@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0
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.
- package/CLAUDE.md +11 -4
- package/README.md +7 -3
- package/changelog/0.6.x/0.6.4.md +14 -0
- package/changelog/0.7.x/0.7.0.md +23 -0
- package/changelog/template.md +1 -1
- package/dist/index.js +2 -0
- package/dist/index.js.map +1 -1
- package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts +30 -0
- package/dist/mcp-server/resources/definitions/brapi-variable.resource.d.ts.map +1 -0
- package/dist/mcp-server/resources/definitions/brapi-variable.resource.js +78 -0
- package/dist/mcp-server/resources/definitions/brapi-variable.resource.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts +81 -0
- package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js +366 -0
- package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts +88 -0
- package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js +494 -0
- package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts +7 -5
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js +67 -120
- package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js +54 -33
- package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js +54 -33
- package/dist/mcp-server/tools/definitions/brapi-find-images.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js +62 -41
- package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js +54 -33
- package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js +52 -33
- package/dist/mcp-server/tools/definitions/brapi-find-studies.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js +54 -33
- package/dist/mcp-server/tools/definitions/brapi-find-variables.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +8 -6
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js +54 -33
- package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts +60 -0
- package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js +416 -0
- package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js.map +1 -0
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-image.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-get-study.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-get.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-raw-search.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-server-info.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts +1 -1
- package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/index.d.ts +225 -61
- package/dist/mcp-server/tools/definitions/index.d.ts.map +1 -1
- package/dist/mcp-server/tools/definitions/index.js +6 -0
- package/dist/mcp-server/tools/definitions/index.js.map +1 -1
- package/dist/mcp-server/tools/shared/canvas-columns.d.ts +32 -0
- package/dist/mcp-server/tools/shared/canvas-columns.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/canvas-columns.js +98 -0
- package/dist/mcp-server/tools/shared/canvas-columns.js.map +1 -0
- package/dist/mcp-server/tools/shared/find-helpers.d.ts +1 -1
- package/dist/mcp-server/tools/shared/find-helpers.d.ts.map +1 -1
- package/dist/mcp-server/tools/shared/find-helpers.js +6 -2
- package/dist/mcp-server/tools/shared/find-helpers.js.map +1 -1
- package/dist/mcp-server/tools/shared/genotype-calls.d.ts +81 -0
- package/dist/mcp-server/tools/shared/genotype-calls.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/genotype-calls.js +172 -0
- package/dist/mcp-server/tools/shared/genotype-calls.js.map +1 -0
- package/dist/mcp-server/tools/shared/observations.d.ts +87 -0
- package/dist/mcp-server/tools/shared/observations.d.ts.map +1 -0
- package/dist/mcp-server/tools/shared/observations.js +285 -0
- package/dist/mcp-server/tools/shared/observations.js.map +1 -0
- package/manifest.json +1 -1
- package/package.json +6 -5
- package/server.json +3 -3
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@@ -43,7 +43,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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readonly when: "No filter catalog is registered for the requested endpoint";
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readonly recovery: "Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).";
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}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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germplasmDbId: import("zod").ZodString;
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alias: import("zod").ZodOptional<import("zod").ZodString>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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@@ -95,7 +95,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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readonly when: "Upstream returned no germplasm record for the requested DbId";
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readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
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}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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alias: import("zod").ZodOptional<import("zod").ZodString>;
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forceRefresh: import("zod").ZodDefault<import("zod").ZodBoolean>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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readonly code: import("@cyanheads/mcp-ts-core/errors").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_server_info.";
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}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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studyDbId: import("zod").ZodString;
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alias: import("zod").ZodOptional<import("zod").ZodString>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
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readonly when: "Upstream returned no study record for the requested DbId";
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readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
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}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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alias: import("zod").ZodOptional<import("zod").ZodString>;
