@cyanheads/brapi-mcp-server 0.7.10 → 0.7.11

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 (99) hide show
  1. package/CLAUDE.md +18 -13
  2. package/Dockerfile +19 -5
  3. package/README.md +6 -3
  4. package/changelog/0.7.x/0.7.11.md +43 -0
  5. package/changelog/template.md +55 -16
  6. package/dist/config/alias-credentials.js.map +1 -1
  7. package/dist/config/builtin-aliases.js.map +1 -1
  8. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts +3 -3
  9. package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map +1 -1
  10. package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts +3 -3
  11. package/dist/mcp-server/resources/definitions/brapi-filters.resource.d.ts.map +1 -1
  12. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts +6 -6
  13. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map +1 -1
  14. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts +3 -3
  15. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map +1 -1
  16. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts +6 -6
  17. package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map +1 -1
  18. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts +6 -6
  19. package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts.map +1 -1
  20. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts +19 -14
  21. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js +34 -0
  23. package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map +1 -1
  24. package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts +12 -12
  25. package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -1
  26. package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts +2 -2
  27. package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map +1 -1
  28. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts +14 -14
  29. package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map +1 -1
  30. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts +9 -4
  31. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map +1 -1
  32. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js +31 -0
  33. package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js.map +1 -1
  34. package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts +6 -6
  35. package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map +1 -1
  36. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts +11 -11
  37. package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map +1 -1
  38. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +11 -11
  39. package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map +1 -1
  40. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts +6 -6
  41. package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map +1 -1
  42. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts +6 -6
  43. package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map +1 -1
  44. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts +6 -6
  45. package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map +1 -1
  46. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +6 -6
  47. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -1
  48. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +6 -6
  49. package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -1
  50. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts +7 -7
  51. package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map +1 -1
  52. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +6 -6
  53. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -1
  54. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts +6 -6
  55. package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts.map +1 -1
  56. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts +6 -6
  57. package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map +1 -1
  58. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts +6 -6
  59. package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts.map +1 -1
  60. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +6 -6
  61. package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -1
  62. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts +6 -6
  63. package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts.map +1 -1
  64. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +7 -7
  65. package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map +1 -1
  66. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +9 -9
  67. package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -1
  68. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts +23 -27
  69. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts.map +1 -1
  70. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js +41 -55
  71. package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map +1 -1
  72. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts +8 -8
  73. package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map +1 -1
  74. package/dist/mcp-server/tools/definitions/index.d.ts +829 -824
  75. package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
  76. package/dist/mcp-server/tools/shared/find-helpers.js.map +1 -1
  77. package/dist/mcp-server/tools/shared/observations.js.map +1 -1
  78. package/dist/mcp-server/tools/shared/orientation-envelope.d.ts +12 -12
  79. package/dist/services/brapi-client/brapi-client.d.ts +2 -3
  80. package/dist/services/brapi-client/brapi-client.d.ts.map +1 -1
  81. package/dist/services/brapi-client/brapi-client.js +11 -14
