@cyanheads/pubmed-mcp-server 2.10.12 → 2.10.14

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 (118) hide show
  1. package/AGENTS.md +39 -20
  2. package/CLAUDE.md +39 -20
  3. package/README.md +89 -121
  4. package/changelog/2.0.x/2.0.0.md +32 -0
  5. package/changelog/2.0.x/2.0.1.md +32 -0
  6. package/changelog/2.1.x/2.1.0.md +17 -0
  7. package/changelog/2.1.x/2.1.1.md +29 -0
  8. package/changelog/2.1.x/2.1.2.md +18 -0
  9. package/changelog/2.1.x/2.1.3.md +10 -0
  10. package/changelog/2.1.x/2.1.4.md +12 -0
  11. package/changelog/2.1.x/2.1.5.md +18 -0
  12. package/changelog/2.1.x/2.1.6.md +15 -0
  13. package/changelog/2.10.x/2.10.0.md +17 -0
  14. package/changelog/2.10.x/2.10.1.md +14 -0
  15. package/changelog/2.10.x/2.10.10.md +22 -0
  16. package/changelog/2.10.x/2.10.11.md +21 -0
  17. package/changelog/2.10.x/2.10.12.md +14 -0
  18. package/changelog/2.10.x/2.10.13.md +28 -0
  19. package/changelog/2.10.x/2.10.14.md +28 -0
  20. package/changelog/2.10.x/2.10.2.md +13 -0
  21. package/changelog/2.10.x/2.10.3.md +26 -0
  22. package/changelog/2.10.x/2.10.4.md +11 -0
  23. package/changelog/2.10.x/2.10.5.md +31 -0
  24. package/changelog/2.10.x/2.10.6.md +30 -0
  25. package/changelog/2.10.x/2.10.7.md +17 -0
  26. package/changelog/2.10.x/2.10.8.md +22 -0
  27. package/changelog/2.10.x/2.10.9.md +15 -0
  28. package/changelog/2.2.x/2.2.0.md +67 -0
  29. package/changelog/2.2.x/2.2.1.md +10 -0
  30. package/changelog/2.2.x/2.2.2.md +20 -0
  31. package/changelog/2.2.x/2.2.3.md +17 -0
  32. package/changelog/2.2.x/2.2.4.md +34 -0
  33. package/changelog/2.2.x/2.2.5.md +10 -0
  34. package/changelog/2.2.x/2.2.6.md +17 -0
  35. package/changelog/2.3.x/2.3.0.md +27 -0
  36. package/changelog/2.3.x/2.3.1.md +15 -0
  37. package/changelog/2.3.x/2.3.10.md +20 -0
  38. package/changelog/2.3.x/2.3.11.md +21 -0
  39. package/changelog/2.3.x/2.3.2.md +27 -0
  40. package/changelog/2.3.x/2.3.3.md +38 -0
  41. package/changelog/2.3.x/2.3.4.md +21 -0
  42. package/changelog/2.3.x/2.3.5.md +24 -0
  43. package/changelog/2.3.x/2.3.6.md +26 -0
  44. package/changelog/2.3.x/2.3.7.md +31 -0
  45. package/changelog/2.3.x/2.3.8.md +19 -0
  46. package/changelog/2.3.x/2.3.9.md +22 -0
  47. package/changelog/2.4.x/2.4.0.md +34 -0
  48. package/changelog/2.4.x/2.4.1.md +32 -0
  49. package/changelog/2.5.x/2.5.0.md +35 -0
  50. package/changelog/2.5.x/2.5.1.md +32 -0
  51. package/changelog/2.5.x/2.5.2.md +23 -0
  52. package/changelog/2.5.x/2.5.3.md +22 -0
  53. package/changelog/2.5.x/2.5.5.md +52 -0
  54. package/changelog/2.5.x/2.5.6.md +33 -0
  55. package/changelog/2.6.x/2.6.0.md +32 -0
  56. package/changelog/2.6.x/2.6.1.md +26 -0
  57. package/changelog/2.6.x/2.6.10.md +16 -0
  58. package/changelog/2.6.x/2.6.11.md +24 -0
  59. package/changelog/2.6.x/2.6.12.md +29 -0
  60. package/changelog/2.6.x/2.6.2.md +23 -0
  61. package/changelog/2.6.x/2.6.3.md +17 -0
  62. package/changelog/2.6.x/2.6.4.md +21 -0
  63. package/changelog/2.6.x/2.6.5.md +30 -0
  64. package/changelog/2.6.x/2.6.6.md +25 -0