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studies: import("zod").ZodArray<import("zod").ZodString>;
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variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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germplasm: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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shape: import("zod").ZodDefault<import("zod").ZodEnum<{
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wide: "wide";
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long: "long";
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}>>;
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aggregate: import("zod").ZodDefault<import("zod").ZodEnum<{
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all: "all";
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mean: "mean";
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median: "median";
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first: "first";
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}>>;
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loadLimit: import("zod").ZodOptional<import("zod").ZodNumber>;
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extraFilters: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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alias: import("zod").ZodString;
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studies: import("zod").ZodArray<import("zod").ZodString>;
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shape: import("zod").ZodEnum<{
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wide: "wide";
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long: "long";
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}>;
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aggregate: import("zod").ZodEnum<{
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all: "all";
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mean: "mean";
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median: "median";
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first: "first";
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}>;
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observationCount: import("zod").ZodNumber;
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germplasmCount: import("zod").ZodNumber;
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variableCount: import("zod").ZodNumber;
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variableLegend: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>;
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dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
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tableName: import("zod").ZodString;
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rowCount: import("zod").ZodNumber;
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columns: import("zod").ZodArray<import("zod").ZodString>;
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createdAt: import("zod").ZodString;
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expiresAt: import("zod").ZodString;
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truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
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maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
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}, import("zod/v4/core").$strip>>;
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warnings: import("zod").ZodArray<import("zod").ZodString>;
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}, import("zod/v4/core").$strip>, readonly [{
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readonly reason: "unknown_alias";
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readonly code: import("@cyanheads/mcp-ts-core/errors").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_build_phenotype_matrix.";
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}, {
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readonly reason: "all_filters_dropped";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
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readonly when: "The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline";
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readonly recovery: "Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.";
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}, {
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readonly reason: "no_observation_path";
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
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readonly when: "Neither /observations nor /observationunits returned data for any requested study after probing both paths";
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readonly recovery: "Verify the studyDbIds exist and the BrAPI server exposes /observations or /observationunits. Use brapi_server_info to inspect the capability list.";
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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baseUrl: import("zod").ZodOptional<import("zod").ZodString>;
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auth: import("zod").ZodOptional<import("zod").ZodDiscriminatedUnion<[import("zod").ZodObject<{
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mode: import("zod").ZodLiteral<"none">;
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readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Forbidden;
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readonly when: "Token endpoint responded but did not return an access_token";
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readonly recovery: "Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.";
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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dataframe: import("zod").ZodOptional<import("zod").ZodString>;
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}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
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tables: import("zod").ZodArray<import("zod").ZodObject<{
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readonly when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
