npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.8.0 → 2.9.1 - Mend

@cyanheads/pubmed-mcp-server 2.8.0 → 2.9.1

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 (48) hide show

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

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

	@@ -1 +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;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~EA8OpC~~,CAAC"}
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;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyPpC,CAAC"}

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

@@ -61,7 +61,7 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
         sort: z
             .string()
             .optional()
-            .describe('Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC.'),
+            .describe('Optional EPMC sort: `<field> asc|desc`. Documented sortable fields: `P_PDATE_D` (publication date), `CITED` (citation count), `AUTH_FIRST` (first author surname), `PUB_YEAR` (publication year). Examples: `P_PDATE_D desc` (newest first), `CITED desc` (most cited). Omit for relevance ranking. Fields outside the documented set are rejected by EPMC. Note: `P_PDATE_D` is ignored for preprint-only (`sources: ["PPR"]`) result sets — preprints have no populated publication date, so use `PUB_YEAR` to order preprints by date.'),
     }),
     output: z.object({
         hits: z
@@ -164,9 +164,22 @@ export const pubmedEuropepmcSearchTool = tool('pubmed_europepmc_search', {
             ...(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;
+        // Europe PMC accepts a `P_PDATE_D` sort but silently ignores it for
+        // preprint-only (PPR) result sets — preprints have no populated publication
+        // date, so results come back relevance-ranked, not date-ordered. Signal it so
+        // a caller asking for "newest first" isn't misled by the silent fallback.
+        // (PUB_YEAR is honored for PPR; only the day-granularity P_PDATE_D is not.)
+        const sortField = input.sort?.trim().split(/\s+/)[0]?.toUpperCase();
+        const isPprOnly = sources.length > 0 && sources.every((s) => s === 'PPR');
+        let notice;
+        if (result.hitCount === 0) {
+            notice =
+                'No results matched your Europe PMC query. Try broadening the query, removing source filters, or running pubmed_spell_check on the term.';
+        }
+        else if (sortField === 'P_PDATE_D' && isPprOnly) {
+            notice =
+                'Europe PMC ignores `P_PDATE_D` sort for preprint-only (PPR) results — preprints have no populated publication date, so records are returned in relevance order, not by date. To order preprints by date, sort by `PUB_YEAR`, or re-rank the returned page by each record’s `firstPublicationDate`.';
+        }
         ctx.log.info('pubmed_europepmc_search completed', {
             hitCount: result.hitCount,
             returnedHits: hits.length,

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

	@@ -1 +1 @@
1	- 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package/dist/services/error-contracts.d.ts CHANGED Viewed

@@ -62,6 +62,24 @@ export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
     readonly recovery: "Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.";
     readonly retryable: true;
 }];
+/**
+ * Failure modes the OpenAlex service layer can surface. Tools that consume
+ * `getOpenAlexService()` / `getOpenAlexServiceOptional()` should spread
+ * these into their `errors[]`.
+ */
+export declare const OPENALEX_SERVICE_ERRORS: readonly [{
+    readonly reason: "openalex_unreachable";
+    readonly code: JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "OpenAlex was unreachable after all retry attempts.";
+    readonly recovery: "Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.";
+    readonly retryable: true;
+}, {
+    readonly reason: "openalex_invalid_response";
+    readonly code: JsonRpcErrorCode.SerializationError;
+    readonly when: "OpenAlex returned a body that could not be parsed (invalid JSON).";
+    readonly recovery: "Retry the request; OpenAlex returned a malformed response that could not be parsed.";
+    readonly retryable: true;
+}];
 /**
  * Failure modes the Europe PMC service layer can surface. Tools that consume
  * `getEuropePmcService()` should spread these into their `errors[]`.
@@ -90,7 +108,7 @@ export declare const EUROPEPMC_SERVICE_ERRORS: readonly [{
  * Tool handlers get a tighter typed union from `ctx.fail` / `ctx.recoveryFor`
  * via the framework — this is the service-side fallback.
  */
-export type ServiceErrorReason = (typeof NCBI_SERVICE_ERRORS)[number]['reason'] | (typeof UNPAYWALL_SERVICE_ERRORS)[number]['reason'] | (typeof EUROPEPMC_SERVICE_ERRORS)[number]['reason'];
+export type ServiceErrorReason = (typeof NCBI_SERVICE_ERRORS)[number]['reason'] | (typeof UNPAYWALL_SERVICE_ERRORS)[number]['reason'] | (typeof EUROPEPMC_SERVICE_ERRORS)[number]['reason'] | (typeof OPENALEX_SERVICE_ERRORS)[number]['reason'];
 /**
  * Service-layer counterpart to `ctx.recoveryFor`. Returns `{ recovery: { hint } }`
  * for the contract reason. Use at every service throw that stamps a `reason` so

