@cyanheads/pubmed-mcp-server 2.10.11 → 2.10.12
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 +1 -1
- package/dist/mcp-server/resources/definitions/database-info.resource.js +6 -6
- package/dist/mcp-server/resources/definitions/database-info.resource.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +13 -0
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +35 -11
- package/dist/services/ncbi/formatting/citation-formatter.js.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/article-parser.js +14 -22
- package/dist/services/ncbi/parsing/article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts +11 -1
- package/dist/services/ncbi/parsing/esummary-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/esummary-parser.js +16 -7
- package/dist/services/ncbi/parsing/esummary-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-article-parser.js +26 -3
- package/dist/services/ncbi/parsing/pmc-article-parser.js.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts +19 -0
- package/dist/services/ncbi/parsing/pmc-xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js +81 -2
- package/dist/services/ncbi/parsing/pmc-xml-helpers.js.map +1 -1
- package/dist/services/ncbi/parsing/xml-helpers.d.ts +29 -3
- package/dist/services/ncbi/parsing/xml-helpers.d.ts.map +1 -1
- package/dist/services/ncbi/parsing/xml-helpers.js +46 -0
- package/dist/services/ncbi/parsing/xml-helpers.js.map +1 -1
- package/dist/services/ncbi/response-handler.d.ts.map +1 -1
- package/dist/services/ncbi/response-handler.js +58 -31
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
package/AGENTS.md
CHANGED
package/CLAUDE.md
CHANGED
package/README.md
CHANGED
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@@ -9,7 +9,7 @@
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-
[](./CHANGELOG.md) [](./LICENSE) [](https://github.com/users/cyanheads/packages/container/package/pubmed-mcp-server) [](https://modelcontextprotocol.io/) [](https://www.npmjs.com/package/@cyanheads/pubmed-mcp-server) [](https://www.typescriptlang.org/) [](https://bun.sh/)
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</div>
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@@ -5,7 +5,7 @@
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*/
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import { resource, z } from '@cyanheads/mcp-ts-core';
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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import { ensureArray, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
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import { ensureArray, getOptionalText, getText } from '../../../services/ncbi/parsing/xml-helpers.js';
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const FieldSchema = z
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.object({
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name: z.string().describe('Short field name used in queries'),
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@@ -33,17 +33,17 @@ export const databaseInfoResource = resource('pubmed://database/info', {
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const eInfoResult = (raw.eInfoResult ?? raw);
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const dbInfo = (eInfoResult.DbInfo ?? eInfoResult);
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const dbName = getText(dbInfo.DbName, 'pubmed');
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const description =
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const count =
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const lastUpdate =
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const description = getOptionalText(dbInfo.Description);
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const count = getOptionalText(dbInfo.Count);
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const lastUpdate = getOptionalText(dbInfo.LastUpdate);
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const fieldListContainer = dbInfo.FieldList;
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let fields;
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if (fieldListContainer) {
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const rawFields = ensureArray(fieldListContainer.Field);
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fields = rawFields.map((f) => ({
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name: getText(f.Name),
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fullName:
