npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.9 → 2.10.11 - Mend

@cyanheads/pubmed-mcp-server 2.10.9 → 2.10.11

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Files changed (83) hide show

package/dist/mcp-server/tools/definitions/find-related.tool.js CHANGED Viewed

@@ -14,6 +14,7 @@ import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
 import { extractBriefSummaries } from '../../../services/ncbi/parsing/esummary-parser.js';
 import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { getOpenAlexServiceOptional } from '../../../services/openalex/openalex-service.js';
+import { OPENALEX_MAX_UPSTREAM_REQUESTS, } from '../../../services/openalex/types.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 import { escapeMarkdownInline } from './_text.js';
@@ -34,6 +35,11 @@ const PROVIDER_LABELS = {
 const PROVIDER_DISABLED = 'provider_disabled';
 /** A provider failure that carried no declared service-contract reason. */
 const UNCLASSIFIED_ERROR = 'unclassified_error';
+/** Declared retryability per reason the two coverage fallbacks can throw. */
+const RETRYABLE_BY_REASON = new Map([...EUROPEPMC_SERVICE_ERRORS, ...OPENALEX_SERVICE_ERRORS].map((entry) => [
+    entry.reason,
+    entry.retryable,
+]));
 // ─── NCBI provider ────────────────────────────────────────────────────────────
 async function ncbiProvider(pmid, relationship, signal) {
     const ncbi = getNcbiService();
@@ -143,7 +149,59 @@ async function openAlexProvider(pmid, relationship, maxNeeded, signal) {
             result = await oa.references(pmid, maxNeeded, signal);
             break;
     }
-    return { allPmids: result.pmids, totalCount: result.totalCount, source: 'openalex' };
+    return {
+        allPmids: result.pmids,
+        totalCount: result.totalCount,
+        source: 'openalex',
+        droppedNoPmid: result.droppedNoPmid,
+        reachCapped: result.reachCapped,
+    };
+}
+/**
+ * Record a coverage-fallback failure with its declared reason. A provider off by
+ * configuration never recovers on retry; an unclassified transport failure is
+ * treated as transient, matching how the fully-failed chain reports one.
+ */
+function coverageFailureFrom(provider, err) {
+    const { reason } = attemptFrom(provider, err);
+    const retryable = reason === PROVIDER_DISABLED ? false : (RETRYABLE_BY_REASON.get(reason) ?? true);
+    return { provider, reason, retryable };
+}
+/** "A", "A or B", "A, B, or C" — the providers a notice may claim answered. */
+function joinWithOr(labels) {
+    if (labels.length <= 1)
+        return labels[0] ?? '';
+    if (labels.length === 2)
+        return `${labels[0]} or ${labels[1]}`;
+    return `${labels.slice(0, -1).join(', ')}, or ${labels[labels.length - 1]}`;
+}
+/** One provider outcome per entry: `Europe PMC (provider_disabled), OpenAlex (openalex_unreachable)`. */
+function summarizeOutcomes(entries) {
+    return entries.map((e) => `${PROVIDER_LABELS[e.provider]} (${e.reason})`).join(', ');
+}
+/**
+ * Trailing clause naming the providers configuration turned off, which no retry
+ * brings back. Empty when every entry is a transient failure.
+ */
+function disabledClause(entries) {
+    const disabled = entries
+        .filter((e) => e.reason === PROVIDER_DISABLED)
+        .map((e) => PROVIDER_LABELS[e.provider]);
+    if (disabled.length === 0)
+        return '';
+    return ` ${disabled.join(' and ')} ${disabled.length > 1 ? 'are' : 'is'} turned off by server configuration and will not recover on retry.`;
+}
+/**
+ * Disclosure for a `references` answer whose coverage check came back short.
+ * Names each provider that failed and its reason, separates a
+ * configuration-disabled provider from the transient failures worth retrying,
+ * and never describes a failed provider as having answered.
+ */
+function coverageIncompleteNotice(failures) {
+    const retryClause = failures.some((f) => f.retryable)
+        ? ' Retry after a brief delay to complete the coverage check.'
