npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.9.10 → 2.10.1 - Mend

@cyanheads/pubmed-mcp-server 2.9.10 → 2.10.1

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 (42) hide show

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

@@ -18,10 +18,19 @@ 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';
 const SourceEnum = z.enum(['MED', 'PMC', 'PPR', 'PAT', 'AGR']);
+/**
+ * Character budget for `abstractSnippet`. Keeps a search page bounded no matter
+ * how many hits carry long abstracts; `pubmed_europepmc_fetch` serves the
+ * complete text for the records a caller actually wants. A cut that would split
+ * a surrogate pair backs off a code unit, so a snippet can come back one
+ * character under the budget. (#93)
+ */
+const ABSTRACT_SNIPPET_LIMIT = 400;
 // ─── 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`.',
+    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`. Abstracts arrive as a bounded `abstractSnippet` with `abstractTruncated` marking the cut ones — pass a hit’s `source` and `epmcId` to `pubmed_europepmc_fetch` for the complete abstract.',
     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',
@@ -71,7 +80,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             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"),
+                .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'),
@@ -94,7 +103,11 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             abstractSnippet: z
                 .string()
                 .optional()
-                .describe('First few hundred characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when `resultType: "core"` is requested'),
+                .describe(`First ${ABSTRACT_SNIPPET_LIMIT} characters of the abstract as display-ready plain text — JATS/HTML markup stripped and HTML entities decoded — when \`resultType: "core"\` is requested, with a trailing … appended when the abstract was cut. Check \`abstractTruncated\` before treating it as the whole abstract.`),
+            abstractTruncated: z
+                .boolean()
+                .optional()
+                .describe('Whether `abstractSnippet` was cut short of the full abstract. Retrieve the complete text with `pubmed_europepmc_fetch` using this record’s `source` and `epmcId`. Present whenever `abstractSnippet` is; omitted when Europe PMC carries no abstract.'),
             citedByCount: z.number().optional().describe('Citation count reported by Europe PMC'),
             epmcUrl: z.string().describe('Europe PMC article URL'),
         })
@@ -151,7 +164,8 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             // un-decoded entities, and soft hyphens (no XML parser runs on it). Clean it
             // to display-ready plain text before truncating, so the snippet budget is
             // spent on text and soft hyphens don't corrupt downstream token matching. (#74)
-            const snippet = h.abstractText ? toDisplayText(h.abstractText) : '';
+            const abstract = h.abstractText ? toDisplayText(h.abstractText) : '';
+            const truncated = abstract.length > ABSTRACT_SNIPPET_LIMIT;
             return {
                 source: h.source,
                 epmcId: h.id,
@@ -165,8 +179,11 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
                 ...(h.doi && { doi: h.doi }),
                 ...(h.isOpenAccess !== undefined && { isOpenAccess: h.isOpenAccess === 'Y' }),
                 ...(h.inPMC !== undefined && { hasFullTextXml: h.inPMC === 'Y' }),
-                ...(snippet && {
-                    abstractSnippet: snippet.length > 400 ? `${snippet.slice(0, 400)}…` : snippet,
+                ...(abstract && {
+                    abstractSnippet: truncated
+                        ? `${sliceCodeUnits(abstract, ABSTRACT_SNIPPET_LIMIT)}…`
+                        : abstract,
+                    abstractTruncated: truncated,
                 }),
                 ...(typeof h.citedByCount === 'number' && { citedByCount: h.citedByCount }),
                 epmcUrl: `https://europepmc.org/article/${h.source}/${h.id}`,
@@ -241,8 +258,12 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
                 if (typeof h.citedByCount === 'number')
                     lines.push(`**Cited by:** ${h.citedByCount}`);
                 lines.push(`**URL:** ${h.epmcUrl}`);
-                if (h.abstractSnippet)
+                if (h.abstractSnippet) {
                     lines.push(`\n${h.abstractSnippet}`);
+                    if (h.abstractTruncated) {
+                        lines.push(`_Abstract truncated at ${ABSTRACT_SNIPPET_LIMIT} characters — call \`pubmed_europepmc_fetch\` with this record's \`source\` and \`epmcId\` for the complete text._`);
+                    }
+                }
             }
         }
         return [{ type: 'text', text: lines.join('\n') }];