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readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.";
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}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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sql: import("zod").ZodString;
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registerAs: import("zod").ZodOptional<import("zod").ZodString>;
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preview: import("zod").ZodOptional<import("zod").ZodNumber>;
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readonly when: "SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)";
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readonly recovery: "Submit a single SELECT statement using only registered dataframes. For changes, use `registerAs` in this tool to materialize a result, or brapi_dataframe_drop to remove a dataframe.";
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}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
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alias: import("zod").ZodOptional<import("zod").ZodString>;
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germplasmDbIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
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variantSetDbId: import("zod").ZodString;
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format: import("zod").ZodEnum<{
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|
430
|
+
plink: "plink";
|
|
431
|
+
"vcf-lite": "vcf-lite";
|
|
432
|
+
"matrix-json": "matrix-json";
|
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433
|
+
}>;
|
|
434
|
+
maxCalls: import("zod").ZodOptional<import("zod").ZodNumber>;
|
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435
|
+
}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
|
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+
alias: import("zod").ZodString;
|
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437
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+
format: import("zod").ZodEnum<{
|
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|
+
plink: "plink";
|
|
439
|
+
"vcf-lite": "vcf-lite";
|
|
440
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+
"matrix-json": "matrix-json";
|
|
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|
+
}>;
|
|
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|
+
rowCount: import("zod").ZodNumber;
|
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443
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+
columnCount: import("zod").ZodNumber;
|
|
444
|
+
variantColumnLegend: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>;
|
|
445
|
+
callFormatting: import("zod").ZodObject<{
|
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446
|
+
expandHomozygotes: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodBoolean>>;
|
|
447
|
+
unknownString: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
448
|
+
sepPhased: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
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449
|
+
sepUnphased: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
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450
|
+
}, import("zod/v4/core").$strip>;
|
|
451
|
+
dataframe: import("zod").ZodObject<{
|
|
452
|
+
tableName: import("zod").ZodString;
|
|
453
|
+
rowCount: import("zod").ZodNumber;
|
|
454
|
+
columns: import("zod").ZodArray<import("zod").ZodString>;
|
|
455
|
+
createdAt: import("zod").ZodString;
|
|
456
|
+
expiresAt: import("zod").ZodString;
|
|
457
|
+
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
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458
|
+
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
459
|
+
}, import("zod/v4/core").$strip>;
|
|
460
|
+
vcf: import("zod").ZodOptional<import("zod").ZodString>;
|
|
461
|
+
ped: import("zod").ZodOptional<import("zod").ZodString>;
|
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462
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+
map: import("zod").ZodOptional<import("zod").ZodString>;
|
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463
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+
truncated: import("zod").ZodBoolean;
|
|
464
|
+
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
465
|
+
}, import("zod/v4/core").$strip>, readonly [{
|
|
466
|
+
readonly reason: "unknown_alias";
|
|
467
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
468
|
+
readonly when: "No connection has been registered under the requested alias";
|
|
469
|
+
readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_export_genotype_matrix.";
|
|
470
|
+
}, {
|
|
471
|
+
readonly reason: "no_filters";
|
|
472
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
473
|
+
readonly when: "No variantSetDbId was provided";
|
|
474
|
+
readonly recovery: "Provide variantSetDbId before retrying — unfiltered genotype-call pulls are too expensive.";
|
|
475
|
+
}, {
|
|
476
|
+
readonly reason: "search_endpoint_disabled";
|
|
477
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
478
|
+
readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
|
|
479
|
+
readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
|
|
480
|
+
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
367
481
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
368
482
|
variantSetDbId: import("zod").ZodOptional<import("zod").ZodString>;
|
|
369
483
|
variantSetDbIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -391,8 +505,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
391
505
|
genotypeValue: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
392
506
|
phaseSet: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
393
507
|
}, import("zod/v4/core").$loose>>;
|
|
394
|
-
returnedCount: import("zod").ZodNumber;
|
|
395
|
-
totalCount: import("zod").ZodNumber;
|
|
396
508
|
hasMore: import("zod").ZodBoolean;
|
|
397
509
|
callFormatting: import("zod").ZodObject<{
|
|
398
510
|
expandHomozygotes: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodBoolean>>;
|
|
@@ -415,8 +527,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
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415
527
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
416
528
|
}, import("zod/v4/core").$strip>>;
|
|
417
529
|