+        : '';
+    return `Reference coverage could not be fully checked — ${summarizeOutcomes(failures)} did not answer.${retryClause}${disabledClause(failures)}`;
 }
 /** Compact, log-safe description of an unknown thrown value. */
 function describeError(err) {
@@ -167,14 +225,7 @@ function attemptFrom(provider, err) {
  * the transient failures worth retrying.
  */
 function allProvidersFailedHint(attempts) {
-    const summary = attempts.map((a) => `${PROVIDER_LABELS[a.provider]} (${a.reason})`).join(', ');
-    const disabled = attempts
-        .filter((a) => a.reason === PROVIDER_DISABLED)
-        .map((a) => PROVIDER_LABELS[a.provider]);
-    const disabledClause = disabled.length
-        ? ` ${disabled.join(' and ')} ${disabled.length > 1 ? 'are' : 'is'} turned off by server configuration and will not recover on retry.`
-        : '';
-    return `Providers attempted: ${summary}. Retry the transient failures after a brief delay.${disabledClause}`;
+    return `Providers attempted: ${summarizeOutcomes(attempts)}. Retry the transient failures after a brief delay.${disabledClause(attempts)}`;
 }
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const findRelatedTool = tool('pubmed_find_related', {
@@ -217,8 +268,30 @@ export const findRelatedTool = tool('pubmed_find_related', {
             .object({
             pmid: z.string().describe('PubMed ID'),
             title: z.string().optional().describe('Article title'),
-            authors: z.string().optional().describe('Author string'),
-            source: z.string().optional().describe('Journal source'),
+            authors: z
+                .string()
+                .optional()
+                .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`."),
+            source: z
+                .string()
+                .optional()
+                .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.'),
+            bookTitle: z
+                .string()
+                .optional()
+                .describe('Title of the book an NCBI Bookshelf record belongs to. Present instead of `source` on a book record; absent on a journal article.'),
+            publisherName: z
+                .string()
+                .optional()
+                .describe('Publisher of the book an NCBI Bookshelf record belongs to. Present only on a book record; absent on a journal article.'),
+            docType: z
+                .string()
+                .optional()
+                .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.'),
+            editors: z
+                .array(z.string().describe('One editor, "Surname Initials" as ESummary renders it'))
+                .optional()
+                .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."),
             pubDate: z.string().optional().describe('Publication date'),
         })
             .describe('Related article with enriched summary'))
@@ -230,18 +303,35 @@ export const findRelatedTool = tool('pubmed_find_related', {
     enrichment: {
         totalCount: z
             .number()
-            .describe('Total related articles found before windowing. A Europe PMC total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned.'),
+            .describe('Total related articles found before windowing. A Europe PMC or OpenAlex total may shrink to the PubMed-addressable count once a request window covers the whole upstream set, since rows without a PubMed PMID cannot be returned.'),
         source: z
             .enum(['ncbi', 'europepmc', 'openalex'])
             .describe('Provider that answered this request'),
         notice: z
             .string()
             .optional()
-            .describe('Guidance when results are empty, a fallback provider answered, offset overshot, or Europe PMC rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page.'),
+            .describe('Guidance when results are empty, a fallback provider answered, offset overshot, a fallback provider could not be reached, or upstream rows were excluded for carrying no PubMed PMID. Absent on a clean NCBI result page.'),
+        coverageFailures: z
+            .array(z
+            .object({
+            provider: z
+                .enum(['europepmc', 'openalex'])
+                .describe('Reference-coverage provider that failed'),
+            reason: z
+                .string()
+                .describe('Declared failure reason, e.g. europepmc_unreachable or provider_disabled'),
+            retryable: z.boolean().describe('Whether a retry can reach this provider'),
+        })
+            .describe('One coverage provider that could not be checked'))
+            .optional()
+            .describe('Reference-coverage fallbacks that failed instead of answering, so the reference set is unverified rather than confirmed absent. Absent when every provider consulted answered.'),
     },
     enrichmentTrailer: {
         totalCount: { label: 'Total Found' },
         source: { label: 'Source' },
+        coverageFailures: {
+            render: (value = []) => `**Coverage not checked:** ${summarizeOutcomes(value)}`,
+        },
     },
     async handler(input, ctx) {
         const ncbi = getNcbiService();
@@ -265,6 +355,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
         // Records WHY a non-primary provider answered, so the provenance notice can
         // distinguish an NCBI outage from references coverage for a non-PMC source.
