@cyanheads/pubmed-mcp-server 2.6.8 → 2.6.10

package/dist/services/ncbi/response-handler.js

@@ -4,9 +4,10 @@
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
  * @module src/services/ncbi/response-handler
  */
-import { serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
+import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
 import { XMLParser as FastXmlParser, XMLValidator } from 'fast-xml-parser';
+import { recoveryFor } from '../../services/error-contracts.js';
 /**
  * jpaths that NCBI may return as either a single value or an array.
  * The `isArray` callback forces these to always parse as arrays for consistency.
@@ -54,6 +55,16 @@ const ERROR_PATHS = [
     'PubmedArticleSet.ErrorList.CannotRetrievePMID',
     'ERROR',
 ];
+/**
+ * NCBI error messages indicating the requested record doesn't exist (permanent
+ * failure). Throwing NotFound for these prevents the retry loop from hammering
+ * NCBI on what is fundamentally a "no such record" response.
+ */
+const NCBI_NOT_FOUND_PATTERNS = [
+    /cannot get document summary/i,
+    /UID=\S+:\s*not found/i,
+    /Empty id list/i,
+];
 const WARNING_PATHS = [
     'eSearchResult.ErrorList.PhraseNotFound',
     'eSearchResult.ErrorList.FieldNotFound',
@@ -232,8 +243,13 @@ export class NcbiResponseHandler {
         });
     }
     /**
-     * Extract a structured error from a parsed NCBI XML body and throw it via
-     * `serviceUnavailable()`. Never returns.
+     * Extract a structured error from a parsed NCBI XML body and throw it as
+     * `notFound()` for permanent "no such record" responses or `serviceUnavailable()`
+     * for transient backend failures. Never returns.
+     *
+     * NCBI returns "cannot get document summary" / "Empty id list" for invalid
+     * UIDs — these are permanent (the record doesn't exist), so we surface them
+     * as NotFound so the retry loop short-circuits instead of hammering NCBI.
      */
     throwNcbiError(parsedXml, endpoint) {
         const errorMessages = this.extractNcbiErrorMessages(parsedXml);
@@ -242,9 +258,19 @@ export class NcbiResponseHandler {
             endpoint,
             errors: errorMessages,
         }));
+        if (errorMessages.some((msg) => NCBI_NOT_FOUND_PATTERNS.some((p) => p.test(msg)))) {
+            throw notFound(`NCBI API Error: ${errorMessages.join('; ')}`, {
+                reason: 'ncbi_resource_not_found',
+                endpoint,
+                ncbiErrors: errorMessages,
+                ...recoveryFor('ncbi_resource_not_found'),
+            });
+        }
         throw serviceUnavailable(`NCBI API Error: ${errorMessages.join('; ')}`, {
+            reason: 'ncbi_unreachable',
             endpoint,
             ncbiErrors: errorMessages,
+            ...recoveryFor('ncbi_unreachable'),
         });
     }
     extractNcbiErrorMessages(parsedXml) {
@@ -281,25 +307,45 @@ export class NcbiResponseHandler {
                 endpoint,
                 retmode,
             }));
+            const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
+            if (isHtml) {
+                logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', requestContextService.createRequestContext({
+                    operation: 'NcbiHtmlResponse',
+                    endpoint,
+                }));
+                throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+            }
+            // NCBI's eLink (and occasionally other endpoints) drops the root element
+            // when the upstream backend connection fails mid-response, yielding just
+            // `<?xml ... ?>` + DOCTYPE with no body. JSON retmode reveals the same
+            // failure as a TXCLIENT EOF in an `ERROR` field; XML just truncates.
+            // Reclassify as transient ServiceUnavailable so the retry chain recovers,
+            // rather than SerializationError which short-circuits retries.
+            const bodyMinusProlog = responseText
+                .replace(/<\?xml[^?]*\?>/gi, '')
+                .replace(/<!DOCTYPE[^>]*>/gi, '')
+                .trim();
+            if (bodyMinusProlog.length === 0) {
+                logger.warning('NCBI returned a prolog-only XML response (upstream backend failure).', requestContextService.createRequestContext({