package/dist/services/error-contracts.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqCtB,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;EAS3B,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;EAyB3B,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;~~AAQxD~~;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}
1	+ {"version":3,"file":"error-contracts.d.ts","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqCtB,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,wBAAwB;;;;;;EAS3B,CAAC;AAEX;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;EAgB1B,CAAC;AAEX;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;;;;;;;EAyB3B,CAAC;AAEX;;;;GAIG;AACH,MAAM,MAAM,kBAAkB,GAC1B,CAAC,OAAO,mBAAmB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GAC9C,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,wBAAwB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,GACnD,CAAC,OAAO,uBAAuB,CAAC,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,CAAC;AAWvD;;;;;;;;;;;;GAYG;AACH,wBAAgB,WAAW,CAAC,MAAM,EAAE,kBAAkB,GAAG;IAAE,QAAQ,EAAE;QAAE,IAAI,EAAE,MAAM,CAAA;KAAE,CAAA;CAAE,CAMtF"}

package/dist/services/error-contracts.js CHANGED Viewed

@@ -70,6 +70,27 @@ export const UNPAYWALL_SERVICE_ERRORS = [
         retryable: true,
     },
 ];
+/**
+ * Failure modes the OpenAlex service layer can surface. Tools that consume
+ * `getOpenAlexService()` / `getOpenAlexServiceOptional()` should spread
+ * these into their `errors[]`.
+ */
+export const OPENALEX_SERVICE_ERRORS = [
+    {
+        reason: 'openalex_unreachable',
+        code: JsonRpcErrorCode.ServiceUnavailable,
+        when: 'OpenAlex was unreachable after all retry attempts.',
+        recovery: 'Retry after a brief delay; OpenAlex was unreachable. NCBI and Europe PMC remain available.',
+        retryable: true,
+    },
+    {
+        reason: 'openalex_invalid_response',
+        code: JsonRpcErrorCode.SerializationError,
+        when: 'OpenAlex returned a body that could not be parsed (invalid JSON).',
+        recovery: 'Retry the request; OpenAlex returned a malformed response that could not be parsed.',
+        retryable: true,
+    },
+];
 /**
  * Failure modes the Europe PMC service layer can surface. Tools that consume
  * `getEuropePmcService()` should spread these into their `errors[]`.
@@ -97,7 +118,12 @@ export const EUROPEPMC_SERVICE_ERRORS = [
         retryable: false,
     },
 ];
-const REASON_TO_RECOVERY = new Map([...NCBI_SERVICE_ERRORS, ...UNPAYWALL_SERVICE_ERRORS, ...EUROPEPMC_SERVICE_ERRORS].map((entry) => [entry.reason, entry.recovery]));
+const REASON_TO_RECOVERY = new Map([
+    ...NCBI_SERVICE_ERRORS,
+    ...UNPAYWALL_SERVICE_ERRORS,
+    ...EUROPEPMC_SERVICE_ERRORS,
+    ...OPENALEX_SERVICE_ERRORS,
+].map((entry) => [entry.reason, entry.recovery]));
 /**
  * Service-layer counterpart to `ctx.recoveryFor`. Returns `{ recovery: { hint } }`
  * for the contract reason. Use at every service throw that stamps a `reason` so

