@cyanheads/brapi-mcp-server 0.7.11 → 0.7.13

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 (135) hide show
  1. package/AGENTS.md +453 -0
  2. package/CLAUDE.md +24 -16
  3. package/README.md +453 -136
  4. package/changelog/0.7.x/0.7.12.md +35 -0
  5. package/changelog/0.7.x/0.7.13.md +38 -0
  6. package/changelog/template.md +9 -26
  7. package/dist/config/alias-credentials.d.ts +1 -1
  8. package/dist/config/alias-credentials.d.ts.map +1 -1
  9. package/dist/config/alias-credentials.js +24 -8
  10. package/dist/config/alias-credentials.js.map +1 -1
  11. package/dist/config/server-config.d.ts +1 -1
  12. package/dist/config/server-config.d.ts.map +1 -1
  13. package/dist/config/server-config.js +3 -1
  14. package/dist/config/server-config.js.map +1 -1
  15. package/dist/index.js +7 -0
  16. package/dist/index.js.map +1 -1
  17. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts +1 -0
  18. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map +1 -1
  19. package/dist/mcp-server/resources/definitions/brapi-calls.resource.js +2 -1
  20. package/dist/mcp-server/resources/definitions/brapi-calls.resource.js.map +1 -1
  21. package/dist/mcp-server/resources/definitions/brapi-filters.resource.js +1 -1
  22. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts +1 -0
  23. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map +1 -1
  24. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js +2 -1
  25. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js.map +1 -1
  26. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts +1 -0
  27. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map +1 -1
  28. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js +2 -1
  29. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js.map +1 -1
  30. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts +1 -0
  31. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map +1 -1
  32. package/dist/mcp-server/resources/definitions/brapi-study.resource.js +2 -1
  33. package/dist/mcp-server/resources/definitions/brapi-study.resource.js.map +1 -1
  34. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts +1 -0
  35. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts.map +1 -1
  36. package/dist/mcp-server/resources/definitions/brapi-variable.resource.js +2 -1
  37. package/dist/mcp-server/resources/definitions/brapi-variable.resource.js.map +1 -1
  38. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts +2 -0
  39. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js +2 -0
  41. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map +1 -1
  42. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts +1 -0
  43. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map +1 -1
  44. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.js +1 -0
  45. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.js.map +1 -1
  46. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts +1 -0
  47. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map +1 -1
  48. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js +1 -0
  49. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js.map +1 -1
  50. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +1 -0
  51. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map +1 -1
  52. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js +1 -0
  53. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js.map +1 -1
  54. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts +2 -0
  55. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map +1 -1
  56. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js +2 -0
  57. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js.map +1 -1
  58. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts +2 -0
  59. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map +1 -1
  60. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js +2 -0
  61. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js.map +1 -1
  62. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts +2 -0
  63. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map +1 -1
  64. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js +2 -0
  65. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js.map +1 -1
  66. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +2 -0
  67. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -1
  68. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js +2 -0
  69. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map +1 -1
  70. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +2 -0
  71. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -1
  72. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js +2 -0
  73. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js.map +1 -1
  74. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts +2 -0
  75. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map +1 -1
  76. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js +2 -0
  77. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js.map +1 -1
  78. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +2 -0
  79. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -1
  80. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js +2 -0
  81. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map +1 -1
  82. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts +1 -0
  83. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts.map +1 -1
  84. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js +1 -0
  85. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js.map +1 -1
  86. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts +1 -0
  87. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map +1 -1
  88. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js +1 -0
  89. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js.map +1 -1