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

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

	@@ -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;~~AA6EjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA8T7B~~,CAAC"}
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;AA+IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2V7B,CAAC"}

package/dist/mcp-server/tools/definitions/search-articles.tool.js CHANGED Viewed

@@ -16,23 +16,67 @@ import { conceptMeta, EDAM_DATABASE_SEARCH, EDAM_PUBMED_ID, SCHEMA_SEARCH_ACTION
  */
 const DATE_RE = /^$|^\d{4}([/\-.]\d{1,2}([/\-.]\d{1,2})?)?$/;
 /**
- * Produces an optional human- and agent-readable hint for edge cases where
- * bare empty arrays leave the caller without enough signal to recover:
+ * NCBI's eSearch serves `retstart` up to 9998 for PubMed and fails the whole
+ * request above it, so the ceiling is enforced at the edge where the caller can
+ * still act on it. The limit is db-specific — it does not apply to db=mesh.
+ */
+const OFFSET_MAX = 9998;
+/** Upper bound on brief summaries fetched per call; shared by the schema and the format() cap message. */
+const SUMMARY_COUNT_MAX = 50;
+/** Renders a diagnostic list as a comma-separated set of backticked clauses. */
+function quoteClauses(clauses) {
+    return clauses.map((clause) => `\`${clause}\``).join(', ');
+}
+/**
+ * Produces an optional human- and agent-readable hint for the cases where the
+ * returned PMIDs alone leave the caller without enough signal to recover.
+ *
+ * The signals are independent and can co-occur, so every applicable one is
+ * collected and joined rather than the first match being returned:
+ * - A `dateRange` with one bound filled, which drops the date filter entirely
+ * - Field tags PubMed did not recognize (results silently unrestricted)
+ * - Phrases PubMed matched nothing for
  * - No matches at all (suggest spell-check / removing filters)
- * - Filters applied but nothing matched (suggest relaxing filters)
  * - Pagination overshoot (offset ≥ totalCount)
+ *
+ * The one precedence rule: an unmatched phrase names the exact clause that
+ * returned nothing, so it replaces the generic empty-result guidance, which
+ * would only guess across every filter the request might have set.
  */
 function buildNotice(args) {
-    const { totalCount, pmidCount, offset, hasFilters } = args;
+    const { totalCount, pmidCount, offset, hasFilters, partialDateBound, errorList, warningList } = args;
+    const notices = [];
+    if (partialDateBound) {
+        const missing = partialDateBound.name === 'minDate' ? 'maxDate' : 'minDate';
+        const sentinel = missing === 'maxDate' ? '3000' : '1800';
+        notices.push(`No date filter was applied: dateRange needs both bounds and only \`${partialDateBound.name}\` ("${partialDateBound.value}") was supplied. Set \`${missing}\` as well — for an open-ended range pass a wide sentinel (e.g. \`${missing}: "${sentinel}"\`).`);
+    }
+    const ignoredFields = [
+        ...(errorList?.FieldNotFound ?? []),
+        ...(warningList?.FieldNotFound ?? []),
+    ];
+    if (ignoredFields.length > 0) {
+        notices.push(`PubMed did not recognize the field tag(s) ${quoteClauses(ignoredFields)} and searched those terms as free text, so these results are not restricted by that field. Correct the tag or drop it.`);
+    }
+    const unmatchedPhrases = [
+        ...(errorList?.PhraseNotFound ?? []),
+        ...(warningList?.PhraseNotFound ?? []),
+        ...(warningList?.QuotedPhraseNotFound ?? []),
+    ];
+    if (unmatchedPhrases.length > 0) {
+        notices.push(`PubMed matched nothing for ${quoteClauses(unmatchedPhrases)}, so that clause contributed no results. Check the spelling, or resolve the term with pubmed_lookup_mesh before filtering on it.`);
+    }
     if (totalCount === 0) {
-        return hasFilters
-            ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
-            : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.';
+        if (unmatchedPhrases.length === 0) {
+            notices.push(hasFilters
+                ? 'No results matched your query with the applied filters. Try removing filters (e.g. dateRange, publicationTypes, meshTerms), broadening dates, or verifying author/journal spelling.'
+                : 'No results matched your query. Try running pubmed_spell_check for a suggested correction or broaden the query.');
+        }
     }
-    if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
-        return `Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`;
+    else if (pmidCount === 0 && offset > 0 && offset >= totalCount) {
+        notices.push(`Offset ${offset} exceeds totalCount (${totalCount}). Reset offset to 0 or reduce it below ${totalCount} to page through results.`);
     }
-    return;
+    return notices.length > 0 ? notices.join(' ') : undefined;
 }
 const AppliedFiltersSchema = z.object({
     dateRange: z
@@ -75,7 +119,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
     input: z.object({
         query: z.string().min(1).describe('PubMed search query (supports full NCBI syntax)'),
         maxResults: z.number().int().min(1).max(1000).default(20).describe('Maximum results to return'),
-        offset: z.number().int().min(0).default(0).describe('Result offset for pagination (0-based)'),
