@cyanheads/pubmed-mcp-server 2.10.13 → 2.10.15

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

@@ -7,29 +7,26 @@
  * from the same `ORDERED_XML_PARSER_OPTIONS` NCBI's ordered parser uses, so
  * `parsePmcArticle` consumes the result without modification.
  *
+ * A search's retry boundary covers fetch and response classification, so
+ * Europe PMC's intermittent empty `{ version }` envelope is retried like an
+ * HTTP outage; only a sort or cursor that explains it is reported as bad input.
+ *
  * 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, validationError, } from '@cyanheads/mcp-ts-core/errors';
-import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
+import { internalError, JsonRpcErrorCode, McpError, serializationError, serviceUnavailable, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 // biome-ignore lint/suspicious/noDeprecatedImports: staying on in-tree XMLValidator — see ncbi/response-handler.ts
 import { XMLParser, XMLValidator } from 'fast-xml-parser';
 import { getServerConfig } from '../../config/server-config.js';
 import { recoveryFor } from '../error-contracts.js';
 import { ORDERED_XML_PARSER_OPTIONS } from '../ncbi/parsing/ordered-xml-parser-options.js';
 import { ensureArray } from '../ncbi/parsing/xml-helpers.js';
-import { isTransient } from '../retry-policy.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)
@@ -70,6 +67,28 @@ function recordLookupQuery({ epmcId, source }) {
     const extIdClause = `(EXT_ID:${epmcId} AND SRC:${source})`;
     return source === 'PMC' ? `${extIdClause} OR (PMCID:${epmcId})` : extIdClause;
 }
+/** The sort fields Europe PMC documents. */
+const DOCUMENTED_SORT_FIELDS = new Set(['P_PDATE_D', 'CITED', 'AUTH_FIRST', 'PUB_YEAR']);
+/**
+ * Whether a sort is the likely cause of an empty `{ version }` envelope: one of
+ * its comma-separated keys has a field outside the documented set, or lacks an
+ * `asc`/`desc` direction. Europe PMC answers those shapes with the envelope on
+ * every request, and orders by every key of a valid list (`PUB_YEAR desc, CITED
+ * desc`). Field and direction compare case-insensitively and tolerate extra
+ * whitespace, matching Europe PMC's own parsing.
+ *
+ * Classification only, never a local allowlist: the request always goes out.
+ * Europe PMC honors some undocumented fields (`ID asc` reorders results) and
+ * silently ignores others (`SCORE desc`), so only the envelope itself decides.
+ */
+function sortExplainsEnvelope(sort) {
+    return sort.split(',').some((key) => {
+        const [field = '', direction = '', ...rest] = key.trim().split(/\s+/);
+        return (rest.length > 0 ||
+            !DOCUMENTED_SORT_FIELDS.has(field.toUpperCase()) ||
+            !/^(asc|desc)$/i.test(direction));
+    });
+}
 /**
  * Facade over the Europe PMC REST API:
  *   - `search()` — keyword search across MED/PMC/PPR/PAT/AGR.
@@ -99,9 +118,21 @@ export class EuropePmcService {
     /**
      * Search Europe PMC. Cursor-based pagination — pass `cursorMark: '*'` (or
      * omit) for the first page; pass the returned `nextCursorMark` for the next.
+     *
+     * The retry boundary covers the fetch and the response classification
+     * together, so an empty envelope retries like any other transient failure
+     * rather than surfacing after the loop has already returned. (#159)
      */
-    async search(params) {
-        const text = await this.queue.enqueue(() => this.withRetry(() => this.client.search(params), 'search', params.signal), 'search', params.signal);
+    search(params) {
+        return this.queue.enqueue(() => this.withRetry((attempt) => this.searchOnce(params, attempt === this.maxRetries), 'search', params.signal), 'search', params.signal);
+    }
+    /**
+     * One search attempt: fetch, parse, and classify the body. `isLastAttempt`
+     * lets an empty envelope that has persisted through the whole retry budget
+     * be attributed to a caller-supplied cursor.
+     */
+    async searchOnce(params, isLastAttempt) {
+        const text = await this.client.search(params);
         let parsed;
         try {
             parsed = JSON.parse(text);
@@ -128,37 +159,51 @@ export class EuropePmcService {
             });
         }
         /**
-         * EPMC silently returns a `{ version }`-only envelope (no `hitCount`, no
-         * `request` echo, no `resultList`) when it rejects a parameter — most
-         * commonly an undocumented `sort` field. Without this guard the response
-         * normalizes to a fake 0-hit success and the caller never learns the sort
-         * was rejected. Route to ValidationError (non-retryable) since retrying
-         * the same input will be rejected again.
+         * EPMC answers some requests with a `{ version }`-only envelope — no
+         * `hitCount`, no `request` echo, no `resultList`. Without this guard the
+         * response normalizes to a fake 0-hit success. Every cause produces the
+         * byte-identical body, so it is classified by its likely cause:
+         *
+         * - A sort that EPMC rejects every time (see `sortExplainsEnvelope`) fails
+         *   fast as non-retryable input — retrying only adds backoff.
+         * - A non-default cursor that draws it on every attempt is most likely
+         *   invalid or expired; EPMC rejects a malformed cursor every time.
+         * - Otherwise it is intermittent upstream noise — valid requests, with or
+         *   without a documented sort, draw it on a fraction of calls and succeed
+         *   when repeated — so it is thrown as a transient `europepmc_unreachable`
+         *   for the retry loop, and never names the caller's input. (#159)
+         *
+         * Each throw keeps the diagnosis (message) apart from the next step
+         * (recovery hint): the framework mirrors `data.recovery.hint` into
+         * `content[]`, and one string passed as both renders byte-identical
+         * Error:/Recovery: blocks. (#75)
          */
         if (parsed.hitCount === undefined &&