truncated: import("zod").ZodBoolean;
|
|
418
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
419
|
-
searchBody: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
420
530
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
421
531
|
readonly reason: "unknown_alias";
|
|
422
532
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -432,7 +542,13 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
432
542
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
433
543
|
readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
|
|
434
544
|
readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
|
|
435
|
-
}]
|
|
545
|
+
}], {
|
|
546
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
547
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
548
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
549
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
550
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
551
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
436
552
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
437
553
|
names: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
438
554
|
germplasmDbIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -470,8 +586,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
470
586
|
type: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
471
587
|
}, import("zod/v4/core").$loose>>>>;
|
|
472
588
|
}, import("zod/v4/core").$loose>>;
|
|
473
|
-
returnedCount: import("zod").ZodNumber;
|
|
474
|
-
totalCount: import("zod").ZodNumber;
|
|
475
589
|
hasMore: import("zod").ZodBoolean;
|
|
476
590
|
distributions: import("zod").ZodObject<{
|
|
477
591
|
commonCropName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
@@ -480,7 +594,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
480
594
|
collection: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
481
595
|
countryOfOriginCode: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
482
596
|
}, import("zod/v4/core").$strip>;
|
|
483
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
484
597
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
485
598
|
tableName: import("zod").ZodString;
|
|
486
599
|
rowCount: import("zod").ZodNumber;
|
|
@@ -490,8 +603,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
490
603
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
491
604
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
492
605
|
}, import("zod/v4/core").$strip>>;
|
|
493
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
494
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
495
606
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
496
607
|
readonly reason: "unknown_alias";
|
|
497
608
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -502,7 +613,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
502
613
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
503
614
|
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.";
|
|
504
615
|
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.";
|
|
505
|
-
}]
|
|
616
|
+
}], {
|
|
617
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
618
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
619
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
620
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
621
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
622
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
623
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
506
624
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
507
625
|
images: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
508
626
|
observationUnits: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -534,8 +652,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
534
652
|
copyright: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
535
653
|
description: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
536
654
|
}, import("zod/v4/core").$loose>>;
|
|
537
|
-
returnedCount: import("zod").ZodNumber;
|
|
538
|
-
totalCount: import("zod").ZodNumber;
|
|
539
655
|
hasMore: import("zod").ZodBoolean;
|
|
540
656
|
distributions: import("zod").ZodObject<{
|
|
541
657
|
mimeType: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
@@ -543,7 +659,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
543
659
|
observationUnitName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
544
660
|
descriptiveOntologyTerms: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
545
661
|
}, import("zod/v4/core").$strip>;
|
|
546
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
547
662
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
548
663
|
tableName: import("zod").ZodString;
|
|
549
664
|
rowCount: import("zod").ZodNumber;
|
|
@@ -553,8 +668,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
553
668
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
554
669
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
555
670
|
}, import("zod/v4/core").$strip>>;
|
|
556
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
557
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
558
671
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
559
672
|
readonly reason: "unknown_alias";
|
|
560
673
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -565,7 +678,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
565
678
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
566
679
|
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.";
|
|
567
680
|
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.";
|
|
568
|
-
}]
|
|
681
|
+
}], {
|
|
682
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
683
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
684
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
685
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
686
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
687
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
688
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
569
689
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
570
690
|
locations: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
571
691
|
locationNames: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -597,14 +717,11 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
597
717
|
instituteAddress: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
598
718
|