  90. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts +1 -0
  91. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts.map +1 -1
  92. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js +1 -0
  93. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.js.map +1 -1
  94. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +1 -0
  95. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -1
  96. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js +1 -0
  97. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map +1 -1
  98. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts +1 -0
  99. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts.map +1 -1
  100. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js +1 -0
  101. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.js.map +1 -1
  102. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +1 -0
  103. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map +1 -1
  104. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js +1 -0
  105. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.js.map +1 -1
  106. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +1 -0
  107. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -1
  108. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.js +1 -0
  109. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.js.map +1 -1
  110. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts +1 -0
  111. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts.map +1 -1
  112. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js +1 -0
  113. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map +1 -1
  114. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts +1 -0
  115. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map +1 -1
  116. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js +1 -0
  117. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js.map +1 -1
  118. package/dist/mcp-server/tools/definitions/index.d.ts +28 -0
  119. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  120. package/dist/services/brapi-client/brapi-client.d.ts +7 -0
  121. package/dist/services/brapi-client/brapi-client.d.ts.map +1 -1
  122. package/dist/services/brapi-client/brapi-client.js +21 -12
  123. package/dist/services/brapi-client/brapi-client.js.map +1 -1
  124. package/dist/services/brapi-client/types.d.ts +1 -1
  125. package/dist/services/brapi-dialect/detect.d.ts +1 -1
  126. package/dist/services/brapi-dialect/index.d.ts +2 -2
  127. package/dist/services/brapi-dialect/index.js +1 -1
  128. package/dist/services/capability-registry/capability-registry.d.ts +1 -1
  129. package/dist/services/capability-registry/capability-registry.js +1 -1
  130. package/dist/services/reference-data-cache/reference-data-cache.d.ts +2 -2
  131. package/dist/services/reference-data-cache/reference-data-cache.js +1 -1
  132. package/dist/services/server-registry/types.d.ts +1 -1
  133. package/manifest.json +8 -6
  134. package/package.json +22 -10
  135. package/server.json +9 -3
package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map CHANGED
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package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts CHANGED
@@ -83,5 +83,6 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
83
83
  readonly code: JsonRpcErrorCode.NotFound;
84
84
  readonly when: 'No connection has been registered under the requested alias';
85
85
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.';
86
+ readonly thrownBy: 'service';
86
87
  }], undefined>;
87
88
  //# sourceMappingURL=brapi-walk-pedigree.tool.d.ts.map
package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-walk-pedigree.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;cA0S7H,CAAC"}
1
+ {"version":3,"file":"brapi-walk-pedigree.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;uBAC/G,SAAS;cA0SvB,CAAC"}
package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js CHANGED
@@ -100,6 +100,7 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
100
100
  code: JsonRpcErrorCode.NotFound,
101
101
  when: 'No connection has been registered under the requested alias',
102
102
  recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.',
103
+ thrownBy: 'service',
103
104
  },
104
105
  ],
105
106
  input: z.object({
package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -107,6 +107,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
107
107
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
108
108
  readonly when: 'No connection has been registered under the requested alias';
109
109
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_study.';
110
+ readonly thrownBy: 'service';
110
111
  }, {
111
112
  readonly reason: 'study_not_found';
112
113
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
@@ -160,6 +161,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
160
161
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
161
162
  readonly when: 'No connection has been registered under the requested alias';
162
163
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_export_genotype_matrix.';
164
+ readonly thrownBy: 'service';
163
165
  }, {
164
166
  readonly reason: 'no_filters';
165
167
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -228,11 +230,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
228
230
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
229
231
  readonly when: 'No connection has been registered under the requested alias';
230
232
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_locations.';
233
+ readonly thrownBy: 'service';
231
234
  }, {
232
235
  readonly reason: 'all_filters_dropped';
233
236
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
234
237
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
235
238