package/dist/services/error-contracts.js.map CHANGED Viewed

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

@@ -36,6 +36,20 @@ export declare class EuropePmcApiClient {
      * doesn't publish a full-text XML for it (very common for preprints).
      */
     fullTextXml(epmcId: string, signal?: AbortSignal): Promise<EuropePmcFullTextFetchResult>;
+    /**
+     * Fetch citations for a PubMed article (articles that cite this one).
+     * Endpoint: GET /MED/{pmid}/citations?page=1&pageSize=N&format=json
+     * Returns the raw JSON response body as a string.
+     */
+    citations(pmid: string, pageSize: number, page: number, signal?: AbortSignal): Promise<string>;
+    /**
+     * Fetch references from a PubMed article (articles this one cites).
+     * Endpoint: GET /MED/{pmid}/references?page=1&pageSize=N&format=json
+     * Returns the raw JSON response body as a string.
+     */
+    references(pmid: string, pageSize: number, page: number, signal?: AbortSignal): Promise<string>;
+    /** Helper: fetch a links (citations/references) JSON URL and return the body. */
+    private fetchLinksJson;
     private buildSearchUrl;
     /**
      * Combine the caller's query with an optional source filter. EPMC's query

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

	@@ -1 +1 @@
1	- {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAsB,KAAK,qBAAqB,EAAE,MAAM,YAAY,CAAC;AAI5E,MAAM,WAAW,wBAAwB;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,MAAM,MAAM,4BAA4B,GACpC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAC9B;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAE9C,+EAA+E;AAC/E,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,wBAAwB;IAE7D;;;;OAIG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC;IAiC5D;;;;OAIG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC;IAmD9F,OAAO,CAAC,cAAc;IActB;;;;OAIG;IACH,OAAO,CAAC,gBAAgB;CAMzB"}
1	+ {"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAWH,OAAO,EAAsB,KAAK,qBAAqB,EAAE,MAAM,YAAY,CAAC;AAI5E,MAAM,WAAW,wBAAwB;IACvC,KAAK,CAAC,EAAE,MAAM,CAAC;IACf,SAAS,EAAE,MAAM,CAAC;CACnB;AAED;;;GAGG;AACH,MAAM,MAAM,4BAA4B,GACpC;IAAE,IAAI,EAAE,OAAO,CAAC;IAAC,GAAG,EAAE,MAAM,CAAA;CAAE,GAC9B;IAAE,IAAI,EAAE,eAAe,CAAC;IAAC,MAAM,EAAE,MAAM,CAAA;CAAE,CAAC;AAE9C,+EAA+E;AAC/E,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;gBAAN,MAAM,EAAE,wBAAwB;IAE7D;;;;OAIG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC;IAiC5D;;;;OAIG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC;IAmD9F;;;;OAIG;IACH,SAAS,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAK9F;;;;OAIG;IACH,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,QAAQ,EAAE,MAAM,EAAE,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,MAAM,CAAC;IAK/F,iFAAiF;YACnE,cAAc;IAkC5B,OAAO,CAAC,cAAc;IActB;;;;OAIG;IACH,OAAO,CAAC,gBAAgB;CAMzB"}

package/dist/services/europe-pmc/api-client.js CHANGED Viewed

@@ -93,6 +93,48 @@ export class EuropePmcApiClient {
         }
         return { kind: 'found', xml };
     }
+    /**
+     * Fetch citations for a PubMed article (articles that cite this one).
+     * Endpoint: GET /MED/{pmid}/citations?page=1&pageSize=N&format=json
+     * Returns the raw JSON response body as a string.
+     */
+    citations(pmid, pageSize, page, signal) {
+        const url = `${EUROPEPMC_API_BASE}/MED/${encodeURIComponent(pmid)}/citations?page=${page}&pageSize=${pageSize}&format=json`;
+        return this.fetchLinksJson(url, 'EuropePmcCitations', pmid, signal);
+    }
+    /**
+     * Fetch references from a PubMed article (articles this one cites).
+     * Endpoint: GET /MED/{pmid}/references?page=1&pageSize=N&format=json
+     * Returns the raw JSON response body as a string.
+     */
+    references(pmid, pageSize, page, signal) {
+        const url = `${EUROPEPMC_API_BASE}/MED/${encodeURIComponent(pmid)}/references?page=${page}&pageSize=${pageSize}&format=json`;
+        return this.fetchLinksJson(url, 'EuropePmcReferences', pmid, signal);
+    }
+    /** Helper: fetch a links (citations/references) JSON URL and return the body. */
+    async fetchLinksJson(url, operation, pmid, signal) {
+        const ctx = requestContextService.createRequestContext({ operation, pmid });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(signal && { signal }),
+            });
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw serviceUnavailable(`Europe PMC links request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
+        }
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'Europe PMC',
+                data: { url, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
+            });
+        }
+        return response.text();
+    }
     buildSearchUrl(params) {
         const finalParams = {
             query: this.buildQueryString(params),

