@cyanheads/pubmed-mcp-server 2.6.11 → 2.7.0

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

@@ -0,0 +1 @@
+{"version":3,"file":"pubmed-europepmc-search.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/pubmed-europepmc-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,wBAAwB,EAAE,MAAM,+BAA+B,CAAC;AACzE,OAAO,EAAE,mBAAmB,EAAE,MAAM,6CAA6C,CAAC;AAClF,OAAO,EACL,qBAAqB,EACrB,yBAAyB,GAE1B,MAAM,gCAAgC,CAAC;AACxC,OAAO,EACL,WAAW,EACX,oBAAoB,EACpB,cAAc,EACd,oBAAoB,GACrB,MAAM,gBAAgB,CAAC;AAExB,MAAM,UAAU,GAAG,CAAC,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,EAAE,KAAK,CAAC,CAAC,CAAC;AAE/D,gFAAgF;AAEhF,MAAM,CAAC,MAAM,yBAAyB,GAAG,IAAI,CAAC,yBAAyB,EAAE;IACvE,WAAW,EACT,4YAA4Y;IAC9Y,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,KAAK,EAAE,WAAW,CAAC,CAAC,oBAAoB,EAAE,oBAAoB,EAAE,cAAc,CAAC,CAAC;IAChF,SAAS,EACP,2HAA2H;IAE7H,MAAM,EAAE;QACN,GAAG,wBAAwB;QAC3B;YACE,MAAM,EAAE,oBAAoB;YAC5B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;YACzC,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EAAE,mFAAmF;SAC9F;KACO;IAEV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CACP,kPAAkP,CACnP;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,GAAG,CAAC,CAAC,CAAC;aACN,GAAG,CAAC,GAAG,CAAC;aACR,OAAO,CAAC,EAAE,CAAC;aACX,QAAQ,CAAC,yCAAyC,CAAC;QACtD,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,OAAO,CAAC,GAAG,CAAC;aACZ,QAAQ,CACP,8HAA8H,CAC/H;QACH,OAAO,EAAE,CAAC;aACP,KAAK,CAAC,UAAU,CAAC;aACjB,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CACP,gDAAgD,yBAAyB,CAAC,IAAI,CAAC,IAAI,CAAC,mGAAmG,qBAAqB,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAC3N;QACH,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;aACtB,OAAO,CAAC,MAAM,CAAC;aACf,QAAQ,CACP,qGAAqG,CACtG;QACH,IAAI,EAAE,CAAC;aACJ,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,0HAA0H,CAC3H;KACJ,CAAC;IAEF,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,6CAA6C,CAAC;QACzE,IAAI,EAAE,CAAC;aACJ,KAAK,CACJ,CAAC;aACE,MAAM,CAAC;YACN,MAAM,EAAE,UAAU,CAAC,QAAQ,CACzB,gHAAgH,CACjH;YACD,MAAM,EAAE,CAAC;iBACN,MAAM,EAAE;iBACR,QAAQ,CAAC,+DAA+D,CAAC;YAC5E,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACtD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;YAClE,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,eAAe,CAAC;YACxD,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YAC3D,oBAAoB,EAAE,CAAC;iBACpB,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CAAC,yCAAyC,CAAC;YACtD,IAAI,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,6BAA6B,CAAC;YACnE,