@cyanheads/pubmed-mcp-server 2.8.0 → 2.9.0

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-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;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA8OpC,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;AAmBjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyPpC,CAAC"}

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

@@ -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

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

@@ -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

@@ -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"}
+{"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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"error-contracts.js","sourceRoot":"","sources":["../../src/services/error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;;GAIG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,iFAAiF;QAC3F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,QAAQ;QAC/B,IAAI,EAAE,uEAAuE;QAC7E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,qEAAqE;QAC3E,QAAQ,EACN,gGAAgG;QAClG,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;;GAIG;AACH,MAAM,CAAC,MAAM,uBAAuB,GAAG;IACrC;QACE,MAAM,EAAE,sBAAsB;QAC9B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,oDAAoD;QAC1D,QAAQ,EACN,4FAA4F;QAC9F,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,2BAA2B;QACnC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,mEAAmE;QACzE,QAAQ,EAAE,qFAAqF;QAC/F,SAAS,EAAE,IAAI;KAChB;CACO,CAAC;AAEX;;;GAGG;AACH,MAAM,CAAC,MAAM,wBAAwB,GAAG;IACtC;QACE,MAAM,EAAE,uBAAuB;QAC/B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,sDAAsD;QAC5D,QAAQ,EACN,iGAAiG;QACnG,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,4BAA4B;QACpC,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,4EAA4E;QAClF,QAAQ,EACN,uFAAuF;QACzF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,yBAAyB;QACjC,IAAI,EAAE,gBAAgB,CAAC,eAAe;QACtC,IAAI,EAAE,+FAA+F;QACrG,QAAQ,EACN,8GAA8G;QAChH,SAAS,EAAE,KAAK;KACjB;CACO,CAAC;AAaX,MAAM,kBAAkB,GAAG,IAAI,GAAG,CAChC;IACE,GAAG,mBAAmB;IACtB,GAAG,wBAAwB;IAC3B,GAAG,wBAAwB;IAC3B,GAAG,uBAAuB;CAC3B,CAAC,GAAG,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,KAAK,CAAC,MAAM,EAAE,KAAK,CAAC,QAAQ,CAAC,CAAC,CACjD,CAAC;AAEF;;;;;;;;;;;;GAYG;AACH,MAAM,UAAU,WAAW,CAAC,MAA0B;IACpD,MAAM,IAAI,GAAG,kBAAkB,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;IAC5C,IAAI,IAAI,KAAK,SAAS,EAAE,CAAC;QACvB,MAAM,IAAI,KAAK,CAAC,wDAAwD,MAAM,GAAG,CAAC,CAAC;IACrF,CAAC;IACD,OAAO,EAAE,QAAQ,EAAE,EAAE,IAAI,EAAE,EAAE,CAAC;AAChC,CAAC"}

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

@@ -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

@@ -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"}
+{"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

@@ -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

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

@@ -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

@@ -1 +1 @@
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+{"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAeH,OAAO,KAAK,EAAE,QAAQ,EAAgB,MAAM,4CAA4C,CAAC;AAEzF,OAAO,EAAE,kBAAkB,EAAE,MAAM,iBAAiB,CAAC;AACrD,OAAO,EAAE,qBAAqB,EAAE,MAAM,oBAAoB,CAAC;AAC3D,OAAO,KAAK,EACV,uBAAuB,EAGvB,sBAAsB,EAEtB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AA2BpB;;;;;;;GAOG;AACH,qBAAa,gBAAgB;IAIzB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAL7B,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAY;gBAG1B,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM;IAmBrC;;;OAGG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC;IAoF3E;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC;IAkBnC;;;;;;;;;OASG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC;IAUlC;;;;;;;;;OASG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC;IAUlC;;;OAGG;YACW,iBAAiB;IA6C/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS;IAgCnD;;;;OAIG;YACW,SAAS;CAsDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAuB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/europe-pmc/europe-pmc-service.js

@@ -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

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package/dist/services/europe-pmc/types.d.ts

@@ -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

@@ -1 +1 @@
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package/dist/services/openalex/api-client.d.ts

@@ -0,0 +1,39 @@
+/**
+ * @fileoverview Low-level HTTP client for the OpenAlex API. Builds URLs,
+ * injects the optional polite-pool email, and exposes single-attempt fetch
+ * calls. Retry logic lives in `OpenAlexService`.
+ * @module src/services/openalex/api-client
+ */
+import { type OpenAlexWork } from './types.js';
+export interface OpenAlexApiClientConfig {
+    /** Admin email for OpenAlex polite pool (mailto= param). Optional. */
+    email?: string;
+    timeoutMs: number;
+}
+/** Low-level HTTP client for OpenAlex. Single-attempt — retries upstream. */
+export declare class OpenAlexApiClient {
+    private readonly config;
+    constructor(config: OpenAlexApiClientConfig);
+    /**
+     * Fetch a single work by PMID. Returns the work record (with related_works
+     * and referenced_works populated) or null when the PMID is unknown.
+     */
+    getWorkByPmid(pmid: string, signal?: AbortSignal): Promise<OpenAlexWork | null>;
+    /**
+     * Batch-resolve a list of OpenAlex work IDs to their PMIDs.
+     * Uses the filter=openalex:W1|W2|... endpoint with select=id,ids.
+     * Returns only records that carry a `pmid` field.
+     */
+    resolveOaIdsToPmids(oaIds: string[], signal?: AbortSignal): Promise<OpenAlexWork[]>;
+    /**
+     * Fetch works that cite a given OpenAlex work ID (the cited_by relationship).
+     * Returns up to `perPage` records with PMIDs.
+     */
+    getCitedBy(oaId: string, perPage: number, signal?: AbortSignal): Promise<{
+        works: OpenAlexWork[];
+        totalCount: number;
+    }>;
+    /** Helper: fetch a /works?... URL and return parsed results. */
+    private fetchWorksList;
+}
+//# sourceMappingURL=api-client.d.ts.map

package/dist/services/openalex/api-client.d.ts.map

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