  65. package/changelog/2.6.x/2.6.7.md +37 -0
  66. package/changelog/2.6.x/2.6.8.md +15 -0
  67. package/changelog/2.6.x/2.6.9.md +36 -0
  68. package/changelog/2.7.x/2.7.0.md +41 -0
  69. package/changelog/2.7.x/2.7.1.md +21 -0
  70. package/changelog/2.7.x/2.7.10.md +13 -0
  71. package/changelog/2.7.x/2.7.11.md +15 -0
  72. package/changelog/2.7.x/2.7.2.md +22 -0
  73. package/changelog/2.7.x/2.7.3.md +18 -0
  74. package/changelog/2.7.x/2.7.4.md +15 -0
  75. package/changelog/2.7.x/2.7.5.md +34 -0
  76. package/changelog/2.7.x/2.7.6.md +14 -0
  77. package/changelog/2.7.x/2.7.7.md +14 -0
  78. package/changelog/2.7.x/2.7.8.md +18 -0
  79. package/changelog/2.7.x/2.7.9.md +16 -0
  80. package/changelog/2.8.x/2.8.0.md +23 -0
  81. package/changelog/2.9.x/2.9.0.md +21 -0
  82. package/changelog/2.9.x/2.9.1.md +12 -0
  83. package/changelog/2.9.x/2.9.10.md +15 -0
  84. package/changelog/2.9.x/2.9.2.md +21 -0
  85. package/changelog/2.9.x/2.9.3.md +11 -0
  86. package/changelog/2.9.x/2.9.4.md +24 -0
  87. package/changelog/2.9.x/2.9.5.md +20 -0
  88. package/changelog/2.9.x/2.9.6.md +22 -0
  89. package/changelog/2.9.x/2.9.7.md +26 -0
  90. package/changelog/2.9.x/2.9.8.md +15 -0
  91. package/changelog/2.9.x/2.9.9.md +35 -0
  92. package/changelog/template.md +151 -0
  93. package/dist/config/server-config.d.ts +4 -4
  94. package/dist/config/server-config.d.ts.map +1 -1
  95. package/dist/config/server-config.js +9 -24
  96. package/dist/config/server-config.js.map +1 -1
  97. package/dist/index.js +1 -0
  98. package/dist/index.js.map +1 -1
  99. package/dist/services/europe-pmc/europe-pmc-service.d.ts.map +1 -1
  100. package/dist/services/europe-pmc/europe-pmc-service.js +3 -10
  101. package/dist/services/europe-pmc/europe-pmc-service.js.map +1 -1
  102. package/dist/services/ncbi/ncbi-service.d.ts +0 -2
  103. package/dist/services/ncbi/ncbi-service.d.ts.map +1 -1
  104. package/dist/services/ncbi/ncbi-service.js +9 -13
  105. package/dist/services/ncbi/ncbi-service.js.map +1 -1
  106. package/dist/services/ncbi/response-handler.d.ts +9 -0
  107. package/dist/services/ncbi/response-handler.d.ts.map +1 -1
  108. package/dist/services/ncbi/response-handler.js +33 -1
  109. package/dist/services/ncbi/response-handler.js.map +1 -1
  110. package/dist/services/openalex/openalex-service.d.ts.map +1 -1
  111. package/dist/services/openalex/openalex-service.js +3 -10
  112. package/dist/services/openalex/openalex-service.js.map +1 -1
  113. package/package.json +23 -12
  114. package/server.json +3 -3
  115. package/dist/services/retry-policy.d.ts +0 -18
  116. package/dist/services/retry-policy.d.ts.map +0 -1
  117. package/dist/services/retry-policy.js +0 -21
  118. package/dist/services/retry-policy.js.map +0 -1
package/dist/services/europe-pmc/europe-pmc-service.js.map CHANGED
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package/dist/services/ncbi/ncbi-service.d.ts CHANGED
@@ -43,8 +43,6 @@ export declare class NcbiService {
43
43
  * Accepts up to 200 IDs in a single request. Only works for articles in PMC.