  82. package/dist/services/brapi-client/brapi-client.js.map +1 -1
  83. package/dist/services/brapi-client/types.d.ts +1 -1
  84. package/dist/services/brapi-dialect/detect.js.map +1 -1
  85. package/dist/services/brapi-dialect/index.js.map +1 -1
  86. package/dist/services/canvas-bridge/canvas-bridge.d.ts +1 -1
  87. package/dist/services/canvas-bridge/canvas-bridge.d.ts.map +1 -1
  88. package/dist/services/canvas-bridge/canvas-bridge.js.map +1 -1
  89. package/dist/services/capability-registry/capability-registry.d.ts.map +1 -1
  90. package/dist/services/capability-registry/capability-registry.js.map +1 -1
  91. package/dist/services/ontology-resolver/ontology-resolver.d.ts.map +1 -1
  92. package/dist/services/ontology-resolver/ontology-resolver.js.map +1 -1
  93. package/dist/services/reference-data-cache/reference-data-cache.d.ts.map +1 -1
  94. package/dist/services/reference-data-cache/reference-data-cache.js.map +1 -1
  95. package/dist/services/server-registry/server-registry.d.ts.map +1 -1
  96. package/dist/services/server-registry/server-registry.js.map +1 -1
  97. package/manifest.json +1 -1
  98. package/package.json +11 -11
  99. package/server.json +3 -3
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4W7B,CAAC"}
1
+ {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,gMAAgM;;;;;;;;EA2VtM,CAAC"}
@@ -59,15 +59,15 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
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  totalCount: z.ZodOptional<z.ZodNumber>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>, readonly [{
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- readonly reason: "unknown_alias";
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+ readonly reason: 'unknown_alias';
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  readonly code: JsonRpcErrorCode.NotFound;
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- readonly when: "No connection has been registered under the requested alias";
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- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_images.";
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+ readonly when: 'No connection has been registered under the requested alias';
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+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_images.';
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  }, {
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- readonly reason: "all_filters_dropped";
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+ readonly reason: 'all_filters_dropped';
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  readonly code: JsonRpcErrorCode.ValidationError;
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- 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.";
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- 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.";
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+ 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.';
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+ 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.';
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  }], {
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  readonly totalCount: z.ZodNumber;
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  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAoS1B,CAAC"}
1
+ {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMd,eAAe;;mBAEjB,6DAA6D;uBAEjE,qHAAqH;;qBAG/G,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,6MAA6M;;;;;;;;EAmRnN,CAAC"}
@@ -63,15 +63,15 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
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  swapped: "swapped";
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  }>;
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  }, z.core.$strip>, readonly [{
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- readonly reason: "unknown_alias";
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+ readonly reason: 'unknown_alias';
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  readonly code: JsonRpcErrorCode.NotFound;
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- readonly when: "No connection has been registered under the requested alias";
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- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_locations.";
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+ readonly when: 'No connection has been registered under the requested alias';
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+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_locations.';
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  }, {
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- readonly reason: "all_filters_dropped";
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+ readonly reason: 'all_filters_dropped';
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  readonly code: JsonRpcErrorCode.ValidationError;
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- 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.";
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- 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.";
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+ 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.';
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+ 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.';
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  }], {
