npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.6.11 → 2.7.0 - Mend

@cyanheads/pubmed-mcp-server 2.6.11 → 2.7.0

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.

Files changed (54) hide show

package/dist/mcp-server/tools/definitions/fetch-fulltext.tool.js.map CHANGED Viewed

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1	- 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package/dist/mcp-server/tools/definitions/find-related.tool.d.ts CHANGED Viewed

@@ -25,7 +25,6 @@ export declare const findRelatedTool: import("@cyanheads/mcp-ts-core").ToolDefin
         authors: z.ZodOptional<z.ZodString>;
         source: z.ZodOptional<z.ZodString>;
         pubDate: z.ZodOptional<z.ZodString>;
-        score: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     totalFound: z.ZodNumber;
     notice: z.ZodOptional<z.ZodString>;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAsCjD~~,eAAO,MAAM,eAAe~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkN1B~~,CAAC"}
1	+ {"version":3,"file":"find-related.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/find-related.tool.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqCjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2L1B,CAAC"}

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

@@ -44,10 +44,6 @@ export const findRelatedTool = tool('pubmed_find_related', {
             authors: z.string().optional().describe('Author string'),
             source: z.string().optional().describe('Journal source'),
             pubDate: z.string().optional().describe('Publication date'),
-            score: z
-                .number()
-                .optional()
-                .describe('NCBI relevance score (arbitrary scale, higher = more related; only present for similar)'),
         })
             .describe('Related article with enriched summary'))
             .describe('Related articles'),
@@ -63,45 +59,34 @@ export const findRelatedTool = tool('pubmed_find_related', {
             pmid: input.pmid,
             relationship: input.relationship,
         });
-        const eLinkParams = {
+        // `cmd=neighbor_score` is unstable on NCBI's side — it intermittently fails
+        // with a TXCLIENT::readAll EOF for high-traffic PMIDs. `cmd=neighbor` returns
+        // the `pubmed_pubmed` list in relevance order anyway, so we keep the ranking
+        // without the (arbitrary-scale) numeric score.
+        const linkName = input.relationship === 'cited_by'
+            ? 'pubmed_pubmed_citedin'
+            : input.relationship === 'references'
+                ? 'pubmed_pubmed_refs'
+                : 'pubmed_pubmed';
+        const eLinkResult = (await ncbi.eLink({
             dbfrom: 'pubmed',
             db: 'pubmed',
             id: input.pmid,
+            cmd: 'neighbor',
+            linkname: linkName,
             retmode: 'xml',
-        };
-        switch (input.relationship) {
-            case 'similar':
-                eLinkParams.cmd = 'neighbor_score';
-                break;
-            case 'cited_by':
-                eLinkParams.cmd = 'neighbor';
-                eLinkParams.linkname = 'pubmed_pubmed_citedin';
-                break;
-            case 'references':
-                eLinkParams.cmd = 'neighbor';
-                eLinkParams.linkname = 'pubmed_pubmed_refs';
-                break;
-        }
-        const eLinkResult = (await ncbi.eLink(eLinkParams, { signal: ctx.signal }));
+        }, { signal: ctx.signal }));
         const eLinkResultsArray = ensureArray(eLinkResult?.eLinkResult);
         const firstResult = eLinkResultsArray[0];
         const linkSet = firstResult?.LinkSet;
         let foundPmids = [];
         if (linkSet?.LinkSetDb) {
             const linkSetDbArray = ensureArray(linkSet.LinkSetDb);
-            const expectedLinkName = input.relationship === 'cited_by'
-                ? 'pubmed_pubmed_citedin'
-                : input.relationship === 'references'
-                    ? 'pubmed_pubmed_refs'
-                    : 'pubmed_pubmed';
-            const targetDb = linkSetDbArray.find((db) => db.LinkName === expectedLinkName) ?? linkSetDbArray[0];
+            const targetDb = linkSetDbArray.find((db) => db.LinkName === linkName) ?? linkSetDbArray[0];
             if (targetDb?.Link) {
                 foundPmids = ensureArray(targetDb.Link)
-                    .map((link) => ({
-                    pmid: extractValue(link.Id),
-                    ...(extractValue(link.Score) ? { score: Number(extractValue(link.Score)) } : {}),
-                }))
-                    .filter((item) => item.pmid && item.pmid !== input.pmid && item.pmid !== '0');
+                    .map((link) => extractValue(link.Id))
+                    .filter((pmid) => pmid && pmid !== input.pmid && pmid !== '0');
             }
         }
         const totalFound = foundPmids.length;
@@ -152,25 +137,21 @@ export const findRelatedTool = tool('pubmed_find_related', {
                 ...(notice && { notice }),
             };
         }
-        if (foundPmids.every((p) => p.score !== undefined)) {
-            foundPmids.sort((a, b) => (b.score ?? 0) - (a.score ?? 0));
-        }
         const pmidsToEnrich = foundPmids.slice(0, input.maxResults);
         const summaryResult = await ncbi.eSummary({
             db: 'pubmed',
-            id: pmidsToEnrich.map((p) => p.pmid).join(','),
+            id: pmidsToEnrich.join(','),
         }, { signal: ctx.signal });
         const briefSummaries = await extractBriefSummaries(summaryResult);
         const summaryMap = new Map(briefSummaries.map((bs) => [bs.pmid, bs]));
-        const articles = pmidsToEnrich.map((p) => {
-            const details = summaryMap.get(p.pmid);
+        const articles = pmidsToEnrich.map((pmid) => {
+            const details = summaryMap.get(pmid);
             return {
-                pmid: p.pmid,
+                pmid,
                 title: details?.title,
                 authors: details?.authors,
                 source: details?.source,
                 pubDate: details?.pubDate,
-                score: p.score,
             };
         });
         return { sourcePmid: input.pmid, relationship: input.relationship, articles, totalFound };
@@ -188,8 +169,7 @@ export const findRelatedTool = tool('pubmed_find_related', {
         }
         else {
             for (const a of result.articles) {
-                const scorePart = a.score !== undefined ? ` (score: ${a.score})` : '';
-                lines.push(`- **[PMID ${a.pmid}](https://pubmed.ncbi.nlm.nih.gov/${a.pmid}/)**${scorePart}`);
+                lines.push(`- **[PMID ${a.pmid}](https://pubmed.ncbi.nlm.nih.gov/${a.pmid}/)**`);
                 if (a.title)
                     lines.push(`  ${a.title}`);
                 if (a.authors)