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

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

@@ -14,7 +14,7 @@
 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, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
+import type { EuropePmcFullTextResult, EuropePmcRelatedResult, EuropePmcSearchParams, EuropePmcSearchResult, EuropePmcSource } from './types.js';
 /**
  * Facade over the Europe PMC REST API. Two methods:
  *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
@@ -43,6 +43,33 @@ export declare class EuropePmcService {
      *     publishes no fullTextXML (404 or empty body).
      */
     fullTextXml(epmcId: string, source: EuropePmcSource, signal?: AbortSignal): Promise<EuropePmcFullTextResult>;
+    /**
+     * Fetch articles that cite the given PubMed article from Europe PMC.
+     * Endpoint: GET /MED/{pmid}/citations?page=N&pageSize=N&format=json
+     * Returns only records with a PMID; others are silently dropped.
+     *
+     * @param pmid  Source PubMed ID
+     * @param pageSize  Number of records to request per page (max 1000 per EPMC)
+     * @param page  1-based page number
+     * @param signal  Optional AbortSignal
+     */
+    citations(pmid: string, pageSize: number, page: number, signal?: AbortSignal): Promise<EuropePmcRelatedResult>;
+    /**
+     * Fetch articles referenced by the given PubMed article from Europe PMC.
+     * Endpoint: GET /MED/{pmid}/references?page=N&pageSize=N&format=json
+     * Returns only records with a PMID; others are silently dropped.
+     *
+     * @param pmid  Source PubMed ID
+     * @param pageSize  Number of records to request per page
+     * @param page  1-based page number
+     * @param signal  Optional AbortSignal
+     */
+    references(pmid: string, pageSize: number, page: number, signal?: AbortSignal): Promise<EuropePmcRelatedResult>;
+    /**
+     * Shared logic for citations() and references(): fetch, parse, extract PMIDs.
+     * Drops records with no PMID — never mints fake IDs.
+     */
+    private fetchRelatedLinks;
     /**
      * Parse a JATS XML string into the ordered node tree consumed by
      * `parsePmcArticle`. Returns the `<article>` JatsNode, or `undefined` when

