@cyanheads/pubmed-mcp-server 2.10.10 → 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 +10 -3
- 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/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 +1 -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 +10 -6
- package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/find-related.tool.d.ts +4 -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 +40 -4
- 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/search-articles.tool.d.ts +4 -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 +37 -2
- package/dist/mcp-server/tools/definitions/search-articles.tool.js.map +1 -1
- package/dist/services/error-contracts.d.ts +17 -0
- package/dist/services/error-contracts.d.ts.map +1 -1
- package/dist/services/error-contracts.js +19 -0
- package/dist/services/error-contracts.js.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.d.ts +4 -20
- package/dist/services/ncbi/formatting/citation-formatter.d.ts.map +1 -1
- package/dist/services/ncbi/formatting/citation-formatter.js +406 -31
- 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 +201 -2
- 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 +48 -8
- 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 +33 -4
- 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 +96 -28
- package/dist/services/ncbi/response-handler.js.map +1 -1
- package/dist/services/ncbi/types.d.ts +172 -2
- package/dist/services/ncbi/types.d.ts.map +1 -1
- package/package.json +1 -1
- package/server.json +3 -3
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@@ -268,8 +268,30 @@ export const findRelatedTool = tool('pubmed_find_related', {
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.object({
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pmid: z.string().describe('PubMed ID'),
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title: z.string().optional().describe('Article title'),
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authors: z
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-
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authors: z
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.string()
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.optional()
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.describe("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 in `editors`."),
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source: z
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.string()
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.optional()
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.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.'),
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bookTitle: z
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.string()
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.optional()
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.describe('Title of the book an NCBI Bookshelf record belongs to. Present instead of `source` on a book record; absent on a journal article.'),
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publisherName: z
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.string()
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.optional()
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.describe('Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.'),
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docType: z
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.string()
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.optional()
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.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.'),
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editors: z
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.array(z.string().describe('One editor, "Surname Initials" as ESummary renders it'))
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.optional()
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.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."),
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pubDate: z.string().optional().describe('Publication date'),
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})
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.describe('Related article with enriched summary'))
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@@ -576,7 +598,12 @@ export const findRelatedTool = tool('pubmed_find_related', {
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// (the article metadata fields are all optional) rather than failing the whole
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// request, so the chain's resilience survives the enrichment step.
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try {
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// Version 2.0 is what carries a Bookshelf record's venue: the version 1
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// DocSum format has no BookTitle, PublisherName or DocType element, and
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// names editors without the AuthType that separates them from the
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// record's own authors. On that older format a book row reports an empty
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// Source and no book fields at all. (#114)
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const summaryResult = await ncbi.eSummary({ db: 'pubmed', version: '2.0', retmode: 'xml', id: window.join(',') }, { signal: ctx.signal });
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const briefSummaries = await extractBriefSummaries(summaryResult);
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const summaryMap = new Map(briefSummaries.map((bs) => [bs.pmid, bs]));
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const articles = window.map((pmid) => {
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@@ -586,6 +613,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
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title: details?.title,
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authors: details?.authors,
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source: details?.source,
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bookTitle: details?.bookTitle,
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publisherName: details?.publisherName,
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docType: details?.docType,
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editors: details?.editors,
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pubDate: details?.pubDate,
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};
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});
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@@ -630,7 +661,12 @@ export const findRelatedTool = tool('pubmed_find_related', {
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lines.push(` ${escapeMarkdownInline(a.title)}`);
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if (a.authors)
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lines.push(` *${escapeMarkdownInline(a.authors)}*`);
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-
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if (a.editors?.length)
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lines.push(` edited by ${escapeMarkdownInline(a.editors.join(', '))}`);
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// A Bookshelf record has no journal: its book and publisher stand in
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// for the source so the row still names a venue. (#114)
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const book = [a.bookTitle, a.publisherName].filter(Boolean).join(' — ');
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const meta = [a.source, book, a.docType, a.pubDate].filter(Boolean).join(', ');
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if (meta)
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lines.push(` ${meta}`);
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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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@@ -1 +1 @@
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{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;
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1
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+
{"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2H9B,CAAC"}
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@@ -7,8 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
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import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
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8
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import { formatCitations, } from '../../../services/ncbi/formatting/citation-formatter.js';
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import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
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-
import {
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11
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-
import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
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+
import { parseArticleSet } from '../../../services/ncbi/parsing/article-parser.js';
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11
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import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
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import { pmidStringSchema } from './_schemas.js';
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13
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const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris', 'vancouver']);
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@@ -56,7 +55,7 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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unavailablePmids: z
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56
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.array(z.string())
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.optional()
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-
.describe('
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+
.describe('PMIDs PubMed returned no record for, so nothing could be cited for them. That is all this reports: PubMed omits a PMID it does not recognize silently, with no error and no reason, so the absence says nothing about whether the PMID exists. Use `pubmed_search_articles` to find PMIDs that do resolve.'),
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}),
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60
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// Recovery guidance when nothing could be formatted — agent-facing context, surfaced
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62
61
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// via ctx.enrich.notice() to both structuredContent and content[]; absent on success.