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  readonly totalCount: z.ZodNumber;
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  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmY7B,CAAC"}
1
+ {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,mLAAmL;;;;;;;;EAkXzL,CAAC"}
@@ -63,15 +63,15 @@ export declare const brapiFindObservations: import("@cyanheads/mcp-ts-core").Too
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  totalCount: z.ZodOptional<z.ZodNumber>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>, readonly [{
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- readonly reason: "unknown_alias";
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+ readonly reason: 'unknown_alias';
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  readonly code: JsonRpcErrorCode.NotFound;
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- readonly when: "No connection has been registered under the requested alias";
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- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_observations.";
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+ readonly when: 'No connection has been registered under the requested alias';
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+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_observations.';
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  }, {
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- readonly reason: "all_filters_dropped";
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+ readonly reason: 'all_filters_dropped';
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  readonly code: JsonRpcErrorCode.ValidationError;
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- 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.";
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- 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.";
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+ 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.';
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+ 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.';
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  }], {
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  readonly totalCount: z.ZodNumber;
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  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+JjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkXhC,CAAC"}
1
+ {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA+JjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMpB,eAAe;;mBAEjB,6DAA6D;uBAEjE,2HAA2H;;qBAGrH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,wLAAwL;;;;;;;;EAiW9L,CAAC"}
@@ -62,15 +62,15 @@ export declare const brapiFindStudies: import("@cyanheads/mcp-ts-core").ToolDefi
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  totalCount: z.ZodOptional<z.ZodNumber>;
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  }, z.core.$strip>>;
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  }, z.core.$strip>, readonly [{
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- readonly reason: "unknown_alias";
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+ readonly reason: 'unknown_alias';
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  readonly code: JsonRpcErrorCode.NotFound;
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- readonly when: "No connection has been registered under the requested alias";
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- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_studies.";
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+ readonly when: 'No connection has been registered under the requested alias';
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+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_studies.';
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  }, {
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- readonly reason: "all_filters_dropped";
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+ readonly reason: 'all_filters_dropped';
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  readonly code: JsonRpcErrorCode.ValidationError;
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- 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.";
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- 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.";
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+ 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.';
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+ 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.';
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  }], {
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  readonly totalCount: z.ZodNumber;
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  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyHjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAsS3B,CAAC"}
1
+ {"version":3,"file":"brapi-find-studies.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-studies.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyHjE,eAAO,MAAM,gBAAgB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMf,eAAe;;mBAEjB,6DAA6D;uBAEjE,sHAAsH;;qBAGhH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,wKAAwK;;;;;;;;EAqR9K,CAAC"}
@@ -63,8 +63,8 @@ export declare const brapiFindVariables: import("@cyanheads/mcp-ts-core").ToolDe
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  synonyms: z.ZodOptional<z.ZodArray<z.ZodString>>;