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,4BAA4B,CAAC;YACnE,GAAG,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,kBAAkB,CAAC;YACvD,YAAY,EAAE,CAAC;iBACZ,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CAAC,gDAAgD,CAAC;YAC7D,cAAc,EAAE,CAAC;iBACd,OAAO,EAAE;iBACT,QAAQ,EAAE;iBACV,QAAQ,CACP,iMAAiM,CAClM;YACH,eAAe,EAAE,CAAC;iBACf,MAAM,EAAE;iBACR,QAAQ,EAAE;iBACV,QAAQ,CACP,qFAAqF,CACtF;YACH,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;YACrF,OAAO,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;SACvD,CAAC;aACD,QAAQ,CAAC,iDAAiD,CAAC,CAC/D;aACA,QAAQ,CAAC,8DAA8D,CAAC;QAC3E,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yCAAyC,CAAC;QACxE,UAAU,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;QAC1F,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kFAAkF,CAAC;QAC/F,cAAc,EAAE,CAAC;aACd,KAAK,CAAC,UAAU,CAAC;aACjB,QAAQ,CAAC,2DAA2D,CAAC;QACxE,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAChF,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,6DAA6D,CAAC;KAC3E,CAAC;IAEF,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,mCAAmC,EAAE,EAAE,KAAK,EAAE,KAAK,CAAC,KAAK,EAAE,CAAC,CAAC;QAC1E,MAAM,IAAI,GAAG,mBAAmB,EAAE,CAAC;QACnC,IAAI,CAAC,IAAI,EAAE,CAAC;YACV,MAAM,GAAG,CAAC,IAAI,CACZ,oBAAoB,EACpB,mFAAmF,EACnF,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,oBAAoB,CAAC,EAAE,CAC7C,CAAC;QACJ,CAAC;QAED,MAAM,OAAO,GAAG,CAAC,KAAK,CAAC,OAAO,IAAI,yBAAyB,CAA+B,CAAC;QAC3F,MAAM,MAAM,GAAG,MAAM,IAAI,CAAC,MAAM,CAAC;YAC/B,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,QAAQ,EAAE,KAAK,CAAC,QAAQ;YACxB,UAAU,EAAE,KAAK,CAAC,UAAU;YAC5B,OAAO;YACP,GAAG,CAAC,KAAK,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,EAAE,CAAC;YACvC,GAAG,CAAC,GAAG,CAAC,MAAM,IAAI,EAAE,MAAM,EAAE,GAAG,CAAC,MAAM,EAAE,CAAC;SAC1C,CAAC,CAAC;QAEH,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC;YACnC,MAAM,EAAE,CAAC,CAAC,MAA+C;YACzD,MAAM,EAAE,CAAC,CAAC,EAAE;YACZ,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;YAClC,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,YAAY,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,YAAY,EAAE,CAAC;YAClD,GAAG,CAAC,CAAC,CAAC,OAAO,IAAI,EAAE,OAAO,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;YACxC,GAAG,CAAC,CAAC,CAAC,oBAAoB,IAAI,EAAE,oBAAoB,EAAE,CAAC,CAAC,oBAAoB,EAAE,CAAC;YAC/E,GAAG,CAAC,CAAC,CAAC,IAAI,IAAI,EAAE,IAAI,EAAE,CAAC,CAAC,IAAI,EAAE,CAAC;YAC/B,GAAG,CAAC,CAAC,CAAC,KAAK,IAAI,EAAE,KAAK,EAAE,CAAC,CAAC,KAAK,EAAE,CAAC;YAClC,GAAG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package/dist/services/error-contracts.d.ts

