@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js

@@ -0,0 +1,366 @@
+/**
+ * @fileoverview `brapi_build_phenotype_matrix` — pull observations across one or
+ * more studies and pivot them into a germplasm × trait matrix materialized as a
+ * canvas dataframe. Returns a dataframe handle plus a summary of dimensions,
+ * aggregate method, and any warnings encountered during the pull.
+ *
+ * The per-study observation pull (with its `/observations` → `/observationunits`
+ * fallback chain) lives in `../shared/observations.ts`, shared with
+ * `brapi_germplasm_performance`.
+ *
+ * Column safety: wide-matrix column names are SQL-safe identifiers derived from
+ * `observationVariableDbId` via `../shared/canvas-columns.ts` — BrAPI DbIds are
+ * routinely numeric (Breedbase) or collide with reserved SQL words, both of
+ * which the canvas identifier gate rejects. A `variableLegend` mapping safe
+ * column → display name is returned so callers can resolve columns back.
+ *
+ * @module mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getServerConfig } from '../../../config/server-config.js';
+import { getBrapiClient } from '../../../services/brapi-client/index.js';
+import { resolveDialect } from '../../../services/brapi-dialect/index.js';
+import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
+import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { buildUniqueColumns } from '../shared/canvas-columns.js';
+import { AliasInput, DataframeHandleSchema, ExtraFiltersInput, LoadLimitInput, renderDataframeHandle, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { pullStudyObservations } from '../shared/observations.js';
+// ---------------------------------------------------------------------------
+// Output schema
+// ---------------------------------------------------------------------------
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    studies: z.array(z.string()).describe('studyDbIds that were queried to build the matrix.'),
+    shape: z
+        .enum(['wide', 'long'])
+        .describe('Matrix shape — wide (one row per germplasm, one column per variable) or long (one row per observation).'),
+    aggregate: z
+        .enum(['mean', 'median', 'first', 'all'])
+        .describe('Aggregation applied to replicate observations (wide shape only). `all` keeps one row per replicate.'),
+    observationCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Total raw observations collected before pivoting.'),
+    germplasmCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of distinct germplasm in the matrix.'),
+    variableCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of distinct observation variables in the matrix.'),
+    variableLegend: z
+        .record(z.string(), z.string())
+        .describe('Mapping of safe column identifier → observationVariableName. Wide-matrix column names are SQL-safe identifiers derived from observationVariableDbId (sanitized for DuckDB); consult this map to resolve a column back to its variable display name.'),
+    dataframe: DataframeHandleSchema.optional().describe('Canvas dataframe handle for the materialized matrix. Omitted when no observations were found. Query with brapi_dataframe_query (SQL). Long-form columns: germplasmDbId, observationVariableDbId, studyDbId, value, replicateIndex. Wide-form columns: germplasmDbId, germplasmName, one column per variable (SQL-safe identifier derived from observationVariableDbId — see variableLegend).'),
+    warnings: z
+        .array(z.string())
+        .describe('Advisory messages (empty studies, non-numeric aggregation skips, fallback paths).'),
+});
+// ---------------------------------------------------------------------------
+// Tool definition
+// ---------------------------------------------------------------------------
+export const brapiBuildPhenotypeMatrix = tool('brapi_build_phenotype_matrix', {
+    description: 'Pull observations across one or more studies and pivot them into a germplasm × trait matrix materialized as a canvas dataframe. Returns a dataframe handle (query with brapi_dataframe_query) plus a summary of dimensions and aggregate method. Long-form output is suitable for downstream GROUP BY analysis by study, germplasm, or variable.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_build_phenotype_matrix.',
+        },
+        {
+            reason: 'all_filters_dropped',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline',
+            recovery: 'Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.',
+        },
+        {
+            reason: 'no_observation_path',
+            code: JsonRpcErrorCode.ServiceUnavailable,
+            when: 'Neither /observations nor /observationunits returned data for any requested study after probing both paths',
+            recovery: 'Verify the studyDbIds exist and the BrAPI server exposes /observations or /observationunits. Use brapi_server_info to inspect the capability list.',
+        },
+    ],
+    input: z.object({
+        alias: AliasInput,
+        studies: z
+            .array(z.string())
+            .min(1)
+            .describe('studyDbIds to include in the matrix. At least one is required — the tool is study-anchored to avoid full-table scans.'),
+        variables: z
+            .array(z.string())
+            .optional()
+            .describe('Optional subset of observationVariableDbIds to include. Omit to include all variables found in the queried studies.'),
+        germplasm: z
+            .array(z.string())
+            .optional()
+            .describe('Optional subset of germplasmDbIds to include. Omit to include all germplasm found in the queried studies.'),
+        shape: z
+            .enum(['wide', 'long'])
+            .default('wide')
+            .describe('Matrix shape. `wide` — one row per germplasm, one column per variable, cell = aggregated value. `long` — one row per observation with columns: germplasmDbId, observationVariableDbId, studyDbId, value, replicateIndex. When `aggregate:"all"` is combined with `shape:"wide"`, the output falls back to long form with a replicateIndex column.'),
+        aggregate: z
+            .enum(['mean', 'median', 'first', 'all'])
+            .default('mean')
+            .describe('How to aggregate replicate observations (multiple readings of the same variable on the same germplasm). `mean` and `median` attempt numeric conversion and skip non-numeric values (e.g. categorical traits). `first` keeps the first value seen. `all` keeps every replicate as a separate row (produces long-form output even when shape is "wide"). Default: `mean`.'),
+        loadLimit: LoadLimitInput,
+        extraFilters: ExtraFiltersInput,
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const client = getBrapiClient();
+        const bridge = getCanvasBridge();
+        const config = getServerConfig();
+        const capabilities = getCapabilityRegistry();
+        const connection = await requireRegisteredConnection(ctx, input.alias);
+        const capabilityLookup = connection.resolvedAuth ? { auth: connection.resolvedAuth } : {};
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const dialect = await resolveDialect(connection, ctx, capabilityLookup);
+        const loadLimit = input.loadLimit ?? config.loadLimit;
+        const warnings = [];
+        const allObs = [];
+        // Collect observations study-by-study. Isolation per study avoids
+        // unbounded queries and preserves studyDbId on each row.