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description:
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fullName: getOptionalText(f.FullName),
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description: getOptionalText(f.Description),
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}));
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}
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ctx.log.info('PubMed database info retrieved', {
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{"version":3,"file":"database-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;
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{"version":3,"file":"database-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/database-info.resource.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,cAAc,EAAE,MAAM,iCAAiC,CAAC;AACjE,OAAO,EAAE,WAAW,EAAE,eAAe,EAAE,OAAO,EAAE,MAAM,wCAAwC,CAAC;AAE/F,MAAM,WAAW,GAAG,CAAC;KAClB,MAAM,CAAC;IACN,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,kCAAkC,CAAC;IAC7D,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;IAC7D,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,mBAAmB,CAAC;CACjE,CAAC;KACD,QAAQ,CAAC,wBAAwB,CAAC,CAAC;AAEtC,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;IAC5C,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,sBAAsB,CAAC;IACnE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,oBAAoB,CAAC;IAC3D,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uBAAuB,CAAC;IACnE,MAAM,EAAE,CAAC,CAAC,KAAK,CAAC,WAAW,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,8CAA8C,CAAC;CACjG,CAAC,CAAC;AAEH,MAAM,CAAC,MAAM,oBAAoB,GAAG,QAAQ,CAAC,wBAAwB,EAAE;IACrE,IAAI,EAAE,eAAe;IACrB,KAAK,EAAE,sBAAsB;IAC7B,WAAW,EAAE,oFAAoF;IACjG,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,EAAE,CAAC;IACpB,MAAM,EAAE,YAAY;IAEpB,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,+BAA+B,CAAC,CAAC;QAE9C,MAAM,GAAG,GAAG,CAAC,MAAM,cAAc,EAAE,CAAC,KAAK,CAAC,EAAE,EAAE,EAAE,QAAQ,EAAE,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAGlF,CAAC;QAEF,MAAM,WAAW,GAAG,CAAC,GAAG,CAAC,WAAW,IAAI,GAAG,CAA4B,CAAC;QACxE,MAAM,MAAM,GAAG,CAAC,WAAW,CAAC,MAAM,IAAI,WAAW,CAA4B,CAAC;QAE9E,MAAM,MAAM,GAAG,OAAO,CAAC,MAAM,CAAC,MAAM,EAAE,QAAQ,CAAC,CAAC;QAChD,MAAM,WAAW,GAAG,eAAe,CAAC,MAAM,CAAC,WAAW,CAAC,CAAC;QACxD,MAAM,KAAK,GAAG,eAAe,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC;QAC5C,MAAM,UAAU,GAAG,eAAe,CAAC,MAAM,CAAC,UAAU,CAAC,CAAC;QAEtD,MAAM,kBAAkB,GAAG,MAAM,CAAC,SAAgD,CAAC;QACnF,IAAI,MAAiD,CAAC;QAEtD,IAAI,kBAAkB,EAAE,CAAC;YACvB,MAAM,SAAS,GAAG,WAAW,CAAC,kBAAkB,CAAC,KAAK,CAA8B,CAAC;YACrF,MAAM,GAAG,SAAS,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;gBAC7B,IAAI,EAAE,OAAO,CAAC,CAAC,CAAC,IAAI,CAAC;gBACrB,QAAQ,EAAE,eAAe,CAAC,CAAC,CAAC,QAAQ,CAAC;gBACrC,WAAW,EAAE,eAAe,CAAC,CAAC,CAAC,WAAW,CAAC;aAC5C,CAAC,CAAC,CAAC;QACN,CAAC;QAED,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,gCAAgC,EAAE;YAC7C,MAAM;YACN,UAAU,EAAE,MAAM,EAAE,MAAM,IAAI,CAAC;SAChC,CAAC,CAAC;QAEH,OAAO,EAAE,MAAM,EAAE,WAAW,EAAE,KAAK,EAAE,UAAU,EAAE,MAAM,EAAE,CAAC;IAC5D,CAAC;IAED,IAAI,EAAE,GAAG,EAAE,CAAC,CAAC;QACX,SAAS,EAAE,CAAC,EAAE,GAAG,EAAE,wBAAwB,EAAE,IAAI,EAAE,sBAAsB,EAAE,CAAC;KAC7E,CAAC;CACH,CAAC,CAAC"}
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import type { ParsedArticle } from '../types.js';
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/** Supported citation output formats. */
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export type CitationStyle = 'apa' | 'mla' | 'bibtex' | 'ris' | 'vancouver';
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/**
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* Format a PubMed article as an APA 7th edition citation.
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*
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* Pattern:
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* ```
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* Authors (Year). Title. *Journal*, *Volume*(Issue), Pages. https://doi.org/DOI
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* ```
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* With no author the title takes the author position (APA 7 §9.12):
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* ```
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* Title. (Year). *Journal*, *Volume*(Issue), Pages. https://doi.org/DOI
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* ```
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* A Bookshelf record routes to {@link formatApaBook}.