@@ -62,12 +62,29 @@ 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 Europe PMC service layer can surface. Tools that consume
+ * `getEuropePmcService()` should spread these into their `errors[]`.
+ */
+export declare const EUROPEPMC_SERVICE_ERRORS: 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;
+}];
 /**
  * Reason identifier union for type-safe authoring on the service layer.
  * 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'];
+export type ServiceErrorReason = (typeof NCBI_SERVICE_ERRORS)[number]['reason'] | (typeof UNPAYWALL_SERVICE_ERRORS)[number]['reason'] | (typeof EUROPEPMC_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;;;;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,CAAC;AASxD;;;;;;;;;;;;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;;;GAGG;AACH,eAAO,MAAM,wBAAwB;;;;;;;;;;;;EAiB3B,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"}

package/dist/services/error-contracts.js

@@ -70,10 +70,27 @@ export const UNPAYWALL_SERVICE_ERRORS = [
         retryable: true,
     },
 ];
-const REASON_TO_RECOVERY = new Map([...NCBI_SERVICE_ERRORS, ...UNPAYWALL_SERVICE_ERRORS].map((entry) => [
-    entry.reason,
-    entry.recovery,
-]));
+/**
+ * Failure modes the Europe PMC service layer can surface. Tools that consume
+ * `getEuropePmcService()` should spread these into their `errors[]`.
+ */
+export const EUROPEPMC_SERVICE_ERRORS = [
+    {
+        reason: 'europepmc_unreachable',
+        code: JsonRpcErrorCode.ServiceUnavailable,
+        when: 'Europe PMC was unreachable after all retry attempts.',
+        recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.',
+        retryable: true,
+    },
+    {
+        reason: 'europepmc_invalid_response',
+        code: JsonRpcErrorCode.SerializationError,
+        when: 'Europe PMC returned a body that could not be parsed (invalid JSON or XML).',
+        recovery: 'Retry the request; Europe PMC returned a malformed response that could not be parsed.',
+        retryable: true,
+    },
+];
+const REASON_TO_RECOVERY = new Map([...NCBI_SERVICE_ERRORS, ...UNPAYWALL_SERVICE_ERRORS, ...EUROPEPMC_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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package/dist/services/europe-pmc/api-client.d.ts

@@ -0,0 +1,47 @@
+/**
+ * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs,
+ * injects the optional contact email, and exposes single-attempt search and
+ * fullTextXML calls. Retry logic lives in `EuropePmcService`.
+ * @module src/services/europe-pmc/api-client
+ */
+import { type EuropePmcSearchParams } from './types.js';
+export interface EuropePmcApiClientConfig {
+    email?: string;
+    timeoutMs: number;
+}
+/**
+ * Outcome of a fullTextXML fetch attempt. Wraps the typed contract so service
+ * callers don't need to inspect raw `Response` objects.
+ */
+export type EuropePmcFullTextFetchResult = {
+    kind: 'found';
+    xml: string;
+} | {
+    kind: 'not-available';
+    reason: string;
+};
+/** Low-level HTTP client for Europe PMC. Single-attempt — retries upstream. */
+export declare class EuropePmcApiClient {
+    private readonly config;
+    constructor(config: EuropePmcApiClientConfig);
+    /**
+     * Execute a search. Returns the raw JSON response body as a string so
+     * `EuropePmcService` can parse and surface SerializationError consistently
+     * when the body is malformed.
+     */
+    search(params: EuropePmcSearchParams): Promise<string>;
+    /**
+     * Fetch the JATS full-text XML for an EPMC record by its internal id.
+     * Returns `{ kind: 'not-available' }` for 404 — EPMC has the record but
+     * doesn't publish a full-text XML for it (very common for preprints).
+     */
+    fullTextXml(epmcId: string, signal?: AbortSignal): Promise<EuropePmcFullTextFetchResult>;
+    private buildSearchUrl;
+    /**
+     * Combine the caller's query with an optional source filter. EPMC's query
+     * syntax supports `SRC:"X"` field tokens — we OR-join the requested sources
+     * into a parenthesized clause and AND it with the user's query.
+     */
+    private buildQueryString;
+}
+//# sourceMappingURL=api-client.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/services/europe-pmc/api-client.js