44
44
  */
45
45
  idConvert(ids: string[], idtype?: string, options?: NcbiCallOptions): Promise<IdConvertRecord[]>;
46
- /** Error codes that are transient and worth retrying with backoff. */
47
- private static readonly RETRYABLE_CODES;
48
46
  /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
49
47
  private static readonly MAX_BACKOFF_MS;
50
48
  /**
package/dist/services/ncbi/ncbi-service.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAeH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAAE,MAAM,uBAAuB,CAAC;AAC5D,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgFpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC,CAIZ;IAED,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CA+BxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;;;;;;;OASG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAmE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CA+E5B;IAED,sEAAsE;IACtE,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,eAAe,CAIpC;IAEH,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAgEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA2BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA8BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
1
+ {"version":3,"file":"ncbi-service.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/ncbi-service.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAcH,OAAO,EAAE,aAAa,EAAE,MAAM,iBAAiB,CAAC;AAChD,OAAO,EAAE,gBAAgB,EAAE,MAAM,oBAAoB,CAAC;AACtD,OAAO,EAAE,mBAAmB,EAA2B,MAAM,uBAAuB,CAAC;AACrF,OAAO,EACL,KAAK,iBAAiB,EACtB,KAAK,eAAe,EAGpB,KAAK,aAAa,EAGlB,KAAK,YAAY,EAEjB,KAAK,cAAc,EACnB,KAAK,eAAe,EAGpB,KAAK,eAAe,EACpB,KAAK,kBAAkB,EACvB,KAAK,iBAAiB,EACtB,KAAK,mBAAmB,EACzB,MAAM,YAAY,CAAC;AAgFpB;;;GAGG;AACH,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,SAAS;IAC1B,OAAO,CAAC,QAAQ,CAAC,KAAK;IACtB,OAAO,CAAC,QAAQ,CAAC,eAAe;IAChC,OAAO,CAAC,QAAQ,CAAC,UAAU;IAC3B,OAAO,CAAC,QAAQ,CAAC,eAAe;IALlC,YACmB,SAAS,EAAE,aAAa,EACxB,KAAK,EAAE,gBAAgB,EACvB,eAAe,EAAE,mBAAmB,EACpC,UAAU,EAAE,MAAM,EAClB,eAAe,EAAE,MAAM,EACtC;IAEE,OAAO,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,aAAa,CAAC,CAoB1F;IAEK,QAAQ,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,cAAc,CAAC,CAO5F;IAED,MAAM,CAAC,CAAC,GAAG;QAAE,gBAAgB,CAAC,EAAE,mBAAmB,CAAA;KAAE,EACnD,MAAM,EAAE,iBAAiB,EACzB,OAAO,GAAE,kBAAuC,GAC/C,OAAO,CAAC,CAAC,CAAC,CAIZ;IAED,KAAK,CAAC,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC/B,MAAM,EAAE,iBAAiB,EACzB,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,CAAC,CAAC,CAKZ;IAEK,MAAM,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,YAAY,CAAC,CA+BxF;IAED,KAAK,CAAC,MAAM,EAAE,iBAAiB,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,OAAO,CAAC,OAAO,CAAC,CAK5E;IAED;;;;;;;;;OASG;IACG,SAAS,CACb,SAAS,EAAE,iBAAiB,EAAE,EAC9B,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CAmE5B;IAED;;;OAGG;IACG,SAAS,CACb,GAAG,EAAE,MAAM,EAAE,EACb,MAAM,CAAC,EAAE,MAAM,EACf,OAAO,CAAC,EAAE,eAAe,GACxB,OAAO,CAAC,eAAe,EAAE,CAAC,CA+E5B;IAED,6FAA6F;IAC7F,OAAO,CAAC,MAAM,CAAC,QAAQ,CAAC,cAAc,CAAU;IAEhD;;;;;OAKG;YACW,eAAe;IAkC7B;;;;;OAKG;YACW,SAAS;IAkEvB;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;CA4BvB;AAMD,qEAAqE;AACrE,wBAAgB,eAAe,IAAI,IAAI,CA8BtC;AAED,mEAAmE;AACnE,wBAAgB,cAAc,IAAI,WAAW,CAG5C"}
package/dist/services/ncbi/ncbi-service.js CHANGED
@@ -5,13 +5,12 @@
5
5
  * @module src/services/ncbi/ncbi-service
6
6
  */
7
7
  import { internalError, JsonRpcErrorCode, McpError, serializationError, timeout, validationError, } from '@cyanheads/mcp-ts-core/errors';