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  ontologyDbId: z.ZodOptional<z.ZodString>;
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  source: z.ZodEnum<{
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- puiMatch: "puiMatch";
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  nameMatch: "nameMatch";
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+ puiMatch: "puiMatch";
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  synonymMatch: "synonymMatch";
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  traitClassMatch: "traitClassMatch";
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  }>;
@@ -81,15 +81,15 @@ export declare const brapiFindVariables: import("@cyanheads/mcp-ts-core").ToolDe
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  totalCount: z.ZodOptional<z.ZodNumber>;
82
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  }, z.core.$strip>>;
83
83
  }, z.core.$strip>, readonly [{
84
- readonly reason: "unknown_alias";
84
+ readonly reason: 'unknown_alias';
85
85
  readonly code: JsonRpcErrorCode.NotFound;
86
- readonly when: "No connection has been registered under the requested alias";
87
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variables.";
86
+ readonly when: 'No connection has been registered under the requested alias';
87
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variables.';
88
88
  }, {
89
- readonly reason: "all_filters_dropped";
89
+ readonly reason: 'all_filters_dropped';
90
90
  readonly code: JsonRpcErrorCode.ValidationError;
91
- 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.";
92
- 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.";
91
+ 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.';
92
+ 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.';
93
93
  }], {
94
94
  readonly totalCount: z.ZodNumber;
95
95
  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW7B,CAAC"}
1
+ {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsKjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMjB,eAAe;;mBAEjB,6DAA6D;uBAEjE,wHAAwH;;qBAGlH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,8KAA8K;;;;;;;;EAuVpL,CAAC"}
@@ -53,15 +53,15 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
53
53
  totalCount: z.ZodOptional<z.ZodNumber>;
54
54
  }, z.core.$strip>>;
55
55
  }, z.core.$strip>, readonly [{
56
- readonly reason: "unknown_alias";
56
+ readonly reason: 'unknown_alias';
57
57
  readonly code: JsonRpcErrorCode.NotFound;
58
- readonly when: "No connection has been registered under the requested alias";
59
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variants.";
58
+ readonly when: 'No connection has been registered under the requested alias';
59
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_variants.';
60
60
  }, {
61
- readonly reason: "all_filters_dropped";
61
+ readonly reason: 'all_filters_dropped';
62
62
  readonly code: JsonRpcErrorCode.ValidationError;
63
- 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.";
64
- 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.";
63
+ 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.';
64
+ 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.';
65
65
  }], {
66
66
  readonly totalCount: z.ZodNumber;
67
67
  readonly returnedCount: z.ZodNumber;
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4P5B,CAAC"}
1
+ {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;;qBAGjH,qBAAqB;;mBAEvB,mNAAmN;uBAEvN,qKAAqK;;;;;;;;EA2O3K,CAAC"}
@@ -48,14 +48,14 @@ export declare const brapiGermplasmPerformance: import("@cyanheads/mcp-ts-core")
48
48
  }, z.core.$strip>>;
49
49
  warnings: z.ZodArray<z.ZodString>;
50
50
  }, z.core.$strip>, readonly [{
51
- readonly reason: "unknown_alias";
51
+ readonly reason: 'unknown_alias';
52
52
  readonly code: JsonRpcErrorCode.NotFound;
53
- readonly when: "No connection has been registered under the requested alias";
54
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.";
53
+ readonly when: 'No connection has been registered under the requested alias';
54
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.';
55
55
  }, {
56
- readonly reason: "germplasm_not_found";
56
+ readonly reason: 'germplasm_not_found';
57
57
  readonly code: JsonRpcErrorCode.NotFound;
58
- readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
59
- readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
58
+ readonly when: 'Upstream returned no germplasm record for the requested germplasmDbId';
59
+ readonly recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.';
60
60
  }], undefined>;
61
61
  //# sourceMappingURL=brapi-germplasm-performance.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-germplasm-performance.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-germplasm-performance.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2LpC,CAAC"}
1
+ {"version":3,"file":"brapi-germplasm-performance.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-germplasm-performance.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMxB,eAAe;;mBAEjB,6DAA6D;uBAEjE,+HAA+H;;qBAGzH,qBAAqB;;mBAEvB,uEAAuE;uBAE3E,mGAAmG;cA0KzG,CAAC"}
@@ -51,14 +51,14 @@ export declare const brapiGetGermplasm: import("@cyanheads/mcp-ts-core").ToolDef
51
51
  directDescendantCount: z.ZodOptional<z.ZodNumber>;
52
52
  warnings: z.ZodArray<z.ZodString>;
53
53
  }, z.core.$strip>, readonly [{
54
- readonly reason: "unknown_alias";
54
+ readonly reason: 'unknown_alias';
55
55
  readonly code: JsonRpcErrorCode.NotFound;
56
- readonly when: "No connection has been registered under the requested alias";
57