             parsed.request === undefined &&
             parsed.resultList === undefined) {
-            // Split the diagnosis (message) from the actionable next step (recovery
-            // hint). The framework mirrors data.recovery.hint into content[], so
-            // passing one string as both renders byte-identical Error:/Recovery:
-            // blocks — the same distinct message-vs-hint shape as the errMsg throw
-            // ~20 lines up. (#75)
-            const { message, hint } = params.sort
-                ? {
-                    message: `Europe PMC silently rejected the request — most likely the invalid sort field "${params.sort}".`,
-                    hint: 'Use a documented sort (`P_PDATE_D desc`, `CITED desc`, `AUTH_FIRST asc`, or `PUB_YEAR desc`), or omit `sort` for relevance ranking.',
-                }
-                : {
-                    message: 'Europe PMC silently rejected the request — empty envelope with no hitCount.',
-                    hint: 'Verify the query syntax, sort field, and cursorMark, then retry.',
-                };
-            throw validationError(message, {
-                reason: 'europepmc_invalid_input',
-                ...(params.sort && { sort: params.sort }),
-                ...(params.cursorMark && params.cursorMark !== '*' && { cursorMark: params.cursorMark }),
-                responseSnippet: text.substring(0, 200),
-                recovery: { hint },
-            });
+            const cursorMark = params.cursorMark && params.cursorMark !== '*' ? params.cursorMark : undefined;
+            if (params.sort && sortExplainsEnvelope(params.sort)) {
+                throw validationError(`Europe PMC silently rejected the request — most likely the sort "${params.sort}", which needs a documented field and an asc/desc direction.`, {
+                    reason: 'europepmc_invalid_input',
+                    sort: params.sort,
+                    ...(cursorMark && { cursorMark }),
+                    responseSnippet: text.substring(0, 200),
+                    recovery: {
+                        hint: 'Use a documented sort (`P_PDATE_D desc`, `CITED desc`, `AUTH_FIRST asc`, or `PUB_YEAR desc`), or omit `sort` for relevance ranking.',
+                    },
+                });
+            }
+            if (cursorMark && isLastAttempt) {
+                throw validationError(`Europe PMC answered every attempt for cursorMark "${cursorMark}" with an empty response — the cursor is most likely invalid or expired.`, {
+                    reason: 'europepmc_invalid_input',
+                    cursorMark,
+                    responseSnippet: text.substring(0, 200),
+                    recovery: {
+                        hint: 'Restart from the first page with `cursorMark: "*"`, or pass the exact `nextCursorMark` from the previous response.',
+                    },
+                });
+            }
+            throw serviceUnavailable('Europe PMC returned an empty response with no hit count or result list.', { reason: 'europepmc_unreachable', ...recoveryFor('europepmc_unreachable') });
         }
         const hits = ensureArray(parsed.resultList?.result);
         const echoed = parsed.request?.queryString ?? params.query;
@@ -338,21 +383,26 @@ export class EuropePmcService {
     /**
      * 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.
+     * caller (typically `ctx.signal`) bounds the total chain. `execute` receives
+     * the zero-based attempt index. On exhaustion the last error keeps its code
+     * and an upstream `retryAfter`, so a 429 still tells the caller how long to
+     * wait. Only a `ServiceUnavailable` gains `europepmc_unreachable` and its hint;
+     * a `Timeout` or `RateLimited` keeps its code with no reason, as the NCBI
+     * service reports them.
      */
     async withRetry(execute, label, signal) {
         for (let attempt = 0; attempt <= this.maxRetries; attempt++) {
             if (signal?.aborted)
                 throw signal.reason;
             try {
-                return await execute();
+                return await execute(attempt);
             }
             catch (error) {
                 if (signal?.aborted)
                     throw signal.reason;
                 if (!(error instanceof McpError))
                     throw error;
-                if (!isTransient(error, RETRYABLE_CODES))
+                if (!defaultIsTransient(error))
                     throw error;
                 if (attempt < this.maxRetries) {
                     const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);
@@ -366,20 +416,18 @@ export class EuropePmcService {
                     continue;
                 }
                 const attempts = this.maxRetries + 1;
-                const msg = error instanceof Error ? error.message : String(error);
-                throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
-                    reason: 'europepmc_unreachable',
+                throw new McpError(error.code, `${error.message} (failed after ${attempts} attempts)`, {
+                    ...(error.code === JsonRpcErrorCode.ServiceUnavailable && {
+                        reason: 'europepmc_unreachable',
+                        ...recoveryFor('europepmc_unreachable'),
+                    }),
                     label,
                     attempts,
-                    ...recoveryFor('europepmc_unreachable'),
+                    ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
                 }, { cause: error });
             }
         }
-        throw internalError('Europe PMC request failed after all retries.', {
-            reason: 'europepmc_unreachable',
-            label,
-            ...recoveryFor('europepmc_unreachable'),
-        });
+        throw internalError('Europe PMC request failed after all retries.', { label });
     }
 }
 // ─── Init / Accessor ────────────────────────────────────────────────────────