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@@ -73,19 +72,18 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
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73
72
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formats,
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74
73
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});
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75
74
|
const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25, signal: ctx.signal });
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76
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-
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-
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-
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83
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-
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84
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-
});
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75
|
+
// Reads both members of the set. Taking `PubmedArticleSet.PubmedArticle`
|
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76
|
+
// alone discards every NCBI Bookshelf record, leaving a chapter or book
|
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77
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+
// uncitable and its PMID reported unavailable. (#114)
|
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78
|
+
const citations = parseArticleSet(raw?.PubmedArticleSet).map((parsed) => ({
|
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79
|
+
pmid: parsed.pmid,
|
|
80
|
+
title: parsed.title,
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81
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+
citations: formatCitations(parsed, formats),
|
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82
|
+
}));
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85
83
|
const returnedPmids = new Set(citations.map((entry) => entry.pmid));
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86
84
|
const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
|
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87
85
|
if (citations.length === 0) {
|
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88
|
-
ctx.enrich.notice('No articles were returned
|
|
86
|
+
ctx.enrich.notice('No articles were returned: PubMed matched no record to any of the submitted PMIDs. It omits a PMID it does not recognize silently, without an error or a reason, so nothing more than that is known here. Try pubmed_search_articles to discover PMIDs that resolve, or pubmed_spell_check if these came from a noisy source.');
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87
|
}
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90
88
|
return {
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91
89
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citations,
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@@ -1 +1 @@
|
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1
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-
{"version":3,"file":"format-citations.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,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,
|
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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,eAAe,EAAE,MAAM,2CAA2C,CAAC;AAC5E,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,EAAE,WAAW,CAAC,CAAC,CAAC;AAE/E;;;;;;GAMG;AACH,MAAM,oBAAoB,GAAG,mCAAmC,iBAAiB,CAAC,OAAO;KACtF,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,IAAI,KAAK,GAAG,CAAC;KAC5B,IAAI,CAAC,GAAG,CAAC,wCAAwC,CAAC;AAErD,MAAM,CAAC,MAAM,mBAAmB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACjE,WAAW,EACT,kKAAkK;IACpK,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,CACJ;YACE,iBAAiB,CAAC,QAAQ,CACxB,kEAAkE,CACnE;YACD,CAAC;iBACE,KAAK,CAAC,iBAAiB,CAAC;iBACxB,GAAG,CAAC,CAAC,CAAC;iBACN,QAAQ,CACP,wFAAwF,CACzF;SACJ,EACD,EAAE,KAAK,EAAE,oBAAoB,EAAE,CAChC;aACA,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CACP,sIAAsI,CACvI;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,CACP,4SAA4S,CAC7S;KACJ,CAAC;IAEF,qFAAqF;IACrF,sFAAsF;IACtF,UAAU,EAAE;QACV,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,gIAAgI,CACjI;KACJ;IAED,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,yEAAyE;QACzE,wEAAwE;QACxE,sDAAsD;QACtD,MAAM,SAAS,GAAG,eAAe,CAAC,GAAG,EAAE,gBAAgB,CAAC,CAAC,GAAG,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;YACxE,IAAI,EAAE,MAAM,CAAC,IAAI;YACjB,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,SAAS,EAAE,eAAe,CAAC,MAAM,EAAE,OAAO,CAAC;SAC5C,CAAC,CAAC,CAAC;QAEJ,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,IAAI,SAAS,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAC3B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,+TAA+T,CAChU,CAAC;QACJ,CAAC;QACD,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,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"}
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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
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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;AAiCjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmT7B,CAAC"}
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@@ -14,6 +14,21 @@ import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTI
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14
14
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function surname(name) {
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15
15
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return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
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16
16
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}
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17
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+
/**
|
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18
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+
* ECitMatch reads each citation as six `|`-delimited fields, and the citations
|
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19
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+
* of one request are joined into a single payload with `\r`. Either character
|
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20
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+
* inside an interpolated field shifts that layout — NCBI mis-parses the line or
|
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21
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+