@@ -0,0 +1,123 @@
+/**
+ * @fileoverview Low-level HTTP client for Europe PMC's REST API. Builds URLs,
+ * injects the optional contact email, and exposes single-attempt search and
+ * fullTextXML calls. Retry logic lives in `EuropePmcService`.
+ * @module src/services/europe-pmc/api-client
+ */
+import { McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
+import { recoveryFor } from '../../services/error-contracts.js';
+import { EUROPEPMC_API_BASE } from './types.js';
+const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
+/** Low-level HTTP client for Europe PMC. Single-attempt — retries upstream. */
+export class EuropePmcApiClient {
+    config;
+    constructor(config) {
+        this.config = config;
+    }
+    /**
+     * Execute a search. Returns the raw JSON response body as a string so
+     * `EuropePmcService` can parse and surface SerializationError consistently
+     * when the body is malformed.
+     */
+    async search(params) {
+        const url = this.buildSearchUrl(params);
+        const ctx = requestContextService.createRequestContext({
+            operation: 'EuropePmcSearch',
+            query: params.query,
+        });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: { Accept: 'application/json', 'User-Agent': USER_AGENT },
+                ...(params.signal && { signal: params.signal }),
+            });
+        }
+        catch (error) {
+            if (error instanceof McpError)
+                throw error;
+            const msg = error instanceof Error ? error.message : String(error);
+            throw serviceUnavailable(`Europe PMC search request failed: ${msg}`, { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') }, { cause: error });
+        }
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'Europe PMC',
+                data: { url, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
+            });
+        }
+        return response.text();
+    }
+    /**
+     * Fetch the JATS full-text XML for an EPMC record by its internal id.
+     * Returns `{ kind: 'not-available' }` for 404 — EPMC has the record but
+     * doesn't publish a full-text XML for it (very common for preprints).
+     */
+    async fullTextXml(epmcId, signal) {
+        const url = `${EUROPEPMC_API_BASE}/${encodeURIComponent(epmcId)}/fullTextXML`;
+        const ctx = requestContextService.createRequestContext({
+            operation: 'EuropePmcFullTextXml',
+            epmcId,
+        });
+        let response;
+        try {
+            response = await fetchWithTimeout(url, this.config.timeoutMs, ctx, {
+                headers: {
+                    Accept: 'application/xml, text/xml, */*;q=0.5',
+                    '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 fullTextXML request failed: ${msg}`, { reason: 'europepmc_unreachable', epmcId, ...recoveryFor('europepmc_unreachable') }, { cause: error });
+        }
+        if (response.status === 404) {
+            return { kind: 'not-available', reason: 'EPMC has no fullTextXML for this record' };
+        }
+        if (!response.ok) {
+            throw await httpErrorFromResponse(response, {
+                service: 'Europe PMC fullTextXML',
+                data: { epmcId, reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') },
+            });
+        }
+        const xml = await response.text();
+        if (!xml.trim()) {
+            logger.debug('Europe PMC returned an empty fullTextXML body.', requestContextService.createRequestContext({
+                operation: 'EuropePmcFullTextXmlEmpty',
+                epmcId,
+            }));
+            return { kind: 'not-available', reason: 'EPMC returned an empty fullTextXML body' };
+        }
+        return { kind: 'found', xml };
+    }
+    buildSearchUrl(params) {
+        const finalParams = {
+            query: this.buildQueryString(params),
+            format: 'json',
+            resultType: params.resultType ?? 'core',
+            pageSize: String(params.pageSize ?? 25),
+            cursorMark: params.cursorMark ?? '*',
+        };
+        if (params.sort)
+            finalParams.sort = params.sort;
+        if (this.config.email)
+            finalParams.email = this.config.email;
+        return `${EUROPEPMC_API_BASE}/search?${new URLSearchParams(finalParams).toString()}`;
+    }
+    /**
+     * Combine the caller's query with an optional source filter. EPMC's query
+     * syntax supports `SRC:"X"` field tokens — we OR-join the requested sources
+     * into a parenthesized clause and AND it with the user's query.
+     */
+    buildQueryString(params) {
+        const base = params.query.trim();
+        if (!params.sources || params.sources.length === 0)
+            return base;
+        const sourceClause = params.sources.map((s) => `SRC:"${s}"`).join(' OR ');
+        return `(${base}) AND (${sourceClause})`;
+    }
+}
+//# sourceMappingURL=api-client.js.map