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*/
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export declare function formatApa(article: ParsedArticle): string;
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export declare function formatMla(article: ParsedArticle): string;
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{"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EACV,aAAa,EAKd,MAAM,aAAa,CAAC;AAErB,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,GAAG,WAAW,CAAC;
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{"version":3,"file":"citation-formatter.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/formatting/citation-formatter.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EACV,aAAa,EAKd,MAAM,aAAa,CAAC;AAErB,yCAAyC;AACzC,MAAM,MAAM,aAAa,GAAG,KAAK,GAAG,KAAK,GAAG,QAAQ,GAAG,KAAK,GAAG,WAAW,CAAC;AAoX3E;;;;;;;;;;;;GAYG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAwDxD;AA6DD,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAwDxD;AAMD;;;;;;;;;;;;GAYG;AACH,wBAAgB,YAAY,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAuH3D;AAMD;;;;;GAKG;AACH,wBAAgB,SAAS,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CA2HxD;AAmGD,wBAAgB,eAAe,CAAC,OAAO,EAAE,aAAa,GAAG,MAAM,CAiD9D;AAMD;;;GAGG;AACH,wBAAgB,cAAc,CAAC,OAAO,EAAE,aAAa,EAAE,KAAK,EAAE,aAAa,GAAG,MAAM,CAanF;AAED;;;GAGG;AACH,wBAAgB,eAAe,CAC7B,OAAO,EAAE,aAAa,EACtB,MAAM,EAAE,aAAa,EAAE,GACtB,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAMxB"}
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// ---------------------------------------------------------------------------
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// APA 7th Edition
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// ---------------------------------------------------------------------------
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/**
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* Format a PubMed article as an APA 7th edition citation.
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* Pattern:
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* ```
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* Authors (Year). Title. *Journal*, *Volume*(Issue), Pages. https://doi.org/DOI
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* ```
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*/
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* Format an editor in APA's "In E. E. Editor (Ed.)," position: initials first,
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* ```
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* editors either — moves its title into the author position instead (APA 7
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* §9.12). Bookshelf makes that common: a whole-book record frequently credits
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* neither. The title is not italicized there, and the year follows it. (#139)
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*/
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function formatApaBook(article) {
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const authorStr = article.authors?.length ? formatAuthorsApa(article.authors) : '';
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/** The record's own title, which stands in the author position when set. */
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parts.push(`${stripTrailingPeriod(leadTitle)}.`);
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}
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parts.push(editorStr ? `In ${editorStr} (${editorLabel}), ${container}.` : `In ${container}.`);
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* ```
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* ```
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// date. It is not italicized there. (#139)
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}
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// Year
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// Title — use as-is from PubMed (sentence case already assumed)
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1
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+
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EAEjB,cAAc,EACd,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EACb,eAAe,EAEf,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAGlB,sBAAsB,EACtB,gBAAgB,EAChB,mBAAmB,EACnB,oBAAoB,EACrB,MAAM,aAAa,CAAC;
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1
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+