+                    operation: 'NcbiEmptyResponse',
+                    endpoint,
+                    responseLength: responseText.length,
+                }));
+                throw serviceUnavailable('NCBI returned an empty response body — the upstream backend likely failed mid-request.', { reason: 'ncbi_unreachable', endpoint, ...recoveryFor('ncbi_unreachable') });
+            }
             const xmlForValidation = responseText.replace(/<!DOCTYPE[^>]*>/gi, '');
             const validationResult = XMLValidator.validate(xmlForValidation);
             if (validationResult !== true) {
-                const isHtml = /^\s*<(!DOCTYPE\s+html|html[\s>])/i.test(responseText);
-                if (isHtml) {
-                    logger.warning('NCBI returned HTML instead of XML (likely rate-limited).', requestContextService.createRequestContext({
-                        operation: 'NcbiHtmlResponse',
-                        endpoint,
-                    }));
-                    throw serviceUnavailable('NCBI API returned an HTML response instead of XML — likely rate-limited.', { endpoint });
-                }
                 logger.error('Invalid XML response from NCBI.', requestContextService.createRequestContext({
                     operation: 'NcbiInvalidXml',
                     endpoint,
                     responseSnippet: responseText.substring(0, 500),
                 }));
                 throw serializationError('Received invalid XML from NCBI.', {
+                    reason: 'ncbi_invalid_response',
                     endpoint,
                     responseSnippet: responseText.substring(0, 200),
+                    ...recoveryFor('ncbi_invalid_response'),
                 });
             }
             const useOrdered = options?.useOrderedParser ?? false;
@@ -328,9 +374,11 @@ export class NcbiResponseHandler {
                     responseSnippet: responseText.substring(0, 500),
                 }));
                 throw serializationError(`Failed to parse XML response from NCBI: ${parserError}`, {
+                    reason: 'ncbi_invalid_response',
                     endpoint,
                     parserError,
                     responseSnippet: responseText.substring(0, 200),
+                    ...recoveryFor('ncbi_invalid_response'),
                 }, { cause: error });
             }
             if (!useOrdered) {
@@ -358,7 +406,12 @@ export class NcbiResponseHandler {
                 parsed = JSON.parse(responseText);
             }
             catch (error) {
-                throw serializationError('Failed to parse NCBI JSON response.', { endpoint, responseSnippet: responseText.substring(0, 200) }, { cause: error });
+                throw serializationError('Failed to parse NCBI JSON response.', {
+                    reason: 'ncbi_invalid_response',
+                    endpoint,
+                    responseSnippet: responseText.substring(0, 200),
+                    ...recoveryFor('ncbi_invalid_response'),
+                }, { cause: error });
             }
             if (parsed && typeof parsed === 'object' && 'error' in parsed) {
                 const errorMessage = String(parsed.error);
@@ -367,9 +420,19 @@ export class NcbiResponseHandler {
                     endpoint,
                     error: errorMessage,
                 }));
+                if (NCBI_NOT_FOUND_PATTERNS.some((p) => p.test(errorMessage))) {
+                    throw notFound(`NCBI API Error: ${errorMessage}`, {
+                        reason: 'ncbi_resource_not_found',
+                        endpoint,
+                        ncbiErrors: [errorMessage],
+                        ...recoveryFor('ncbi_resource_not_found'),
+                    });
+                }
                 throw serviceUnavailable(`NCBI API Error: ${errorMessage}`, {
+                    reason: 'ncbi_unreachable',
                     endpoint,
                     ncbiError: errorMessage,
+                    ...recoveryFor('ncbi_unreachable'),
                 });
             }
             logger.debug('Successfully parsed JSON response.', requestContextService.createRequestContext({ operation: 'NcbiParseJsonOk', endpoint }));