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_germplasm.";
56
+ readonly when: 'No connection has been registered under the requested alias';
57
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_germplasm.';
58
58
  }, {
59
- readonly reason: "germplasm_not_found";
59
+ readonly reason: 'germplasm_not_found';
60
60
  readonly code: JsonRpcErrorCode.NotFound;
61
- readonly when: "Upstream returned no germplasm record for the requested DbId";
62
- readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
61
+ readonly when: 'Upstream returned no germplasm record for the requested DbId';
62
+ readonly recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.';
63
63
  }], undefined>;
64
64
  //# sourceMappingURL=brapi-get-germplasm.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2P5B,CAAC"}
1
+ {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMhB,eAAe;;mBAEjB,6DAA6D;uBAEjE,uHAAuH;;qBAGjH,qBAAqB;;mBAEvB,8DAA8D;uBAElE,mGAAmG;cA0OzG,CAAC"}
@@ -49,14 +49,14 @@ export declare const brapiGetImage: import("@cyanheads/mcp-ts-core").ToolDefinit
49
49
  warning: z.ZodString;
50
50
  }, z.core.$strip>>;
51
51
  }, z.core.$strip>, readonly [{
52
- readonly reason: "unknown_alias";
52
+ readonly reason: 'unknown_alias';
53
53
  readonly code: JsonRpcErrorCode.NotFound;
54
- readonly when: "No connection has been registered under the requested alias";
55
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_image.";
54
+ readonly when: 'No connection has been registered under the requested alias';
55
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_image.';
56
56
  }, {
57
- readonly reason: "images_unsupported";
57
+ readonly reason: 'images_unsupported';
58
58
  readonly code: JsonRpcErrorCode.NotFound;
59
- readonly when: "BrAPI server does not advertise /images in /serverinfo";
60
- readonly recovery: "Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /images.";
59
+ readonly when: 'BrAPI server does not advertise /images in /serverinfo';
60
+ readonly recovery: 'Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /images.';
61
61
  }], undefined>;
62
62
  //# sourceMappingURL=brapi-get-image.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-get-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-image.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAiKxB,CAAC"}
1
+ {"version":3,"file":"brapi-get-image.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-image.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiFjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAKZ,eAAe;;mBAEjB,6DAA6D;uBAEjE,mHAAmH;;qBAG7G,oBAAoB;;mBAEtB,wDAAwD;uBAE5D,4IAA4I;cAiJlJ,CAAC"}
@@ -68,14 +68,14 @@ export declare const brapiGetStudy: import("@cyanheads/mcp-ts-core").ToolDefinit
68
68
  variableCount: z.ZodOptional<z.ZodNumber>;
69
69
  warnings: z.ZodArray<z.ZodString>;
70
70
  }, z.core.$strip>, readonly [{
71
- readonly reason: "unknown_alias";
71
+ readonly reason: 'unknown_alias';
72
72
  readonly code: JsonRpcErrorCode.NotFound;
73
- readonly when: "No connection has been registered under the requested alias";
74
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_study.";
73
+ readonly when: 'No connection has been registered under the requested alias';
74
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_get_study.';
75
75
  }, {
76
- readonly reason: "study_not_found";
76
+ readonly reason: 'study_not_found';
77
77
  readonly code: JsonRpcErrorCode.NotFound;
78
- readonly when: "Upstream returned no study record for the requested DbId";
79
- readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
78
+ readonly when: 'Upstream returned no study record for the requested DbId';
79
+ readonly recovery: 'Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.';
80
80
  }], undefined>;
81
81
  //# sourceMappingURL=brapi-get-study.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmJjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8QxB,CAAC"}
1
+ {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmJjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMZ,eAAe;;mBAEjB,6DAA6D;uBAEjE,mHAAmH;;qBAG7G,iBAAiB;;mBAEnB,0DAA0D;uBAE9D,6FAA6F;cA6PnG,CAAC"}
@@ -44,14 +44,14 @@ export declare const brapiRawGet: import("@cyanheads/mcp-ts-core").ToolDefinitio
44
44
  totalCount: z.ZodOptional<z.ZodNumber>;
45
45
  }, z.core.$strip>>;
46
46
  }, z.core.$strip>, readonly [{
47
- readonly reason: "unknown_alias";
47
+ readonly reason: 'unknown_alias';
48
48
  readonly code: JsonRpcErrorCode.NotFound;
49
- readonly when: "No connection has been registered under the requested alias";
50
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_get.";
49
+ readonly when: 'No connection has been registered under the requested alias';
50
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_get.';
51
51
  }, {
52
- readonly reason: "cross_origin_path";
52
+ readonly reason: 'cross_origin_path';
53
53
  readonly code: JsonRpcErrorCode.ValidationError;
54
- readonly when: "path argument was a full URL instead of a relative BrAPI route";
55
- readonly recovery: "Pass a path like \"/samples\" or \"/methods\" — the connection alias supplies the baseUrl.";
54
+ readonly when: 'path argument was a full URL instead of a relative BrAPI route';
55
+ readonly recovery: 'Pass a path like "/samples" or "/methods" — the connection alias supplies the baseUrl.';
56
56
  }], undefined>;
57
57
  //# sourceMappingURL=brapi-raw-get.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-raw-get.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-get.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAuDjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoItB,CAAC"}