8
- import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
8
+ import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
9
9
  import { getServerConfig } from '../../config/server-config.js';
10
10
  import { recoveryFor } from '../error-contracts.js';
11
- import { isTransient } from '../retry-policy.js';
12
11
  import { NcbiApiClient } from './api-client.js';
13
12
  import { NcbiRequestQueue } from './request-queue.js';
14
- import { NcbiResponseHandler } from './response-handler.js';
13
+ import { NcbiResponseHandler, reclassifyNcbiHttpError } from './response-handler.js';
15
14
  import { NCBI_PMC_IDCONV_URL, } from './types.js';
16
15
  /**
17
16
  * Per-idType expected-format hints surfaced when PMC ID Converter rejects a
@@ -294,12 +293,6 @@ export class NcbiService {
294
293
  }
295
294
  return parsed.records ?? [];
296
295
  }
297
- /** Error codes that are transient and worth retrying with backoff. */
298
- static RETRYABLE_CODES = new Set([
299
- JsonRpcErrorCode.ServiceUnavailable,
300
- JsonRpcErrorCode.Timeout,
301
- JsonRpcErrorCode.RateLimited,
302
- ]);
303
296
  /** Maximum backoff delay per retry (prevents exponential explosion at high retry counts). */
304
297
  static MAX_BACKOFF_MS = 30_000;
305
298
  /**
@@ -350,7 +343,7 @@ export class NcbiService {
350
343
  if (!(error instanceof McpError)) {
351
344
  throw error;
352
345
  }
353
- if (!isTransient(error, NcbiService.RETRYABLE_CODES)) {
346
+ if (!defaultIsTransient(error)) {
354
347
  throw error;
355
348
  }
356
349
  if (attempt < this.maxRetries) {
@@ -371,10 +364,12 @@ export class NcbiService {
371
364
  // RateLimited) keep their original code with no reason — `ncbi_deadline_exceeded`
372
365
  // and `queue_full` are stamped at their own throw sites.
373
366
  const reason = error.code === JsonRpcErrorCode.ServiceUnavailable ? 'ncbi_unreachable' : undefined;
367
+ const ncbiErrors = error.data?.ncbiErrors;
374
368
  throw new McpError(error.code, `${msg} (failed after ${attempts} attempts)`, {
375
369
  ...(reason && { reason, ...recoveryFor(reason) }),
376
370
  endpoint: label,
377
371
  attempts,
372
+ ...(ncbiErrors !== undefined && { ncbiErrors }),
378
373
  }, { cause: error });
379
374
  }
380
375
  }
@@ -395,9 +390,10 @@ export class NcbiService {
395
390
  */
396
391
  performRequest(endpoint, params, options) {
397
392
  return this.runWithDeadline((signal) => this.queue.enqueue(() => this.withRetry(async () => {
398
- const text = await this.apiClient.makeRequest(endpoint, params, {
399
- ...options,
400
- signal,
393
+ const text = await this.apiClient
394
+ .makeRequest(endpoint, params, { ...options, signal })
395
+ .catch((error) => {
396
+ throw reclassifyNcbiHttpError(error, endpoint);
401
397
  });
402
398
  return this.responseHandler.parseAndHandleResponse(text, endpoint, options);
403
399
  }, endpoint, signal), endpoint, params, signal), options?.signal);
package/dist/services/ncbi/ncbi-service.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/ncbi/response-handler.d.ts CHANGED
@@ -5,6 +5,15 @@
5
5
  * @module src/services/ncbi/response-handler
6
6
  */
7
7
  import type { NcbiRequestOptions } from './types.js';
8
+ /**
9
+ * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
10
+ * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
11
+ * response as caller error (400 → InvalidParams), which the retry gate never retries.