  readonly recovery: 'Drop the unsupported filters and rescope by locations, locationNames, countryCodes, locationTypes, abbreviations, or bbox — these filter paths are honored on the active dialect.';
239
+ readonly thrownBy: 'service';
236
240
  }], {
237
241
  readonly totalCount: import("zod").ZodNumber;
238
242
  readonly returnedCount: import("zod").ZodNumber;
@@ -289,11 +293,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
289
293
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
290
294
  readonly when: 'No connection has been registered under the requested alias';
291
295
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variants.';
296
+ readonly thrownBy: 'service';
292
297
  }, {
293
298
  readonly reason: 'all_filters_dropped';
294
299
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
295
300
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
296
301
  readonly recovery: 'Drop the unsupported filters and rescope by variants, variantSets, references, or referenceName + start/end — these filter paths are honored on the active dialect.';
302
+ readonly thrownBy: 'service';
297
303
  }], {
298
304
  readonly totalCount: import("zod").ZodNumber;
299
305
  readonly returnedCount: import("zod").ZodNumber;
@@ -336,6 +342,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
336
342
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
337
343
  readonly when: 'No connection has been registered under the requested alias';
338
344
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_get.';
345
+ readonly thrownBy: 'service';
339
346
  }, {
340
347
  readonly reason: 'cross_origin_path';
341
348
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -482,11 +489,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
482
489
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
483
490
  readonly when: 'No connection has been registered under the requested alias';
484
491
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_build_phenotype_matrix.';
492
+ readonly thrownBy: 'service';
485
493
  }, {
486
494
  readonly reason: 'all_filters_dropped';
487
495
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
488
496
  readonly when: 'The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline';
489
497
  readonly recovery: 'Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.';
498
+ readonly thrownBy: 'service';
490
499
  }, {
491
500
  readonly reason: 'no_observation_path';
492
501
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
@@ -563,6 +572,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
563
572
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
564
573
  readonly when: 'No connection has been registered under the requested alias';
565
574
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_server_info.';
575
+ readonly thrownBy: 'service';
566
576
  }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
567
577
  alias: import("zod").ZodOptional<import("zod").ZodString>;
568
578
  crop: import("zod").ZodOptional<import("zod").ZodString>;
@@ -620,11 +630,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
620
630
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
621
631
  readonly when: 'No connection has been registered under the requested alias';
622
632
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_studies.';
633
+ readonly thrownBy: 'service';
623
634
  }, {
624
635
  readonly reason: 'all_filters_dropped';
625
636
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
626
637
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
627
638
  readonly recovery: 'Drop the unsupported filters and rescope by crop, trialTypes, seasons, programs, trials, studyNames, or active — these filter paths are honored on the active dialect.';
639
+ readonly thrownBy: 'service';
628
640
  }], {
629
641
  readonly totalCount: import("zod").ZodNumber;
630
642
  readonly returnedCount: import("zod").ZodNumber;
@@ -694,11 +706,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
694
706
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
695
707
  readonly when: 'No connection has been registered under the requested alias';
696
708
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_germplasm.';
709
+ readonly thrownBy: 'service';
697
710
  }, {
698
711
  readonly reason: 'all_filters_dropped';
699
712
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
700
713
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
701
714
  readonly recovery: 'Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.';
715
+ readonly thrownBy: 'service';
702
716
  }], {
703
717
  readonly totalCount: import("zod").ZodNumber;
704
718
  readonly returnedCount: import("zod").ZodNumber;
@@ -753,6 +767,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
753
767
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
754
768
  readonly when: 'No connection has been registered under the requested alias';
755
769
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_germplasm.';
770
+ readonly thrownBy: 'service';
756
771
  }, {
757
772
  readonly reason: 'germplasm_not_found';
758
773
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
@@ -831,6 +846,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
831
846
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
832
847
  readonly when: 'No connection has been registered under the requested alias';
833
848
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.';
849
+ readonly thrownBy: 'service';
834
850
  }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
835
851
  alias: import("zod").ZodOptional<import("zod").ZodString>;
836
852
  germplasmDbId: import("zod").ZodString;
@@ -861,6 +877,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
861
877
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
862
878
  readonly when: 'No connection has been registered under the requested alias';
863
879
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.';
880