         let fallbackKind;
+        // Reference-coverage fallbacks that threw. NCBI answering successfully with
+        // an empty set is not the same fact as a provider never being reached, so a
+        // failure here is carried to the caller instead of logged and dropped.
+        const coverageFailures = [];
         // 1. NCBI (primary)
         try {
             providerResult = await ncbiProvider(input.pmid, input.relationship, ctx.signal);
@@ -369,20 +463,34 @@ export const findRelatedTool = tool('pubmed_find_related', {
             // likely a transient NCBI issue, not a real "no references".
             if (input.relationship === 'references' && sourceSummary?.title) {
                 let refFallback = null;
+                // Providers that actually answered — the only ones a "no references"
+                // notice may claim to have checked.
+                const coverageChecked = ['ncbi'];
                 const refAttempts = [
-                    () => epmcProvider(input.pmid, 'references', input.offset, input.maxResults, ctx.signal),
-                    () => openAlexProvider(input.pmid, 'references', input.offset + input.maxResults, ctx.signal),
+                    {
+                        provider: 'europepmc',
+                        run: () => epmcProvider(input.pmid, 'references', input.offset, input.maxResults, ctx.signal),
+                    },
+                    {
+                        provider: 'openalex',
+                        run: () => openAlexProvider(input.pmid, 'references', input.offset + input.maxResults, ctx.signal),
+                    },
                 ];
                 for (const attempt of refAttempts) {
                     try {
-                        const result = await attempt();
+                        const result = await attempt.run();
+                        coverageChecked.push(attempt.provider);
                         if (result.allPmids.length > 0) {
                             refFallback = result;
                             break;
                         }
                     }
                     catch (err) {
-                        ctx.log.warning('References fallback provider failed', { err: describeError(err) });
+                        ctx.log.warning('References fallback provider failed', {
+                            provider: attempt.provider,
+                            err: describeError(err),
+                        });
+                        coverageFailures.push(coverageFailureFrom(attempt.provider, err));
                     }
                 }
                 if (refFallback) {
@@ -392,10 +500,16 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 else {
                     ctx.enrich({ source: 'ncbi' });
                     ctx.enrich.total(0);
+                    if (coverageFailures.length > 0)
+                        ctx.enrich({ coverageFailures });
                     const sourcePmcId = sourceSummary.pmcId;
-                    ctx.enrich.notice(sourcePmcId
-                        ? `No reference list found for PMID ${input.pmid} (PMCID ${sourcePmcId}) via NCBI, Europe PMC, or OpenAlex.`
-                        : `No reference list available for PMID ${input.pmid} via NCBI, Europe PMC, or OpenAlex. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`);
+                    const checked = joinWithOr(coverageChecked.map((p) => PROVIDER_LABELS[p]));
+                    const noReferences = sourcePmcId
+                        ? `No reference list found for PMID ${input.pmid} (PMCID ${sourcePmcId}) via ${checked}.`
+                        : `No reference list available for PMID ${input.pmid} via ${checked}. Use pubmed_fetch_articles to inspect the article record, or try relationship: "similar" / "cited_by".`;
+                    ctx.enrich.notice(coverageFailures.length > 0
+                        ? `${noReferences} ${coverageIncompleteNotice(coverageFailures)}`
+                        : noReferences);
                     return {
                         sourcePmid: input.pmid,
                         relationship: input.relationship,
@@ -421,6 +535,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
         const { allPmids, totalCount, source, droppedNoPmid = 0, reachCapped = false } = providerResult;
         ctx.enrich({ source });
         ctx.enrich.total(totalCount);
+        // A provider that failed before another one answered still shapes how far
+        // this reference set was actually checked.
