@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.11
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 +13 -5
- package/dist/mcp-server/tools/definitions/_schemas.d.ts +16 -0
- package/dist/mcp-server/tools/definitions/_schemas.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/_schemas.js +20 -0
- package/dist/mcp-server/tools/definitions/_schemas.js.map +1 -1
- package/dist/mcp-server/tools/definitions/convert-ids.tool.d.ts +6 -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 +28 -3
- package/dist/mcp-server/tools/definitions/convert-ids.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/fetch-articles.tool.d.ts +27 -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 +166 -24
- 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 +307 -68
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +12 -0
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.js +171 -27
- package/dist/mcp-server/tools/definitions/find-related.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/format-citations.tool.js +11 -13
- package/dist/mcp-server/tools/definitions/format-citations.tool.js.map +1 -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 +42 -8
- package/dist/mcp-server/tools/definitions/lookup-citation.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js +14 -3
- package/dist/mcp-server/tools/definitions/lookup-mesh.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts +10 -0
- package/dist/mcp-server/tools/definitions/search-articles.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/search-articles.tool.js +52 -5
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts +6 -0
- package/dist/mcp-server/tools/definitions/spell-check.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/spell-check.tool.js +15 -3
- package/dist/mcp-server/tools/definitions/spell-check.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +39 -2
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +43 -2
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +0 -29
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +381 -30
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/ncbi-service.d.ts +3 -2
- package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
- package/dist/services/ncbi/ncbi-service.js +22 -10
- package/dist/services/ncbi/ncbi-service.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts +45 -2
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +208 -1
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +32 -1
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts +24 -4
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +505 -57
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +42 -1
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +215 -2
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/dist/services/openalex/api-client.d.ts +13 -4
- package/dist/services/openalex/api-client.d.ts.map +1 -1
- package/dist/services/openalex/api-client.js +19 -8
- package/dist/services/openalex/api-client.js.map +1 -1
- package/dist/services/openalex/openalex-service.d.ts +34 -17
- package/dist/services/openalex/openalex-service.d.ts.map +1 -1
- package/dist/services/openalex/openalex-service.js +119 -35
- package/dist/services/openalex/openalex-service.js.map +1 -1
- package/dist/services/openalex/types.d.ts +34 -1
- package/dist/services/openalex/types.d.ts.map +1 -1
- package/dist/services/openalex/types.js +20 -0
- package/dist/services/openalex/types.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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+
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@@ -52,6 +52,12 @@ export declare const lookupMeshTool: import("@cyanheads/mcp-ts-core").ToolDefini
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52
52
|
readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
|
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53
53
|
readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
|
|
54
54
|
readonly retryable: false;
|
|
55
|
+
}, {
|
|
56
|
+
readonly reason: 'blank_query';
|
|
57
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
58
|
+
readonly when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.';
|
|
59
|
+
readonly recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.';
|
|
60
|
+
readonly retryable: false;
|
|
55
61
|
}], {
|
|
56
62
|
readonly totalCount: z.ZodNumber;
|
|
57
63
|
readonly notice: z.ZodOptional<z.ZodString>;
|
|
@@ -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;;;;;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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsMzB,CAAC"}
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|
@@ -5,7 +5,7 @@
