@cyanheads/pubmed-mcp-server 2.10.4 → 2.10.6

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

@@ -2,11 +2,12 @@
  * @fileoverview PubMed related articles tool — finds articles related to a
  * source article via a provider chain: NCBI ELink (primary) → Europe PMC →
  * OpenAlex. First success wins; results are never merged across sources.
- * Supports offset pagination on the returned window.
+ * Supports offset pagination on the returned window. A served empty answer is a
+ * success; only a chain where every eligible provider failed is an error.
  * @module src/mcp-server/tools/definitions/find-related.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
-import { McpError } from '@cyanheads/mcp-ts-core/errors';
+import { configurationError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
 import { EUROPEPMC_SERVICE_ERRORS, NCBI_SERVICE_ERRORS, OPENALEX_SERVICE_ERRORS, } from '../../../services/error-contracts.js';
 import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
 import { getNcbiService } from '../../../services/ncbi/ncbi-service.js';
@@ -15,6 +16,7 @@ import { ensureArray } from '../../../services/ncbi/parsing/xml-helpers.js';
 import { getOpenAlexServiceOptional } from '../../../services/openalex/openalex-service.js';
 import { conceptMeta, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE } from './_concepts.js';
 import { pmidStringSchema } from './_schemas.js';
+import { escapeMarkdownInline } from './_text.js';
 function extractValue(field) {
     if (field === undefined || field === null)
         return '';
@@ -22,6 +24,16 @@ function extractValue(field) {
         return field['#text'] !== undefined ? String(field['#text']) : '';
     return String(field);
 }
+/** Human-facing provider names for notices and recovery hints. */
+const PROVIDER_LABELS = {
+    ncbi: 'NCBI',
+    europepmc: 'Europe PMC',
+    openalex: 'OpenAlex',
+};
+/** A provider the server never reached because configuration turned it off. */
+const PROVIDER_DISABLED = 'provider_disabled';
+/** A provider failure that carried no declared service-contract reason. */
+const UNCLASSIFIED_ERROR = 'unclassified_error';
 // ─── NCBI provider ────────────────────────────────────────────────────────────
 async function ncbiProvider(pmid, relationship, signal) {
     const ncbi = getNcbiService();
@@ -61,31 +73,64 @@ async function ncbiProvider(pmid, relationship, signal) {
 function epmcSupports(relationship) {
     return relationship === 'cited_by' || relationship === 'references';
 }
+/** Europe PMC's per-request row ceiling — 1001 is rejected with an `errMsg`. */
+const EPMC_MAX_PAGE_SIZE = 1000;
+/** Upper bound on Europe PMC pages pulled for one request. */
+const EPMC_MAX_PAGES = 10;
 /**
- * Fetch enough pages to cover [offset, offset+maxResults) from EPMC.
- * EPMC uses 1-based page numbers and its endpoint supports pageSize up to 1000.
- * We fetch one page containing the window we need.
+ * Fetch enough Europe PMC pages to cover [offset, offset+maxResults) in
+ * PMID-addressable rows. Europe PMC pages count every upstream record, but
+ * non-MED rows carry no PubMed PMID and are dropped, so a single page sized on
+ * the raw window can under-fill it. Pages share one size (the endpoint pages by
+ * number, so the size must stay constant) and are pulled until the filtered
+ * array reaches the window, upstream runs out, or `EPMC_MAX_PAGES` is hit.
  */
 async function epmcProvider(pmid, relationship, offset, maxResults, signal) {
     const epmc = getEuropePmcService();
-    if (!epmc)
-        throw new Error('Europe PMC service not available');
-    // EPMC is 1-based; we need the page covering [offset, offset+maxResults).
-    // Simplest approach: fetch one page starting at the right position.
-    // pageSize = maxResults, page = floor(offset/maxResults) + 1 won't align
-    // cleanly. Instead, use a large pageSize and slice client-side, capped at 100.