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

@@ -163,6 +163,65 @@ export class EuropePmcService {
         }
         return { kind: 'found', xml: outcome.xml, epmcId, source };
     }
+    /**
+     * Fetch articles that cite the given PubMed article from Europe PMC.
+     * Endpoint: GET /MED/{pmid}/citations?page=N&pageSize=N&format=json
+     * Returns only records with a PMID; others are silently dropped.
+     *
+     * @param pmid  Source PubMed ID
+     * @param pageSize  Number of records to request per page (max 1000 per EPMC)
+     * @param page  1-based page number
+     * @param signal  Optional AbortSignal
+     */
+    citations(pmid, pageSize, page, signal) {
+        return this.fetchRelatedLinks(() => this.client.citations(pmid, pageSize, page, signal), 'citations', pmid, (parsed) => ensureArray(parsed.citationList?.citation), signal);
+    }
+    /**
+     * Fetch articles referenced by the given PubMed article from Europe PMC.
+     * Endpoint: GET /MED/{pmid}/references?page=N&pageSize=N&format=json
+     * Returns only records with a PMID; others are silently dropped.
+     *
+     * @param pmid  Source PubMed ID
+     * @param pageSize  Number of records to request per page
+     * @param page  1-based page number
+     * @param signal  Optional AbortSignal
+     */
+    references(pmid, pageSize, page, signal) {
+        return this.fetchRelatedLinks(() => this.client.references(pmid, pageSize, page, signal), 'references', pmid, (parsed) => ensureArray(parsed.referenceList?.reference), signal);
+    }
+    /**
+     * Shared logic for citations() and references(): fetch, parse, extract PMIDs.
+     * Drops records with no PMID — never mints fake IDs.
+     */
+    async fetchRelatedLinks(fetch, kind, pmid, extractRecords, signal) {
+        const text = await this.queue.enqueue(() => this.withRetry(fetch, `${kind}(${pmid})`, signal), `${kind}(${pmid})`, signal);
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch (error) {
+            throw serializationError(`Failed to parse Europe PMC ${kind} JSON response.`, {
+                reason: 'europepmc_invalid_response',
+                responseSnippet: text.substring(0, 200),
+                ...recoveryFor('europepmc_invalid_response'),
+            }, { cause: error });
+        }
+        const records = extractRecords(parsed);
+        const pmids = [];
+        for (const rec of records) {
+            // EPMC citation/reference records carry no `pmid` field: for a MED-source
+            // record the `id` IS the PubMed ID. Non-MED records (PPR/PMC/PAT/AGR) have
+            // no PubMed PMID and are dropped. A `pmid` field is honored if ever present.
+            const candidate = rec.pmid ?? (rec.source === 'MED' ? rec.id : undefined);
+            const p = candidate?.trim();
+            if (p && /^\d+$/.test(p))
+                pmids.push(p);
+        }
+        return {
+            pmids,
+            totalCount: parsed.hitCount ?? records.length,
+        };
+    }
     /**
      * Parse a JATS XML string into the ordered node tree consumed by
      * `parsePmcArticle`. Returns the `<article>` JatsNode, or `undefined` when

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

@@ -124,4 +124,35 @@ export type EuropePmcFullTextResult = {
     kind: 'not-available';
     reason: string;
 };
+/**
+ * Single record from the citations or references endpoint.
+ * Only fields the server uses are typed; `pmid` is the key field.
+ */
+export interface EuropePmcRelatedRecord {
+    authorString?: string;
+    doi?: string;
+    id: string;
+    journalTitle?: string;
+    pmid?: string;
+    pubYear?: string;
+    source?: string;
+    title?: string;
+    [key: string]: unknown;
+}
+/** Top-level shape of a Europe PMC citations/references JSON response. */
+export interface EuropePmcLinksResponse {
+    citationList?: {
+        citation?: EuropePmcRelatedRecord[] | EuropePmcRelatedRecord;
+    };
+    hitCount?: number;
+    nextPageUrl?: string;
+    referenceList?: {
+        reference?: EuropePmcRelatedRecord[] | EuropePmcRelatedRecord;
+    };
+}
+/** Normalized result from citations() or references(). */
+export interface EuropePmcRelatedResult {
+    pmids: string[];
+    totalCount: number;
+}
 //# sourceMappingURL=types.d.ts.map

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

	@@ -1 +1 @@
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package/dist/services/ncbi/parsing/pmc-article-parser.d.ts CHANGED Viewed

@@ -19,9 +19,11 @@ export declare function extractJatsAuthors(contribGroup: JatsNode | undefined):
  */
 export declare function extractBodySections(body: JatsNode | undefined): ParsedPmcSection[];
 /**
- * Extract references from a `<back>` node. Prefers mixed-citation over
- * element-citation, descending into `<citation-alternatives>` when a ref carries
- * both forms there rather than as direct children of `<ref>`.
+ * Extract references from a `<back>` node. Prefers `<mixed-citation>` over
+ * `<element-citation>`, descending into `<citation-alternatives>` when a ref
+ * carries both forms there rather than as direct children of `<ref>`. Mixed
+ * citations are read verbatim; structured element citations are rendered
+ * field-by-field with separators (see `renderElementCitation`).
  */
 export declare function extractReferences(back: JatsNode | undefined): ParsedPmcReference[];
 /**

package/dist/services/ncbi/parsing/pmc-article-parser.d.ts.map CHANGED Viewed

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