+ readonly thrownBy: 'service';
864
881
  }, {
865
882
  readonly reason: 'germplasm_not_found';
866
883
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
@@ -942,11 +959,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
942
959
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
943
960
  readonly when: 'No connection has been registered under the requested alias';
944
961
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variables.';
962
+ readonly thrownBy: 'service';
945
963
  }, {
946
964
  readonly reason: 'all_filters_dropped';
947
965
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
948
966
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
949
967
  readonly recovery: 'Drop the unsupported filters and rescope by variables, traitClasses, ontologyDbIds, methodDbIds, scaleDbIds, or text — these filter paths are honored on the active dialect.';
968
+ readonly thrownBy: 'service';
950
969
  }], {
951
970
  readonly totalCount: import("zod").ZodNumber;
952
971
  readonly returnedCount: import("zod").ZodNumber;
@@ -1012,11 +1031,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
1012
1031
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1013
1032
  readonly when: 'No connection has been registered under the requested alias';
1014
1033
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_observations.';
1034
+ readonly thrownBy: 'service';
1015
1035
  }, {
1016
1036
  readonly reason: 'all_filters_dropped';
1017
1037
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
1018
1038
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
1019
1039
  readonly recovery: 'Drop the unsupported filters and rescope by germplasm, variables, observationUnits, observations, seasons, programs, or trials — these filter paths are honored on the active dialect.';
1040
+ readonly thrownBy: 'service';
1020
1041
  }], {
1021
1042
  readonly totalCount: import("zod").ZodNumber;
1022
1043
  readonly returnedCount: import("zod").ZodNumber;
@@ -1079,11 +1100,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
1079
1100
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1080
1101
  readonly when: 'No connection has been registered under the requested alias';
1081
1102
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_images.';
1103
+ readonly thrownBy: 'service';
1082
1104
  }, {
1083
1105
  readonly reason: 'all_filters_dropped';
1084
1106
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
1085
1107
  readonly when: 'The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.';
1086
1108
  readonly recovery: 'Drop the unsupported filters and rescope by images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — these filter paths are honored on the active dialect.';
1109
+ readonly thrownBy: 'service';
1087
1110
  }], {
1088
1111
  readonly totalCount: import("zod").ZodNumber;
1089
1112
  readonly returnedCount: import("zod").ZodNumber;
@@ -1135,6 +1158,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
1135
1158
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1136
1159
  readonly when: 'No connection has been registered under the requested alias';
1137
1160
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_image.';
1161
+ readonly thrownBy: 'service';
1138
1162
  }, {
1139
1163
  readonly reason: 'images_unsupported';
1140
1164
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
@@ -1197,6 +1221,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
1197
1221
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1198
1222
  readonly when: 'No connection has been registered under the requested alias';
1199
1223
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_genotype_calls.';
1224
+ readonly thrownBy: 'service';
1200
1225
  }, {
1201
1226
  readonly reason: 'no_filters';
1202
1227
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -1300,6 +1325,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
1300
1325
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1301
1326
  readonly when: 'No connection has been registered under the requested alias';
1302
1327
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_search.';
1328
+ readonly thrownBy: 'service';
1303
1329
  }, {
1304
1330
  readonly reason: 'search_endpoint_disabled';
1305
1331
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -1364,6 +1390,7 @@ export declare const exportToolDefinitions: import("@cyanheads/mcp-ts-core").Too
1364
1390
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
1365
1391
  readonly when: 'filename contains path separators or traversal segments';
1366
1392
  readonly recovery: 'Provide a filename without "/", "\\", or ".." — leave it unset to use the default.';
1393
+ readonly thrownBy: 'service';
1367
1394
  }, {
1368
1395
  readonly reason: 'mutually_exclusive_projection';
1369
1396
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
@@ -1449,6 +1476,7 @@ export declare const writeToolDefinitions: import("@cyanheads/mcp-ts-core").Tool
1449
1476
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
1450
1477
  readonly when: 'No connection has been registered under the requested alias';
1451
1478
  readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_submit_observations.';
1479
+ readonly thrownBy: 'service';
1452
1480
  }, {
1453
1481
  readonly reason: 'observations_unsupported';
1454
1482
  readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AA4BH;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAuBnC,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;;yDAAuB,CAAC;AAExD;;;;GAIG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;gBAAyB,CAAC;AAE5D,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;gBAA4B,CAAC"}
package/dist/services/brapi-client/brapi-client.d.ts CHANGED
@@ -72,6 +72,13 @@ export declare class BrapiClient {
72
72
  * sleeps `searchPollIntervalMs` and retries until `searchPollTimeoutMs`.