documentationURL: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
599
719
|
}, import("zod/v4/core").$loose>>;
|
|
600
|
-
returnedCount: import("zod").ZodNumber;
|
|
601
|
-
totalCount: import("zod").ZodNumber;
|
|
602
720
|
hasMore: import("zod").ZodBoolean;
|
|
603
721
|
distributions: import("zod").ZodObject<{
|
|
604
722
|
countryCode: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
605
723
|
locationType: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
606
724
|
}, import("zod/v4/core").$strip>;
|
|
607
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
608
725
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
609
726
|
tableName: import("zod").ZodString;
|
|
610
727
|
rowCount: import("zod").ZodNumber;
|
|
@@ -614,8 +731,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
614
731
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
615
732
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
616
733
|
}, import("zod/v4/core").$strip>>;
|
|
617
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
618
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
619
734
|
coordinateAxisOrder: import("zod").ZodEnum<{
|
|
620
735
|
spec: "spec";
|
|
621
736
|
swapped: "swapped";
|
|
@@ -630,7 +745,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
630
745
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
631
746
|
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.";
|
|
632
747
|
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.";
|
|
633
|
-
}]
|
|
748
|
+
}], {
|
|
749
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
750
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
751
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
752
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
753
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
754
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
755
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
634
756
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
635
757
|
studies: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
636
758
|
germplasm: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -664,8 +786,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
664
786
|
collector: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
665
787
|
uploadedBy: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
666
788
|
}, import("zod/v4/core").$loose>>;
|
|
667
|
-
returnedCount: import("zod").ZodNumber;
|
|
668
|
-
totalCount: import("zod").ZodNumber;
|
|
669
789
|
hasMore: import("zod").ZodBoolean;
|
|
670
790
|
distributions: import("zod").ZodObject<{
|
|
671
791
|
observationVariableName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
@@ -674,7 +794,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
674
794
|
observationLevel: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
675
795
|
season: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
676
796
|
}, import("zod/v4/core").$strip>;
|
|
677
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
678
797
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
679
798
|
tableName: import("zod").ZodString;
|
|
680
799
|
rowCount: import("zod").ZodNumber;
|
|
@@ -684,8 +803,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
684
803
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
685
804
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
686
805
|
}, import("zod/v4/core").$strip>>;
|
|
687
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
688
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
689
806
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
690
807
|
readonly reason: "unknown_alias";
|
|
691
808
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -696,7 +813,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
696
813
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
697
814
|
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.";
|
|
698
815
|
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.";
|
|
699
|
-
}]
|
|
816
|
+
}], {
|
|
817
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
818
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
819
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
820
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
821
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
822
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
823
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
700
824
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
701
825
|
crop: import("zod").ZodOptional<import("zod").ZodString>;
|
|
702
826
|
trialTypes: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -729,8 +853,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
729
853
|
studyCode: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
730
854
|
studyPUI: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
731
855
|
}, import("zod/v4/core").$loose>>;
|
|
732
|
-
returnedCount: import("zod").ZodNumber;
|
|
733
|
-
totalCount: import("zod").ZodNumber;
|
|
734
856
|
hasMore: import("zod").ZodBoolean;
|
|
735
857
|
distributions: import("zod").ZodObject<{
|
|
736
858
|
programName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
@@ -739,7 +861,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
739
861
|
locationName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
740
862
|
commonCropName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
741
863
|
}, import("zod/v4/core").$strip>;
|
|
742
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
743
864
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
744
865
|
tableName: import("zod").ZodString;
|
|
745
866
|
rowCount: import("zod").ZodNumber;
|
|
@@ -749,8 +870,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
749
870
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
750
871
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
751
872
|
}, import("zod/v4/core").$strip>>;
|
|
752
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
753
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
754
873
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
755
874
|
readonly reason: "unknown_alias";
|
|
756
875
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -761,7 +880,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
761
880
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
762
881
|