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|
|
5
5
|
* @module src/mcp-server/tools/definitions/lookup-mesh.tool
|
|
6
6
|
*/
|
|
7
7
|
import { tool, z } from '@cyanheads/mcp-ts-core';
|
|
8
|
-
import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
8
|
+
import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
9
9
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
10
10
|
import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
|
|
11
11
|
import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_ONTOLOGY_TERMINOLOGY, SCHEMA_DEFINED_TERM, SCHEMA_DEFINED_TERM_SET, } from './_concepts.js';
|
|
@@ -100,9 +100,12 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
|
|
|
100
100
|
EDAM_DATA_RETRIEVAL,
|
|
101
101
|
]),
|
|
102
102
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/lookup-mesh.tool.ts',
|
|
103
|
-
errors: [...NCBI_SERVICE_ERRORS],
|
|
103
|
+
errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
|
|
104
104
|
input: z.object({
|
|
105
|
-
query: z
|
|
105
|
+
query: z
|
|
106
|
+
.string()
|
|
107
|
+
.min(1)
|
|
108
|
+
.describe('MeSH descriptor name or free-text term to look up. Must carry a term: a blank or whitespace-only value is rejected rather than searched.'),
|
|
106
109
|
maxResults: z.number().int().min(1).max(50).default(10).describe('Maximum results'),
|
|
107
110
|
offset: z
|
|
108
111
|
.number()
|
|
@@ -158,6 +161,14 @@ export const lookupMeshTool = tool('pubmed_lookup_mesh', {
|
|
|
158
161
|
const { query, maxResults, offset, includeDetails } = input;
|
|
159
162
|
const ncbi = getNcbiService();
|
|
160
163
|
ctx.log.debug('MeSH lookup started', { query, maxResults, offset, includeDetails });
|
|
164
|
+
// ESearch on db=mesh answers a blank term with Count=0 and a WarningList
|
|
165
|
+
// rather than an error, so the empty-result branch would report "no MeSH
|
|
166
|
+
// descriptors matched" for a term that was never really searched. (#133)
|
|
167
|
+
if (query.trim().length === 0) {
|
|
168
|
+
throw ctx.fail('blank_query', 'The `query` is blank — there is no term to look up.', {
|
|
169
|
+
...ctx.recoveryFor('blank_query'),
|
|
170
|
+
});
|
|
171
|
+
}
|
|
161
172
|
const hasFieldTag = /\[.+\]/.test(query);
|
|
162
173
|
const callOpts = { signal: ctx.signal };
|
|
163
174
|
const broadSearch = ncbi.eSearch({ db: 'mesh', term: query, retmax: maxResults, retstart: offset }, callOpts);
|
|
@@ -1 +1 @@
|
|
|
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,mBAAmB,EAAE,MAAM,+BAA+B,CAAC;
|
|
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,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,2FAA2F,CAC5F;YACH,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,iBAAiB,CAAC;YAC5C,WAAW,EAAE,CAAC;iBACX,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;iBACjB,QAAQ,EAAE;iBACV,QAAQ,CACP,2KAA2K,CAC5K;YACH,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,YAAY,CAAC;YACvD,UAAU,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SAC9E,CAAC;aACD,QAAQ,CAAC,iCAAiC,CAAC,CAC/C;aACA,QAAQ,CAAC,uBAAuB,CAAC;KACrC,CAAC;IAEF,sFAAsF;IACtF,gFAAgF;IAChF,yEAAyE;IACzE,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,CAAC,+EAA+E,CAAC;QAC5F,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,2LAA2L,CAC5L;KACJ;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,cAAc,EAAE,GAAG,KAAK,CAAC;QAC5D,MAAM,IAAI,GAAG,cAAc,EAAE,CAAC;QAC9B,GAAG,CAAC,GAAG,CAAC,KAAK,CAAC,qBAAqB,EAAE,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,cAAc,EAAE,CAAC,CAAC;QAEpF,yEAAyE;QACzE,yEAAyE;QACzE,yEAAyE;QACzE,IAAI,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC9B,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,qDAAqD,EAAE;gBACnF,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC;aAClC,CAAC,CAAC;QACL,CAAC;QAED,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,CAC9B,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,EAAE,MAAM,EAAE,UAAU,EAAE,QAAQ,EAAE,MAAM,EAAE,EACjE,QAAQ,CACT,CAAC;QACF,kFAAkF;QAClF,mFAAmF;QACnF,+EAA+E;QAC/E,MAAM,WAAW,GAAG,WAAW;YAC7B,CAAC,CAAC,SAAS;YACX,CAAC,CAAC,IAAI,CAAC,OAAO,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,IAAI,EAAE,GAAG,KAAK,MAAM,EAAE,MAAM,EAAE,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QAC5E,MAAM,CAAC,WAAW,EAAE,WAAW,CAAC,GAAG,MAAM,OAAO,CAAC,GAAG,CAAC,CAAC,WAAW,EAAE,WAAW,CAAC,CAAC,CAAC;QAEjF,MAAM,UAAU,GAAG,WAAW,CAAC,KAAK,CAAC;QACrC,MAAM,SAAS,GAAG,WAAW,EAAE,MAAM,CAAC,CAAC,CAAC,CAAC;QACzC,MAAM,GAAG,GAAa,EAAE,CAAC;QACzB,IAAI,SAAS,KAAK,SAAS,IAAI,MAAM,KAAK,CAAC;YAAE,GAAG,CAAC,IAAI,CAAC,SAAS,CAAC,CAAC;QACjE,+EAA+E;QAC/E,6EAA6E;QAC7E,+EAA+E;QAC/E,IAAI,QAAQ,GAAG,CAAC,CAAC;QACjB,KAAK,MAAM,EAAE,IAAI,WAAW,CAAC,MAAM,EAAE,CAAC;YACpC,+EAA+E;YAC/E,8EAA8E;YAC9E,IAAI,EAAE,KAAK,SAAS,EAAE,CAAC;gBACrB,QAAQ,EAAE,CAAC;gBACX,SAAS;YACX,CAAC;YACD,IAAI,GAAG,CAAC,MAAM,IAAI,UAAU;gBAAE,MAAM;YACpC,QAAQ,EAAE,CAAC;YACX,GAAG,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,CAAC;QAED,MAAM,UAAU,GAAG,MAAM,GAAG,QAAQ,CAAC;QACrC,MAAM,OAAO,GAAG,QAAQ,GAAG,CAAC,IAAI,UAAU,GAAG,UAAU,CAAC;QAExD,IAAI,GAAG,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACrB,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;YAC7B,IAAI,MAAc,CAAC;YACnB,IAAI,UAAU,KAAK,CAAC,EAAE,CAAC;gBACrB,MAAM,GAAG,gCAAgC,KAAK,iKAAiK,CAAC;YAClN,CAAC;iBAAM,IAAI,QAAQ,GAAG,CAAC,EAAE,CAAC;gBACxB,iFAAiF;gBACjF,MAAM,GAAG,UAAU,MAAM,8CAA8C,KAAK,2CAC1E,OAAO,CAAC,CAAC,CAAC,yBAAyB,UAAU,GAAG,CAAC,CAAC,CAAC,EACrD,EAAE,CAAC;YACL,CAAC;iBAAM,CAAC;gBACN,MAAM,GAAG,UAAU,MAAM,2BAA2B,KAAK,aAAa,UAAU,4DAA4D,UAAU,GAAG,CAAC;YAC5J,CAAC;YACD,GAAG,CAAC,MAAM,CAAC,MAAM,CAAC,MAAM,CAAC,CAAC;YAC1B,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,OAAO,IAAI,EAAE,UAAU,EAAE,CAAC,EAAE,OAAO,EAAE,EAAE,EAAE,CAAC;QACxE,CAAC;QAED,MAAM,WAAW,GAAG,MAAM,IAAI,CAAC,QAAQ,CAAC,EAAE,EAAE,EAAE,MAAM,EAAE,EAAE,EAAE,GAAG,CAAC,IAAI,CAAC,GAAG,CAAC,EAAE,EAAE,QAAQ,CAAC,CAAC;QACrF,MAAM,OAAO,GAAG,mBAAmB,CAAC,WAAW,EAAE,GAAG,EAAE,cAAc,CAAC,CAAC;QAEtE,MAAM,UAAU,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;QACvC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;YACpB,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,MAAM,MAAM,GAAG,CAAC,CAAC,IAAI,CAAC,WAAW,EAAE,KAAK,UAAU,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;YAC3D,OAAO,MAAM,GAAG,MAAM,CAAC;QACzB,CAAC,CAAC,CAAC;QAEH,GAAG,CAAC,MAAM,CAAC,KAAK,CAAC,UAAU,CAAC,CAAC;QAC7B,8EAA8E;QAC9E,4EAA4E;QAC5E,0BAA0B;QAC1B,IAAI,QAAQ,KAAK,CAAC,IAAI,UAAU,GAAG,CAAC,EAAE,CAAC;YACrC,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,kDAAkD,UAAU,iCAAiC,UAAU,0BAA0B,KAAK,IAAI,CAC3I,CAAC;QACJ,CAAC;QACD,OAAO,EAAE,KAAK,EAAE,MAAM,EAAE,GAAG,CAAC,OAAO,IAAI,EAAE,UAAU,EAAE,CAAC,EAAE,OAAO,EAAE,CAAC;IACpE,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAG;YACZ,mBAAmB,MAAM,CAAC,KAAK,GAAG;YAClC,WAAW,MAAM,CAAC,OAAO,CAAC,MAAM,4BAA4B,MAAM,CAAC,MAAM,KAAK;SAC/E,CAAC;QACF,IAAI,MAAM,CAAC,UAAU,KAAK,SAAS,EAAE,CAAC;YACpC,KAAK,CAAC,IAAI,CAAC,8CAA8C,MAAM,CAAC,UAAU,KAAK,CAAC,CAAC;QACnF,CAAC;QACD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,QAAQ,CAAC,CAAC,IAAI,EAAE,CAAC,CAAC;YAC7B,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC;YACzC,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAC/C,IAAI,CAAC,CAAC,WAAW,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,uBAAuB,CAAC,CAAC,WAAW,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACzF,IAAI,CAAC,CAAC,SAAS;gBAAE,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC,SAAS,EAAE,CAAC,CAAC;YAChE,IAAI,CAAC,CAAC,UAAU,EAAE,MAAM;gBAAE,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC,UAAU,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACxF,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC"}
|
|
@@ -44,6 +44,10 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
44
44
|
title: z.ZodOptional<z.ZodString>;
|
|
45
45
|
authors: z.ZodOptional<z.ZodString>;
|
|
46
46
|
source: z.ZodOptional<z.ZodString>;
|
|
47
|
+
bookTitle: z.ZodOptional<z.ZodString>;
|
|
48
|
+
publisherName: z.ZodOptional<z.ZodString>;
|
|
49
|
+
docType: z.ZodOptional<z.ZodString>;
|
|
50
|
+
editors: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
|
47
51
|
pubDate: z.ZodOptional<z.ZodString>;
|
|
48
52
|
doi: z.ZodOptional<z.ZodString>;
|
|
49
53
|
pmcId: z.ZodOptional<z.ZodString>;
|
|
@@ -81,6 +85,12 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
|
|
|
81
85
|
readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
|
|
82
86
|
readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
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readonly retryable: false;
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+
}, {
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+
readonly reason: 'blank_query';
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90
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.';
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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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readonly retryable: false;
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94
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}], {
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readonly effectiveQuery: z.ZodString;
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readonly totalCount: z.ZodNumber;
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"search-articles.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/search-articles.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAgJjD,eAAO,MAAM,kBAAkB
|