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

@@ -1 +1 @@
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+{"version":3,"file":"unpaywall-service.d.ts","sourceRoot":"","sources":["../../../src/services/unpaywall/unpaywall-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAYH,OAAO,EAEL,KAAK,gBAAgB,EACrB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EAEzB,MAAM,YAAY,CAAC;AAIpB;;;GAGG;AACH,qBAAa,gBAAgB;IAEzB,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,SAAS;gBADT,KAAK,EAAE,MAAM,EACb,SAAS,EAAE,MAAM;IAGpC;;;;OAIG;IACG,OAAO,CAAC,GAAG,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,mBAAmB,CAAC;IA0D9E;;;;;OAKG;IACG,YAAY,CAAC,QAAQ,EAAE,iBAAiB,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,gBAAgB,CAAC;YAsBlF,OAAO;CAkDtB;AAiBD;;;;GAIG;AACH,wBAAgB,oBAAoB,IAAI,IAAI,CAc3C;AAED,qFAAqF;AACrF,wBAAgB,mBAAmB,IAAI,gBAAgB,GAAG,SAAS,CAElE"}

package/dist/services/unpaywall/unpaywall-service.js

@@ -10,6 +10,7 @@
 import { serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
 import { fetchWithTimeout, httpErrorFromResponse, logger, requestContextService, } from '@cyanheads/mcp-ts-core/utils';
 import { getServerConfig } from '../../config/server-config.js';
+import { recoveryFor } from '../../services/error-contracts.js';
 import { UNPAYWALL_API_BASE, } from './types.js';
 const USER_AGENT = 'pubmed-mcp-server (+https://github.com/cyanheads/pubmed-mcp-server)';
 /**
@@ -43,7 +44,11 @@ export class UnpaywallService {
         }
         catch (error) {
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Unpaywall request failed: ${msg}`, { doi: normalized }, { cause: error });
+            throw serviceUnavailable(`Unpaywall request failed: ${msg}`, {
+                reason: 'unpaywall_unreachable',
+                doi: normalized,
+                ...recoveryFor('unpaywall_unreachable'),
+            }, { cause: error });
         }
         if (response.status === 404)
             return { kind: 'no-oa', reason: 'DOI unknown to Unpaywall' };
@@ -114,7 +119,7 @@ export class UnpaywallService {
         }
         catch (error) {
             const msg = error instanceof Error ? error.message : String(error);
-            throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { url }, { cause: error });
+            throw serviceUnavailable(`Unpaywall content fetch failed: ${msg}`, { reason: 'unpaywall_unreachable', url, ...recoveryFor('unpaywall_unreachable') }, { cause: error });
         }
         if (!response.ok) {
             throw await httpErrorFromResponse(response, {

package/dist/services/unpaywall/unpaywall-service.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@cyanheads/pubmed-mcp-server",
-  "version": "2.6.8",
+  "version": "2.6.10",
   "mcpName": "io.github.cyanheads/pubmed-mcp-server",
   "description": "MCP server for PubMed/NCBI E-utilities integration. Search articles, fetch metadata and open-access full text (PMC + Unpaywall), generate citations, explore MeSH terms, and discover related research.",
   "type": "module",
@@ -71,7 +71,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.8.19",
+    "@cyanheads/mcp-ts-core": "^0.8.20",
     "defuddle": "^0.18.1",
     "fast-xml-parser": "^5.7.3",
     "linkedom": "^0.18.12",
@@ -80,7 +80,7 @@
     "unpdf": "^1.6.2"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.14",
+    "@biomejs/biome": "^2.4.15",
     "@types/node": "^25.6.2",
     "@types/sanitize-html": "^2.16.1",
     "@vitest/coverage-istanbul": "^4.1.5",

package/server.json

@@ -6,7 +6,7 @@
     "url": "https://github.com/cyanheads/pubmed-mcp-server",
     "source": "github"
   },
-  "version": "2.6.8",
+  "version": "2.6.10",
   "remotes": [
     {
       "type": "streamable-http",
@@ -19,7 +19,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.8",
+      "version": "2.6.10",
       "packageArguments": [
         {
           "type": "positional",
@@ -66,7 +66,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/pubmed-mcp-server",
       "runtimeHint": "bun",
-      "version": "2.6.8",
+      "version": "2.6.10",
       "packageArguments": [
         {
           "type": "positional",

