@cyanheads/brapi-mcp-server 0.6.4 → 0.7.1

package/dist/mcp-server/tools/definitions/index.d.ts

@@ -230,6 +230,66 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no study record for the requested DbId";
     readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
+}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    alias: import("zod").ZodOptional<import("zod").ZodString>;
+    studies: import("zod").ZodArray<import("zod").ZodString>;
+    variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    germplasm: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    shape: import("zod").ZodDefault<import("zod").ZodEnum<{
+        wide: "wide";
+        long: "long";
+    }>>;
+    aggregate: import("zod").ZodDefault<import("zod").ZodEnum<{
+        all: "all";
+        mean: "mean";
+        median: "median";
+        first: "first";
+    }>>;
+    loadLimit: import("zod").ZodOptional<import("zod").ZodNumber>;
+    extraFilters: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodUnknown>>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    alias: import("zod").ZodString;
+    studies: import("zod").ZodArray<import("zod").ZodString>;
+    shape: import("zod").ZodEnum<{
+        wide: "wide";
+        long: "long";
+    }>;
+    aggregate: import("zod").ZodEnum<{
+        all: "all";
+        mean: "mean";
+        median: "median";
+        first: "first";
+    }>;
+    observationCount: import("zod").ZodNumber;
+    germplasmCount: import("zod").ZodNumber;
+    variableCount: import("zod").ZodNumber;
+    variableLegend: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>;
+    dataframe: import("zod").ZodOptional<import("zod").ZodObject<{
+        tableName: import("zod").ZodString;
+        rowCount: import("zod").ZodNumber;
+        columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
+        createdAt: import("zod").ZodString;
+        expiresAt: import("zod").ZodString;
+        truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
+        maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
+    }, import("zod/v4/core").$strip>>;
+    warnings: import("zod").ZodArray<import("zod").ZodString>;
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_build_phenotype_matrix.";
+}, {
+    readonly reason: "all_filters_dropped";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline";
+    readonly recovery: "Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.";
+}, {
+    readonly reason: "no_observation_path";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ServiceUnavailable;
+    readonly when: "Neither /observations nor /observationunits returned data for any requested study after probing both paths";
+    readonly recovery: "Verify the studyDbIds exist and the BrAPI server exposes /observations or /observationunits. Use brapi_server_info to inspect the capability list.";
 }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     baseUrl: import("zod").ZodOptional<import("zod").ZodString>;
     auth: import("zod").ZodOptional<import("zod").ZodDiscriminatedUnion<[import("zod").ZodObject<{
@@ -363,6 +423,62 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
     readonly when: "SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)";
     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.";
+}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    alias: import("zod").ZodOptional<import("zod").ZodString>;
+    germplasmDbIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    variantSetDbId: import("zod").ZodString;
+    format: import("zod").ZodEnum<{
+        plink: "plink";
+        "vcf-lite": "vcf-lite";
+        "matrix-json": "matrix-json";
+    }>;
+    maxCalls: import("zod").ZodOptional<import("zod").ZodNumber>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    alias: import("zod").ZodString;
+    format: import("zod").ZodEnum<{
+        plink: "plink";
+        "vcf-lite": "vcf-lite";
+        "matrix-json": "matrix-json";
+    }>;
+    rowCount: import("zod").ZodNumber;
+    columnCount: import("zod").ZodNumber;
+    variantColumnLegend: import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>;
+    callFormatting: import("zod").ZodObject<{
+        expandHomozygotes: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodBoolean>>;
+        unknownString: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
+        sepPhased: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
+        sepUnphased: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
+    }, import("zod/v4/core").$strip>;
+    dataframe: import("zod").ZodObject<{