12
+ * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
13
+ * Matches the body text rather than parsing it, since the framework captures only a
14
+ * bounded prefix. (#153)
15
+ */
16
+ export declare function reclassifyNcbiHttpError(error: unknown, endpoint: string): unknown;
8
17
  /**
9
18
  * Flattens inline mixed-content markup (`<sup>`, `<sub>`, `<inf>`, `<i>`,
10
19
  * `<b>`, `<u>`, `<sc>`) inside PubMed/MEDLINE XML before fast-xml-parser
package/dist/services/ncbi/response-handler.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAsBH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AA2OrD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAeD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}
1
+ {"version":3,"file":"response-handler.d.ts","sourceRoot":"","sources":["../../../src/services/ncbi/response-handler.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AA2BH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,YAAY,CAAC;AAkGrD;;;;;;;GAOG;AACH,wBAAgB,uBAAuB,CAAC,KAAK,EAAE,OAAO,EAAE,QAAQ,EAAE,MAAM,GAAG,OAAO,CAqBjF;AAsJD;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAMvD;AAeD;;;GAGG;AACH,qBAAa,mBAAmB;IAC9B,OAAO,CAAC,QAAQ,CAAC,SAAS,CAAgB;IAC1C;;;;OAIG;IACH,OAAO,CAAC,QAAQ,CAAC,gBAAgB,CAAgB;IACjD;;;;;;;;;OASG;IACH,OAAO,CAAC,QAAQ,CAAC,iBAAiB,CAAgB;IAElD,cAkBC;IAED;;;;;;;;OAQG;IACH,OAAO,CAAC,cAAc;IA2BtB,wBAAwB,CAAC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAoBrE;IAED,sBAAsB,CAAC,CAAC,EACtB,YAAY,EAAE,MAAM,EACpB,QAAQ,EAAE,MAAM,EAChB,OAAO,CAAC,EAAE,kBAAkB,GAC3B,CAAC,CAsOH;CACF"}
package/dist/services/ncbi/response-handler.js CHANGED
@@ -4,7 +4,7 @@
4
4
  * NCBI's inconsistent XML structures where single-element lists are collapsed to scalars.
5
5
  * @module src/services/ncbi/response-handler
6
6
  */
7
- import { notFound, serializationError, serviceUnavailable } from '@cyanheads/mcp-ts-core/errors';
7
+ import { McpError, notFound, serializationError, serviceUnavailable, } from '@cyanheads/mcp-ts-core/errors';
8
8
  import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
9
9
  /**
10
10
  * fast-xml-parser 5.8.0 marks the in-tree `XMLValidator` as `@deprecated` in
@@ -99,9 +99,41 @@ const ERROR_PATHS = [
99
99
  'eLinkResult.ERROR',
100
100
  'eSearchResult.ERROR',
101
101
  'eSummaryResult.ERROR',
102
+ 'eFetchResult.ERROR',
102
103
  'PubmedArticleSet.ErrorList.CannotRetrievePMID',
103
104
  'ERROR',
104
105
  ];
106
+ /**
107
+ * NCBI `<ERROR>` messages describing a backend failure rather than the request.
108
+ * EFetch sends the viewer-timeout envelope under HTTP 200 and HTTP 400 alike, so
109
+ * the status cannot tell it from a malformed request; the message can. (#153)
110
+ */
111
+ const NCBI_TRANSIENT_ERROR_PATTERNS = [/External viewer error/i, /Status:\s*Timeout/i];
112
+ /** Captures the text of each uppercase `<ERROR>` element in a raw response body. */
113
+ const ERROR_TEXT_REGEX = /<ERROR(?:\s[^>]*)?>([^<]*)<\/ERROR>/g;
114
+ /**
115
+ * Reclassifies an HTTP error from a eutils request whose captured body is an NCBI
116
+ * `<ERROR>` envelope reporting a backend failure. The status-derived code reads such a
117
+ * response as caller error (400 → InvalidParams), which the retry gate never retries.
118
+ * Any other error — including a genuine invalid-parameter 400 — is returned unchanged.