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.";
|
|
763
882
|
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.";
|
|
764
|
-
}]
|
|
883
|
+
}], {
|
|
884
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
885
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
886
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
887
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
888
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
889
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
890
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
765
891
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
766
892
|
variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
767
893
|
variableNames: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -801,8 +927,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
801
927
|
methodName: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
|
|
802
928
|
}, import("zod/v4/core").$loose>>>;
|
|
803
929
|
}, import("zod/v4/core").$loose>>;
|
|
804
|
-
returnedCount: import("zod").ZodNumber;
|
|
805
|
-
totalCount: import("zod").ZodNumber;
|
|
806
930
|
hasMore: import("zod").ZodBoolean;
|
|
807
931
|
distributions: import("zod").ZodObject<{
|
|
808
932
|
ontologyDbId: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
@@ -823,7 +947,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
823
947
|
traitClassMatch: "traitClassMatch";
|
|
824
948
|
}>;
|
|
825
949
|
}, import("zod/v4/core").$strip>>;
|
|
826
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
827
950
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
828
951
|
tableName: import("zod").ZodString;
|
|
829
952
|
rowCount: import("zod").ZodNumber;
|
|
@@ -833,8 +956,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
833
956
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
834
957
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
835
958
|
}, import("zod/v4/core").$strip>>;
|
|
836
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
837
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
838
959
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
839
960
|
readonly reason: "unknown_alias";
|
|
840
961
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -845,7 +966,14 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
845
966
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
846
967
|
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.";
|
|
847
968
|
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.";
|
|
848
|
-
}]
|
|
969
|
+
}], {
|
|
970
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
971
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
972
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
973
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
974
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
975
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
976
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
849
977
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
850
978
|
variantSets: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
851
979
|
variants: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
@@ -872,15 +1000,12 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
872
1000
|
filtersApplied: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodBoolean>>;
|
|
873
1001
|
filtersFailed: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodArray<import("zod").ZodString>>>;
|
|
874
1002
|
}, import("zod/v4/core").$loose>>;
|
|
875
|
-
returnedCount: import("zod").ZodNumber;
|
|
876
|
-
totalCount: import("zod").ZodNumber;
|
|
877
1003
|
hasMore: import("zod").ZodBoolean;
|
|
878
1004
|
distributions: import("zod").ZodObject<{
|
|
879
1005
|
variantType: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
880
1006
|
referenceName: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
881
1007
|
variantSetDbId: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodNumber>;
|
|
882
1008
|
}, import("zod/v4/core").$strip>;
|
|
883
|
-
refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
884
1009
|
dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
|
|
885
1010
|
tableName: import("zod").ZodString;
|
|
886
1011
|
rowCount: import("zod").ZodNumber;
|
|
@@ -890,8 +1015,6 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
890
1015
|
truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
|
|
891
1016
|
maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
892
1017
|
}, import("zod/v4/core").$strip>>;
|
|
893
|
-
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
894
|
-
appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
895
1018
|
}, import("zod/v4/core").$strip>, readonly [{
|
|
896
1019
|
readonly reason: "unknown_alias";
|
|
897
1020
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
@@ -902,7 +1025,48 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
902
1025
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
903
1026
|
readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
|
|
904
1027
|
readonly recovery: "Drop the unsupported filters and rescope by variants, variantSets, references, or referenceName + start/end — these filter paths are honored on the active dialect.";
|
|
905
|
-
}]
|
|
1028
|
+
}], {
|
|
1029
|
+
readonly totalCount: import("zod").ZodNumber;
|
|
1030
|
+
readonly returnedCount: import("zod").ZodNumber;
|
|
1031
|
+
readonly appliedFilters: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
1032
|
+
readonly refinementHint: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1033
|
+
readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1034
|
+
readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
1035
|
+
}> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1036
|
+
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1037
|
+
germplasmDbId: import("zod").ZodString;
|
|
1038
|
+
variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
|
|
1039
|
+
}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
|
|
1040
|
+
alias: import("zod").ZodString;
|
|
1041
|
+
germplasmDbId: import("zod").ZodString;
|
|
1042
|
+
germplasmName: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1043
|
+
studyCount: import("zod").ZodNumber;
|
|
1044
|
+
studyDbIds: import("zod").ZodArray<import("zod").ZodString>;
|
|
1045
|
+
perVariable: import("zod").ZodArray<import("zod").ZodObject<{