-    const pageSize = Math.min(offset + maxResults, 100);
-    const page = 1;
-    const result = relationship === 'cited_by'
-        ? await epmc.citations(pmid, pageSize, page, signal)
-        : await epmc.references(pmid, pageSize, page, signal);
-    return { allPmids: result.pmids, totalCount: result.totalCount, source: 'europepmc' };
+    if (!epmc) {
+        throw configurationError('Europe PMC is turned off by server configuration.', {
+            reason: PROVIDER_DISABLED,
+            provider: 'europepmc',
+        });
+    }
+    const needed = offset + maxResults;
+    const pageSize = Math.min(needed, EPMC_MAX_PAGE_SIZE);
+    const allPmids = [];
+    let droppedNoPmid = 0;
+    let hitCount = 0;
+    let exhausted = false;
+    for (let page = 1; page <= EPMC_MAX_PAGES && allPmids.length < needed; page++) {
+        const result = relationship === 'cited_by'
+            ? await epmc.citations(pmid, pageSize, page, signal)
+            : await epmc.references(pmid, pageSize, page, signal);
+        allPmids.push(...result.pmids);
+        droppedNoPmid += result.droppedNoPmid;
+        hitCount = result.hitCount;
+        const served = result.pmids.length + result.droppedNoPmid;
+        if (served < pageSize || page * pageSize >= hitCount) {
+            exhausted = true;
+            break;
+        }
+    }
+    return {
+        allPmids,
+        // Exhausting upstream makes the addressable count exact; otherwise only
+        // Europe PMC's own total is known.
+        totalCount: exhausted ? allPmids.length : hitCount,
+        source: 'europepmc',
+        droppedNoPmid,
+        reachCapped: !exhausted && allPmids.length < needed,
+    };
 }
 // ─── OpenAlex provider ────────────────────────────────────────────────────────
 async function openAlexProvider(pmid, relationship, maxNeeded, signal) {
     const oa = getOpenAlexServiceOptional();
-    if (!oa)
-        throw new Error('OpenAlex service not available');
+    if (!oa) {
+        throw configurationError('OpenAlex is not configured on this server.', {
+            reason: PROVIDER_DISABLED,
+            provider: 'openalex',
+        });
+    }
     let result;
     switch (relationship) {
         case 'similar':
@@ -104,6 +149,33 @@ async function openAlexProvider(pmid, relationship, maxNeeded, signal) {
 function describeError(err) {
     return err instanceof Error ? err.message : String(err);
 }
+/**
+ * Record a provider failure with the declared service-contract reason it
+ * carries, so the aggregate error names each origin's own failure mode instead
+ * of collapsing the chain into one opaque message.
+ */
+function attemptFrom(provider, err) {
+    const reason = err instanceof McpError
+        ? (err.data?.reason ?? UNCLASSIFIED_ERROR)
+        : UNCLASSIFIED_ERROR;
+    return { provider, reason, message: describeError(err) };
+}
+/**
+ * Recovery hint for a fully failed chain. Names only the providers actually
+ * attempted and their observed outcomes — never another origin's health — and
+ * separates a configuration-disabled provider, which no retry brings back, from
+ * 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}`;
+}
 // ─── Tool Definition ─────────────────────────────────────────────────────────
 export const findRelatedTool = tool('pubmed_find_related', {
     description: 'Find articles related to a source article — similar content (similar), articles citing this one (cited_by), or articles this one cites (references). Uses NCBI ELink as the primary source; falls back to Europe PMC then OpenAlex when NCBI is unavailable.',
@@ -114,6 +186,13 @@ export const findRelatedTool = tool('pubmed_find_related', {
         ...NCBI_SERVICE_ERRORS,
         ...EUROPEPMC_SERVICE_ERRORS,
         ...OPENALEX_SERVICE_ERRORS,
+        {
+            reason: 'all_providers_failed',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Every provider eligible for the requested relationship failed; none answered.',
+            recovery: 'Read data.attempted for each provider outcome, then retry the transient failures after a brief delay; an entry marked provider_disabled is turned off by server configuration and will not recover.',
+            retryable: true,
+        },
     ],
     input: z.object({
         pmid: pmidStringSchema.describe('Source PubMed ID'),
@@ -149,14 +228,16 @@ export const findRelatedTool = tool('pubmed_find_related', {
     // the answering provider, and recovery guidance. Surfaced via ctx.enrich(...)