119
+ * Matches the body text rather than parsing it, since the framework captures only a
120
+ * bounded prefix. (#153)
121
+ */
122
+ export function reclassifyNcbiHttpError(error, endpoint) {
123
+ if (!(error instanceof McpError) || typeof error.data?.body !== 'string')
124
+ return error;
125
+ const ncbiErrors = [...error.data.body.matchAll(ERROR_TEXT_REGEX)].map((match) => decodeHtmlEntities(match[1] ?? '').trim());
126
+ if (!ncbiErrors.some((msg) => NCBI_TRANSIENT_ERROR_PATTERNS.some((p) => p.test(msg)))) {
127
+ return error;
128
+ }
129
+ return serviceUnavailable(`NCBI API Error: ${ncbiErrors.join('; ')}`, {
130
+ reason: 'ncbi_unreachable',
131
+ endpoint,
132
+ status: error.data.status,
133
+ ncbiErrors,
134
+ ...recoveryFor('ncbi_unreachable'),
135
+ }, { cause: error });
136
+ }
105
137
  /**
106
138
  * NCBI error messages indicating the requested record doesn't exist (permanent
107
139
  * failure). Throwing NotFound for these prevents the retry loop from hammering
package/dist/services/ncbi/response-handler.js.map CHANGED
@@ -1 +1 @@
1
- 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1
+ 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package/dist/services/openalex/openalex-service.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAQH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AAmFpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
1
+ {"version":3,"file":"openalex-service.d.ts","sourceRoot":"","sources":["../../../src/services/openalex/openalex-service.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAOH,OAAO,EAAE,iBAAiB,EAAE,MAAM,iBAAiB,CAAC;AACpD,OAAO,EAIL,KAAK,qBAAqB,EAE3B,MAAM,YAAY,CAAC;AA4EpB,gFAAgF;AAChF,qBAAa,eAAe;IAExB,OAAO,CAAC,QAAQ,CAAC,MAAM;IACvB,OAAO,CAAC,QAAQ,CAAC,UAAU;IAF7B,YACmB,MAAM,EAAE,iBAAiB,EACzB,UAAU,EAAE,MAAM,EACjC;IAEJ;;;;OAIG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW3F;IAED;;;;;;;;OAQG;IACG,OAAO,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CA4B3F;IAED;;;OAGG;IACG,UAAU,CAAC,IAAI,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,WAAW,GAAG,OAAO,CAAC,qBAAqB,CAAC,CAW9F;IAED,8EAA8E;IAC9E,OAAO,CAAC,SAAS;IAQjB;;;;;;;;;OASG;YACW,iBAAiB;IAiC/B;;;;OAIG;IACH,OAAO,CAAC,MAAM;IAcd,8EAA8E;YAChE,SAAS;CAmDxB;AAMD,yEAAyE;AACzE,wBAAgB,mBAAmB,IAAI,IAAI,CAmB1C;AAED,uEAAuE;AACvE,wBAAgB,kBAAkB,IAAI,eAAe,CAIpD;AAED,kFAAkF;AAClF,wBAAgB,0BAA0B,IAAI,eAAe,GAAG,SAAS,CAExE"}
package/dist/services/openalex/openalex-service.js CHANGED
@@ -17,19 +17,12 @@
17
17
  *
18
18
  * @module src/services/openalex/openalex-service
19
19
  */
20
- import { internalError, JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
21
- import { logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
20
+ import { internalError, McpError } from '@cyanheads/mcp-ts-core/errors';
21
+ import { defaultIsTransient, logger, requestContextService } from '@cyanheads/mcp-ts-core/utils';
22
22
  import { getServerConfig } from '../../config/server-config.js';
23
23
  import { recoveryFor } from '../error-contracts.js';
24
- import { isTransient } from '../retry-policy.js';
25
24
  import { OpenAlexApiClient } from './api-client.js';
26
25
  import { OPENALEX_MAX_FILTER_VALUES, OPENALEX_MAX_PAGE_SIZE, OPENALEX_MAX_UPSTREAM_REQUESTS, } from './types.js';
27
- /** Transient codes eligible for retry. */
28
- const RETRYABLE_CODES = new Set([
29
- JsonRpcErrorCode.ServiceUnavailable,
30
- JsonRpcErrorCode.Timeout,
31
- JsonRpcErrorCode.RateLimited,
32
- ]);
33
26
  const MAX_BACKOFF_MS = 30_000;
34
27
  /** Strip the `https://openalex.org/` prefix an OA ID may carry. */
35
28
  function bareOaId(id) {