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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;AAgJjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsa7B,CAAC"}
|
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@@ -5,7 +5,7 @@
|
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5
5
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*/
|
|
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';
|
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8
|
+
import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
9
9
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
10
10
|
import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
|
|
11
11
|
import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
|
|
@@ -116,9 +116,12 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
116
116
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
117
117
|
_meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
|
|
118
118
|
sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/search-articles.tool.ts',
|
|
119
|
-
errors: [...NCBI_SERVICE_ERRORS],
|
|
119
|
+
errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
|
|
120
120
|
input: z.object({
|
|
121
|
-
query: z
|
|
121
|
+
query: z
|
|
122
|
+
.string()
|
|
123
|
+
.min(1)
|
|
124
|
+
.describe('PubMed search query (supports full NCBI syntax). Must carry a search term: a value that is blank once markup is stripped is rejected rather than sent to PubMed as an empty term.'),
|
|
122
125
|
maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
|
|
123
126
|
offset: z
|
|
124
127
|
.number()
|
|
@@ -179,8 +182,30 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
179
182
|
.object({
|
|
180
183
|
pmid: z.string().describe('PubMed ID'),
|
|
181
184
|
title: z.string().optional().describe('Article title'),
|
|
182
|
-
authors: z
|
|
183
|
-
|
|
185
|
+
authors: z
|
|
186
|
+
.string()
|
|
187
|
+
.optional()
|
|
188
|
+
.describe("Formatted author string — the first three of the record's own authors, then \"et al.\". On an NCBI Bookshelf chapter these are the chapter's authors; the book's editors are reported separately in `editors`."),
|
|
189
|
+
source: z
|
|
190
|
+
.string()
|
|
191
|
+
.optional()
|
|
192
|
+
.describe('Journal the article appeared in. Absent on an NCBI Bookshelf record, which has no journal — its venue is in `bookTitle` and `publisherName` instead, and `docType` says which kind of record it is.'),
|
|
193
|
+
bookTitle: z
|
|
194
|
+
.string()
|
|
195
|
+
.optional()
|
|
196
|
+
.describe('Title of the book an NCBI Bookshelf record belongs to, e.g. "GeneReviews(®)". Present instead of `source` on a book record; absent on a journal article.'),
|
|
197
|
+
publisherName: z
|
|
198
|
+
.string()
|
|
199
|
+
.optional()
|
|
200
|
+
.describe('Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.'),
|
|
201
|
+
docType: z
|
|
202
|
+
.string()
|
|
203
|
+
.optional()
|
|
204
|
+
.describe('What PubMed classifies this record as: "chapter" or "book" for an NCBI Bookshelf record, "citation" for an ordinary journal article. Absent when PubMed supplies none.'),
|
|
205
|
+
editors: z
|
|
206
|
+
.array(z.string().describe('One editor, "Surname Initials" as ESummary renders it'))
|
|
207
|
+
.optional()
|
|
208
|
+
.describe("Editors of the containing book, kept out of `authors` so they cannot displace the record's own authors. Absent on a journal article and on a book that credits no editors."),
|
|
184
209
|
pubDate: z.string().optional().describe('Publication date'),
|
|
185
210
|
doi: z
|
|
186
211
|
.string()
|
|
@@ -248,6 +273,15 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
248
273
|
ctx.log.info('Executing pubmed_search', { query: input.query });
|
|
249
274
|
const ncbi = getNcbiService();
|
|
250
275
|
let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
|
|
276
|
+
// `min(1)` counts whitespace, and the sanitizer reduces markup with no text
|
|
277
|
+
// content to an empty string, so both reach here as a blank term. NCBI
|
|
278
|
+
// answers a blank term with HTTP 200 and an embedded <ERROR> reading
|
|
279
|
+
// "Search is temporarily unavailable", which classifies as a retryable
|
|
280
|
+
// outage — the caller would spend the whole retry deadline on a
|
|
281
|
+
// deterministic input mistake. Reject before the call instead. (#122)
|
|
282
|
+
if (effectiveQuery.trim().length === 0) {
|
|
283
|
+
throw ctx.fail('blank_query', 'The `query` carries no search term — it is blank after markup is stripped.', { ...ctx.recoveryFor('blank_query') });
|
|
284
|
+
}
|
|
251
285
|
// Build filters — capture normalized values for both query construction and appliedFilters
|
|
252
286
|
let normalizedDateRange;
|
|
253
287
|
const { dateRange } = input;
|
|