     // to structuredContent and content[]; kept out of the domain return.
     enrichment: {
-        totalCount: z.number().describe('Total related articles found before windowing'),
+        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.'),
         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, or offset overshot. Absent on a clean NCBI result page.'),
+            .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.'),
     },
     enrichmentTrailer: {
         totalCount: { label: 'Total Found' },
@@ -174,7 +255,13 @@ export const findRelatedTool = tool('pubmed_find_related', {
         // success wins, never merged). A non-PMC `references` source returns an empty
         // NCBI set rather than throwing — that structural fallback is handled below.
         let providerResult = null;
-        let providerError;
+        // Europe PMC's served-but-empty answer, held so a later OpenAlex failure
+        // falls back to it: an answer of zero is still an answer, not an outage.
+        let epmcEmpty = null;
+        // Every provider the chain actually reached, with its outcome. Structurally
+        // ineligible providers (Europe PMC for `similar`) and unconfigured ones are
+        // never attempted, so they never appear here.
+        const attempts = [];
         // 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;
@@ -187,7 +274,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 pmid: input.pmid,
                 err: describeError(err),
             });
-            providerError = err;
+            attempts.push(attemptFrom('ncbi', err));
         }
         // 2. Europe PMC (fallback for cited_by / references only). An empty EPMC
         //    result is not "served" — fall through to OpenAlex rather than return 0.
@@ -198,45 +285,48 @@ export const findRelatedTool = tool('pubmed_find_related', {
                     providerResult = epmcResult;
                     fallbackKind = 'outage';
                 }
-                providerError = undefined;
+                else {
+                    epmcEmpty = epmcResult;
+                }
             }
             catch (err) {
                 ctx.log.warning('Europe PMC fallback failed, trying OpenAlex', {
                     pmid: input.pmid,
                     err: describeError(err),
                 });
-                providerError = err;
+                attempts.push(attemptFrom('europepmc', err));
             }
         }
         // 3. OpenAlex (last resort for all relationships)
         if (providerResult === null) {
-            const oa = getOpenAlexServiceOptional();
-            if (oa) {
-                try {
-                    providerResult = await openAlexProvider(input.pmid, input.relationship, input.offset + input.maxResults, ctx.signal);
-                    fallbackKind = 'outage';
-                    providerError = undefined;
-                }
-                catch (err) {
-                    ctx.log.warning('OpenAlex fallback failed', {
-                        pmid: input.pmid,
-                        err: describeError(err),
-                    });
-                    providerError = err;
-                }
+            try {
+                providerResult = await openAlexProvider(input.pmid, input.relationship, input.offset + input.maxResults, ctx.signal);
+                fallbackKind = 'outage';
+            }
+            catch (err) {
+                ctx.log.warning('OpenAlex fallback failed', {
+                    pmid: input.pmid,
+                    err: describeError(err),
+                });
+                attempts.push(attemptFrom('openalex', err));
             }
         }
-        // ── Every provider failed ─────────────────────────────────────────────────
+        if (providerResult === null && epmcEmpty) {
+            providerResult = epmcEmpty;
+            fallbackKind = 'outage';
+        }
+        // ── Every eligible provider failed ────────────────────────────────────────
+        // A request no source answered is a failure, not an empty result set: a
+        // success-shaped payload here would invent a provenance and a count for an
+        // answer nobody gave. A provider that genuinely answered with zero records
+        // set `providerResult` above and never reaches this branch.