+        tableName: import("zod").ZodString;
+        rowCount: import("zod").ZodNumber;
+        columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
+        createdAt: import("zod").ZodString;
+        expiresAt: import("zod").ZodString;
+        truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
+        maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
+    }, import("zod/v4/core").$strip>;
+    vcf: import("zod").ZodOptional<import("zod").ZodString>;
+    ped: import("zod").ZodOptional<import("zod").ZodString>;
+    map: import("zod").ZodOptional<import("zod").ZodString>;
+    truncated: import("zod").ZodBoolean;
+    warnings: import("zod").ZodArray<import("zod").ZodString>;
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_export_genotype_matrix.";
+}, {
+    readonly reason: "no_filters";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "No variantSetDbId was provided";
+    readonly recovery: "Provide variantSetDbId before retrying — unfiltered genotype-call pulls are too expensive.";
+}, {
+    readonly reason: "search_endpoint_disabled";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.ValidationError;
+    readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
+    readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
 }], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     alias: import("zod").ZodOptional<import("zod").ZodString>;
     variantSetDbId: import("zod").ZodOptional<import("zod").ZodString>;
@@ -407,6 +523,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -484,6 +601,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -549,6 +667,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -612,6 +731,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -684,6 +804,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -751,6 +872,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -837,6 +959,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -896,6 +1019,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -919,6 +1043,40 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     readonly notice: import("zod").ZodOptional<import("zod").ZodString>;
     readonly warnings: import("zod").ZodArray<import("zod").ZodString>;
 }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+    alias: import("zod").ZodOptional<import("zod").ZodString>;
+    germplasmDbId: import("zod").ZodString;
+    variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+}, import("zod/v4/core").$strip>, import("zod").ZodObject<{
+    alias: import("zod").ZodString;
+    germplasmDbId: import("zod").ZodString;
+    germplasmName: import("zod").ZodOptional<import("zod").ZodString>;
+    studyCount: import("zod").ZodNumber;
+    studyDbIds: import("zod").ZodArray<import("zod").ZodString>;
+    perVariable: import("zod").ZodArray<import("zod").ZodObject<{
+        observationVariableDbId: import("zod").ZodString;
+        observationVariableName: import("zod").ZodOptional<import("zod").ZodString>;
+        n: import("zod").ZodNumber;
+        mean: import("zod").ZodOptional<import("zod").ZodNumber>;
+        median: import("zod").ZodOptional<import("zod").ZodNumber>;
+        sd: import("zod").ZodOptional<import("zod").ZodNumber>;
+        min: import("zod").ZodOptional<import("zod").ZodString>;
+        max: import("zod").ZodOptional<import("zod").ZodString>;
+        studyCount: import("zod").ZodNumber;
+        studyDbIds: import("zod").ZodArray<import("zod").ZodString>;
+        seasons: import("zod").ZodArray<import("zod").ZodString>;
+    }, import("zod/v4/core").$strip>>;
+    warnings: import("zod").ZodArray<import("zod").ZodString>;
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.";
+}, {
+    readonly reason: "germplasm_not_found";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;
+    readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
+    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+}], undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     imageDbIds: import("zod").ZodArray<import("zod").ZodString>;
     alias: import("zod").ZodOptional<import("zod").ZodString>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
@@ -990,6 +1148,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
@@ -1032,6 +1191,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         tableName: import("zod").ZodString;
         rowCount: import("zod").ZodNumber;
         columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
         createdAt: import("zod").ZodString;
         expiresAt: import("zod").ZodString;
         truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;