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

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

@@ -0,0 +1,71 @@
+/**
+ * @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.
+ *
+ * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
+ * default). `getEuropePmcService()` returns `undefined` when disabled so
+ * callers can skip the chain step gracefully.
+ *
+ * @module src/services/europe-pmc/europe-pmc-service
+ */
+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';
+/**
+ * Facade over the Europe PMC REST API. Two methods:
+ *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
+ *   - `fullTextXml()` — JATS full text for an EPMC record.
+ *
+ * Both honor `ctx.signal` for cancellation and retry transient failures with
+ * capped exponential backoff plus jitter.
+ */
+export declare class EuropePmcService {
+    private readonly client;
+    private readonly queue;
+    private readonly maxRetries;
+    private readonly orderedXmlParser;
+    constructor(client: EuropePmcApiClient, queue: EuropePmcRequestQueue, maxRetries: number);
+    /**
+     * Search Europe PMC. Cursor-based pagination — pass `cursorMark: '*'` (or
+     * omit) for the first page; pass the returned `nextCursorMark` for the next.
+     */
+    search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
+    /**
+     * Fetch the JATS full text for an EPMC record. Returns:
+     *   - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable
+     *     directly by tool callers that hold their own parser, or via
+     *     `parseFullTextXml()` for the parsed tree.
+     *   - `{ kind: 'not-available', reason }` — EPMC has the record but
+     *     publishes no fullTextXML (404 or empty body).
+     */
+    fullTextXml(epmcId: string, source: EuropePmcSource, signal?: AbortSignal): Promise<EuropePmcFullTextResult>;
+    /**
+     * Parse a JATS XML string into the ordered node tree consumed by
+     * `parsePmcArticle`. Returns the `<article>` JatsNode, or `undefined` when
+     * the body doesn't contain an article element (malformed / empty).
+     *
+     * Throws `SerializationError` only for fundamentally invalid XML; an
+     * article-free but well-formed body returns `undefined` so callers can
+     * surface a `no-epmc-fulltext` outcome without a hard failure.
+     */
+    parseFullTextXml(xml: string): JatsNode | undefined;
+    /**
+     * Retry wrapper for transient errors. Mirrors NCBI's `withRetry` minus the
+     * service-level deadline — EPMC requests are cheaper individually and the
+     * caller (typically `ctx.signal`) bounds the total chain.
+     */
+    private withRetry;
+}
+/**
+ * Initialize the Europe PMC service when enabled. Safe to call regardless of
+ * config — `EUROPEPMC_ENABLED=false` leaves the service unset so callers see
+ * `undefined` and skip the chain step.
+ */
+export declare function initEuropePmcService(): void;
+/** Returns the initialized service, or `undefined` when EPMC is disabled. */
+export declare function getEuropePmcService(): EuropePmcService | undefined;
+//# sourceMappingURL=europe-pmc-service.d.ts.map