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

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package/dist/services/ncbi/ncbi-service.d.ts

@@ -1,11 +1,13 @@
 /**
  * @fileoverview High-level service for interacting with NCBI E-utilities.
  * Orchestrates the API client, request queue, and response handler to provide
- * typed methods for each E-utility endpoint. Uses init/accessor pattern.
+ * typed methods for each E-utility endpoint. Every call runs as a retry loop around
+ * the shared request queue — each attempt re-queued and re-paced — under one total
+ * deadline that covers queue wait, attempts, and backoff. Uses init/accessor pattern.
  * @module src/services/ncbi/ncbi-service
  */
+import { type Pacer } from '@cyanheads/mcp-ts-core/utils';
 import { NcbiApiClient } from './api-client.js';
-import { NcbiRequestQueue } from './request-queue.js';
 import { NcbiResponseHandler } from './response-handler.js';
 import { type ECitMatchCitation, type ECitMatchResult, type ESearchResult, type ESpellResult, type ESummaryResult, type IdConvertRecord, type NcbiCallOptions, type NcbiRequestOptions, type NcbiRequestParams, type XmlPubmedArticleSet } from './types.js';
 /**
@@ -18,7 +20,7 @@ export declare class NcbiService {
     private readonly responseHandler;
     private readonly maxRetries;
     private readonly totalDeadlineMs;
-    constructor(apiClient: NcbiApiClient, queue: NcbiRequestQueue, responseHandler: NcbiResponseHandler, maxRetries: number, totalDeadlineMs: number);
+    constructor(apiClient: NcbiApiClient, queue: Pacer, responseHandler: NcbiResponseHandler, maxRetries: number, totalDeadlineMs: number);
     eSearch(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESearchResult>;
     eSummary(params: NcbiRequestParams, options?: NcbiCallOptions): Promise<ESummaryResult>;
     eFetch<T = {
@@ -43,32 +45,22 @@ export declare class NcbiService {
      * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
      */
     idConvert(ids: string[], idtype?: string, options?: NcbiCallOptions): Promise<IdConvertRecord[]>;
-    /** Error codes that are transient and worth retrying with backoff. */
-    private static readonly RETRYABLE_CODES;
-    /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
-    private static readonly MAX_BACKOFF_MS;
     /**
-     * Wraps a task with a service-level deadline. Returns a combined AbortSignal
-     * (internal deadline OR'd with the caller's `ctx.signal`, if any) that the
-     * task must forward to both the HTTP call and any backoff sleep so cancellation
-     * interrupts the full retry chain — not just the next attempt.
-     */
-    private runWithDeadline;
-    /**
-     * Retry wrapper for transient NCBI errors (ServiceUnavailable, Timeout, RateLimited).
-     * Non-transient McpErrors and unexpected plain Errors fail immediately.
-     * Uses capped exponential backoff with jitter. Backoff sleep is abortable via
-     * `signal`, so deadline expiration or caller cancel short-circuits the chain.
+     * Runs one NCBI call: a retry loop around the shared request queue, so every
+     * attempt re-queues and is re-paced (and a 429 closes the gate for all callers,
+     * not just this one). One deadline covers queue wait, attempts, and backoff. Its
+     * signal — joined with the caller's — reaches the queue wait, the backoff sleep,
+     * and the HTTP request, and each attempt offers the queue only the time left, so
+     * a call that cannot start in time is shed at once instead of waiting it out.
+     *
+     * A caller abort rethrows the caller's own reason; every other failure is mapped
+     * onto this service's reasons by {@link toServiceError}, after the loop.
      */
-    private withRetry;
+    private runPaced;
     /**
-     * Runs a request under a service-level deadline that bounds queue wait time
-     * + retry chain + HTTP execution. The deadline is constructed *outside* the
-     * queue so a backlog can't burn a request's budget before it even dispatches.
-     *
-     * The combined deadline+caller signal is threaded into the queue (cancels a
-     * still-waiting task), the retry chain (cancels pending backoff sleeps),
-     * and the HTTP fetch (cancels wedged requests).
+     * One eutils request through {@link runPaced}: fetch, classify, parse. EFetch's
+     * all-invalid-ID rejection resolves as the empty set NCBI returns for an unknown
+     * ID, and a backend-failure envelope is reclassified as transient so it retries.
      */
     private performRequest;
 }

package/dist/services/ncbi/ncbi-service.d.ts.map

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