         if (providerResult === null) {
-            ctx.enrich({ source: 'ncbi' });
-            ctx.enrich.total(0);
-            ctx.enrich.notice(`All providers failed to retrieve related articles (NCBI, Europe PMC, OpenAlex). Last error: ${describeError(providerError ?? 'unknown')}. Retry after a brief delay.`);
-            return {
+            throw ctx.fail('all_providers_failed', `No provider could return ${input.relationship} for PMID ${input.pmid}.`, {
                 sourcePmid: input.pmid,
                 relationship: input.relationship,
-                offset: input.offset,
-                articles: [],
-            };
+                attempted: attempts,
+                recovery: { hint: allProvidersFailedHint(attempts) },
+            });
         }
         // ── NCBI returned an empty set ──────────────────────────────────────────────
         // ELink returns an empty LinkSet for both invalid source PMIDs and valid PMIDs
@@ -328,11 +418,11 @@ export const findRelatedTool = tool('pubmed_find_related', {
             }
         }
         // ── Window the result set + enrich ──────────────────────────────────────────
-        const { allPmids, totalCount, source } = providerResult;
+        const { allPmids, totalCount, source, droppedNoPmid = 0, reachCapped = false } = providerResult;
         ctx.enrich({ source });
         ctx.enrich.total(totalCount);
         // For NCBI the full neighbor set is in memory; for EPMC/OpenAlex the provider
-        // pre-fetched enough to cover the window. Slice the requested page either way.
+        // pre-fetched enough PMID-addressable rows to cover the window.
         const window = allPmids.slice(input.offset, input.offset + input.maxResults);
         // Only the LAST ctx.enrich.notice survives, so collect the applicable
         // fragments (overshoot, provenance, enrichment-degraded) and emit them once.
@@ -341,7 +431,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
             notices.push(`Offset ${input.offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
         }
         if (source !== 'ncbi') {
-            const providerName = source === 'europepmc' ? 'Europe PMC' : 'OpenAlex';
+            const providerName = PROVIDER_LABELS[source];
             const detail = source === 'openalex'
                 ? input.relationship === 'similar'
                     ? 'related_works — OpenAlex similarity, not PubMed’s neighbor algorithm'
@@ -353,6 +443,16 @@ 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
+        // 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.`);
+        }
+        // The page cap bounds how far into Europe PMC's set one request can reach.
+        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.`);
+        }
         if (window.length === 0) {
             if (notices.length > 0)
                 ctx.enrich.notice(notices.join(' '));
@@ -419,9 +519,9 @@ export const findRelatedTool = tool('pubmed_find_related', {
             for (const a of result.articles) {
                 lines.push(`- **[PMID ${a.pmid}](https://pubmed.ncbi.nlm.nih.gov/${a.pmid}/)**`);
                 if (a.title)
-                    lines.push(`  ${a.title}`);
+                    lines.push(`  ${escapeMarkdownInline(a.title)}`);
                 if (a.authors)
-                    lines.push(`  *${a.authors}*`);
+                    lines.push(`  *${escapeMarkdownInline(a.authors)}*`);
                 const meta = [a.source, a.pubDate].filter(Boolean).join(', ');
                 if (meta)
                     lines.push(`  ${meta}`);

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pubmed-europepmc-fetch.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkFjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;EAsJjG,CAAC"}
+{"version":3,"file":"pubmed-europepmc-fetch.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkGjE,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWvB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;EA+JjG,CAAC"}

package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js

@@ -18,6 +18,7 @@ import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-ser
 import { EUROPEPMC_ALL_SOURCES } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
 import { conceptMeta, EDAM_ACCESSION, EDAM_DATA_RETRIEVAL, SCHEMA_SCHOLARLY_ARTICLE, } from './_concepts.js';
+import { escapeMarkdownInline } from './_text.js';
 const SourceEnum = z.enum(EUROPEPMC_ALL_SOURCES);
 /**
  * Europe PMC ids are identifier tokens (`PPR1283828`, `KR20120031038`,