* splits one citation into two response rows, and the citation's real match is
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22
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* lost. Rejected at the schema so the constraint is advertised as a JSON-Schema
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23
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+
* `pattern` and a hazardous citation never reaches NCBI, rather than silently
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24
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+
* rewriting what the caller asked for. (#125)
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+
*
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26
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+
* `key` is exempt: it is a label echoed onto the result and is never put on the
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+
* wire (the service submits positional tokens instead), so it stays free-form.
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+
*/
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+
const BDATA_FIELD_RE = /^[^|\r\n]*$/;
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30
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+
const BDATA_FIELD_HINT = 'Cannot contain a pipe ("|") or a line break.';
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+
const BDATA_FIELD_ERROR = `${BDATA_FIELD_HINT} Those characters shift ECitMatch's field layout — remove them or replace them with a space.`;
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17
32
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export const lookupCitationTool = tool('pubmed_lookup_citation', {
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18
33
|
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 journal or year (ECitMatch primary-keys on journal+volume+page; author-only or volume-only inputs guarantee no match); more fields = better match accuracy.`,
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34
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annotations: { readOnlyHint: true, openWorldHint: true },
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@@ -26,19 +41,33 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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41
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.object({
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27
42
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journal: z
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28
43
|
.string()
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44
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+
.regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
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45
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+
.optional()
|
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46
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+
.describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${BDATA_FIELD_HINT}`),
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47
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+
year: z
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48
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+
.string()
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49
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+
.regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
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50
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.optional()
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.describe(`Publication year (e.g., "1991"). ${BDATA_FIELD_HINT}`),
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52
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+
volume: z
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53
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+
.string()
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54
|
+
.regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
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55
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+
.optional()
|
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56
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+
.describe(`Volume number. ${BDATA_FIELD_HINT}`),
|
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57
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+
firstPage: z
|
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58
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+
.string()
|
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59
|
+
.regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
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60
|
.optional()
|
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30
|
-
.describe(
|
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31
|
-
year: z.string().optional().describe('Publication year (e.g., "1991")'),
|
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32
|
-
volume: z.string().optional().describe('Volume number'),
|
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33
|
-
firstPage: z.string().optional().describe('First page number'),
|
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61
|
+
.describe(`First page number. ${BDATA_FIELD_HINT}`),
|
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34
62
|
authorName: z
|
|
35
63
|
.string()
|
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64
|
+
.regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
|
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36
65
|
.optional()
|
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37
|
-
.describe(
|
|
66
|
+
.describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${BDATA_FIELD_HINT}`),
|
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38
67
|
key: z
|
|
39
68
|
.string()
|
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40
69
|
.optional()
|
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41
|
-
.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
|
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70
|
+
.describe('Arbitrary label to track this citation in results. Auto-assigned if omitted. Echoed back unchanged and never sent to NCBI, so any character is accepted here.'),
|
|
42
71
|
})
|
|
43
72
|
.describe('Citation to match against PubMed. Must include at least journal or year — ECitMatch primary-keys on journal+volume+page, so author-only or volume-only inputs guarantee no match.')