@@ -332,6 +366,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
332
366
|
title: s.title,
|
|
333
367
|
authors: s.authors,
|
|
334
368
|
source: s.source,
|
|
369
|
+
bookTitle: s.bookTitle,
|
|
370
|
+
publisherName: s.publisherName,
|
|
371
|
+
docType: s.docType,
|
|
372
|
+
editors: s.editors,
|
|
335
373
|
pubDate: s.pubDate,
|
|
336
374
|
doi: s.doi,
|
|
337
375
|
pmcId: s.pmcId,
|
|
@@ -404,8 +442,17 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
404
442
|
lines.push(`**PMID:** ${s.pmid}`);
|
|
405
443
|
if (s.authors)
|
|
406
444
|
lines.push(`**Authors:** ${s.authors}`);
|
|
445
|
+
if (s.editors?.length)
|
|
446
|
+
lines.push(`**Editors:** ${s.editors.join(', ')}`);
|
|
407
447
|
if (s.source)
|
|
408
448
|
lines.push(`**Source:** ${s.source}`);
|
|
449
|
+
// A Bookshelf record has no journal, so its venue takes the Source
|
|
450
|
+
// slot rather than leaving the summary without one. (#114)
|
|
451
|
+
if (s.bookTitle || s.publisherName) {
|
|
452
|
+
lines.push(`**Book:** ${[s.bookTitle, s.publisherName].filter(Boolean).join(' — ')}`);
|
|
453
|
+
}
|
|
454
|
+
if (s.docType)
|
|
455
|
+
lines.push(`**Doc Type:** ${s.docType}`);
|
|
409
456
|
if (s.pubDate)
|
|
410
457
|
lines.push(`**Published:** ${s.pubDate}`);
|
|
411
458
|
if (s.doi)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -40,5 +40,11 @@ export declare const spellCheckTool: import("@cyanheads/mcp-ts-core").ToolDefini
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40
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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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42
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readonly retryable: false;
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43
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+
}, {
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44
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+
readonly reason: 'blank_query';
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45
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+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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46
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+
readonly when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.';
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47
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+
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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48
|
+
readonly retryable: false;
|
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43
49
|
}], undefined>;
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44
50
|
//# sourceMappingURL=spell-check.tool.d.ts.map
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@@ -1 +1 @@
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1
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-
{"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
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1
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+
{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA+DzB,CAAC"}
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@@ -4,7 +4,7 @@
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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
|
+
import { NCBI_QUERY_INPUT_ERRORS, NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
|
|
8
8
|
import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
|
|
9
9
|
import { conceptMeta, SCHEMA_SEARCH_ACTION } from './_concepts.js';
|
|
10
10
|
export const spellCheckTool = tool('pubmed_spell_check', {
|
|
@@ -12,9 +12,12 @@ export const spellCheckTool = tool('pubmed_spell_check', {
|
|
|
12
12
|
annotations: { readOnlyHint: true, openWorldHint: true },
|
|
13
13
|
_meta: conceptMeta([SCHEMA_SEARCH_ACTION]),
|
|
14
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],
|
|
15
|
+
errors: [...NCBI_SERVICE_ERRORS, ...NCBI_QUERY_INPUT_ERRORS],
|
|
16
16
|
input: z.object({
|
|
17
|
-
query: z
|
|
17
|
+
query: z
|
|
18
|
+
.string()
|
|
19
|
+
.min(2)
|
|
20
|
+
.describe('PubMed search query to spell-check. Must carry a term: a blank or whitespace-only value is rejected rather than sent to ESpell.'),
|
|
18
21
|
}),
|
|
19
22
|
output: z.object({
|
|
20
23
|
original: z.string().describe('Original query'),
|
|
@@ -23,6 +26,15 @@ export const spellCheckTool = tool('pubmed_spell_check', {
|
|
|
23
26
|
}),
|
|
24
27
|
async handler(input, ctx) {
|
|
25
28
|
ctx.log.info('Executing pubmed_spell_check tool', { query: input.query });
|
|
29
|
+
// `min(2)` counts the spaces, so a whitespace-only query passes the schema.