@@ -41,9 +42,18 @@ const FetchedRecordSchema = z
     .object({
     source: SourceEnum.describe('Europe PMC source the record was resolved from'),
     epmcId: z.string().describe("Europe PMC's internal record id"),
-    title: z.string().optional().describe('Record title'),
-    authors: z.string().optional().describe('Formatted author string'),
-    journal: z.string().optional().describe('Journal title'),
+    title: z
+        .string()
+        .optional()
+        .describe('Record title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
+    authors: z
+        .string()
+        .optional()
+        .describe('Formatted author string as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
+    journal: z
+        .string()
+        .optional()
+        .describe('Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
     pubYear: z.string().optional().describe('Publication year'),
     firstPublicationDate: z.string().optional().describe('First publication date (ISO YYYY-MM-DD)'),
     pmid: z.string().optional().describe('PMID when present in PubMed'),
@@ -115,16 +125,23 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
         }
         const hits = await epmc.fetchRecords(input.records, ctx.signal);
         const records = hits.map((h) => {
-            // EPMC returns abstractText as a raw JSON string carrying JATS/HTML markup,
-            // un-decoded entities, and soft hyphens (no XML parser runs on it). The
-            // cleanup mirrors pubmed_europepmc_search; only the truncation is dropped.
+            // EPMC returns these as raw JSON strings carrying JATS/HTML markup,
+            // un-decoded entities, and soft hyphens (no XML parser runs on them).
+            // Title is the confirmed live vector — preprints carry italicized species
+            // and gene names — but authors and journal are free-text upstream fields
+            // on the same footing, so all three take the single-pass normalization
+            // the abstract already gets. (#102) The cleanup mirrors
+            // pubmed_europepmc_search; only the truncation is dropped.
             const abstract = h.abstractText ? toDisplayText(h.abstractText) : '';
+            const title = h.title ? toDisplayText(h.title) : '';
+            const authors = h.authorString ? toDisplayText(h.authorString) : '';
+            const journal = h.journalTitle ? toDisplayText(h.journalTitle) : '';
             return {
                 source: h.source,
                 epmcId: h.id,
-                ...(h.title && { title: h.title }),
-                ...(h.authorString && { authors: h.authorString }),
-                ...(h.journalTitle && { journal: h.journalTitle }),
+                ...(title && { title }),
+                ...(authors && { authors }),
+                ...(journal && { journal }),
                 ...(h.pubYear && { pubYear: h.pubYear }),
                 ...(h.firstPublicationDate && { firstPublicationDate: h.firstPublicationDate }),
                 ...(h.pmid && { pmid: h.pmid }),
@@ -180,12 +197,14 @@ export const pubmedEuropepmcFetchTool = tool('pubmed_europepmc_fetch', {
             lines.push(`**Not found:** ${result.notFound.map((r) => `${r.source}/${r.epmcId}`).join(', ')}`);
         }
         for (const r of result.records) {
-            lines.push(`\n### ${r.title ?? r.epmcId}`);
+            // Escaping is render-time only — the structuredContent values above stay
+            // plain text; only these interpolations are neutralized. (#102)
+            lines.push(`\n### ${escapeMarkdownInline(r.title ?? r.epmcId)}`);
             lines.push(`**Source:** ${r.source} | **EPMC ID:** ${r.epmcId}`);
             if (r.authors)
-                lines.push(`**Authors:** ${r.authors}`);
+                lines.push(`**Authors:** ${escapeMarkdownInline(r.authors)}`);
             if (r.journal)
-                lines.push(`**Journal:** ${r.journal}`);
+                lines.push(`**Journal:** ${escapeMarkdownInline(r.journal)}`);
             if (r.firstPublicationDate)
                 lines.push(`**Published:** ${r.firstPublicationDate}`);
             if (r.pubYear)

package/dist/mcp-server/tools/definitions/pubmed-europepmc-fetch.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAyQjG,CAAC"}
+{"version":3,"file":"pubmed-europepmc-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8BjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWxB,oBAAoB;;mBAEtB,6DAA6D;uBACzD,mFAAmF;;;;;;;;;;;;EAiSjG,CAAC"}