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

@@ -1 +1 @@
-{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAyBH;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAoBnC,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"}
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AA4BH;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAuBnC,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;;yDAAuB,CAAC;AAExD;;;;GAIG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;gBAAyB,CAAC;AAE5D,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;gBAA4B,CAAC"}

package/dist/mcp-server/tools/definitions/index.js

@@ -10,12 +10,14 @@
  *
  * @module mcp-server/tools/definitions/index
  */
+import { brapiBuildPhenotypeMatrix } from './brapi-build-phenotype-matrix.tool.js';
 import { brapiConnect } from './brapi-connect.tool.js';
 import { brapiDataframeDescribe } from './brapi-dataframe-describe.tool.js';
 import { brapiDataframeDrop } from './brapi-dataframe-drop.tool.js';
 import { brapiDataframeExport } from './brapi-dataframe-export.tool.js';
 import { brapiDataframeQuery } from './brapi-dataframe-query.tool.js';
 import { brapiDescribeFilters } from './brapi-describe-filters.tool.js';
+import { brapiExportGenotypeMatrix } from './brapi-export-genotype-matrix.tool.js';
 import { brapiFindGenotypeCalls } from './brapi-find-genotype-calls.tool.js';
 import { brapiFindGermplasm } from './brapi-find-germplasm.tool.js';
 import { brapiFindImages } from './brapi-find-images.tool.js';
@@ -24,6 +26,7 @@ import { brapiFindObservations } from './brapi-find-observations.tool.js';
 import { brapiFindStudies } from './brapi-find-studies.tool.js';
 import { brapiFindVariables } from './brapi-find-variables.tool.js';
 import { brapiFindVariants } from './brapi-find-variants.tool.js';
+import { brapiGermplasmPerformance } from './brapi-germplasm-performance.tool.js';
 import { brapiGetGermplasm } from './brapi-get-germplasm.tool.js';
 import { brapiGetImage } from './brapi-get-image.tool.js';
 import { brapiGetStudy } from './brapi-get-study.tool.js';
@@ -39,6 +42,7 @@ import { brapiWalkPedigree } from './brapi-walk-pedigree.tool.js';
  */
 export const readOnlyToolDefinitions = [
     brapiConnect,
+    brapiBuildPhenotypeMatrix,
     brapiServerInfo,
     brapiDescribeFilters,
     brapiFindStudies,
@@ -46,6 +50,7 @@ export const readOnlyToolDefinitions = [
     brapiFindGermplasm,
     brapiGetGermplasm,
     brapiWalkPedigree,
+    brapiGermplasmPerformance,
     brapiFindVariables,
     brapiFindObservations,
     brapiFindImages,
@@ -53,6 +58,7 @@ export const readOnlyToolDefinitions = [
     brapiFindLocations,
     brapiFindVariants,
     brapiFindGenotypeCalls,
+    brapiExportGenotypeMatrix,
     brapiDataframeDescribe,
     brapiDataframeQuery,
     brapiRawGet,

package/dist/mcp-server/tools/definitions/index.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/canvas-columns.d.ts

@@ -0,0 +1,55 @@
+/**
+ * @fileoverview Shared canvas column-name sanitizer. The two matrix-building
+ * tools (`brapi_build_phenotype_matrix`, `brapi_export_genotype_matrix`) pivot
+ * upstream IDs (`observationVariableDbId`, `variantDbId`) into dataframe column
+ * names. The framework's canvas registers tables through `assertValidIdentifier`,
+ * which rejects any column whose name fails `/^[A-Za-z_][A-Za-z0-9_]{0,62}$/` or
+ * matches a reserved SQL keyword. BrAPI DbIds are routinely numeric (Breedbase
+ * uses integers) or collide with reserved words, so column names must be
+ * sanitized to SQL-safe identifiers before registration — paired with a legend
+ * mapping the safe name back to the original ID so the correlation is never lost.
+ *
+ * `sanitizeRowColumns` applies the same rules to whole spilled rows at the
+ * `CanvasBridge.registerDataframe` choke point, so every generic `find_*`
+ * spillover (not just the matrix pivots) is protected — a `/variants` row's
+ * reserved `end` key no longer fails registration.
+ *
+ * @module mcp-server/tools/shared/canvas-columns
+ */
+/**
+ * Sanitize an arbitrary upstream ID into a valid DuckDB column identifier.
+ * Mirrors the framework's `CANVAS_IDENTIFIER_REGEX` (`/^[A-Za-z_][A-Za-z0-9_]{0,62}$/`):
+ * replace illegal characters with `_`, prefix `v_` when the result would start
+ * with a digit, truncate to 63 chars, and suffix `_` when the result collides
+ * with a reserved SQL keyword.
+ */
+export declare function sanitizeColumnName(raw: string): string;
+/**
+ * Sanitize a list of IDs into unique column names, preserving input order. When
+ * two IDs sanitize to the same name, later collisions get a numeric suffix
+ * (`_2`, `_3`, …). Returns the column names in order plus a legend mapping each
+ * safe column name back to its original ID.
+ */
+export declare function buildUniqueColumns(ids: readonly string[]): {
+    columns: string[];
+    toOriginal: Record<string, string>;
+};
+/**
+ * Sanitize every column key across a spilled row set into SQL-safe DuckDB
+ * identifiers, reusing {@link buildUniqueColumns}. Returns the (possibly
+ * rewritten) rows plus a legend mapping each *renamed* safe column back to its
+ * original upstream key — entries are added only for columns that actually
+ * changed. When every key is already a valid identifier the input rows are
+ * returned by reference and the legend is empty, so the common (all-safe) path
+ * stays allocation-free.
+ *
+ * Centralizing this at `CanvasBridge.registerDataframe` keeps every spill
+ * consumer safe by construction: a row carrying a reserved word (`end`,
+ * `order`, …) or a digit-leading key no longer trips the framework's
+ * `assertValidIdentifier` gate at table registration.
+ */
+export declare function sanitizeRowColumns(rows: ReadonlyArray<Record<string, unknown>>): {
+    legend: Record<string, string>;
+    rows: Record<string, unknown>[];
+};
+//# sourceMappingURL=canvas-columns.d.ts.map

package/dist/mcp-server/tools/shared/canvas-columns.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/shared/canvas-columns.js