+        offset: z
+            .number()
+            .int()
+            .min(0)
+            .max(OFFSET_MAX)
+            .default(0)
+            .describe(`Result offset for pagination (0-based). PubMed serves at most the first ${OFFSET_MAX + 1} records of a result set, so this caps at ${OFFSET_MAX}; narrow the query or add filters to reach anything beyond it.`),
         sort: z
             .enum(['relevance', 'pub_date', 'author', 'journal'])
             .default('relevance')
@@ -115,9 +165,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             .number()
             .int()
             .min(0)
-            .max(50)
+            .max(SUMMARY_COUNT_MAX)
             .default(0)
-            .describe('Fetch brief summaries for top N results (0 = PMIDs only)'),
+            .describe(`Fetch brief summaries for top N results (0 = PMIDs only). Above the ${SUMMARY_COUNT_MAX} cap, pass the remaining PMIDs to pubmed_fetch_articles.`),
     }),
     output: z.object({
         query: z.string().describe('Original query'),
@@ -153,7 +203,7 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         notice: z
             .string()
             .optional()
-            .describe('Optional guidance when results are empty or paging overshot — e.g. how to broaden filters or reset offset. Absent on successful result pages.'),
+            .describe('Optional guidance when the result set does not reflect what was asked for — a field tag PubMed ignored, a phrase it matched nothing for, a dateRange dropped for having one bound, no matches at all, or paging past the end. Absent when nothing applies.'),
     },
     // content[] trailer presentation for the enrichment block. structuredContent always
     // carries the full structured value; this only shapes the human-facing trailer line.
@@ -196,14 +246,24 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
         let effectiveQuery = await sanitization.sanitizeString(input.query, { context: 'text' });
         // Build filters — capture normalized values for both query construction and appliedFilters
         let normalizedDateRange;
-        if (input.dateRange?.minDate && input.dateRange?.maxDate) {
+        const { dateRange } = input;
+        const minDate = dateRange?.minDate.trim() ?? '';
+        const maxDate = dateRange?.maxDate.trim() ?? '';
+        if (dateRange && minDate && maxDate) {
             normalizedDateRange = {
-                minDate: input.dateRange.minDate.trim().replace(/[-.]/g, '/'),
-                maxDate: input.dateRange.maxDate.trim().replace(/[-.]/g, '/'),
-                dateType: input.dateRange.dateType,
+                minDate: minDate.replace(/[-.]/g, '/'),
+                maxDate: maxDate.replace(/[-.]/g, '/'),
+                dateType: dateRange.dateType,
             };
             effectiveQuery += ` AND (${normalizedDateRange.minDate}[${normalizedDateRange.dateType}] : ${normalizedDateRange.maxDate}[${normalizedDateRange.dateType}])`;
         }
+        // Both bounds are required for the filter to apply, so one filled bound is a
+        // dropped date range the caller gets no other signal about.
+        const partialDateBound = minDate && !maxDate
+            ? { name: 'minDate', value: minDate }
+            : maxDate && !minDate
+                ? { name: 'maxDate', value: maxDate }
+                : undefined;
         let sanitizedPubTypes;
         if (input.publicationTypes?.length) {
             sanitizedPubTypes = await Promise.all(input.publicationTypes.map((pt) => sanitization.sanitizeString(pt, { context: 'text' })));
@@ -297,6 +357,9 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             pmidCount: pmids.length,
             offset: input.offset,
             hasFilters: Object.keys(appliedFilters).length > 0,
+            ...(partialDateBound && { partialDateBound }),
+            ...(esResult.errorList && { errorList: esResult.errorList }),
+            ...(esResult.warningList && { warningList: esResult.warningList }),
         });
         ctx.enrich({ effectiveQuery, appliedFilters });
         ctx.enrich.total(esResult.count);
@@ -321,7 +384,13 @@ export const searchArticlesTool = tool('pubmed_search_articles', {
             lines.push(`\n**PMIDs:** ${result.pmids.join(', ')}`);
         if (result.summaries?.length) {
             if (result.summaries.length < result.pmids.length) {
-                lines.push(`\n> Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs. Increase \`summaryCount\` (max 50) to fetch more.`);
+                const shown = `Summaries shown for top ${result.summaries.length} of ${result.pmids.length} PMIDs`;
+                lines.push(
+                // At the cap there is no knob left to raise, so point at the tool that
+                // can read the rest instead of at `summaryCount`.
+                result.summaries.length >= SUMMARY_COUNT_MAX
+                    ? `\n> ${shown} — \`summaryCount\` is at its maximum (${SUMMARY_COUNT_MAX}). Fetch the remaining ${result.pmids.length - result.summaries.length} with \`pubmed_fetch_articles\` using the PMIDs above.`
+                    : `\n> ${shown}. Increase \`summaryCount\` (max ${SUMMARY_COUNT_MAX}) to fetch more.`);
             }
             lines.push('\n### Summaries');
             for (const s of result.summaries) {