{"version":3,"file":"article-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/article-parser.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EACV,aAAa,EACb,mBAAmB,EACnB,iBAAiB,EAEjB,cAAc,EACd,WAAW,EACX,iBAAiB,EAEjB,cAAc,EACd,uBAAuB,EAEvB,UAAU,EAEV,gBAAgB,EAEhB,aAAa,EACb,eAAe,EAEf,YAAY,EAEZ,UAAU,EAEV,cAAc,EACd,kBAAkB,EAElB,kBAAkB,EAGlB,sBAAsB,EACtB,gBAAgB,EAChB,mBAAmB,EACnB,oBAAoB,EACrB,MAAM,aAAa,CAAC;AAUrB;;GAEG;AACH,MAAM,WAAW,gBAAgB;IAC/B,YAAY,EAAE,MAAM,EAAE,CAAC;IACvB,OAAO,EAAE,mBAAmB,EAAE,CAAC;CAChC;AAED;;;;;;GAMG;AACH,wBAAgB,cAAc,CAAC,aAAa,CAAC,EAAE,aAAa,GAAG,gBAAgB,CAqD9E;AA2BD;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAChC,UAAU,CAAC,EAAE,UAAU,EACvB,UAAU,CAAC,EAAE,UAAU,GACtB,iBAAiB,GAAG,SAAS,CAmC/B;AAED;;;;GAIG;AACH,wBAAgB,gBAAgB,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,cAAc,EAAE,CA8B1F;AAED;;;;GAIG;AACH,wBAAgB,aAAa,CAAC,YAAY,CAAC,EAAE,YAAY,GAAG,WAAW,EAAE,CAmBxE;AAED;;;;;;;GAOG;AACH,wBAAgB,UAAU,CACxB,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAyCpB;AAED;;;;;;GAMG;AACH,wBAAgB,YAAY,CAC1B,UAAU,CAAC,EAAE,UAAU,EACvB,uBAAuB,CAAC,EAAE,gBAAgB,GACzC,MAAM,GAAG,SAAS,CAsBpB;AAED;;;;GAIG;AACH,wBAAgB,uBAAuB,CAAC,sBAAsB,CAAC,EAAE,sBAAsB,GAAG,MAAM,EAAE,CAIjG;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAAC,eAAe,CAAC,EAAE,cAAc,EAAE,GAAG,cAAc,GAAG,MAAM,EAAE,CAa7F;AAED;;;;;;GAMG;AACH,wBAAgB,mBAAmB,CAAC,WAAW,CAAC,EAAE,UAAU,CAAC,UAAU,CAAC,GAAG,MAAM,GAAG,SAAS,CAyB5F;AAED;;;;GAIG;AACH,wBAAgB,WAAW,CAAC,kBAAkB,CAAC,EAAE,kBAAkB,GAAG,MAAM,GAAG,SAAS,CAGvF;AAED;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,UAAU,CAAC,EAAE,UAAU,GAAG,iBAAiB,EAAE,CAShF;AAED;;;;;;GAMG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,gBAAgB,EAC5B,OAAO,GAAE,uBAA4B,GACpC,aAAa,CAkCf;AAkCD;;;;;;;;;GASG;AACH,wBAAgB,eAAe,CAAC,eAAe,EAAE,eAAe,GAAG,cAAc,CAgDhF;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,oBAAoB,CAAC,cAAc,EAAE,oBAAoB,GAAG,aAAa,CAsDxF;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,eAAe,CAC7B,UAAU,EAAE,mBAAmB,GAAG,SAAS,EAC3C,OAAO,GAAE,uBAA4B,GACpC,aAAa,EAAE,CAejB"}
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@@ -4,7 +4,7 @@
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4
4
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* @module src/services/ncbi/parsing/article-parser
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5
5
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*/
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6
6
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import { decodeHtmlEntities } from './text-helpers.js';
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7
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-
import { ensureArray, getAttribute, getText } from './xml-helpers.js';
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7
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+
import { ensureArray, getAttribute, getOptionalAttribute, getOptionalText, getText, } from './xml-helpers.js';
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8
8
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/**
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9
9
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* Extracts and formats author information from XML, deduplicating affiliations.
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10
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* Affiliations are collected into a single array; each author references them by index.
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@@ -77,11 +77,11 @@ export function extractAuthors(authorListXml) {
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77
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function extractELocationId(articleXml) {
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78
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const candidates = ensureArray(articleXml?.ELocationID).filter((eloc) => getAttribute(eloc, 'EIdType') !== 'doi' &&
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79
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getAttribute(eloc, 'ValidYN') !== 'N' &&
|
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80
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-
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80
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+
getOptionalText(eloc));
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81
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const locator = candidates.find((eloc) => getAttribute(eloc, 'ValidYN') === 'Y') ?? candidates[0];
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if (!locator)
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83
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return;
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84
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-
const type =
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84
|
+
const type = getOptionalAttribute(locator, 'EIdType');
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85
85
|
return { value: getText(locator), ...(type && { type }) };
|
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86
86
|
}
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87
87
|
/**
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@@ -394,25 +394,17 @@ export function parseFullArticle(xmlArticle, options = {}) {
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394
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};
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395
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}
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// ─── Bookshelf records (PubmedBookArticle) ──────────────────────────────────
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397
|
-
/**
|
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398
|
-
* Text of an XML element, with an absent or empty element reported as absent.