|
|
30
|
+
// ESpell answers a blank term with an empty `<ERROR/>` element the response
|
|
31
|
+
// handler does not detect, and the tool would report the blank input as
|
|
32
|
+
// spell-checked. Reject before the call. (#133)
|
|
33
|
+
if (input.query.trim().length === 0) {
|
|
34
|
+
throw ctx.fail('blank_query', 'The `query` is blank — there is nothing to spell-check.', {
|
|
35
|
+
...ctx.recoveryFor('blank_query'),
|
|
36
|
+
});
|
|
37
|
+
}
|
|
26
38
|
const result = await getNcbiService().eSpell({ db: 'pubmed', term: input.query }, { signal: ctx.signal });
|
|
27
39
|
return {
|
|
28
40
|
original: result.original,
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.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;
|
|
1
|
+
{"version":3,"file":"spell-check.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/spell-check.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;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,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAEnE,MAAM,CAAC,MAAM,cAAc,GAAG,IAAI,CAAC,oBAAoB,EAAE;IACvD,WAAW,EACT,8FAA8F;IAChG,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,CAAC,CAAC;IAC1C,SAAS,EACP,+GAA+G;IAEjH,MAAM,EAAE,CAAC,GAAG,mBAAmB,EAAE,GAAG,uBAAuB,CAAU;IAErE,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,iIAAiI,CAClI;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gBAAgB,CAAC;QAC/C,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,qDAAqD,CAAC;QACrF,aAAa,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,qCAAqC,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,4EAA4E;QAC5E,4EAA4E;QAC5E,wEAAwE;QACxE,gDAAgD;QAChD,IAAI,KAAK,CAAC,KAAK,CAAC,IAAI,EAAE,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YACpC,MAAM,GAAG,CAAC,IAAI,CAAC,aAAa,EAAE,yDAAyD,EAAE;gBACvF,GAAG,GAAG,CAAC,WAAW,CAAC,aAAa,CAAC;aAClC,CAAC,CAAC;QACL,CAAC;QACD,MAAM,MAAM,GAAG,MAAM,cAAc,EAAE,CAAC,MAAM,CAC1C,EAAE,EAAE,EAAE,QAAQ,EAAE,IAAI,EAAE,KAAK,CAAC,KAAK,EAAE,EACnC,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CACvB,CAAC;QACF,OAAO;YACL,QAAQ,EAAE,MAAM,CAAC,QAAQ;YACzB,SAAS,EAAE,MAAM,CAAC,SAAS;YAC3B,aAAa,EAAE,MAAM,CAAC,aAAa;SACpC,CAAC;IACJ,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,IAAI,MAAM,CAAC,aAAa,EAAE,CAAC;YACzB,OAAO;gBACL;oBACE,IAAI,EAAE,MAAM;oBACZ,IAAI,EAAE,oBAAoB,MAAM,CAAC,SAAS,iBAAiB,MAAM,CAAC,QAAQ,IAAI;iBAC/E;aACF,CAAC;QACJ,CAAC;QACD,OAAO;YACL;gBACE,IAAI,EAAE,MAAM;gBACZ,IAAI,EAAE,0BAA0B,MAAM,CAAC,QAAQ,+BAA+B;aAC/E;SACF,CAAC;IACJ,CAAC;CACF,CAAC,CAAC"}
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@@ -1,6 +1,8 @@
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/**
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* @fileoverview Canonical
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*
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* @fileoverview Canonical error contracts. Single source of truth for the
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* failure modes services throw and tools declare in `errors[]`, plus the
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* input rejections shared by the tools that forward a free-text query
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* upstream.