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

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

@@ -0,0 +1,87 @@
+/**
+ * @fileoverview Europe PMC search tool. Surfaces records PubMed-only search
+ * can't reach: preprints (source `PPR`), Agricola (`AGR`), patents (`PAT`),
+ * and EPMC-only OA articles. Uses EPMC's cursor-based pagination
+ * (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
+ * because EPMC's search API doesn't support offset.
+ *
+ * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
+ * fails fast with a configuration error if the service is unset, since the
+ * tool wouldn't be registered in that case.
+ *
+ * @module src/mcp-server/tools/definitions/pubmed-europepmc-search.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const pubmedEuropepmcSearchTool: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    query: z.ZodString;
+    pageSize: z.ZodDefault<z.ZodNumber>;
+    cursorMark: z.ZodDefault<z.ZodString>;
+    sources: z.ZodOptional<z.ZodArray<z.ZodEnum<{
+        MED: "MED";
+        PMC: "PMC";
+        PPR: "PPR";
+        PAT: "PAT";
+        AGR: "AGR";
+    }>>>;
+    resultType: z.ZodDefault<z.ZodEnum<{
+        core: "core";
+        lite: "lite";
+    }>>;
+    sort: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    query: z.ZodString;
+    hits: z.ZodArray<z.ZodObject<{
+        source: z.ZodEnum<{
+            MED: "MED";
+            PMC: "PMC";
+            PPR: "PPR";
+            PAT: "PAT";
+            AGR: "AGR";
+        }>;
+        epmcId: z.ZodString;
+        title: z.ZodOptional<z.ZodString>;
+        authors: z.ZodOptional<z.ZodString>;
+        journal: z.ZodOptional<z.ZodString>;
+        pubYear: z.ZodOptional<z.ZodString>;
+        firstPublicationDate: z.ZodOptional<z.ZodString>;
+        pmid: z.ZodOptional<z.ZodString>;
+        pmcId: z.ZodOptional<z.ZodString>;
+        doi: z.ZodOptional<z.ZodString>;
+        isOpenAccess: z.ZodOptional<z.ZodBoolean>;
+        hasFullTextXml: z.ZodOptional<z.ZodBoolean>;
+        abstractSnippet: z.ZodOptional<z.ZodString>;
+        citedByCount: z.ZodOptional<z.ZodNumber>;
+        epmcUrl: z.ZodString;
+    }, z.core.$strip>>;
+    hitCount: z.ZodNumber;
+    cursorMark: z.ZodString;
+    nextCursorMark: z.ZodOptional<z.ZodString>;
+    appliedSources: z.ZodArray<z.ZodEnum<{
+        MED: "MED";
+        PMC: "PMC";
+        PPR: "PPR";
+        PAT: "PAT";
+        AGR: "AGR";
+    }>>;
+    searchUrl: z.ZodString;
+    notice: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "europepmc_unreachable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Europe PMC was unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.";
+    readonly retryable: true;
+}, {
+    readonly reason: "europepmc_invalid_response";
+    readonly code: JsonRpcErrorCode.SerializationError;
+    readonly when: "Europe PMC returned a body that could not be parsed (invalid JSON or XML).";
+    readonly recovery: "Retry the request; Europe PMC returned a malformed response that could not be parsed.";
+    readonly retryable: true;
+}, {
+    readonly reason: "europepmc_disabled";
+    readonly code: JsonRpcErrorCode.ConfigurationError;
+    readonly when: "Europe PMC service is disabled via EUROPEPMC_ENABLED=false.";
+    readonly recovery: "Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.";
+}]>;
+//# sourceMappingURL=pubmed-europepmc-search.tool.d.ts.map