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399
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-
* `getText(x, undefined)` cannot do this: `undefined` triggers the parameter's
|
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400
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-
* own `''` default, so it returns the empty string for a missing element.
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401
|
-
*/
|
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402
|
-
function optionalText(element) {
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403
|
-
return getText(element) || undefined;
|
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404
|
-
}
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405
397
|
/** Year text from a `PubDate`-shaped element, falling back to a `MedlineDate` span. */
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406
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|
function extractYear(dateXml) {
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407
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|
if (!dateXml)
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408
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|
return;
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409
|
-
return
|
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401
|
+
return getOptionalText(dateXml.Year) ?? getText(dateXml.MedlineDate).match(/\d{4}/)?.[0];
|
|
410
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|
}
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|
411
403
|
/** First `ArticleId` of the given `IdType`, or undefined. */
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412
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|
function findArticleId(idListXml, idType) {
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413
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for (const articleId of ensureArray(idListXml?.ArticleId)) {
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|
414
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|
if (getAttribute(articleId, 'IdType') === idType) {
|
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415
|
-
const value =
|
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407
|
+
const value = getOptionalText(articleId);
|
|
416
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|
if (value)
|
|
417
409
|
return value;
|
|
418
410
|
}
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|
@@ -448,21 +440,21 @@ export function extractBookInfo(bookDocumentXml) {
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|
448
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|
...(collectiveName && { collectiveName }),
|
|
449
441
|
}));
|
|
450
442
|
const isbns = ensureArray(book?.Isbn)
|
|
451
|
-
.map(
|
|
443
|
+
.map(getOptionalText)
|
|
452
444
|
.filter((isbn) => isbn !== undefined);
|
|
453
445
|
const bookDoi = ensureArray(book?.ELocationID)
|
|
454
446
|
.filter((eloc) => getAttribute(eloc, 'EIdType') === 'doi')
|
|
455
|
-
.map(
|
|
447
|
+
.map(getOptionalText)
|
|
456
448
|
.find(Boolean);
|
|
457
|
-
const title =
|
|
458
|
-
const publisher =
|
|
459
|
-
const publisherLocation =
|
|
449
|
+
const title = getOptionalText(book?.BookTitle);
|
|
450
|
+
const publisher = getOptionalText(book?.Publisher?.PublisherName);
|
|
451
|
+
const publisherLocation = getOptionalText(book?.Publisher?.PublisherLocation);
|
|
460
452
|
const pubDate = extractYear(book?.PubDate);
|
|
461
453
|
const beginningDate = extractYear(book?.BeginningDate);
|
|
462
454
|
const endingDate = extractYear(book?.EndingDate);
|
|
463
|
-
const medium =
|
|
464
|
-
const edition =
|
|
465
|
-
const collectionTitle =
|
|
455
|
+
const medium = getOptionalText(book?.Medium);
|
|
456
|
+
const edition = getOptionalText(book?.Edition);
|
|
457
|
+
const collectionTitle = getOptionalText(book?.CollectionTitle);
|
|
466
458
|
const accession = findArticleId(bookDocumentXml.ArticleIdList, 'bookaccession');
|
|
467
459
|
return {
|
|
468
460
|
...(title && { title }),
|
|
@@ -498,7 +490,7 @@ export function extractBookInfo(bookDocumentXml) {
|
|
|
498
490
|
export function parseFullBookArticle(xmlBookArticle) {
|
|
499
491
|
const bookDocument = xmlBookArticle.BookDocument;
|
|
500
492
|
const book = extractBookInfo(bookDocument);
|
|
501
|
-
const chapterTitle =
|
|
493
|
+
const chapterTitle = getOptionalText(bookDocument?.ArticleTitle);
|
|
502
494
|
const bookAuthorLists = ensureArray(bookDocument?.Book?.AuthorList).filter((list) => getAttribute(list, 'Type') !== 'editors');