+        if (coverageFailures.length > 0)
+            ctx.enrich({ coverageFailures });
         // For NCBI the full neighbor set is in memory; for EPMC/OpenAlex the provider
         // pre-fetched enough PMID-addressable rows to cover the window.
         const window = allPmids.slice(input.offset, input.offset + input.maxResults);
@@ -443,15 +561,27 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 ? `NCBI has no PMC-indexed reference list for PMID ${input.pmid} — references served by ${providerName} (${detail}).`
                 : `NCBI eLink unavailable — related articles served by ${providerName} (${detail}).`);
         }
-        // Europe PMC counts every upstream record, but only MED-source rows carry a
-        // PubMed PMID. Disclose the gap so an empty or short window reads as an
+        // Both fallbacks count every upstream record, but only some rows carry a
+        // PubMed PMID — Europe PMC's non-MED sources, OpenAlex works with no PubMed
+        // record. Disclose the gap so an empty or short window reads as an
         // excluded-rows effect rather than an exhausted result set.
         if (droppedNoPmid > 0) {
-            notices.push(`Europe PMC served ${allPmids.length + droppedNoPmid} upstream rows for this request, ${droppedNoPmid} with no PubMed PMID (non-MED sources such as preprints); those rows cannot be returned here.`);
+            const excluded = source === 'europepmc'
+                ? 'non-MED sources such as preprints'
+                : 'works OpenAlex indexes with no PubMed record';
+            notices.push(`${PROVIDER_LABELS[source]} served ${allPmids.length + droppedNoPmid} upstream rows for this request, ${droppedNoPmid} with no PubMed PMID (${excluded}); those rows cannot be returned here.`);
         }
-        // The page cap bounds how far into Europe PMC's set one request can reach.
+        // The request cap bounds how far into a fallback's set one request can
+        // reach. It counts pages for Europe PMC and for OpenAlex's `cites:` filter,
+        // but OpenAlex serves `similar` and `references` from the source work's own
+        // ID list, which it resolves in batches — so the same cap names a different
+        // unit of work there.
         if (reachCapped) {
-            notices.push(`Europe PMC paging stopped after ${EPMC_MAX_PAGES} pages (${allPmids.length} PubMed-addressable rows) without reaching offset ${input.offset}; lower the offset.`);
+            const cap = source === 'europepmc' ? EPMC_MAX_PAGES : OPENALEX_MAX_UPSTREAM_REQUESTS;
+            const walk = source === 'europepmc' || input.relationship === 'cited_by'
+                ? `paging stopped after ${cap} pages`
+                : `ID resolution stopped after ${cap} batches`;
+            notices.push(`${PROVIDER_LABELS[source]} ${walk} (${allPmids.length} PubMed-addressable rows) without reaching offset ${input.offset}; lower the offset.`);
         }
         if (window.length === 0) {
             if (notices.length > 0)
@@ -468,7 +598,12 @@ export const findRelatedTool = tool('pubmed_find_related', {
         // (the article metadata fields are all optional) rather than failing the whole
         // request, so the chain's resilience survives the enrichment step.