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*
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* Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
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* `recoveryFor(reason)` from this module into the error factory's `data` arg.
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@@ -50,6 +52,41 @@ export declare const NCBI_SERVICE_ERRORS: readonly [{
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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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}];
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/**
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* Input failure the NCBI query tools reject before any call is made. Declared
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* here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
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* throw it advertise it — a tool that takes no free-text query can never
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* produce it, and declaring it there would advertise a failure mode that
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*
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* Unlike the service arrays in this module, this one is thrown from a tool
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* through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
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*/
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export declare const NCBI_QUERY_INPUT_ERRORS: readonly [{
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readonly reason: 'blank_query';
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.';
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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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readonly retryable: false;
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}];
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/**
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* Input failure the identifier-conversion path rejects before any call is made.
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* Separate from {@link NCBI_QUERY_INPUT_ERRORS} for the same reason that array
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* is separate from the service contracts: only a tool that takes caller-supplied
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* identifiers can produce it.
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*
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* Thrown from a tool handler via `ctx.fail('malformed_id', …)`, so its recovery
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* {@link ServiceErrorReason}.
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export declare const NCBI_ID_INPUT_ERRORS: readonly [{
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readonly reason: 'malformed_id';
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readonly code: JsonRpcErrorCode.ValidationError;
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readonly when: 'An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records.';
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readonly recovery: 'Submit one identifier per `ids` element, in the declared idType format; the same packed value will be rejected again.';
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}];
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/**
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* Failure modes the Unpaywall service layer can surface. Tools that consume
|
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@@ -1 +1 @@
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-
{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA
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1
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{"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;aAE5B,MAAM,EAAE,YAAY;aACpB,IAAI;aACJ,IAAI,EAAE,0CAA0C;aAChD,QAAQ,EAAE,qEAAqE;aAC/E,SAAS;;aAGT,MAAM,EAAE,kBAAkB;aAC1B,IAAI;aACJ,IAAI,EAAE,2DAA2D;aACjE,QAAQ,EAAE,4EAA4E;aACtF,SAAS;;aAGT,MAAM,EAAE,wBAAwB;aAChC,IAAI;aACJ,IAAI,EAAE,iEAAiE;aACvE,QAAQ,EAAE,+DAA+D;aACzE,SAAS;;aAGT,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,iFAAiF;aAC3F,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,uEAAuE;aAC7E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;;;;;;;GAUG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,aAAa;aACrB,IAAI;aACJ,IAAI,EAAE,yIAAyI;aAC/I,QAAQ,EACN,2GAA2G;aAC7G,SAAS;EAEH,CAAC;AAEX;;;;;;;;;GASG;AACH,eAAO,MAAM,oBAAoB;aAE7B,MAAM,EAAE,cAAc;aACtB,IAAI;aACJ,IAAI,EAAE,0LAA0L;aAChM,QAAQ,EACN,uHAAuH;aACzH,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,qEAAqE;aAC3E,QAAQ,EACN,gGAAgG;aAClG,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;aAEhC,MAAM,EAAE,sBAAsB;aAC9B,IAAI;aACJ,IAAI,EAAE,oDAAoD;aAC1D,QAAQ,EACN,4FAA4F;aAC9F,SAAS;;aAGT,MAAM,EAAE,2BAA2B;aACnC,IAAI;aACJ,IAAI,EAAE,mEAAmE;aACzE,QAAQ,EAAE,qFAAqF;aAC/F,SAAS;EAEH,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;aAEjC,MAAM,EAAE,uBAAuB;aAC/B,IAAI;aACJ,IAAI,EAAE,sDAAsD;aAC5D,QAAQ,EACN,iGAAiG;aACnG,SAAS;;aAGT,MAAM,EAAE,4BAA4B;aACpC,IAAI;aACJ,IAAI,EAAE,4EAA4E;aAClF,QAAQ,EACN,uFAAuF;aACzF,SAAS;;aAGT,MAAM,EAAE,yBAAyB;aACjC,IAAI;aACJ,IAAI,EAAE,+FAA+F;aACrG,QAAQ,EACN,8GAA8G;aAChH,SAAS;EAEH,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
|
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@@ -1,6 +1,8 @@
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/**
|
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* @fileoverview Canonical
|
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|
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*
|
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2
|
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* @fileoverview Canonical error contracts. Single source of truth for the
|
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3
|
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* failure modes services throw and tools declare in `errors[]`, plus the
|
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4
|
+
* input rejections shared by the tools that forward a free-text query
|
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5
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+
* upstream.