|
|
1046
|
+
observationVariableDbId: import("zod").ZodString;
|
|
1047
|
+
observationVariableName: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1048
|
+
n: import("zod").ZodNumber;
|
|
1049
|
+
mean: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
1050
|
+
median: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
1051
|
+
sd: import("zod").ZodOptional<import("zod").ZodNumber>;
|
|
1052
|
+
min: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1053
|
+
max: import("zod").ZodOptional<import("zod").ZodString>;
|
|
1054
|
+
studyCount: import("zod").ZodNumber;
|
|
1055
|
+
studyDbIds: import("zod").ZodArray<import("zod").ZodString>;
|
|
1056
|
+
seasons: import("zod").ZodArray<import("zod").ZodString>;
|
|
1057
|
+
}, import("zod/v4/core").$strip>>;
|
|
1058
|
+
warnings: import("zod").ZodArray<import("zod").ZodString>;
|
|
1059
|
+
}, import("zod/v4/core").$strip>, readonly [{
|
|
1060
|
+
readonly reason: "unknown_alias";
|
|
1061
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
1062
|
+
readonly when: "No connection has been registered under the requested alias";
|
|
1063
|
+
readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.";
|
|
1064
|
+
}, {
|
|
1065
|
+
readonly reason: "germplasm_not_found";
|
|
1066
|
+
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
1067
|
+
readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
|
|
1068
|
+
readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
|
|
1069
|
+
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
906
1070
|
imageDbIds: import("zod").ZodArray<import("zod").ZodString>;
|
|
907
1071
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
908
1072
|
}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
|
|
@@ -951,7 +1115,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
951
1115
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
952
1116
|
readonly when: "BrAPI server does not advertise /images in /serverinfo";
|
|
953
1117
|
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.";
|
|
954
|
-
}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1118
|
+
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
955
1119
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
956
1120
|
path: import("zod").ZodString;
|
|
957
1121
|
params: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber, import("zod").ZodBoolean, import("zod").ZodArray<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>]>>>;
|
|
@@ -989,7 +1153,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
989
1153
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
990
1154
|
readonly when: "path argument was a full URL instead of a relative BrAPI route";
|
|
991
1155
|
readonly recovery: "Pass a path like \"/samples\" or \"/methods\" — the connection alias supplies the baseUrl.";
|
|
992
|
-
}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1156
|
+
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
993
1157
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
994
1158
|
noun: import("zod").ZodString;
|
|
995
1159
|
body: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>;
|
|
@@ -1031,7 +1195,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
1031
1195
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
1032
1196
|
readonly when: "The active dialect declares this POST /search/{noun} route as known-dead on this server";
|
|
1033
1197
|
readonly recovery: "Use the curated find_* tool for this noun — it routes through GET filters instead and avoids the dead search route.";
|
|
1034
|
-
}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1198
|
+
}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1035
1199
|
germplasmDbIds: import("zod").ZodArray<import("zod").ZodString>;
|
|
1036
1200
|
direction: import("zod").ZodDefault<import("zod").ZodEnum<{
|
|
1037
1201
|
both: "both";
|
|
@@ -1081,7 +1245,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
|
|
|
1081
1245
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
|
|
1082
1246
|
readonly when: "No connection has been registered under the requested alias";
|
|
1083
1247
|
readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.";
|
|
1084
|
-
}]>)[];
|
|
1248
|
+
}], undefined>)[];
|
|
1085
1249
|
/**
|
|
1086
1250
|
* Drop tool — opt-in via `BRAPI_CANVAS_DROP_ENABLED`. Off by default; the
|
|
1087
1251
|
* underlying canvas tables expire via TTL when left unmanaged, so explicit
|
|
@@ -1093,7 +1257,7 @@ export declare const dropToolDefinitions: import("@cyanheads/mcp-ts-core").ToolD
|
|
|
1093
1257
|
}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
|
|
1094
1258
|
dataframe: import("zod").ZodString;
|
|
1095
1259
|
dropped: import("zod").ZodBoolean;
|
|
1096
|
-
}, import("zod/v4/core").$strip>, undefined>[];
|
|
1260
|
+
}, import("zod/v4/core").$strip>, undefined, undefined>[];
|
|
1097
1261
|
/**
|
|
1098
1262
|
* Export tool — gated by `BRAPI_EXPORT_DIR` (the opt-in) AND
|
|
1099
1263
|
* `MCP_TRANSPORT_TYPE=stdio` (path output is meaningful only when the server
|
|
@@ -1145,7 +1309,7 @@ export declare const exportToolDefinitions: import("@cyanheads/mcp-ts-core").Too
|
|
|
1145
1309
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
|
|
1146
1310
|
readonly when: "Both `columns` and `sql` were supplied";
|
|
1147
1311
|
readonly recovery: "Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.";
|
|
1148
|
-
}]>[];
|
|
1312
|
+
}], undefined>[];
|
|
1149
1313
|
/** Write tools — registered only when `BRAPI_ENABLE_WRITES=true`. */
|
|
1150
1314
|
export declare const writeToolDefinitions: import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
|
|
1151
1315
|
alias: import("zod").ZodOptional<import("zod").ZodString>;
|
|
@@ -1255,5 +1419,5 @@ export declare const writeToolDefinitions: import("@cyanheads/mcp-ts-core").Tool
|
|
|
1255
1419
|
readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Forbidden;
|
|
1256
1420
|
readonly when: "User declined the elicitation prompt for the apply write";
|
|
1257
1421
|
readonly recovery: "Re-run the tool when the user is ready to confirm the write.";
|
|
1258
|
-
}]>[];
|
|
1422
|
+
}], undefined>[];
|
|
1259
1423
|
//# sourceMappingURL=index.d.ts.map
|
|
@@ -1 +1 @@
|
|
|
1
|
-
{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;
|
|
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"}
|