package/dist/mcp-server/tools/definitions/_error-contracts.d.ts

@@ -1,41 +0,0 @@
-/**
- * @fileoverview Shared `errors[]` contract entries for tool definitions.
- *
- * The NCBI service layer (queue, retry loop, deadline) throws three failure
- * modes that any NCBI-consuming tool can surface. They're collected here so
- * tool definitions can spread them into their own `errors[]` without
- * duplicating the contract — keeping the public failure surface consistent
- * and machine-readable across the whole server.
- *
- * Service-layer throws stamp `data.reason` to match these entries (see
- * `src/services/ncbi/request-queue.ts` and `src/services/ncbi/ncbi-service.ts`)
- * so wire payloads carry the same `error.data.reason` clients see from
- * `ctx.fail` in tool handlers.
- *
- * @module src/mcp-server/tools/definitions/_error-contracts
- */
-import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-/**
- * Cross-tool error reasons shared by every tool that calls the NCBI service.
- * Spread these into a tool's `errors[]` alongside any tool-specific entries.
- */
-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 retryable: true;
-}, {
-    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 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;
-}];
-//# sourceMappingURL=_error-contracts.d.ts.map

package/dist/mcp-server/tools/definitions/_error-contracts.d.ts.map

@@ -1 +0,0 @@
-{"version":3,"file":"_error-contracts.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;EAsBtB,CAAC"}

package/dist/mcp-server/tools/definitions/_error-contracts.js

@@ -1,45 +0,0 @@
-/**
- * @fileoverview Shared `errors[]` contract entries for tool definitions.
- *
- * The NCBI service layer (queue, retry loop, deadline) throws three failure
- * modes that any NCBI-consuming tool can surface. They're collected here so
- * tool definitions can spread them into their own `errors[]` without
- * duplicating the contract — keeping the public failure surface consistent
- * and machine-readable across the whole server.
- *
- * Service-layer throws stamp `data.reason` to match these entries (see
- * `src/services/ncbi/request-queue.ts` and `src/services/ncbi/ncbi-service.ts`)
- * so wire payloads carry the same `error.data.reason` clients see from
- * `ctx.fail` in tool handlers.
- *
- * @module src/mcp-server/tools/definitions/_error-contracts
- */
-import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-/**
- * Cross-tool error reasons shared by every tool that calls the NCBI service.
- * Spread these into a tool's `errors[]` alongside any tool-specific entries.
- */
-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.',
-        retryable: true,
-    },
-    {
-        reason: 'ncbi_unreachable',
-        code: JsonRpcErrorCode.ServiceUnavailable,
-        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,
-    },
-    {
-        reason: 'ncbi_deadline_exceeded',
-        code: JsonRpcErrorCode.Timeout,
-        when: 'Total request deadline expired before NCBI returned a response.',
-        recovery: 'Reduce batch size or retry; NCBI may be under temporary load.',
-        retryable: true,
-    },
-];
-//# sourceMappingURL=_error-contracts.js.map

package/dist/mcp-server/tools/definitions/_error-contracts.js.map

@@ -1 +0,0 @@
-{"version":3,"file":"_error-contracts.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/_error-contracts.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;GAeG;AAEH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAEjE;;;GAGG;AACH,MAAM,CAAC,MAAM,mBAAmB,GAAG;IACjC;QACE,MAAM,EAAE,YAAY;QACpB,IAAI,EAAE,gBAAgB,CAAC,WAAW;QAClC,IAAI,EAAE,0CAA0C;QAChD,QAAQ,EAAE,qEAAqE;QAC/E,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,kBAAkB;QAC1B,IAAI,EAAE,gBAAgB,CAAC,kBAAkB;QACzC,IAAI,EAAE,2DAA2D;QACjE,QAAQ,EAAE,4EAA4E;QACtF,SAAS,EAAE,IAAI;KAChB;IACD;QACE,MAAM,EAAE,wBAAwB;QAChC,IAAI,EAAE,gBAAgB,CAAC,OAAO;QAC9B,IAAI,EAAE,iEAAiE;QACvE,QAAQ,EAAE,+DAA+D;QACzE,SAAS,EAAE,IAAI;KAChB;CACO,CAAC"}