@@ -218,7 +211,7 @@ export class OpenAlexService {
218
211
  throw signal.reason;
219
212
  if (!(error instanceof McpError))
220
213
  throw error;
221
- if (!isTransient(error, RETRYABLE_CODES))
214
+ if (!defaultIsTransient(error))
222
215
  throw error;
223
216
  if (attempt < this.maxRetries) {
224
217
  const baseDelay = Math.min(1000 * 2 ** attempt, MAX_BACKOFF_MS);
package/dist/services/openalex/openalex-service.js.map CHANGED
@@ -1 +1 @@
1
- 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package/package.json CHANGED
@@ -1,6 +1,6 @@
1
1
  {
2
2
  "name": "@cyanheads/pubmed-mcp-server",
3
- "version": "2.10.12",
3
+ "version": "2.10.14",
4
4
  "mcpName": "io.github.cyanheads/pubmed-mcp-server",
5
5
  "description": "Search PubMed/Europe PMC, fetch articles and full text (PMC/EPMC/Unpaywall), citations, MeSH terms via MCP. STDIO or Streamable HTTP.",
6
6
  "type": "module",
@@ -9,7 +9,16 @@
9
9
  "bin": {
10
10
  "pubmed-mcp-server": "dist/index.js"
11
11
  },
12
- "files": ["dist/", "README.md", "LICENSE", "CLAUDE.md", "AGENTS.md", "Dockerfile", "server.json"],
12
+ "files": [
13
+ "changelog/",
14
+ "dist/",
15
+ "README.md",
16
+ "LICENSE",
17
+ "CLAUDE.md",
18
+ "AGENTS.md",
19
+ "Dockerfile",
20
+ "server.json"
21
+ ],
13
22
  "scripts": {
14
23
  "build": "bun run scripts/build.ts",
15
24
  "rebuild": "bun run scripts/clean.ts && bun run build",
@@ -19,6 +28,8 @@
19
28
  "format": "biome check --write .",
20
29
  "format:unsafe": "biome check --write --unsafe .",
21
30
  "test": "bunx vitest run",
31
+ "test:coverage": "bunx vitest run --coverage",
32
+ "audit:fix": "bun audit fix",
22
33
  "audit:refresh": "rm -f bun.lock && bun install && bun audit",
23
34
  "list-skills": "bun run scripts/list-skills.ts",
24
35
  "lint:mcp": "bun run scripts/lint-mcp.ts",
@@ -74,34 +85,34 @@
74
85
  "license": "Apache-2.0",
75
86
  "packageManager": "bun@1.4.0",
76
87
  "engines": {
77
- "bun": ">=1.3.0",
88
+ "bun": ">=1.4.0",
78
89
  "node": ">=24.0.0"
79
90
  },
80
91
  "publishConfig": {
81
92
  "access": "public"
82
93
  },
83
94
  "dependencies": {
84
- "@cyanheads/mcp-ts-core": "^0.12.8",
95
+ "@cyanheads/mcp-ts-core": "^0.13.4",
85
96
  "defuddle": "^0.19.3",
86
97
  "fast-xml-parser": "^5.11.1",
87
98
  "linkedom": "^0.18.13",
88
99
  "pino-pretty": "^13.1.3",
89
100
  "sanitize-html": "^2.17.7",
90
101
  "unpdf": "^1.8.1",
91
- "zod": "^4.5.4"
102
+ "zod": "^4.6.5"
92
103
  },
93
104
  "devDependencies": {
94
- "@biomejs/biome": "^2.5.12",
105
+ "@biomejs/biome": "^2.5.13",
95
106
  "@socketsecurity/bun-security-scanner": "^1.1.2",
96
- "@types/node": "^26.4.1",
107
+ "@types/node": "^26.5.1",
97
108
  "@types/sanitize-html": "^2.16.1",
98
- "@vitest/coverage-istanbul": "^5.0.0",
109
+ "@vitest/coverage-istanbul": "^5.0.1",
99
110
  "depcheck": "^1.4.7",
100
- "fast-check": "^4.9.0",
101
- "ignore": "^7.0.8",
102
- "tsc-alias": "^1.9.4",
111
+ "fast-check": "^4.10.0",
112
+ "ignore": "^7.0.9",
113
+ "tsc-alias": "^1.9.5",
103
114
  "typescript": "^7.0.2",
104
- "vitest": "^5.0.0"
115
+ "vitest": "^5.0.1"
105
116
  },
106
117
  "overrides": {
107
118
  "@hono/node-server": "^2.0.11",
package/server.json CHANGED
@@ -6,7 +6,7 @@
6
6
  "url": "https://github.com/cyanheads/pubmed-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "2.10.12",
9
+ "version": "2.10.14",
10
10
  "remotes": [
11
11
  {
12
12
  "type": "streamable-http",
@@ -19,7 +19,7 @@
19
19
  "registryBaseUrl": "https://registry.npmjs.org",
20
20
  "identifier": "@cyanheads/pubmed-mcp-server",
21
21
  "runtimeHint": "bun",
22
- "version": "2.10.12",
22