package/dist/mcp-server/tools/definitions/pubmed-europepmc-search.tool.js

@@ -18,7 +18,7 @@ import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-ser
 import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
 import { toDisplayText } from '../../../services/ncbi/parsing/text-helpers.js';
 import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
-import { sliceCodeUnits } from './_text.js';
+import { escapeMarkdownInline, sliceCodeUnits } from './_text.js';
 const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
 /**
  * Character budget for `abstractSnippet`. Keeps a search page bounded no matter
@@ -81,9 +81,18 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             epmcId: z
                 .string()
                 .describe("Europe PMC's internal record id. Pass it with this hit's `source` to `pubmed_europepmc_fetch` for the complete record. Europe PMC's `fullTextXML` is keyed on `pmcId`, not on this id, so records without a PMC counterpart have no full text to fetch."),
-            title: z.string().optional().describe('Article title'),
-            authors: z.string().optional().describe('Formatted author string'),
-            journal: z.string().optional().describe('Journal title'),
+            title: z
+                .string()
+                .optional()
+                .describe('Article title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
+            authors: z
+                .string()
+                .optional()
+                .describe('Formatted author string as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
+            journal: z
+                .string()
+                .optional()
+                .describe('Journal title as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded.'),
             pubYear: z.string().optional().describe('Publication year'),
             firstPublicationDate: z
                 .string()
@@ -169,12 +178,19 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             // spent on text and soft hyphens don't corrupt downstream token matching. (#74)
             const abstract = h.abstractText ? toDisplayText(h.abstractText) : '';
             const truncated = abstract.length > ABSTRACT_SNIPPET_LIMIT;
+            // Title, authors, and journal arrive on the same footing as the abstract —
+            // raw JSON strings no XML parser has touched — so they take the same
+            // single-pass normalization. Title is the confirmed live vector:
+            // preprints carry italicized species and gene names. (#102)
+            const title = h.title ? toDisplayText(h.title) : '';
+            const authors = h.authorString ? toDisplayText(h.authorString) : '';
+            const journal = h.journalTitle ? toDisplayText(h.journalTitle) : '';
             return {
                 source: h.source,
                 epmcId: h.id,
-                ...(h.title && { title: h.title }),
-                ...(h.authorString && { authors: h.authorString }),
-                ...(h.journalTitle && { journal: h.journalTitle }),
+                ...(title && { title }),
+                ...(authors && { authors }),
+                ...(journal && { journal }),
                 ...(h.pubYear && { pubYear: h.pubYear }),
                 ...(h.firstPublicationDate && { firstPublicationDate: h.firstPublicationDate }),
                 ...(h.pmid && { pmid: h.pmid }),
@@ -237,12 +253,14 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         if (result.hits.length > 0) {
             lines.push('\n### Hits');
             for (const h of result.hits) {
-                lines.push(`\n#### ${h.title ?? h.epmcId}`);
+                // Escaping is render-time only — the structuredContent values above stay
+                // plain text; only these interpolations are neutralized. (#102)
+                lines.push(`\n#### ${escapeMarkdownInline(h.title ?? h.epmcId)}`);
                 lines.push(`**Source:** ${h.source} | **EPMC ID:** ${h.epmcId}`);
                 if (h.authors)
-                    lines.push(`**Authors:** ${h.authors}`);
+                    lines.push(`**Authors:** ${escapeMarkdownInline(h.authors)}`);
                 if (h.journal)
-                    lines.push(`**Journal:** ${h.journal}`);
+                    lines.push(`**Journal:** ${escapeMarkdownInline(h.journal)}`);
                 if (h.firstPublicationDate)
                     lines.push(`**Published:** ${h.firstPublicationDate}`);
                 if (h.pubYear)