npm - @cyanheads/pubmed-mcp-server - Versions diffs - 2.10.14 → 2.10.15 - Mend

@cyanheads/pubmed-mcp-server 2.10.14 → 2.10.15

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 (57) hide show

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

@@ -1,7 +1,9 @@
 /**
  * @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`.
+ * injects the optional contact email, and exposes single-attempt search,
+ * fullTextXML, and citation-link calls. Classifies each endpoint's HTTP
+ * failures — a failed search as `europepmc_unreachable`, a missing fullTextXML
+ * as `not-available` — while retry logic lives in `EuropePmcService`.
  * @module src/services/europe-pmc/api-client
  */
 import { JsonRpcErrorCode, McpError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
@@ -27,6 +29,16 @@ export class EuropePmcApiClient {
      * 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.
+     *
+     * A failed `/search` is an outage, never "no match" — a genuine zero-hit
+     * query is HTTP 200 with `hitCount: 0`. A 404 is reclassified from its
+     * status-mapped `NotFound` to `ServiceUnavailable` so the service retries it.
+     * A retryable 5xx keeps its code, so a 504 stays `Timeout`. Only a failure
+     * that ends up `ServiceUnavailable` carries `europepmc_unreachable` and its
+     * recovery hint, the one code that reason is declared for. An upstream
+     * `retryAfter` is kept. A 429 and every other 4xx pass through unchanged, as
+     * does a 501, whose `data.retryable: false` keeps it out of the retry loop.
+     * (#152)
      */
     async search(params) {
         const url = this.buildSearchUrl(params);
@@ -42,8 +54,22 @@ export class EuropePmcApiClient {
             });
         }
         catch (error) {
-            if (error instanceof McpError)
-                throw error;
+            if (error instanceof McpError) {
+                const status = error.data?.status;
+                const isOutage = status === 404 ||
+                    (typeof status === 'number' && status >= 500 && error.data?.retryable !== false);
+                if (!isOutage)
+                    throw error;
+                const code = status === 404 ? JsonRpcErrorCode.ServiceUnavailable : error.code;
+                throw new McpError(code, `Europe PMC search request failed: ${error.message}`, {
+                    ...(code === JsonRpcErrorCode.ServiceUnavailable && {
+                        reason: 'europepmc_unreachable',
+                        ...recoveryFor('europepmc_unreachable'),
+                    }),
+                    status,
+                    ...(error.data?.retryAfter !== undefined && { retryAfter: error.data.retryAfter }),
+                }, { cause: 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 });
         }

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

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

@@ -7,6 +7,10 @@
  * 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.
@@ -36,8 +40,18 @@ export declare 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)
      */
     search(params: EuropePmcSearchParams): Promise<EuropePmcSearchResult>;
+    /**
+     * 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.
+     */
+    private searchOnce;
     /**
      * Look up specific records by `source` + EPMC id. One search request covers
      * the whole batch: each ref becomes a `recordLookupQuery` clause, OR-joined
@@ -103,7 +117,12 @@ export declare 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.
      */
     private withRetry;
 }

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"europe-pmc-service.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/europe-pmc-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAiBH,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,EAEvB,kBAAkB,EAElB,sBAAsB,EACtB,kBAAkB,EAClB,qBAAqB,EAErB,qBAAqB,EACrB,eAAe,EAChB,MAAM,YAAY,CAAC;AAqEpB;;;;;;;;;GASG;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;IAE7C,YACmB,MAAM,EAAE,kBAAkB,EAC1B,KAAK,EAAE,qBAAqB,EAC5B,UAAU,EAAE,MAAM,EAQpC;IAED;;;;;;;OAOG;IACH,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAWpE;IAED;;;;OAIG;YACW,UAAU;IAsHxB;;;;;;;;;;OAUG;IACG,YAAY,CAChB,IAAI,EAAE,SAAS,kBAAkB,EAAE,EACnC,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,kBAAkB,EAAE,CAAC,CAQ/B;IAED;;;;;;;OAOG;IACG,WAAW,CACf,MAAM,EAAE,MAAM,EACd,MAAM,EAAE,eAAe,EACvB,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,uBAAuB,CAAC,CAgBlC;IAED;;;;;;;;;;OAUG;IACH,SAAS,CACP,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;;;;;;OAUG;IACH,UAAU,CACR,IAAI,EAAE,MAAM,EACZ,QAAQ,EAAE,MAAM,EAChB,IAAI,EAAE,MAAM,EACZ,MAAM,CAAC,EAAE,WAAW,GACnB,OAAO,CAAC,sBAAsB,CAAC,CAQjC;IAED;;;;;OAKG;YACW,iBAAiB;IAsE/B;;;;;;;;OAQG;IACH,gBAAgB,CAAC,GAAG,EAAE,MAAM,GAAG,QAAQ,GAAG,SAAS,CA8BlD;IAED;;;;;;;;;OASG;YACW,SAAS;CAkDxB;AAMD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAyB3C;AAED,6EAA6E;AAC7E,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

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

@@ -7,13 +7,17 @@
  * 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, McpError, serializationError, validationError, } from '@cyanheads/mcp-ts-core/errors';
+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';
@@ -63,6 +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.
@@ -92,9 +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);
@@ -121,37 +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;
@@ -331,14 +383,19 @@ 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)
@@ -359,20 +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 CHANGED Viewed

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

@@ -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 = {
@@ -43,30 +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[]>;
-    /** 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;
 }

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