         try {
-            const summaryResult = await ncbi.eSummary({ db: 'pubmed', id: window.join(',') }, { signal: ctx.signal });
+            // Version 2.0 is what carries a Bookshelf record's venue: the version 1
+            // DocSum format has no BookTitle, PublisherName or DocType element, and
+            // names editors without the AuthType that separates them from the
+            // record's own authors. On that older format a book row reports an empty
+            // Source and no book fields at all. (#114)
+            const summaryResult = await ncbi.eSummary({ db: 'pubmed', version: '2.0', retmode: 'xml', id: window.join(',') }, { signal: ctx.signal });
             const briefSummaries = await extractBriefSummaries(summaryResult);
             const summaryMap = new Map(briefSummaries.map((bs) => [bs.pmid, bs]));
             const articles = window.map((pmid) => {
@@ -478,6 +613,10 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     title: details?.title,
                     authors: details?.authors,
                     source: details?.source,
+                    bookTitle: details?.bookTitle,
+                    publisherName: details?.publisherName,
+                    docType: details?.docType,
+                    editors: details?.editors,
                     pubDate: details?.pubDate,
                 };
             });
@@ -522,7 +661,12 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     lines.push(`  ${escapeMarkdownInline(a.title)}`);
                 if (a.authors)
                     lines.push(`  *${escapeMarkdownInline(a.authors)}*`);
-                const meta = [a.source, a.pubDate].filter(Boolean).join(', ');
+                if (a.editors?.length)
+                    lines.push(`  edited by ${escapeMarkdownInline(a.editors.join(', '))}`);
+                // A Bookshelf record has no journal: its book and publisher stand in
+                // for the source so the row still names a venue. (#114)
+                const book = [a.bookTitle, a.publisherName].filter(Boolean).join(' — ');
+                const meta = [a.source, book, a.docType, a.pubDate].filter(Boolean).join(', ');
                 if (meta)
                     lines.push(`  ${meta}`);
             }

package/dist/mcp-server/tools/definitions/find-related.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/format-citations.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA0BjD~~,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2H9B,CAAC"}
1	+ {"version":3,"file":"format-citations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/format-citations.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAwBjD,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2H9B,CAAC"}

package/dist/mcp-server/tools/definitions/format-citations.tool.js CHANGED Viewed

@@ -7,8 +7,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { NCBI_SERVICE_ERRORS } from '../../../services/error-contracts.js';
 import { formatCitations, } from '../../../services/ncbi/formatting/citation-formatter.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
-import { parseFullArticle } from '../../../services/ncbi/parsing/article-parser.js';
-import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
+import { parseArticleSet } from '../../../services/ncbi/parsing/article-parser.js';
 import { conceptMeta, EDAM_DATA_FORMATTING, SCHEMA_CREATIVE_WORK } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
 const CitationStyleEnum = z.enum(['apa', 'mla', 'bibtex', 'ris', 'vancouver']);
@@ -56,7 +55,7 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
         unavailablePmids: z
             .array(z.string())
             .optional()
-            .describe('Requested PMIDs that did not return article metadata'),
+            .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.'),
     }),
     // Recovery guidance when nothing could be formatted — agent-facing context, surfaced
     // via ctx.enrich.notice() to both structuredContent and content[]; absent on success.
@@ -73,19 +72,18 @@ export const formatCitationsTool = tool('pubmed_format_citations', {
             formats,
         });
         const raw = await getNcbiService().eFetch({ db: 'pubmed', id: input.pmids.join(','), retmode: 'xml' }, { retmode: 'xml', usePost: input.pmids.length >= 25, signal: ctx.signal });
-        const xmlArticles = ensureArray(raw?.PubmedArticleSet?.PubmedArticle);
-        const citations = xmlArticles.map((xmlArticle) => {
-            const parsed = parseFullArticle(xmlArticle);
-            return {
-                pmid: parsed.pmid,
-                title: parsed.title,
-                citations: formatCitations(parsed, formats),
-            };
-        });
+        // Reads both members of the set. Taking `PubmedArticleSet.PubmedArticle`
+        // alone discards every NCBI Bookshelf record, leaving a chapter or book
+        // uncitable and its PMID reported unavailable. (#114)
+        const citations = parseArticleSet(raw?.PubmedArticleSet).map((parsed) => ({
+            pmid: parsed.pmid,
+            title: parsed.title,
+            citations: formatCitations(parsed, formats),
+        }));
         const returnedPmids = new Set(citations.map((entry) => entry.pmid));
         const unavailablePmids = input.pmids.filter((pmid) => !returnedPmids.has(pmid));
         if (citations.length === 0) {
-            ctx.enrich.notice('No articles were returned for the submitted PMIDs. They may be invalid, unpublished, or withdrawn. Try pubmed_search_articles to discover valid PMIDs, or pubmed_spell_check if these came from a noisy source.');
+            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.');
         }
         return {
             citations,

package/dist/mcp-server/tools/definitions/format-citations.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/lookup-citation.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAiBjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~cA4R7B~~,CAAC"}
1	+ {"version":3,"file":"lookup-citation.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/lookup-citation.tool.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAiCjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmT7B,CAAC"}

package/dist/mcp-server/tools/definitions/lookup-citation.tool.js CHANGED Viewed

@@ -14,6 +14,21 @@ import { conceptMeta, EDAM_DATA_RETRIEVAL, EDAM_PUBMED_ID, SCHEMA_SCHOLARLY_ARTI
 function surname(name) {
     return name.trim().split(/\s+/)[0]?.toLowerCase() ?? '';
 }
+/**
+ * ECitMatch reads each citation as six `|`-delimited fields, and the citations
+ * of one request are joined into a single payload with `\r`. Either character
+ * inside an interpolated field shifts that layout — NCBI mis-parses the line or
+ * splits one citation into two response rows, and the citation's real match is
+ * lost. Rejected at the schema so the constraint is advertised as a JSON-Schema
+ * `pattern` and a hazardous citation never reaches NCBI, rather than silently
+ * rewriting what the caller asked for. (#125)
+ *
+ * `key` is exempt: it is a label echoed onto the result and is never put on the
+ * wire (the service submits positional tokens instead), so it stays free-form.
