAC;IAEF,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,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@@ -76,5 +76,35 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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76
76
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}, z.core.$strip>>;
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|
searchUrl: z.ZodString;
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78
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notice: z.ZodOptional<z.ZodString>;
|
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79
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-
}, z.core.$strip>,
|
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79
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+
}, z.core.$strip>, readonly [{
|
|
80
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+
readonly reason: "queue_full";
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81
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
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82
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+
readonly when: "Local NCBI request queue is at capacity.";
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83
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+
readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
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84
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+
readonly retryable: true;
|
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85
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+
}, {
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86
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+
readonly reason: "ncbi_unreachable";
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87
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
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88
|
+
readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
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89
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+
readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
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90
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+
readonly retryable: true;
|
|
91
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+
}, {
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|
92
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+
readonly reason: "ncbi_deadline_exceeded";
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93
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
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94
|
+
readonly when: "Total request deadline expired before NCBI returned a response.";
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|
95
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+
readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
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96
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+
readonly retryable: true;
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97
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+
}, {
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98
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+
readonly reason: "ncbi_invalid_response";
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99
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
|
100
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+
readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
|
|
101
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+
readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
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102
|
+
readonly retryable: true;
|
|
103
|
+
}, {
|
|
104
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+
readonly reason: "ncbi_resource_not_found";
|
|
105
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
106
|
+
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
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107
|
+
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
|
108
|
+
readonly retryable: false;
|
|
109
|
+
}]>;
|
|
80
110
|
//# sourceMappingURL=search-articles.tool.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;
|
|
1
|
+
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyT7B,CAAC"}
|
|
@@ -5,6 +5,7 @@
|
|
|
5
5
|
*/
|
|
6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
7
|
import { sanitization } from '@cyanheads/mcp-ts-core/utils';
|
|
8
|
+
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
8
9
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
9
10
|
import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
|
|
10
11
|
import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
|
|
@@ -70,6 +71,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
70
71
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
71
72
|
_meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
|
|
72
73
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
|
|
74
|
+
errors: [...NCBI_SERVICE_ERRORS],
|
|
73
75
|
input: z.object({
|
|
74
76
|
query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
|
|
75
77
|
maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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+