@@ -0,0 +1,151 @@
+/**
+ * @fileoverview Shared canvas column-name sanitizer. The two matrix-building
+ * tools (`brapi_build_phenotype_matrix`, `brapi_export_genotype_matrix`) pivot
+ * upstream IDs (`observationVariableDbId`, `variantDbId`) into dataframe column
+ * names. The framework's canvas registers tables through `assertValidIdentifier`,
+ * which rejects any column whose name fails `/^[A-Za-z_][A-Za-z0-9_]{0,62}$/` or
+ * matches a reserved SQL keyword. BrAPI DbIds are routinely numeric (Breedbase
+ * uses integers) or collide with reserved words, so column names must be
+ * sanitized to SQL-safe identifiers before registration — paired with a legend
+ * mapping the safe name back to the original ID so the correlation is never lost.
+ *
+ * `sanitizeRowColumns` applies the same rules to whole spilled rows at the
+ * `CanvasBridge.registerDataframe` choke point, so every generic `find_*`
+ * spillover (not just the matrix pivots) is protected — a `/variants` row's
+ * reserved `end` key no longer fails registration.
+ *
+ * @module mcp-server/tools/shared/canvas-columns
+ */
+/**
+ * Reserved SQL keywords rejected by the framework canvas gate
+ * (`assertValidIdentifier`, reason `identifierReserved`). Kept in sync with the
+ * framework's `RESERVED_IDENTIFIERS` set — a sanitized name matching one of
+ * these (case-insensitive) is suffixed with `_` to clear the gate.
+ */
+const RESERVED_IDENTIFIERS = new Set([
+    'select',
+    'from',
+    'where',
+    'order',
+    'group',
+    'having',
+    'limit',
+    'offset',
+    'union',
+    'intersect',
+    'except',
+    'all',
+    'distinct',
+    'as',
+    'and',
+    'or',
+    'not',
+    'null',
+    'true',
+    'false',
+    'case',
+    'when',
+    'then',
+    'else',
+    'end',
+    'join',
+    'inner',
+    'outer',
+    'left',
+    'right',
+    'full',
+    'cross',
+    'on',
+    'using',
+    'with',
+    'recursive',
+]);
+/**
+ * Sanitize an arbitrary upstream ID into a valid DuckDB column identifier.
+ * Mirrors the framework's `CANVAS_IDENTIFIER_REGEX` (`/^[A-Za-z_][A-Za-z0-9_]{0,62}$/`):
+ * replace illegal characters with `_`, prefix `v_` when the result would start
+ * with a digit, truncate to 63 chars, and suffix `_` when the result collides
+ * with a reserved SQL keyword.
+ */
+export function sanitizeColumnName(raw) {
+    let name = raw.replace(/[^A-Za-z0-9_]/g, '_');
+    if (/^[0-9]/.test(name))
+        name = `v_${name}`;
+    if (name.length > 63)
+        name = name.slice(0, 63);
+    if (name.length === 0)
+        name = 'v_unknown';
+    if (RESERVED_IDENTIFIERS.has(name.toLowerCase())) {
+        name = name.length >= 63 ? `${name.slice(0, 62)}_` : `${name}_`;
+    }
+    return name;
+}
+/**
+ * Sanitize a list of IDs into unique column names, preserving input order. When
+ * two IDs sanitize to the same name, later collisions get a numeric suffix
+ * (`_2`, `_3`, …). Returns the column names in order plus a legend mapping each
+ * safe column name back to its original ID.
+ */
+export function buildUniqueColumns(ids) {
+    const used = new Map();
+    const columns = [];
+    const toOriginal = {};
+    for (const id of ids) {
+        const base = sanitizeColumnName(id);
+        const count = (used.get(base) ?? 0) + 1;
+        used.set(base, count);
+        const colName = count === 1 ? base : `${base}_${count}`;
+        columns.push(colName);
+        toOriginal[colName] = id;
+    }
+    return { columns, toOriginal };
+}
+/**
+ * Sanitize every column key across a spilled row set into SQL-safe DuckDB
+ * identifiers, reusing {@link buildUniqueColumns}. Returns the (possibly
+ * rewritten) rows plus a legend mapping each *renamed* safe column back to its
+ * original upstream key — entries are added only for columns that actually
+ * changed. When every key is already a valid identifier the input rows are
+ * returned by reference and the legend is empty, so the common (all-safe) path
+ * stays allocation-free.
+ *
+ * Centralizing this at `CanvasBridge.registerDataframe` keeps every spill
+ * consumer safe by construction: a row carrying a reserved word (`end`,
+ * `order`, …) or a digit-leading key no longer trips the framework's
+ * `assertValidIdentifier` gate at table registration.
+ */
+export function sanitizeRowColumns(rows) {
+    // Ordered union of keys across all (sparse) rows — later rows may introduce
+    // columns the first row lacks.
+    const order = [];
+    const seen = new Set();
+    for (const row of rows) {
+        for (const key of Object.keys(row)) {
+            if (!seen.has(key)) {
+                seen.add(key);
+                order.push(key);
+            }
+        }
+    }
+    const { columns } = buildUniqueColumns(order);
+    const rename = new Map();
+    const legend = {};
+    order.forEach((original, i) => {
+        const safe = columns[i] ?? original;
+        rename.set(original, safe);
+        if (safe !== original)
+            legend[safe] = original;
+    });
+    if (Object.keys(legend).length === 0) {
+        return { rows: rows, legend: {} };
+    }
+    const rewritten = rows.map((row) => {
+        const out = {};
+        for (const [key, value] of Object.entries(row)) {
+            out[rename.get(key) ?? key] = value;
+        }
+        return out;
+    });
+    return { rows: rewritten, legend };
+}
+//# sourceMappingURL=canvas-columns.js.map