+ "version": "2.10.14",
23
23
  "packageArguments": [
24
24
  {
25
25
  "type": "positional",
@@ -66,7 +66,7 @@
66
66
  "registryBaseUrl": "https://registry.npmjs.org",
67
67
  "identifier": "@cyanheads/pubmed-mcp-server",
68
68
  "runtimeHint": "bun",
69
- "version": "2.10.12",
69
+ "version": "2.10.14",
70
70
  "packageArguments": [
71
71
  {
72
72
  "type": "positional",
package/dist/services/retry-policy.d.ts DELETED
@@ -1,18 +0,0 @@
1
- /**
2
- * @fileoverview Shared transience check for the hand-rolled retry loops in the NCBI,
3
- * OpenAlex, and Europe PMC services. Mirrors the framework's `defaultIsTransient`
4
- * (`withRetry`, `@cyanheads/mcp-ts-core/utils`) so the three gates classify identically
5
- * to the framework path they don't use.
6
- * @module src/services/retry-policy
7
- */
8
- import type { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
9
- /**
10
- * Whether a thrown `McpError` should be retried. An explicit `data.retryable === false`
11
- * opt-out wins over code-based classification; absent (or `true`) the code decides.
12
- *
13
- * The HTTP helpers stamp the opt-out on an upstream 501, which classifies as
14
- * `ServiceUnavailable` — a transient code — but re-asks for a method the upstream has
15
- * declared absent, so it must fail on the first attempt.
16
- */
17
- export declare function isTransient(error: McpError, transientCodes: ReadonlySet<JsonRpcErrorCode>): boolean;
18
- //# sourceMappingURL=retry-policy.d.ts.map
package/dist/services/retry-policy.d.ts.map DELETED
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package/dist/services/retry-policy.js DELETED
@@ -1,21 +0,0 @@
1
- /**
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- * @fileoverview Shared transience check for the hand-rolled retry loops in the NCBI,
3
- * OpenAlex, and Europe PMC services. Mirrors the framework's `defaultIsTransient`
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- * (`withRetry`, `@cyanheads/mcp-ts-core/utils`) so the three gates classify identically
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- * to the framework path they don't use.
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- * @module src/services/retry-policy
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- */
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- /**
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- * Whether a thrown `McpError` should be retried. An explicit `data.retryable === false`
10
- * opt-out wins over code-based classification; absent (or `true`) the code decides.
11
- *
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- * The HTTP helpers stamp the opt-out on an upstream 501, which classifies as
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- * `ServiceUnavailable` — a transient code — but re-asks for a method the upstream has
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- * declared absent, so it must fail on the first attempt.
15
- */
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- export function isTransient(error, transientCodes) {
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- if (error.data?.retryable === false)
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- return false;
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- return transientCodes.has(error.code);
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- }
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- //# sourceMappingURL=retry-policy.js.map
package/dist/services/retry-policy.js.map DELETED
@@ -1 +0,0 @@
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