|
|
44
73
|
.refine((c) => !!(c.journal || c.year), {
|
|
@@ -197,8 +226,13 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
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|
197
226
|
if (result.totalWarnings > 0) {
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198
227
|
lines.push(`**Warnings:** ${result.totalWarnings}`);
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199
228
|
}
|
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-
|
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201
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-
|
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229
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+
// The heading leads with the citation's 1-based submission index, which is
|
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230
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+
// unique across the batch. `key` is a caller-supplied label that may repeat,
|
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231
|
+
// and text-only clients read this markdown instead of structuredContent — so
|
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232
|
+
// without the index two results can render under identical headings with no
|
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233
|
+
// way to tell which block answers which submitted citation. (#128)
|
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234
|
+
for (const [i, r] of result.results.entries()) {
|
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235
|
+
lines.push(`\n### ${i + 1} · ${r.key}`);
|
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202
236
|
if (r.pmid)
|
|
203
237
|
lines.push(`**PMID:** ${r.pmid}`);
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238
|
if (r.matchedFirstAuthor)
|
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@@ -1 +1 @@
|
|
|
1
|
-
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|
|
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;;;;;;;;;;;GAWG;AACH,MAAM,cAAc,GAAG,aAAa,CAAC;AACrC,MAAM,gBAAgB,GAAG,8CAA8C,CAAC;AACxE,MAAM,iBAAiB,GAAG,GAAG,gBAAgB,8FAA8F,CAAC;AAE5I,MAAM,CAAC,MAAM,kBAAkB,GAAG,IAAI,CAAC,wBAAwB,EAAE;IAC/D,WAAW,EAAE,qbAAqb;IAClc,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,KAAK,CAAC,cAAc,EAAE,iBAAiB,CAAC;iBACxC,QAAQ,EAAE;iBACV,QAAQ,CACP,yEAAyE,gBAAgB,EAAE,CAC5F;YACH,IAAI,EAAE,CAAC;iBACJ,MAAM,EAAE;iBACR,KAAK,CAAC,cAAc,EAAE,iBAAiB,CAAC;iBACxC,QAAQ,EAAE;iBACV,QAAQ,CAAC,oCAAoC,gBAAgB,EAAE,CAAC;YACnE,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,KAAK,CAAC,cAAc,EAAE,iBAAiB,CAAC;iBACxC,QAAQ,EAAE;iBACV,QAAQ,CAAC,kBAAkB,gBAAgB,EAAE,CAAC;YACjD,SAAS,EAAE,CAAC;iBACT,MAAM,EAAE;iBACR,KAAK,CAAC,cAAc,EAAE,iBAAiB,CAAC;iBACxC,QAAQ,EAAE;iBACV,QAAQ,CAAC,sBAAsB,gBAAgB,EAAE,CAAC;YACrD,UAAU,EAAE,CAAC;iBACV,MAAM,EAAE;iBACR,KAAK,CAAC,cAAc,EAAE,iBAAiB,CAAC;iBACxC,QAAQ,EAAE;iBACV,QAAQ,CACP,iEAAiE,gBAAgB,EAAE,CACpF;YACH,GAAG,EAAE,CAAC;iBACH,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,+JAA+J,CAChK;SACJ,CAAC;aACD,QAAQ,CACP,mLAAmL,CACpL;aACA,MAAM,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,IAAI,CAAC,EAAE;YACtC,OAAO,EACL,uKAAuK;SAC1K,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,2EAA2E;QAC3E,4EAA4E;QAC5E,2EAA2E;QAC3E,6CAA6C;QAC7C,MAAM,OAAO,GAAG,MAAM,IAAI,CAAC,SAAS,CAAC,SAAS,EAAE,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC;QAExE,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,EAG1B,CAAC;QACJ,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,WAAW,EAAE,MAAM,IAAI,EAAE,WAAW,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;oBAC5D,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;iBACzC,CAAC,CAAC;YACL,CAAC;QACH,CAAC;QAkBD,MAAM,MAAM,GAAmB,OAAO,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE;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@@ -44,6 +44,10 @@ export declare const searchArticlesTool: import("@cyanheads/mcp-ts-core").ToolDe
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44
44
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title: z.ZodOptional<z.ZodString>;
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45
45
|
authors: z.ZodOptional<z.ZodString>;
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46
46
|
source: z.ZodOptional<z.ZodString>;
|
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47
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+