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

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

@@ -0,0 +1,243 @@
+/**
+ * @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.
+ *
+ * Optional service: only constructed when `EUROPEPMC_ENABLED=true` (the
+ * default). `getEuropePmcService()` returns `undefined` when disabled so
+ * callers can skip the chain step gracefully.
+ *
+ * @module src/services/europe-pmc/europe-pmc-service
+ */
+import { internalError, JsonRpcErrorCode, McpError, serializationError, } from '@cyanheads/mcp-ts-core/errors';
+import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { XMLParser, XMLValidator } from 'fast-xml-parser';
+import { getServerConfig } from '../../config/server-config.js';
+import { recoveryFor } from '../../services/error-contracts.js';
+import { ensureArray } from '../../services/ncbi/parsing/xml-helpers.js';
+import { EuropePmcApiClient } from './api-client.js';
+import { EuropePmcRequestQueue } from './request-queue.js';
+/** Retryable transient codes — same set NCBI uses. */
+const RETRYABLE_CODES = new Set([
+    JsonRpcErrorCode.ServiceUnavailable,
+    JsonRpcErrorCode.Timeout,
+    JsonRpcErrorCode.RateLimited,
+]);
+const MAX_BACKOFF_MS = 30_000;
+function abortableSleep(ms, signal) {
+    if (!signal)
+        return new Promise((r) => setTimeout(r, ms));
+    if (signal.aborted)
+        return Promise.reject(signal.reason);
+    return new Promise((resolve, reject) => {
+        const onAbort = () => {
+            clearTimeout(timer);
+            reject(signal.reason);
+        };
+        const timer = setTimeout(() => {
+            signal.removeEventListener('abort', onAbort);
+            resolve();
+        }, ms);
+        signal.addEventListener('abort', onAbort, { once: true });
+    });
+}
+/**
+ * Facade over the Europe PMC REST API. Two methods:
+ *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
+ *   - `fullTextXml()` — JATS full text for an EPMC record.
+ *
+ * Both honor `ctx.signal` for cancellation and retry transient failures with
+ * capped exponential backoff plus jitter.
+ */
+export class EuropePmcService {
+    client;
+    queue;
+    maxRetries;
+    orderedXmlParser;
+    constructor(client, queue, maxRetries) {
+        this.client = client;
+        this.queue = queue;
+        this.maxRetries = maxRetries;
+        /**
+         * EPMC's fullTextXML is JATS Z39.96 — same DTD PMC uses — so the parser
+         * config mirrors `NcbiResponseHandler.orderedXmlParser`. `preserveOrder`
+         * keeps inline mixed content readable; `trimValues: false` retains spaces
+         * between text and inline children.
+         */
+        this.orderedXmlParser = new XMLParser({
+            preserveOrder: true,
+            ignoreAttributes: false,
+            attributeNamePrefix: '@_',
+            parseTagValue: true,
+            trimValues: false,
+            processEntities: true,
+            htmlEntities: true,
+        });
+    }
+    /**
+     * Search Europe PMC. Cursor-based pagination — pass `cursorMark: '*'` (or
+     * omit) for the first page; pass the returned `nextCursorMark` for the next.
+     */
+    async search(params) {
+        const text = await this.queue.enqueue(() => this.withRetry(() => this.client.search(params), 'search', params.signal), 'search', params.signal);
+        let parsed;
+        try {
+            parsed = JSON.parse(text);
+        }
+        catch (error) {
+            throw serializationError('Failed to parse Europe PMC search JSON response.', {
+                reason: 'europepmc_invalid_response',
+                responseSnippet: text.substring(0, 200),
+                ...recoveryFor('europepmc_invalid_response'),
+            }, { cause: error });
+        }
+        const hits = ensureArray(parsed.resultList?.result);
+        const echoed = parsed.request?.queryString ?? params.query;
+        // EPMC echoes back the input cursor mark on the final page, so absence of
+        // an explicit "next" or equality with the request's cursor marks the end.
+        const cursorMark = parsed.request?.cursorMark ?? params.cursorMark ?? '*';
+        const nextCursor = parsed.nextCursorMark && parsed.nextCursorMark !== cursorMark
+            ? parsed.nextCursorMark
+            : undefined;
+        return {
+            hits,
+            hitCount: parsed.hitCount ?? hits.length,
+            ...(nextCursor && { nextCursorMark: nextCursor }),
+            cursorMark,
+            query: echoed,
+        };
+    }
+    /**
+     * Fetch the JATS full text for an EPMC record. Returns:
+     *   - `{ kind: 'found', xml, epmcId, source }` — JATS XML string usable
+     *     directly by tool callers that hold their own parser, or via
+     *     `parseFullTextXml()` for the parsed tree.
+     *   - `{ kind: 'not-available', reason }` — EPMC has the record but
+     *     publishes no fullTextXML (404 or empty body).
+     */
+    async fullTextXml(epmcId, source, signal) {
+        const outcome = await this.queue.enqueue(() => this.withRetry(() => this.client.fullTextXml(epmcId, signal), `fullTextXml(${epmcId})`, signal), `fullTextXml(${epmcId})`, signal);
+        if (outcome.kind === 'not-available') {
+            return { kind: 'not-available', reason: outcome.reason };
+        }
+        return { kind: 'found', xml: outcome.xml, epmcId, source };