|
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4
6
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*
|
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5
7
|
* Service-layer code can't reach `ctx.recoveryFor` (no Context), so it spreads
|
|
6
8
|
* `recoveryFor(reason)` from this module into the error factory's `data` arg.
|
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@@ -56,6 +58,45 @@ export const NCBI_SERVICE_ERRORS = [
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retryable: false,
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},
|
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];
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/**
|
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* Input failure the NCBI query tools reject before any call is made. Declared
|
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63
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+
* here rather than inside `NCBI_SERVICE_ERRORS` so only the tools that actually
|
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64
|
+
* throw it advertise it — a tool that takes no free-text query can never
|
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65
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+
* produce it, and declaring it there would advertise a failure mode that
|
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66
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* cannot happen.
|
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67
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*
|
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+
* Unlike the service arrays in this module, this one is thrown from a tool
|
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69
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+
* handler via `ctx.fail('blank_query', …)`, so its recovery hint resolves
|
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70
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* through `ctx.recoveryFor` and it stays out of {@link ServiceErrorReason}.
|
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*/
|
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72
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export const NCBI_QUERY_INPUT_ERRORS = [
|
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{
|
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+
reason: 'blank_query',
|
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75
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code: JsonRpcErrorCode.ValidationError,
|
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when: 'The query holds no search term once whitespace, and any markup the tool strips first, are removed — so NCBI would receive a blank term.',
|
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recovery: 'Supply a nonblank search term; NCBI cannot search a blank term and retrying the same input will not help.',
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retryable: false,
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},
|
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];
|
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/**
|
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* Input failure the identifier-conversion path rejects before any call is made.
|
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83
|
+
* Separate from {@link NCBI_QUERY_INPUT_ERRORS} for the same reason that array
|
|
84
|
+
* is separate from the service contracts: only a tool that takes caller-supplied
|
|
85
|
+
* identifiers can produce it.
|
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86
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+
*
|
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87
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+
* Thrown from a tool handler via `ctx.fail('malformed_id', …)`, so its recovery
|
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* hint resolves through `ctx.recoveryFor` and it stays out of
|
|
89
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* {@link ServiceErrorReason}.
|
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+
*/
|
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export const NCBI_ID_INPUT_ERRORS = [
|
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{
|
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reason: 'malformed_id',
|
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code: JsonRpcErrorCode.ValidationError,
|
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+
when: 'An `ids` element does not match the declared `idType` — most often several identifiers packed into one element, which the comma-delimited upstream batch would split into extra records.',
|
|
96
|
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recovery: 'Submit one identifier per `ids` element, in the declared idType format; the same packed value will be rejected again.',
|
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retryable: false,
|
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},
|
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];
|
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|
/**
|
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|
* Failure modes the Unpaywall service layer can surface. Tools that consume
|
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|
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|
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@@ -1 +1 @@
|
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{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA
|
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1
|
+
{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;GAgBG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;;;;;;;GAUG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,aAAa;QACrB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,yIAAyI;QAC/I,QAAQ,EACN,2GAA2G;QAC7G,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;;;;;;GASG;AACH,MAAM,CAAC,MAAM,oBAAoB,GAAG;IAClC;QACE,MAAM,EAAE,cAAc;QACtB,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,0LAA0L;QAChM,QAAQ,EACN,uHAAuH;QACzH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qEAAqE;QAC3E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,sBAAsB;QAC9B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,oDAAoD;QAC1D,QAAQ,EACN,4FAA4F;QAC9F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,2BAA2B;QACnC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,qFAAqF;QAC/F,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;GAGG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,sDAAsD;QAC5D,QAAQ,EACN,iGAAiG;QACnG,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,4BAA4B;QACpC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,4EAA4E;QAClF,QAAQ,EACN,uFAAuF;QACzF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,+FAA+F;QACrG,QAAQ,EACN,8GAA8G;QAChH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAaX,MAAM,kBAAkB,GAAG,IAAI,GAAG,CAChC;IACE,GAAG,mBAAmB;IACtB,GAAG,wBAAwB;IAC3B,GAAG,wBAAwB;IAC3B,GAAG,uBAAuB;CAC3B,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAC;AAEF;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,MAA0B;IACpD,MAAM,IAAI,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,wDAAwD,MAAM,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;AAChC,CAAC"}
|