bookTitle: z.ZodOptional<z.ZodString>;
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48
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+
publisherName: z.ZodOptional<z.ZodString>;
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49
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+
docType: z.ZodOptional<z.ZodString>;
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50
|
+
editors: z.ZodOptional<z.ZodArray<z.ZodString>>;
|
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47
51
|
pubDate: z.ZodOptional<z.ZodString>;
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|
48
52
|
doi: z.ZodOptional<z.ZodString>;
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|
49
53
|
pmcId: z.ZodOptional<z.ZodString>;
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|
@@ -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;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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@@ -182,8 +182,30 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
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|
182
182
|
.object({
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|
183
183
|
pmid: z.string().describe('PubMed ID'),
|
|
184
184
|
title: z.string().optional().describe('Article title'),
|
|
185
|
-
authors: z
|
|
186
|
-
|
|
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."),
|
|
187
209
|
pubDate: z.string().optional().describe('Publication date'),
|
|
188
210
|
doi: z
|
|
189
211
|
.string()
|
|
@@ -344,6 +366,10 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
344
366
|
title: s.title,
|
|
345
367
|
authors: s.authors,
|
|
346
368
|
source: s.source,
|
|
369
|
+
bookTitle: s.bookTitle,
|
|
370
|
+
publisherName: s.publisherName,
|
|
371
|
+
docType: s.docType,
|
|
372
|
+
editors: s.editors,
|
|
347
373
|
pubDate: s.pubDate,
|
|
348
374
|
doi: s.doi,
|
|
349
375
|
pmcId: s.pmcId,
|
|
@@ -416,8 +442,17 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
|
|
|
416
442
|
lines.push(`**PMID:** ${s.pmid}`);
|
|
417
443
|
if (s.authors)
|
|
418
444
|
lines.push(`**Authors:** ${s.authors}`);
|
|
445
|
+
if (s.editors?.length)
|
|
446
|
+
lines.push(`**Editors:** ${s.editors.join(', ')}`);
|
|
419
447
|
if (s.source)
|
|
420
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}`);
|
|
421
456
|
if (s.pubDate)
|
|
422
457
|
lines.push(`**Published:** ${s.pubDate}`);
|
|
423
458
|
if (s.doi)
|
|
@@ -1 +1 @@
|
|
|
1
|
-
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1
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@@ -70,6 +70,23 @@ export declare const NCBI_QUERY_INPUT_ERRORS: readonly [{
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|
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70
70
|
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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71
71
|
readonly retryable: false;
|
|
72
72
|
}];
|
|
73
|
+
/**
|
|
74
|
+
* Input failure the identifier-conversion path rejects before any call is made.
|
|
75
|
+
* Separate from {@link NCBI_QUERY_INPUT_ERRORS} for the same reason that array
|
|
76
|
+
* is separate from the service contracts: only a tool that takes caller-supplied
|
|
77
|
+
* identifiers can produce it.
|
|
78
|
+
*
|
|
79
|
+
* Thrown from a tool handler via `ctx.fail('malformed_id', …)`, so its recovery
|
|
80
|
+
* hint resolves through `ctx.recoveryFor` and it stays out of
|
|
81
|
+
* {@link ServiceErrorReason}.
|
|
82
|
+
*/
|
|
83
|
+
export declare const NCBI_ID_INPUT_ERRORS: readonly [{
|
|
84
|
+
readonly reason: 'malformed_id';
|
|
85
|
+
readonly code: JsonRpcErrorCode.ValidationError;
|
|
86
|
+
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.';
|
|
87
|
+
readonly recovery: 'Submit one identifier per `ids` element, in the declared idType format; the same packed value will be rejected again.';
|
|
88
|
+
readonly retryable: false;
|
|
89
|
+
}];
|
|
73
90
|
/**
|
|
74
91
|
* Failure modes the Unpaywall service layer can surface. Tools that consume
|
|
75
92
|
* `getUnpaywallService()` (currently `pubmed_fetch_fulltext`) should spread
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"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;;;;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"}
|
|
1
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