package/dist/mcp-server/tools/definitions/search-articles.tool.js.map CHANGED Viewed

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package/dist/services/europe-pmc/europe-pmc-service.d.ts CHANGED Viewed

@@ -1,9 +1,11 @@
 /**
  * @fileoverview Europe PMC service. Wraps the EPMC REST API with rate-limiting,
- * retries, and JATS XML parsing. Two methods: `search()` for keyword discovery
- * across the EPMC corpus (MED/PMC/PPR/PAT/AGR) and `fullTextXml()` for fetching
- * a record's full-text JATS. The XML parser matches NCBI's ordered config so
- * `parsePmcArticle` consumes the result without modification.
+ * retries, and JATS XML parsing. `search()` covers keyword discovery across the
+ * EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
+ * by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
+ * `citations()` / `references()` walk EPMC's link graph. The XML parser matches
+ * NCBI's ordered config so `parsePmcArticle` consumes the result without
+ * modification.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so
@@ -14,13 +16,15 @@
 import type { JatsNode } from '../../services/ncbi/parsing/pmc-xml-helpers.js';
 import { EuropePmcApiClient } from './api-client.js';
 import { EuropePmcRequestQueue } from './request-queue.js';
-import type { EuropePmcFullTextResult, EuropePmcRelatedResult, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
+import type { EuropePmcFullTextResult, EuropePmcRecordRef, EuropePmcRelatedResult, EuropePmcSearchHit, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
 /**
- * Facade over the Europe PMC REST API. Two methods:
+ * Facade over the Europe PMC REST API:
  *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
+ *   - `fetchRecords()` — batch lookup of specific records by source + EPMC id.
  *   - `fullTextXml()` — JATS full text for an EPMC record.
+ *   - `citations()` / `references()` — EPMC's link graph for a PubMed article.
  *
- * Both honor `ctx.signal` for cancellation and retry transient failures with
+ * All honor `ctx.signal` for cancellation and retry transient failures with
  * capped exponential backoff plus jitter.
  */
 export declare class EuropePmcService {
@@ -34,6 +38,16 @@ export declare class EuropePmcService {
      * omit) for the first page; pass the returned `nextCursorMark` for the next.
      */
     search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
+    /**
+     * Look up specific records by `source` + EPMC id. One search request covers
+     * the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
+     * clause, OR-joined into a single query.
+     *
+     * Returns the hits Europe PMC resolved, in the order it returned them.
+     * Unmatched refs are simply absent — callers diff against their own request
+     * to report misses rather than getting a padded array back.
+     */
+    fetchRecords(refs: readonly EuropePmcRecordRef[], signal?: AbortSignal): Promise<EuropePmcSearchHit[]>;
     /**
      * Fetch the JATS full text for an EPMC record. Returns:
      *   - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable

package/dist/services/europe-pmc/europe-pmc-service.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/europe-pmc-service.js CHANGED Viewed