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

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+/**
+ * @fileoverview Europe PMC search tool. Surfaces records PubMed-only search
+ * can't reach: preprints (source `PPR`), Agricola (`AGR`), patents (`PAT`),
+ * and EPMC-only OA articles. Uses EPMC's cursor-based pagination
+ * (`cursorMark`) — unlike `pubmed_search_articles`'s offset-based paging,
+ * because EPMC's search API doesn't support offset.
+ *
+ * Only registered when `EUROPEPMC_ENABLED=true` (the default). The handler
+ * fails fast with a configuration error if the service is unset, since the
+ * tool wouldn't be registered in that case.
+ *
+ * @module src/mcp-server/tools/definitions/pubmed-europepmc-search.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { EUROPEPMC_SERVICE_ERRORS } from '../../../services/error-contracts.js';
+import { getEuropePmcService } from '../../../services/europe-pmc/europe-pmc-service.js';
+import { EUROPEPMC_ALL_SOURCES, EUROPEPMC_DEFAULT_SOURCES, } from '../../../services/europe-pmc/types.js';
+import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION, } from './_concepts.js';
+const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
+// ─── Tool Definition ─────────────────────────────────────────────────────────
+export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
+    description: 'Search Europe PMC, a broad open-access biomedical corpus. Surfaces preprints (`source: PPR`), patents (`source: PAT`), Agricola (`source: AGR`), plus everything in PubMed (`MED`) and PMC. Use when additional coverage is needed — preprints and EPMC-only OA records are the typical recovery. Paginate via `cursorMark`. Defaults to `MED`, `PMC`, and `PPR`; pass `sources` to include `PAT` / `AGR`.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    _meta: conceptMeta([SCHEMA_SEARCH_ACTION, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID]),
+    sourceUrl: 'https://github.com/cyanheads/pubmed-mcp-server/blob/main/src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts',
+    errors: [
+        ...EUROPEPMC_SERVICE_ERRORS,
+        {
+            reason: 'europepmc_disabled',
+            code: JsonRpcErrorCode.ConfigurationError,
+            when: 'Europe PMC service is disabled via EUROPEPMC_ENABLED=false.',
+            recovery: 'Set EUROPEPMC_ENABLED=true (the default) and restart the server to use this tool.',
+        },
+    ],
+    input: z.object({
+        query: z
+            .string()
+            .min(1)
+            .describe('Europe PMC search query. Supports field tokens like `AUTH:"<name>"`, `JOURNAL:"<title>"`, `TITLE:"<words>"`, `PUB_YEAR:[2020 TO 2024]`, `DOI:"..."`, `EXT_ID:"<pmid>" AND SRC:MED`. Free text is matched broadly across abstract/title/keywords.'),
+        pageSize: z
+            .number()
+            .int()
+            .min(1)
+            .max(100)
+            .default(25)
+            .describe('Results per page. Max 100 per EPMC API.'),
+        cursorMark: z
+            .string()
+            .default('*')
+            .describe("Pagination cursor. Use `*` (default) for the first page; pass the previous response's `nextCursorMark` for subsequent pages."),
+        sources: z
+            .array(SourceEnum)
+            .min(1)
+            .optional()
+            .describe(`Filter to specific EPMC sources. Defaults to ${EUROPEPMC_DEFAULT_SOURCES.join(', ')} when omitted. Pass an explicit array including PAT or AGR to broaden coverage. Allowed values: ${EUROPEPMC_ALL_SOURCES.join(', ')}.`),
+        resultType: z
+            .enum(['core', 'lite'])
+            .default('core')
+            .describe('`core` returns abstract, IDs, dates, license; `lite` is a smaller payload with IDs and titles only.'),
+        sort: z
+            .string()
+            .optional()
