@cyanheads/pubmed-mcp-server 2.10.13 → 2.10.15

package/dist/services/error-contracts.d.ts

@@ -12,45 +12,55 @@
  *
  * Tool definitions import the contract arrays directly and spread them into
  * their `errors: [...]` declarations to surface the failure modes to the LLM.
+ * Every service-array entry carries `thrownBy: 'service'` so the linter's
+ * `error-contract-unthrown` check skips it while still checking the handler's
+ * own reasons. Spread a service array only into a tool whose handler lets that
+ * service's errors propagate — a tool that catches them all never produces
+ * those reasons.
  *
  * @module src/services/error-contracts
  */
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 /**
- * Failure modes the NCBI service layer can surface. Tools that consume
- * `getNcbiService()` should spread these into their own `errors[]` so the
- * declared contract matches what actually reaches the wire.
+ * Failure modes the NCBI service layer can surface. Tools whose handler lets
+ * `getNcbiService()` failures propagate spread these into their own `errors[]`
+ * so the declared contract matches what actually reaches the wire.
  */
 export declare const NCBI_SERVICE_ERRORS: readonly [{
     readonly reason: 'queue_full';
     readonly code: JsonRpcErrorCode.RateLimited;
-    readonly when: 'Local NCBI request queue is at capacity.';
-    readonly recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.';
+    readonly when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).';
+    readonly recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_unreachable';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
     readonly when: 'NCBI E-utilities is unreachable after all retry attempts.';
     readonly recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_deadline_exceeded';
     readonly code: JsonRpcErrorCode.Timeout;
     readonly when: 'Total request deadline expired before NCBI returned a response.';
     readonly recovery: 'Reduce batch size or retry; NCBI may be under temporary load.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_invalid_response';
     readonly code: JsonRpcErrorCode.SerializationError;
     readonly when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).';
     readonly recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'ncbi_resource_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: 'NCBI returned a structured "not found" error for the requested ID(s).';
     readonly recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.';
     readonly retryable: false;
+    readonly thrownBy: 'service';
 }];
 /**
  * Input failure the NCBI query tools reject before any call is made. Declared
@@ -98,11 +108,12 @@ export declare const UNPAYWALL_SERVICE_ERRORS: readonly [{
     readonly when: 'Unpaywall was unreachable when resolving a DOI or fetching content.';
     readonly recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }];
 /**
- * Failure modes the OpenAlex service layer can surface. Tools that consume
- * `getOpenAlexService()` / `getOpenAlexServiceOptional()` should spread
- * these into their `errors[]`.
+ * Failure modes the OpenAlex service layer can surface. Tools whose handler
+ * lets `getOpenAlexService()` / `getOpenAlexServiceOptional()` failures
+ * propagate spread these into their `errors[]`.
  */
 export declare const OPENALEX_SERVICE_ERRORS: readonly [{
     readonly reason: 'openalex_unreachable';
@@ -110,35 +121,41 @@ export declare const OPENALEX_SERVICE_ERRORS: readonly [{
     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 thrownBy: 'service';
 }, {
     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;
+    readonly thrownBy: 'service';
 }];
 /**
- * Failure modes the Europe PMC service layer can surface. Tools that consume
- * `getEuropePmcService()` should spread these into their `errors[]`.
+ * Failure modes the Europe PMC service layer can surface. Tools whose handler
+ * lets `getEuropePmcService()` failures propagate 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 when: 'Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results.';
     readonly recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.';
     readonly retryable: true;
+    readonly thrownBy: 'service';
 }, {
     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;
+    readonly thrownBy: 'service';
 }, {
     readonly reason: 'europepmc_invalid_input';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).';
-    readonly recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.';
+    readonly when: 'Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt.';
+    readonly recovery: 'Adjust the input — the query, the sort, or the cursorMark — before retrying; the same input will be rejected again.';
     readonly retryable: false;
+    readonly thrownBy: 'service';
 }];
 /**
  * Reason identifier union for type-safe authoring on the service layer.

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

@@ -1 +1 @@
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package/dist/services/error-contracts.js