73
73
  */
74
74
  getSearchResults<T>(baseUrl: string, noun: string, searchResultsDbId: string, ctx: Context, options?: BrapiRequestOptions): Promise<BrapiEnvelope<T>>;
75
+ /**
76
+ * `init.signal` lets a `withRetry` caller pass the per-attempt
77
+ * `RetryAttempt.signal` — `AbortSignal.any` over the caller abort and the
78
+ * retry deadline clock — so an expiry firing mid-attempt aborts the request
79
+ * already in flight instead of overshooting it. Callers outside a retry
80
+ * ladder omit it and fall back to the caller signal.
81
+ */
75
82
  private doFetch;
76
83
  private buildUrl;
77
84
  private buildHeaders;
package/dist/services/brapi-client/brapi-client.d.ts.map CHANGED
@@ -1 +1 @@
1
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1
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package/dist/services/brapi-client/brapi-client.js CHANGED
@@ -8,7 +8,7 @@
8
8
  *
9
9
  * @module services/brapi-client/brapi-client
10
10
  */
11
- import { forbidden, internalError, JsonRpcErrorCode, McpError, notFound, rateLimited, serviceUnavailable, unauthorized, validationError, } from '@cyanheads/mcp-ts-core/errors';
11
+ import { forbidden, JsonRpcErrorCode, McpError, notFound, rateLimited, requestCancelled, serviceUnavailable, timeout, unauthorized, validationError, } from '@cyanheads/mcp-ts-core/errors';
12
12
  import { fetchWithTimeout, withRetry } from '@cyanheads/mcp-ts-core/utils';
13
13
  import { DIALECT_ALL_DROPPED_REASON } from './types.js';
14
14
  const defaultFetcher = (url, timeoutMs, context, options) => fetchWithTimeout(url, timeoutMs, context, options);
@@ -30,8 +30,8 @@ export class BrapiClient {
30
30
  */
31
31
  async get(baseUrl, path, ctx, options = {}) {
32
32
  const params = applyDialectToParams(path, options);
33
- return await withRetry(async () => {
34
- const response = await this.doFetch(this.buildUrl(baseUrl, path, params), ctx, { method: 'GET', headers: this.buildHeaders(options.auth) }, options.timeoutMs, options.singleton === true);
33
+ return await withRetry(async ({ signal }) => {
34
+ const response = await this.doFetch(this.buildUrl(baseUrl, path, params), ctx, { method: 'GET', headers: this.buildHeaders(options.auth), signal }, options.timeoutMs, options.singleton === true);
35
35
  return this.parseEnvelope(response);
36
36
  }, {
37
37
  operation: `brapi.get ${path}`,
@@ -47,10 +47,10 @@ export class BrapiClient {
47
47
  * overrides the default `image/*`.
48
48
  */
49
49
  getBinary(baseUrl, path, ctx, options = {}) {
50
- return withRetry(async () => {
50
+ return withRetry(async ({ signal }) => {
51
51
  const headers = this.buildHeaders(options.auth);
52
52
  headers.Accept = options.accept ?? 'image/*';
53
- const response = await this.doFetch(this.buildUrl(baseUrl, path, options.params), ctx, { method: 'GET', headers }, options.timeoutMs);
53
+ const response = await this.doFetch(this.buildUrl(baseUrl, path, options.params), ctx, { method: 'GET', headers, signal }, options.timeoutMs);
54
54
  const buffer = await response.arrayBuffer();
55
55
  const contentType = response.headers.get('Content-Type') ?? 'application/octet-stream';
56
56
  return { bytes: new Uint8Array(buffer), contentType };
@@ -81,7 +81,7 @@ export class BrapiClient {
81
81
  * `searchResultsDbId` the caller must poll via `getSearchResults`.