package/dist/mcp-server/tools/shared/canvas-columns.js.map

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package/dist/mcp-server/tools/shared/find-helpers.d.ts

@@ -239,6 +239,7 @@ export declare const DataframeHandleSchema: z.ZodObject<{
     tableName: z.ZodString;
     rowCount: z.ZodNumber;
     columns: z.ZodArray<z.ZodString>;
+    columnLegend: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodString>>;
     createdAt: z.ZodString;
     expiresAt: z.ZodString;
     truncated: z.ZodOptional<z.ZodBoolean>;

package/dist/mcp-server/tools/shared/find-helpers.d.ts.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.js

@@ -367,6 +367,10 @@ export const DataframeHandleSchema = z.object({
     columns: z
         .array(z.string().describe('Column name from the materialized rows.'))
         .describe('Full column list of the dataframe.'),
+    columnLegend: z
+        .record(z.string(), z.string())
+        .optional()
+        .describe('Maps a sanitized column name back to its original upstream key, for columns renamed to clear the SQL-safe-identifier gate (e.g. `end` → `end_`). Present only when a column was renamed — write SQL against the sanitized (left-hand) names.'),
     createdAt: z.string().describe('ISO 8601 timestamp the dataframe was created.'),
     expiresAt: z
         .string()
@@ -396,6 +400,12 @@ export function renderDataframeHandle(handle) {
         `- createdAt: ${handle.createdAt}`,
         `- expiresAt: ${handle.expiresAt} (${formatExpiresIn(handle.expiresAt)})`,
     ];
+    if (handle.columnLegend && Object.keys(handle.columnLegend).length > 0) {
+        const pairs = Object.entries(handle.columnLegend)
+            .map(([safe, original]) => `${safe} → ${original}`)
+            .join(', ');
+        lines.push(`- renamedColumns: ${pairs} (query using the left-hand names)`);
+    }
     if (handle.truncated)
         lines.push(`- truncated: true`);
     if (typeof handle.maxRows === 'number')
@@ -436,6 +446,8 @@ export function toDataframeHandle(result) {
         createdAt: result.createdAt,
         expiresAt: result.expiresAt,
     };
+    if (result.columnLegend)
+        handle.columnLegend = result.columnLegend;
     if (result.truncated)
         handle.truncated = true;
     if (typeof result.maxRows === 'number')