@@ -12,22 +12,28 @@
  *
  * Tool definitions import the contract arrays directly and spread them into
  * their `errors: [...]` declarations to surface the failure modes to the LLM.
+ * Every service-array entry carries `thrownBy: 'service'` so the linter's
+ * `error-contract-unthrown` check skips it while still checking the handler's
+ * own reasons. Spread a service array only into a tool whose handler lets that
+ * service's errors propagate — a tool that catches them all never produces
+ * those reasons.
  *
  * @module src/services/error-contracts
  */
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 /**
- * Failure modes the NCBI service layer can surface. Tools that consume
- * `getNcbiService()` should spread these into their own `errors[]` so the
- * declared contract matches what actually reaches the wire.
+ * Failure modes the NCBI service layer can surface. Tools whose handler lets
+ * `getNcbiService()` failures propagate spread these into their own `errors[]`
+ * so the declared contract matches what actually reaches the wire.
  */
 export const NCBI_SERVICE_ERRORS = [
     {
         reason: 'queue_full',
         code: JsonRpcErrorCode.RateLimited,
-        when: 'Local NCBI request queue is at capacity.',
-        recovery: 'Retry after 1-2 seconds; the request queue hit the NCBI rate limit.',
+        when: 'The local NCBI request queue shed the call — the queue is full, or the call cannot start before its total deadline (for example behind the cooldown that follows an NCBI 429).',
+        recovery: 'Wait the number of seconds in `retryAfter`, then retry; the NCBI request queue is saturated or cooling down after a rate limit.',
         retryable: true,
+        thrownBy: 'service',
     },
     {
         reason: 'ncbi_unreachable',
@@ -35,6 +41,7 @@ export const NCBI_SERVICE_ERRORS = [
         when: 'NCBI E-utilities is unreachable after all retry attempts.',
         recovery: 'Retry after a brief delay; NCBI was unreachable across all retry attempts.',
         retryable: true,
+        thrownBy: 'service',
     },
     {
         reason: 'ncbi_deadline_exceeded',
@@ -42,6 +49,7 @@ export const NCBI_SERVICE_ERRORS = [
         when: 'Total request deadline expired before NCBI returned a response.',
         recovery: 'Reduce batch size or retry; NCBI may be under temporary load.',
         retryable: true,
+        thrownBy: 'service',
     },
     {
         reason: 'ncbi_invalid_response',
@@ -49,6 +57,7 @@ export const NCBI_SERVICE_ERRORS = [
         when: 'NCBI returned a body that could not be parsed (invalid XML/JSON).',
         recovery: 'Retry the request; NCBI returned a malformed response that could not be parsed.',
         retryable: true,
+        thrownBy: 'service',
     },
     {
         reason: 'ncbi_resource_not_found',
@@ -56,6 +65,7 @@ export const NCBI_SERVICE_ERRORS = [
         when: 'NCBI returned a structured "not found" error for the requested ID(s).',
         recovery: 'Verify the ID exists in PubMed; the resource was not found in NCBI and retrying will not help.',
         retryable: false,
+        thrownBy: 'service',
     },
 ];
 /**
@@ -109,12 +119,13 @@ export const UNPAYWALL_SERVICE_ERRORS = [
         when: 'Unpaywall was unreachable when resolving a DOI or fetching content.',
         recovery: 'Retry after a brief delay; Unpaywall was unreachable. The PMC source remains the primary path.',
         retryable: true,
+        thrownBy: 'service',
     },
 ];
 /**
- * Failure modes the OpenAlex service layer can surface. Tools that consume
- * `getOpenAlexService()` / `getOpenAlexServiceOptional()` should spread
- * these into their `errors[]`.
+ * Failure modes the OpenAlex service layer can surface. Tools whose handler
+ * lets `getOpenAlexService()` / `getOpenAlexServiceOptional()` failures
+ * propagate spread these into their `errors[]`.
  */
 export const OPENALEX_SERVICE_ERRORS = [
     {
@@ -123,6 +134,7 @@ export const OPENALEX_SERVICE_ERRORS = [
         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,
+        thrownBy: 'service',
     },
     {
         reason: 'openalex_invalid_response',
@@ -130,19 +142,22 @@ export const OPENALEX_SERVICE_ERRORS = [
         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,
+        thrownBy: 'service',
     },
 ];
 /**
- * Failure modes the Europe PMC service layer can surface. Tools that consume
- * `getEuropePmcService()` should spread these into their `errors[]`.
+ * Failure modes the Europe PMC service layer can surface. Tools whose handler
+ * lets `getEuropePmcService()` failures propagate 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.',
+        when: 'Europe PMC failed on every retry attempt — unreachable, an HTTP 404 or 5xx other than a 504 timeout from its search endpoint, or an empty response with no results.',
         recovery: 'Retry after a brief delay; Europe PMC was unreachable. NCBI PMC and Unpaywall remain available.',
         retryable: true,
+        thrownBy: 'service',
     },
     {
         reason: 'europepmc_invalid_response',
@@ -150,13 +165,15 @@ export const EUROPEPMC_SERVICE_ERRORS = [
         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,
+        thrownBy: 'service',
     },
     {
         reason: 'europepmc_invalid_input',
         code: JsonRpcErrorCode.ValidationError,
-        when: 'Europe PMC rejected the request input (empty query, unknown sort field, malformed parameter).',
-        recovery: 'Adjust the input — usually the query or sort field — before retrying; the same input will be rejected again.',
+        when: 'Europe PMC rejected the request input — an error message such as an empty query, an empty response to a sort with an undocumented field or no asc/desc direction, or an empty response to a pagination cursor on every attempt.',
+        recovery: 'Adjust the input — the query, the sort, or the cursorMark — before retrying; the same input will be rejected again.',
         retryable: false,
+        thrownBy: 'service',
     },
 ];
 const REASON_TO_RECOVERY = new Map([

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

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

@@ -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 { type EuropePmcSearchParams } from './types.js';
@@ -36,6 +38,16 @@ export declare 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)
      */
     search(params: EuropePmcSearchParams): Promise<string>;
     /**

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

@@ -1 +1 @@
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+{"version":3,"file":"api-client.d.ts","sourceRoot":"","sources":["../../../src/services/europe-pmc/api-client.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAMH,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;;;;;;;;GAQG;AACH,qBAAa,kBAAkB;IACjB,OAAO,CAAC,QAAQ,CAAC,MAAM;IAAnC,YAA6B,MAAM,EAAE,wBAAwB,EAAI;IAEjE;;;;;;;;;;;;;;OAcG;IACG,MAAM,CAAC,MAAM,EAAE,qBAAqB,GAAG,OAAO,CAAC,MAAM,CAAC,CA4C3D;IAED;;;;;;;;;OASG;IACG,WAAW,CAAC,MAAM,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,4BAA4B,CAAC,CA4C7F;IAED;;;;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,CAG7F;IAED;;;;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,CAG9F;IAED,iFAAiF;YACnE,cAAc;IA8B5B,OAAO,CAAC,cAAc;IActB;;;;OAIG;IACH,OAAO,CAAC,gBAAgB;CAMzB"}

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

@@ -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

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

@@ -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

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