1
+ {"version":3,"file":"brapi-raw-get.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-get.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAuDjE,eAAO,MAAM,WAAW;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMV,eAAe;;mBAEjB,6DAA6D;uBAEjE,iHAAiH;;qBAG3G,mBAAmB;;mBAErB,gEAAgE;uBAEpE,wFAAwF;cAmH9F,CAAC"}
@@ -21,8 +21,8 @@ export declare const brapiRawSearch: import("@cyanheads/mcp-ts-core").ToolDefini
21
21
  alias: z.ZodString;
22
22
  noun: z.ZodString;
23
23
  kind: z.ZodEnum<{
24
- sync: "sync";
25
24
  async: "async";
25
+ sync: "sync";
26
26
  }>;
27
27
  searchResultsDbId: z.ZodOptional<z.ZodString>;
28
28
  metadata: z.ZodObject<{
@@ -47,14 +47,14 @@ export declare const brapiRawSearch: import("@cyanheads/mcp-ts-core").ToolDefini
47
47
  totalCount: z.ZodOptional<z.ZodNumber>;
48
48
  }, z.core.$strip>>;
49
49
  }, z.core.$strip>, readonly [{
50
- readonly reason: "unknown_alias";
50
+ readonly reason: 'unknown_alias';
51
51
  readonly code: JsonRpcErrorCode.NotFound;
52
- readonly when: "No connection has been registered under the requested alias";
53
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_search.";
52
+ readonly when: 'No connection has been registered under the requested alias';
53
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_raw_search.';
54
54
  }, {
55
- readonly reason: "search_endpoint_disabled";
55
+ readonly reason: 'search_endpoint_disabled';
56
56
  readonly code: JsonRpcErrorCode.ValidationError;
57
- readonly when: "The active dialect declares this POST /search/{noun} route as known-dead on this server";
58
- readonly recovery: "Use the curated find_* tool for this noun — it routes through GET filters instead and avoids the dead search route.";
57
+ readonly when: 'The active dialect declares this POST /search/{noun} route as known-dead on this server';
58
+ readonly recovery: 'Use the curated find_* tool for this noun — it routes through GET filters instead and avoids the dead search route.';
59
59
  }], undefined>;
60
60
  //# sourceMappingURL=brapi-raw-search.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-raw-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6DjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmKzB,CAAC"}
1
+ {"version":3,"file":"brapi-raw-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6DjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMb,eAAe;;mBAEjB,6DAA6D;uBAEjE,oHAAoH;;qBAG9G,0BAA0B;;mBAE5B,yFAAyF;uBAE7F,qHAAqH;cAkJ3H,CAAC"}
@@ -25,11 +25,11 @@ export declare const brapiServerInfo: import("@cyanheads/mcp-ts-core").ToolDefin
25
25
  }, z.core.$strip>;
26
26
  auth: z.ZodObject<{
27
27
  mode: z.ZodEnum<{
28
- none: "none";
29
- sgn: "sgn";
30
- oauth2: "oauth2";
31
28
  api_key: "api_key";
32
29
  bearer: "bearer";
30
+ none: "none";
31
+ oauth2: "oauth2";
32
+ sgn: "sgn";
33
33
  }>;
34
34
  headerName: z.ZodOptional<z.ZodString>;
35
35
  expiresAt: z.ZodOptional<z.ZodString>;
@@ -43,10 +43,10 @@ export declare const brapiServerInfo: import("@cyanheads/mcp-ts-core").ToolDefin
43
43
  id: z.ZodString;
44
44
  source: z.ZodEnum<{
45
45
  "env-override": "env-override";
46
- "url-pattern": "url-pattern";
47
- "server-name": "server-name";
48
- "organization-name": "organization-name";
49
46
  fallback: "fallback";
47
+ "organization-name": "organization-name";
48
+ "server-name": "server-name";
49
+ "url-pattern": "url-pattern";
50
50
  }>;
51
51
  envVar: z.ZodString;
52
52
  disabledSearchEndpoints: z.ZodArray<z.ZodString>;
@@ -70,9 +70,9 @@ export declare const brapiServerInfo: import("@cyanheads/mcp-ts-core").ToolDefin
70
70
  notes: z.ZodArray<z.ZodString>;
71
71
  fetchedAt: z.ZodString;
72
72
  }, z.core.$strip>, readonly [{
73
- readonly reason: "unknown_alias";
73
+ readonly reason: 'unknown_alias';
74
74
  readonly code: JsonRpcErrorCode.NotFound;
75
- readonly when: "No connection has been registered under the requested alias";
76
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_server_info.";
75
+ readonly when: 'No connection has been registered under the requested alias';
76
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_server_info.';
77
77
  }], undefined>;
78
78
  //# sourceMappingURL=brapi-server-info.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-server-info.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-server-info.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAUjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA0C1B,CAAC"}
1
+ {"version":3,"file":"brapi-server-info.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-server-info.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAUjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMd,eAAe;;mBAEjB,6DAA6D;uBAEjE,qHAAqH;cAgC3H,CAAC"}
@@ -3,9 +3,10 @@
3
3
  * observations for a study. Two-phase write: `mode: 'preview'` validates rows
4
4
  * against the study's observation variables and returns a routing breakdown
5
5
  * (POST for new rows, PUT for rows carrying `observationDbId`); `mode: 'apply'`
6
- * elicits confirmation when supported, fans the rows out to POST + PUT in
7
- * parallel, then verifies the post-state with a cheap `pageSize=1` count.
8
- * Additive write — no observation is destroyed by this tool.
6
+ * asks the caller to confirm via a multi-round-trip `input_required` result,
7
+ * then fans the rows out to POST + PUT in parallel and verifies the post-state
8
+ * with a cheap `pageSize=1` count. Additive write — no observation is destroyed
9
+ * by this tool.