+ */
+const BDATA_FIELD_RE = /^[^|\r\n]*$/;
+const BDATA_FIELD_HINT = 'Cannot contain a pipe ("|") or a line break.';
+const BDATA_FIELD_ERROR = `${BDATA_FIELD_HINT} Those characters shift ECitMatch's field layout — remove them or replace them with a space.`;
 export const lookupCitationTool = tool('pubmed_lookup_citation', {
     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.`,
     annotations: { readOnlyHint: true, openWorldHint: true },
@@ -26,19 +41,33 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
             .object({
             journal: z
                 .string()
+                .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
+                .optional()
+                .describe(`Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a"). ${BDATA_FIELD_HINT}`),
+            year: z
+                .string()
+                .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
+                .optional()
+                .describe(`Publication year (e.g., "1991"). ${BDATA_FIELD_HINT}`),
+            volume: z
+                .string()
+                .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
+                .optional()
+                .describe(`Volume number. ${BDATA_FIELD_HINT}`),
+            firstPage: z
+                .string()
+                .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
                 .optional()
-                .describe('Journal title or ISO abbreviation (e.g., "proc natl acad sci u s a")'),
-            year: z.string().optional().describe('Publication year (e.g., "1991")'),
-            volume: z.string().optional().describe('Volume number'),
-            firstPage: z.string().optional().describe('First page number'),
+                .describe(`First page number. ${BDATA_FIELD_HINT}`),
             authorName: z
                 .string()
+                .regex(BDATA_FIELD_RE, BDATA_FIELD_ERROR)
                 .optional()
-                .describe('Author name, typically "lastname initials" (e.g., "mann bj")'),
+                .describe(`Author name, typically "lastname initials" (e.g., "mann bj"). ${BDATA_FIELD_HINT}`),
             key: z
                 .string()
                 .optional()
-                .describe('Arbitrary label to track this citation in results. Auto-assigned if omitted.'),
+                .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.'),
         })
             .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.')
             .refine((c) => !!(c.journal || c.year), {
@@ -197,8 +226,13 @@ export const lookupCitationTool = tool('pubmed_lookup_citation', {
         if (result.totalWarnings > 0) {
             lines.push(`**Warnings:** ${result.totalWarnings}`);
         }
-        for (const r of result.results) {
-            lines.push(`\n### ${r.key}`);
+        // The heading leads with the citation's 1-based submission index, which is
+        // unique across the batch. `key` is a caller-supplied label that may repeat,
+        // and text-only clients read this markdown instead of structuredContent — so
+        // without the index two results can render under identical headings with no
+        // way to tell which block answers which submitted citation. (#128)
+        for (const [i, r] of result.results.entries()) {
+            lines.push(`\n### ${i + 1} · ${r.key}`);
             if (r.pmid)
                 lines.push(`**PMID:** ${r.pmid}`);
             if (r.matchedFirstAuthor)