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AAE,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,OAAO;YACL,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,cAAc;YACd,cAAc;YACd,UAAU,EAAE,QAAQ,CAAC,KAAK;YAC1B,MAAM,EAAE,KAAK,CAAC,MAAM;YACpB,KAAK;YACL,SAAS;YACT,SAAS;YACT,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,CAAC;SAC1B,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,0BAA0B;YAC1B,cAAc,MAAM,CAAC,KAAK,EAAE;YAC5B,wBAAwB,MAAM,CAAC,cAAc,EAAE;YAC/C,oBAAoB,MAAM,CAAC,UAAU,oBAAoB,MAAM,CAAC,KAAK,CAAC,MAAM,kBAAkB,MAAM,CAAC,MAAM,EAAE;YAC7G,mBAAmB,MAAM,CAAC,SAAS,EAAE;SACtC,CAAC;QACF,IAAI,MAAM,CAAC,IAAI,CAAC,MAAM,CAAC,cAAc,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAClD,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC;YACpC,IAAI,MAAM,CAAC,cAAc,CAAC,SAAS,EAAE,CAAC;gBACpC,KAAK,CAAC,IAAI,CACR,mBAAmB,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,QAAQ,QAAQ,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,OAAO,OAAO,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,OAAO,EAAE,CAC3J,CAAC;YACJ,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,gBAAgB,EAAE,MAAM,EAAE,CAAC;gBACnD,KAAK,CAAC,IAAI,CAAC,4BAA4B,MAAM,CAAC,cAAc,CAAC,gBAAgB,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAC9F,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC;gBACjC,KAAK,CAAC,IAAI,CAAC,iBAAiB,MAAM,CAAC,cAAc,CAAC,MAAM,EAAE,CAAC,CAAC;YAC9D,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,kBAAkB,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,CAAC,CAAC;YAChE,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,SAAS,EAAE,MAAM,EAAE,CAAC;gBAC5C,KAAK,CAAC,IAAI,CAAC,qBAAqB,MAAM,CAAC,cAAc,CAAC,SAAS,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YAChF,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,QAAQ,EAAE,CAAC;gBACnC,KAAK,CAAC,IAAI,CAAC,mBAAmB,MAAM,CAAC,cAAc,CAAC,QAAQ,EAAE,CAAC,CAAC;YAClE,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,WAAW,EAAE,CAAC;gBACtC,KAAK,CAAC,IAAI,CAAC,yBAAyB,CAAC,CAAC;YACxC,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,YAAY,EAAE,CAAC;gBACvC,KAAK,CAAC,IAAI,CAAC,2BAA2B,CAAC,CAAC;YAC1C,CAAC;YACD,IAAI,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,CAAC;gBAClC,KAAK,CAAC,IAAI,CAAC,kBAAkB,MAAM,CAAC,cAAc,CAAC,OAAO,EAAE,CAAC,CAAC;YAChE,CAAC;QACH,CAAC;QACD,IAAI,MAAM,CAAC,MAAM;YAAE,KAAK,CAAC,IAAI,CAAC,OAAO,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC;QACtD,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"}
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@@ -10,5 +10,35 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
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10
10
|
original: z.ZodString;
|
|
11
11
|
corrected: z.ZodString;
|
|
12
12
|
hasSuggestion: z.ZodBoolean;
|
|
13
|
-
}, z.core.$strip>,
|
|
13
|
+
}, z.core.$strip>, readonly [{
|
|
14
|
+
readonly reason: "queue_full";
|
|
15
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.RateLimited;
|
|
16
|
+
readonly when: "Local NCBI request queue is at capacity.";
|
|
17
|
+
readonly recovery: "Retry after 1-2 seconds; the request queue hit the NCBI rate limit.";
|
|
18
|
+
readonly retryable: true;
|
|
19
|
+
}, {
|
|
20
|
+
readonly reason: "ncbi_unreachable";
|
|
21
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
|
|
22
|
+
readonly when: "NCBI E-utilities is unreachable after all retry attempts.";
|
|
23
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+
readonly recovery: "Retry after a brief delay; NCBI was unreachable across all retry attempts.";
|
|
24
|
+
readonly retryable: true;
|
|
25
|
+
}, {
|
|
26
|
+
readonly reason: "ncbi_deadline_exceeded";
|
|
27
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Timeout;
|
|
28
|
+
readonly when: "Total request deadline expired before NCBI returned a response.";
|
|
29
|
+
readonly recovery: "Reduce batch size or retry; NCBI may be under temporary load.";
|
|
30
|
+
readonly retryable: true;
|
|
31
|
+
}, {
|
|
32
|
+
readonly reason: "ncbi_invalid_response";
|
|
33
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.SerializationError;
|
|
34
|
+
readonly when: "NCBI returned a body that could not be parsed (invalid XML/JSON).";
|
|
35
|
+
readonly recovery: "Retry the request; NCBI returned a malformed response that could not be parsed.";
|
|
36
|
+
readonly retryable: true;
|
|
37
|
+
}, {
|
|
38
|
+
readonly reason: "ncbi_resource_not_found";
|
|
39
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
40
|
+
readonly when: "NCBI returned a structured \"not found\" error for the requested ID(s).";
|
|
41
|
+
readonly recovery: "Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.";
|
|
42
|
+
readonly retryable: false;
|
|
43
|
+
}]>;
|
|
14
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;
|
|
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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8CzB,CAAC"}
|
|
@@ -4,6 +4,7 @@
|
|
|
4
4
|
* @module src/mcp-server/tools/definitions/spell-check.tool
|
|
5
5
|
*/
|
|
6
6
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
7
|
+
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
7
8
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
8
9
|
import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
|
|
9
10
|
export const spellCheckTool = tool('pubmed_spell_check', {
|
|
@@ -11,6 +12,7 @@ export const spellCheckTool = tool('pubmed_spell_check', {
|
|
|
11
12
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
12
13
|
_meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
|
|
13
14
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/spell-check.tool.ts',
|
|
15
|
+
errors: [...NCBI_SERVICE_ERRORS],
|
|
14
16
|
input: z.object({
|
|
15
17
|
query: z.string().min(2).describe('PubMed search query to spell-check'),
|
|
16
18
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}),
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@@ -1 +1 @@
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1
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-
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1
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+
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