9
10
  *
10
11
  * @module mcp-server/tools/definitions/brapi-submit-observations.tool
11
12
  */
@@ -35,8 +36,8 @@ export declare const brapiSubmitObservations: import("@cyanheads/mcp-ts-core").T
35
36
  }, z.core.$strip>>;
36
37
  }, z.core.$strip>>;
37
38
  mode: z.ZodDefault<z.ZodEnum<{
38
- preview: "preview";
39
39
  apply: "apply";
40
+ preview: "preview";
40
41
  }>>;
41
42
  force: z.ZodDefault<z.ZodBoolean>;
42
43
  }, z.core.$strip>, z.ZodObject<{
@@ -85,39 +86,34 @@ export declare const brapiSubmitObservations: import("@cyanheads/mcp-ts-core").T
85
86
  warnings: z.ZodOptional<z.ZodArray<z.ZodString>>;
86
87
  }, z.core.$strip>], "mode">;
87
88
  }, z.core.$strip>, readonly [{
88
- readonly reason: "unknown_alias";
89
+ readonly reason: 'unknown_alias';
89
90
  readonly code: JsonRpcErrorCode.NotFound;
90
- readonly when: "No connection has been registered under the requested alias";
91
- readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_submit_observations.";
91
+ readonly when: 'No connection has been registered under the requested alias';
92
+ readonly recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_submit_observations.';
92
93
  }, {
93
- readonly reason: "observations_unsupported";
94
+ readonly reason: 'observations_unsupported';
94
95
  readonly code: JsonRpcErrorCode.ValidationError;
95
- readonly when: "BrAPI server does not advertise /observations";
96
- readonly recovery: "Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /observations.";
96
+ readonly when: 'BrAPI server does not advertise /observations';
97
+ readonly recovery: 'Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /observations.';
97
98
  }, {
98
- readonly reason: "study_not_found";
99
+ readonly reason: 'study_not_found';
99
100
  readonly code: JsonRpcErrorCode.NotFound;
100
- readonly when: "Upstream returned no study record for the requested studyDbId";
101
- readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs before retrying.";
101
+ readonly when: 'Upstream returned no study record for the requested studyDbId';
102
+ readonly recovery: 'Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs before retrying.';
102
103
  }, {
103
- readonly reason: "post_unsupported";
104
+ readonly reason: 'post_unsupported';
104
105
  readonly code: JsonRpcErrorCode.ValidationError;
105
- readonly when: "Server does not advertise POST on /observations but new rows were submitted";
106
- readonly recovery: "Remove the rows that lack observationDbId (those are the new rows) before retrying, or connect to a different server that supports POST on /observations.";
106
+ readonly when: 'Server does not advertise POST on /observations but new rows were submitted';
107
+ readonly recovery: 'Remove the rows that lack observationDbId (those are the new rows) before retrying, or connect to a different server that supports POST on /observations.';
107
108
  }, {
108
- readonly reason: "put_unsupported";
109
+ readonly reason: 'put_unsupported';
109
110
  readonly code: JsonRpcErrorCode.ValidationError;
110
- readonly when: "Server does not advertise PUT on /observations but update rows were submitted";
111
- readonly recovery: "Connect to a different server that supports PUT on /observations — dropping observationDbId would route as POST and create duplicates instead of updating the existing rows.";
112
- }, {
113
- readonly reason: "elicit_unavailable";
114
- readonly code: JsonRpcErrorCode.Forbidden;
115
- readonly when: "Apply mode invoked but client does not expose ctx.elicit and force was false";
116
- readonly recovery: "Set force=true only with explicit user authorization, or use a client that supports elicitation.";
111
+ readonly when: 'Server does not advertise PUT on /observations but update rows were submitted';
112
+ readonly recovery: 'Connect to a different server that supports PUT on /observations — dropping observationDbId would route as POST and create duplicates instead of updating the existing rows.';
117
113
  }, {
118
- readonly reason: "user_declined";
114
+ readonly reason: 'user_declined';
119
115
  readonly code: JsonRpcErrorCode.Forbidden;
120
- readonly when: "User declined the elicitation prompt for the apply write";
121
- readonly recovery: "Re-run the tool when the user is ready to confirm the write.";
116
+ readonly when: 'The confirmation round came back declined, cancelled, or without a true `confirm` value';
117
+ readonly recovery: 'Re-run brapi_submit_observations when the user is ready to confirm, or pass force=true with explicit out-of-band authorization.';
122
118
  }], undefined>;
123
119
  //# sourceMappingURL=brapi-submit-observations.tool.d.ts.map
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA2C,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACpF,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkPjE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmTlC,CAAC"}
1
+ {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAqC,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC9E,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgPjE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAjDxB,eAAe;;mBAEjB,6DAA6D;uBAEjE,6HAA6H;;qBAGvH,0BAA0B;;mBAE5B,+CAA+C;uBAEnD,kJAAkJ;;qBAG5I,iBAAiB;;mBAEnB,+DAA+D;uBAEnE,6GAA6G;;qBAGvG,kBAAkB;;mBAEpB,6EAA6E;uBAEjF,2JAA2J;;qBAGrJ,iBAAiB;;mBAEnB,+EAA+E;uBAEnF,8KAA8K;;qBAGxK,eAAe;;mBAEjB,yFAAyF;uBAE7F,iIAAiI;cA4UrI,CAAC"}