+            .describe('Optional EPMC sort spec, e.g. `FIRST_PIDATE desc` (newest first) or `CITED desc` (most cited). Omit for relevance order.'),
+    }),
+    output: z.object({
+        query: z.string().describe('Effective query string echoed by Europe PMC'),
+        hits: z
+            .array(z
+            .object({
+            source: SourceEnum.describe('Europe PMC source — `MED` (PubMed), `PMC` (PubMed Central), `PPR` (preprint), `PAT` (patent), `AGR` (Agricola)'),
+            epmcId: z
+                .string()
+                .describe("Europe PMC's internal record id; key for `fullTextXML` lookup"),
+            title: z.string().optional().describe('Article title'),
+            authors: z.string().optional().describe('Formatted author string'),
+            journal: z.string().optional().describe('Journal title'),
+            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'),
+            pmcId: z.string().optional().describe('PMC ID when present in PMC'),
+            doi: z.string().optional().describe('DOI when present'),
+            isOpenAccess: z
+                .boolean()
+                .optional()
+                .describe('Whether EPMC reports the record as open access'),
+            hasFullTextXml: z
+                .boolean()
+                .optional()
+                .describe('Whether Europe PMC publishes a fullTextXML for this record. Derived from `inPMC` — only records with a PMC counterpart have JATS via EPMC; preprints (`PPR`) and MED-only records return false.'),
+            abstractSnippet: z
+                .string()
+                .optional()
+                .describe('First few hundred characters of the abstract when `resultType: "core"` is requested'),
+            citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
+            epmcUrl: z.string().describe('Europe PMC article URL'),
+        })
+            .describe('Single Europe PMC record returned by the search'))
+            .describe('Matching Europe PMC records, in the order EPMC returned them'),
+        hitCount: z.number().describe('Total matching records across all pages'),
+        cursorMark: z.string().describe('Cursor used for this response (echoed from the request)'),
+        nextCursorMark: z
+            .string()
+            .optional()
+            .describe('Cursor to pass back as `cursorMark` for the next page. Absent on the final page.'),
+        appliedSources: z
+            .array(SourceEnum)
+            .describe('Sources the query was filtered against (defaults applied)'),
+        searchUrl: z.string().describe("Europe PMC's website search URL for this query"),
+        notice: z
+            .string()
+            .optional()
+            .describe('Optional guidance when results are empty or paging overshot'),
+    }),
+    async handler(input, ctx) {
+        ctx.log.info('Executing pubmed_europepmc_search', { query: input.query });
+        const epmc = getEuropePmcService();
+        if (!epmc) {
+            throw ctx.fail('europepmc_disabled', 'Europe PMC service is not available. Set EUROPEPMC_ENABLED=true to use this tool.', { ...ctx.recoveryFor('europepmc_disabled') });
+        }
+        const sources = (input.sources ?? EUROPEPMC_DEFAULT_SOURCES);
+        const result = await epmc.search({
+            query: input.query,
+            resultType: input.resultType,
+            pageSize: input.pageSize,
+            cursorMark: input.cursorMark,
+            sources,
+            ...(input.sort && { sort: input.sort }),
+            ...(ctx.signal && { signal: ctx.signal }),
+        });
+        const hits = result.hits.map((h) => ({
+            source: h.source,
+            epmcId: h.id,
+            ...(h.title && { title: h.title }),
+            ...(h.authorString && { authors: h.authorString }),
+            ...(h.journalTitle && { journal: h.journalTitle }),