82
82
  */
83
83
  postSearch(baseUrl, noun, body, ctx, options = {}) {
84
- return withRetry(async () => {
84
+ return withRetry(async ({ signal }) => {
85
85
  const response = await this.doFetch(this.buildUrl(baseUrl, `/search/${noun}`), ctx, {
86
86
  method: 'POST',
87
87
  headers: {
@@ -89,6 +89,7 @@ export class BrapiClient {
89
89
  'Content-Type': 'application/json',
90
90
  },
91
91
  body: JSON.stringify(body),
92
+ signal,
92
93
  }, options.timeoutMs);
93
94
  const envelope = await this.parseEnvelope(response);
94
95
  const asyncId = extractAsyncId(envelope);
@@ -120,7 +121,7 @@ export class BrapiClient {
120
121
  return this.sendJson('PUT', baseUrl, path, body, ctx, options);
121
122
  }
122
123
  sendJson(method, baseUrl, path, body, ctx, options = {}) {
123
- return withRetry(async () => {
124
+ return withRetry(async ({ signal }) => {
124
125
  const response = await this.doFetch(this.buildUrl(baseUrl, path, options.params), ctx, {
125
126
  method,
126
127
  headers: {
@@ -128,6 +129,7 @@ export class BrapiClient {
128
129
  'Content-Type': 'application/json',
129
130
  },
130
131
  body: JSON.stringify(body),
132
+ signal,
131
133
  }, options.timeoutMs);
132
134
  return this.parseEnvelope(response);
133
135
  }, {
@@ -150,13 +152,13 @@ export class BrapiClient {
150
152
  const startedAt = Date.now();
151
153
  for (;;) {
152
154
  if (ctx.signal.aborted) {
153
- throw internalError('Async search polling aborted by caller', {
155
+ throw requestCancelled('Async search polling aborted by caller', {
154
156
  noun,
155
157
  searchResultsDbId,
156
158
  });
157
159
  }
158
160
  if (Date.now() - startedAt > pollTimeoutMs) {
159
- throw serviceUnavailable(`Async search ${noun}/${searchResultsDbId} timed out after ${pollTimeoutMs}ms`, { noun, searchResultsDbId, pollTimeoutMs });
161
+ throw timeout(`Async search ${noun}/${searchResultsDbId} timed out after ${pollTimeoutMs}ms`, { noun, searchResultsDbId, pollTimeoutMs });
160
162
  }
161
163
  const response = await this.doFetch(url, ctx, { method: 'GET', headers: this.buildHeaders(options.auth) }, options.timeoutMs);
162
164
  if (response.status === 202) {
@@ -166,11 +168,18 @@ export class BrapiClient {
166
168
  return this.parseEnvelope(response);
167
169
  }
168
170
  }
171
+ /**
172
+ * `init.signal` lets a `withRetry` caller pass the per-attempt
173
+ * `RetryAttempt.signal` — `AbortSignal.any` over the caller abort and the
174
+ * retry deadline clock — so an expiry firing mid-attempt aborts the request
175
+ * already in flight instead of overshooting it. Callers outside a retry
176
+ * ladder omit it and fall back to the caller signal.
177
+ */
169
178
  async doFetch(url, ctx, init, timeoutMs, singleton = false) {
170
179
  try {
171
180
  return await this.fetcher(url, timeoutMs ?? this.serverConfig.requestTimeoutMs, ctx, {
172
181
  ...init,
173
- signal: ctx.signal,
182
+ signal: init.signal ?? ctx.signal,
174
183
  rejectPrivateIPs: !this.serverConfig.allowPrivateIps,
175
184
  // Every singleton caller catches the not-found and reports it as an
176
185
  // absent record, so a 404 here is an outcome, not an incident — log it
@@ -357,7 +366,7 @@ function extractAsyncId(envelope) {
357
366
  function sleep(ms, ctx) {
358
367
  return new Promise((resolve, reject) => {
359
368
  if (ctx.signal.aborted) {
360
- reject(internalError('Sleep aborted by caller'));
369
+ reject(requestCancelled('Sleep aborted by caller'));
361
370
  return;
362
371
  }
363
372
  const timer = setTimeout(() => {
@@ -366,7 +375,7 @@ function sleep(ms, ctx) {
366
375
  }, ms);
367
376
  const onAbort = () => {
368
377
  clearTimeout(timer);
369
- reject(internalError('Sleep aborted by caller'));
378
+ reject(requestCancelled('Sleep aborted by caller'));
370
379
  };
371
380
  ctx.signal.addEventListener('abort', onAbort, { once: true });
372
381
  });