@@ -1,9 +1,11 @@
 /**
  * @fileoverview Europe PMC service. Wraps the EPMC REST API with rate-limiting,
- * retries, and JATS XML parsing. Two methods: `search()` for keyword discovery
- * across the EPMC corpus (MED/PMC/PPR/PAT/AGR) and `fullTextXml()` for fetching
- * a record's full-text JATS. The XML parser matches NCBI's ordered config so
- * `parsePmcArticle` consumes the result without modification.
+ * retries, and JATS XML parsing. `search()` covers keyword discovery across the
+ * EPMC corpus (MED/PMC/PPR/PAT/AGR), `fetchRecords()` resolves specific records
+ * by `source` + EPMC id, `fullTextXml()` fetches a record's full-text JATS, and
+ * `citations()` / `references()` walk EPMC's link graph. The XML parser matches
+ * NCBI's ordered config so `parsePmcArticle` consumes the result without
+ * modification.
  *
  * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
  * default). `getEuropePmcService()` returns `undefined` when disabled so
@@ -45,11 +47,24 @@ function abortableSleep(ms, signal) {
     });
 }
 /**
- * Facade over the Europe PMC REST API. Two methods:
+ * Europe PMC lookup clause for one record addressed by `source` + EPMC id.
+ *
+ * The unquoted form is load-bearing: Europe PMC matches zero records for
+ * `EXT_ID:"<id>" AND SRC:<source>` — quotes survive on an identifier token only
+ * while no `AND SRC:` clause follows it. Callers pass ids through a schema that
+ * restricts them to identifier characters, so no escaping is applied here.
+ */
+function recordLookupQuery({ epmcId, source }) {
+    return `(EXT_ID:${epmcId} AND SRC:${source})`;
+}
+/**
+ * Facade over the Europe PMC REST API:
  *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
+ *   - `fetchRecords()` — batch lookup of specific records by source + EPMC id.
  *   - `fullTextXml()` — JATS full text for an EPMC record.
+ *   - `citations()` / `references()` — EPMC's link graph for a PubMed article.
  *
- * Both honor `ctx.signal` for cancellation and retry transient failures with
+ * All honor `ctx.signal` for cancellation and retry transient failures with
  * capped exponential backoff plus jitter.
  */
 export class EuropePmcService {
@@ -159,6 +174,24 @@ export class EuropePmcService {
             query: echoed,
         };
     }
+    /**
+     * Look up specific records by `source` + EPMC id. One search request covers
+     * the whole batch: each ref becomes an `(EXT_ID:<id> AND SRC:<source>)`
+     * clause, OR-joined into a single query.
+     *
+     * Returns the hits Europe PMC resolved, in the order it returned them.
+     * Unmatched refs are simply absent — callers diff against their own request
+     * to report misses rather than getting a padded array back.
+     */
+    async fetchRecords(refs, signal) {
+        const result = await this.search({
+            query: refs.map(recordLookupQuery).join(' OR '),
+            resultType: 'core',
+            pageSize: refs.length,
+            ...(signal && { signal }),
+        });
+        return result.hits;
+    }
     /**
      * Fetch the JATS full text for an EPMC record. Returns:
      *   - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable

package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/europe-pmc/types.d.ts CHANGED Viewed

@@ -114,6 +114,15 @@ export interface EuropePmcSearchParams {
     /** Allowed sources, comma-joined into the query as `(SRC:"MED" OR ...)`. */
     sources?: readonly EuropePmcSource[];
 }
+/**
+ * Address of one Europe PMC record: the corpus it lives in plus EPMC's own
+ * identifier within that corpus. The pair is the only identifier many PPR,
+ * PAT, and AGR records carry — they frequently have no PMID and no DOI.
+ */
+export interface EuropePmcRecordRef {
+    epmcId: string;
+    source: EuropePmcSource;
+}
 /** Outcome of a fullTextXML lookup. */
 export type EuropePmcFullTextResult = {
     kind: 'found';

package/dist/services/europe-pmc/types.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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