|
|
503
495
|
const chapterAuthors = extractAuthors(mergeAuthorLists(ensureArray(bookDocument?.AuthorList)));
|
|
504
496
|
const { authors, affiliations } = chapterAuthors.authors.length
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -5,7 +5,7 @@
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* @module src/services/ncbi/parsing/esummary-parser
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*/
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import type { RequestContext } from '@cyanheads/mcp-ts-core/utils';
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8
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-
import type { ESummaryResult, ParsedBriefSummary, ESummaryAuthor as XmlESummaryAuthor } from '../types.js';
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8
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+
import type { ESummaryDocumentSummary, ESummaryResult, ParsedBriefSummary, ESummaryAuthor as XmlESummaryAuthor } from '../types.js';
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/**
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* Formats an array of ESummary authors into a string.
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* Limits to the first 3 authors and adds 'et al.' if more exist.
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@@ -26,6 +26,16 @@ export declare function parseNcbiDate(dateStr: string): string | undefined;
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* chrono-node via the framework's dateParser for anything unexpected.
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*/
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export declare function standardizeESummaryDate(dateStr?: string, parentContext?: RequestContext): Promise<string | undefined>;
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+
/**
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+
* Read the contributor list of a `DocumentSummarySet` summary.
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+
*
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+
* `authtype` and `clusterid` are omitted rather than written as empty strings
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+
* when the record carries neither — NCBI ships `<ClusterID/>` on every author of
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+
* a Bookshelf summary, and a field present with no value is the same absence to
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* every consumer. (#137)
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+
* @internal exported for direct unit tests
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+
*/
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+
export declare function parseESummaryAuthorsFromDocumentSummary(docSummary: ESummaryDocumentSummary): XmlESummaryAuthor[];
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39
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/**
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30
40
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* Extracts and formats brief summaries from ESummary XML result.
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31
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* Handles both DocumentSummarySet (newer) and older DocSum structures.
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@@ -1 +1 @@
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1
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-
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,
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1
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+
{"version":3,"file":"esummary-parser.d.ts","sourceRoot":"","sources":["../../../../src/services/ncbi/parsing/esummary-parser.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAEH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,8BAA8B,CAAC;AAEnE,OAAO,KAAK,EAGV,uBAAuB,EAEvB,cAAc,EACd,kBAAkB,EAClB,cAAc,IAAI,iBAAiB,EAEpC,MAAM,aAAa,CAAC;AAGrB;;;GAGG;AACH,wBAAgB,qBAAqB,CAAC,OAAO,CAAC,EAAE,iBAAiB,EAAE,GAAG,MAAM,CAQ3E;AA8BD;;;;;;;GAOG;AACH,wBAAgB,aAAa,CAAC,OAAO,EAAE,MAAM,GAAG,MAAM,GAAG,SAAS,CAajE;AAED;;;;GAIG;AACH,wBAAsB,uBAAuB,CAC3C,OAAO,CAAC,EAAE,MAAM,EAChB,aAAa,CAAC,EAAE,cAAc,GAC7B,OAAO,CAAC,MAAM,GAAG,SAAS,CAAC,CA+B7B;AAmBD;;;;;;;;GAQG;AACH,wBAAgB,uCAAuC,CACrD,UAAU,EAAE,uBAAuB,GAClC,iBAAiB,EAAE,CAuGrB;AAyKD;;;GAGG;AACH,wBAAsB,qBAAqB,CACzC,cAAc,CAAC,EAAE,cAAc,EAC/B,OAAO,CAAC,EAAE,cAAc,GACvB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAwD/B"}
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