+            ...(h.pubYear && { pubYear: h.pubYear }),
+            ...(h.firstPublicationDate && { firstPublicationDate: h.firstPublicationDate }),
+            ...(h.pmid && { pmid: h.pmid }),
+            ...(h.pmcid && { pmcId: h.pmcid }),
+            ...(h.doi && { doi: h.doi }),
+            ...(h.isOpenAccess !== undefined && { isOpenAccess: h.isOpenAccess === 'Y' }),
+            ...(h.inPMC !== undefined && { hasFullTextXml: h.inPMC === 'Y' }),
+            ...(h.abstractText && {
+                abstractSnippet: h.abstractText.length > 400 ? `${h.abstractText.slice(0, 400)}…` : h.abstractText,
+            }),
+            ...(typeof h.citedByCount === 'number' && { citedByCount: h.citedByCount }),
+            epmcUrl: `https://europepmc.org/article/${h.source}/${h.id}`,
+        }));
+        const notice = result.hitCount === 0
+            ? 'No results matched your Europe PMC query. Try broadening the query, removing source filters, or running pubmed_spell_check on the term.'
+            : undefined;
+        ctx.log.info('pubmed_europepmc_search completed', {
+            hitCount: result.hitCount,
+            returnedHits: hits.length,
+            hasNextPage: !!result.nextCursorMark,
+        });
+        return {
+            query: result.query,
+            hits,
+            hitCount: result.hitCount,
+            cursorMark: result.cursorMark ?? '*',
+            ...(result.nextCursorMark && { nextCursorMark: result.nextCursorMark }),
+            appliedSources: [...sources],
+            searchUrl: `https://europepmc.org/search?query=${encodeURIComponent(input.query)}`,
+            ...(notice && { notice }),
+        };
+    },
+    format: (result) => {
+        const lines = [
+            '## Europe PMC Search Results',
+            `**Query:** ${result.query}`,
+            `**Total Hits:** ${result.hitCount} | **Returned:** ${result.hits.length}`,
+            `**Sources:** ${result.appliedSources.join(', ')}`,
+            `**Cursor:** ${result.cursorMark}${result.nextCursorMark ? ` → \`${result.nextCursorMark}\` (next page)` : ' (final page)'}`,
+            `**Search URL:** ${result.searchUrl}`,
+        ];
+        if (result.notice)
+            lines.push(`\n> ${result.notice}`);
+        if (result.hits.length > 0) {
+            lines.push('\n### Hits');
+            for (const h of result.hits) {
+                lines.push(`\n#### ${h.title ?? h.epmcId}`);
+                lines.push(`**Source:** ${h.source} | **EPMC ID:** ${h.epmcId}`);
+                if (h.authors)
+                    lines.push(`**Authors:** ${h.authors}`);
+                if (h.journal)
+                    lines.push(`**Journal:** ${h.journal}`);
+                if (h.firstPublicationDate)
+                    lines.push(`**Published:** ${h.firstPublicationDate}`);
+                if (h.pubYear)
+                    lines.push(`**Year:** ${h.pubYear}`);
+                if (h.pmid)
+                    lines.push(`**PMID:** ${h.pmid}`);
+                if (h.pmcId)
+                    lines.push(`**PMCID:** ${h.pmcId}`);
+                if (h.doi)
+                    lines.push(`**DOI:** ${h.doi}`);
+                if (h.isOpenAccess !== undefined)
+                    lines.push(`**Open Access:** ${h.isOpenAccess ? 'yes' : 'no'}`);
+                if (h.hasFullTextXml !== undefined) {
+                    lines.push(`**Full-text XML in EPMC:** ${h.hasFullTextXml ? 'yes' : 'no'}`);
+                }
+                if (typeof h.citedByCount === 'number')
+                    lines.push(`**Cited by:** ${h.citedByCount}`);
+                lines.push(`**URL:** ${h.epmcUrl}`);
+                if (h.abstractSnippet)
+                    lines.push(`\n${h.abstractSnippet}`);
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+//# sourceMappingURL=pubmed-europepmc-search.tool.js.map