+    }
+    /**
+     * Parse a JATS XML string into the ordered node tree consumed by
+     * `parsePmcArticle`. Returns the `<article>` JatsNode, or `undefined` when
+     * the body doesn't contain an article element (malformed / empty).
+     *
+     * Throws `SerializationError` only for fundamentally invalid XML; an
+     * article-free but well-formed body returns `undefined` so callers can
+     * surface a `no-epmc-fulltext` outcome without a hard failure.
+     */
+    parseFullTextXml(xml) {
+        const validationResult = XMLValidator.validate(xml.replace(/<!DOCTYPE[^>]*>/gi, ''));
+        if (validationResult !== true) {
+            throw serializationError('Received invalid XML from Europe PMC.', {
+                reason: 'europepmc_invalid_response',
+                responseSnippet: xml.substring(0, 200),
+                ...recoveryFor('europepmc_invalid_response'),
+            });
+        }
+        let parsed;
+        try {
+            parsed = this.orderedXmlParser.parse(xml);
+        }
+        catch (error) {
+            const parserError = error instanceof Error ? error.message : String(error);
+            throw serializationError(`Failed to parse Europe PMC fullTextXML response: ${parserError}`, {
+                reason: 'europepmc_invalid_response',
+                parserError,
+                responseSnippet: xml.substring(0, 200),
+                ...recoveryFor('europepmc_invalid_response'),
+            }, { cause: error });
+        }
+        if (!Array.isArray(parsed))
+            return;
+        const nodes = parsed;
+        return nodes.find((n) => 'article' in n);
+    }
+    /**
+     * Retry wrapper for transient errors. Mirrors NCBI's `withRetry` minus the
+     * service-level deadline — EPMC requests are cheaper individually and the
+     * caller (typically `ctx.signal`) bounds the total chain.
+     */
+    async withRetry(execute, label, signal) {
+        for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
+            if (signal?.aborted)
+                throw signal.reason;
+            try {
+                return await execute();
+            }
+            catch (error) {
+                if (signal?.aborted)
+                    throw signal.reason;
+                if (!(error instanceof McpError))
+                    throw error;
+                if (!RETRYABLE_CODES.has(error.code))
+                    throw error;
+                if (attempt < this.maxRetries) {
+                    const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);
+                    const jitter = baseDelay * (0.75 + 0.5 * Math.random());
+                    const retryDelay = Math.round(jitter);
+                    logger.warning(`Europe PMC ${label} failed. Retrying (${attempt + 1}/${this.maxRetries}) in ${retryDelay}ms.`, requestContextService.createRequestContext({
+                        operation: 'EuropePmcRetry',
+                        label,
+                        attempt: attempt + 1,
+                        retryDelay,
+                    }));
+                    await abortableSleep(retryDelay, signal);
+                    continue;
+                }
+                const attempts = this.maxRetries + 1;
+                const msg = error instanceof Error ? error.message : String(error);
+                throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
+                    reason: 'europepmc_unreachable',
+                    label,
+                    attempts,
+                    ...recoveryFor('europepmc_unreachable'),
+                }, { cause: error });
+            }
+        }
+        throw internalError('Europe PMC request failed after all retries.', {
+            reason: 'europepmc_unreachable',
+            label,
+            ...recoveryFor('europepmc_unreachable'),
+        });
+    }
+}
+// ─── Init / Accessor ────────────────────────────────────────────────────────
+let _service;
+/**
+ * Initialize the Europe PMC service when enabled. Safe to call regardless of
+ * config — `EUROPEPMC_ENABLED=false` leaves the service unset so callers see
+ * `undefined` and skip the chain step.
+ */
+export function initEuropePmcService() {
+    const config = getServerConfig();
+    if (!config.europepmcEnabled) {
+        logger.info('Europe PMC service disabled (EUROPEPMC_ENABLED=false).');
+        return;
+    }
+    const client = new EuropePmcApiClient({
+        timeoutMs: config.europepmcTimeoutMs,
+        ...(config.europepmcEmail && { email: config.europepmcEmail }),
+    });
+    const queue = new EuropePmcRequestQueue(config.europepmcRequestDelayMs);
+    _service = new EuropePmcService(client, queue, config.europepmcMaxRetries);
+    logger.info('Europe PMC service initialized.', requestContextService.createRequestContext({
+        operation: 'EuropePmcInit',
+        requestDelayMs: config.europepmcRequestDelayMs,
+        maxRetries: config.europepmcMaxRetries,
+        timeoutMs: config.europepmcTimeoutMs,
+        hasEmail: !!config.europepmcEmail,
+    }));
+}
+/** Returns the initialized service, or `undefined` when EPMC is disabled. */
+export function getEuropePmcService() {
+    return _service;
+}
+//# sourceMappingURL=europe-pmc-service.js.map

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

@@ -0,0 +1 @@
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