+        for (const studyDbId of input.studies) {
+            const studyObs = await pullStudyObservations({
+                studyDbId,
+                input,
+                client,
+                connection,
+                profile: profile.supported,
+                dialect,
+                config,
+                loadLimit,
+                warnings,
+                ctx,
+            });
+            if (studyObs === null) {
+                throw ctx.fail('no_observation_path', `Neither /observations nor /observationunits returned a usable path for study '${studyDbId}'. Check brapi_server_info for the capability list.`, { ...ctx.recoveryFor('no_observation_path'), studyDbId });
+            }
+            allObs.push(...studyObs);
+        }
+        // Apply variable and germplasm filters if requested
+        const filteredObs = filterObservations(allObs, input.variables, input.germplasm);
+        if (filteredObs.length === 0) {
+            warnings.push('No observations matched after collecting from the requested studies. The matrix will be empty.');
+        }
+        // Build variable column plan: distinct variables in encounter order →
+        // SQL-safe column names, plus a legend mapping safe column → display name.
+        const varOrder = [];
+        const varDisplay = new Map();
+        for (const o of filteredObs) {
+            if (!varDisplay.has(o.observationVariableDbId)) {
+                varDisplay.set(o.observationVariableDbId, o.observationVariableName);
+                varOrder.push(o.observationVariableDbId);
+            }
+        }
+        const { columns: variableColumns, toOriginal: columnToVariable } = buildUniqueColumns(varOrder);
+        const variableLegend = {};
+        for (const col of variableColumns) {
+            const varId = columnToVariable[col];
+            if (varId !== undefined)
+                variableLegend[col] = varDisplay.get(varId) ?? varId;
+        }
+        // Determine effective shape — `all` replicates force long form
+        const effectiveShape = input.shape === 'wide' && input.aggregate === 'all' ? 'long' : input.shape;
+        if (input.shape === 'wide' && input.aggregate === 'all') {
+            warnings.push('`shape:"wide"` combined with `aggregate:"all"` produces long-form output with a replicateIndex column (no pivot possible when all replicates are kept).');
+        }
+        // Build the matrix rows
+        let matrixRows;
+        if (effectiveShape === 'long') {
+            matrixRows = buildLongRows(filteredObs);
+        }
+        else {
+            matrixRows = buildWideRows(filteredObs, input.aggregate, variableColumns, columnToVariable, warnings);
+        }
+        // Distinct germplasm count (from filteredObs, not matrixRows)
+        const germplasmSet = new Set(filteredObs.map((o) => o.germplasmDbId));
+        const result = {
+            alias: connection.alias,
+            studies: input.studies,
+            shape: input.shape,
+            aggregate: input.aggregate,
+            observationCount: filteredObs.length,
+            germplasmCount: germplasmSet.size,
+            variableCount: varOrder.length,
+            variableLegend,
+            warnings,
+        };
+        // Only materialize when there are actual rows — DuckDB rejects an empty
+        // schema (no columns), and an empty dataframe handle is misleading.
+        if (matrixRows.length > 0) {
+            const dataframe = await bridge.registerDataframe(ctx, {
+                source: 'build_phenotype_matrix',
+                baseUrl: connection.baseUrl,
+                query: {
+                    studies: input.studies,
+                    variables: input.variables,
+                    germplasm: input.germplasm,
+                    shape: input.shape,
+                    aggregate: input.aggregate,
+                },
+                rows: matrixRows,
+            });
+            result.dataframe = {
+                tableName: dataframe.tableName,
+                rowCount: dataframe.rowCount,
+                columns: dataframe.columns,
+                createdAt: dataframe.createdAt,
+                expiresAt: dataframe.expiresAt,
+            };
+        }
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# Phenotype matrix — ${result.germplasmCount} germplasm × ${result.variableCount} variables — \`${result.alias}\``);
+        lines.push('');
+        lines.push(`Shape: **${result.shape}** · Aggregate: **${result.aggregate}** · Observations collected: ${result.observationCount}`);
+        lines.push(`Studies queried: ${result.studies.join(', ')}`);
+        lines.push('');
+        // Variable legend
+        const legendEntries = Object.entries(result.variableLegend);
+        if (legendEntries.length > 0) {
+            lines.push('## Variable legend');
+            for (const [col, name] of legendEntries) {
+                lines.push(`- \`${col}\` → ${name}`);
+            }
+            lines.push('');
+        }
+        // Dataframe handle
+        if (result.dataframe) {
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
+            lines.push('');
+        }
+        else {
+            lines.push('_No observations found — dataframe not materialized._');
+            lines.push('');
+        }
+        if (result.warnings.length > 0) {
+            lines.push('## Warnings');
+            for (const w of result.warnings) {
+                lines.push(`- ${w}`);
+            }
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+// ---------------------------------------------------------------------------
+// Filter helpers
+// ---------------------------------------------------------------------------
+function filterObservations(obs, variables, germplasm) {
+    let result = obs;
+    if (variables?.length) {
+        const set = new Set(variables);
+        result = result.filter((o) => set.has(o.observationVariableDbId));
+    }
+    if (germplasm?.length) {
+        const set = new Set(germplasm);
+        result = result.filter((o) => set.has(o.germplasmDbId));
+    }
+    return result;
+}
+// ---------------------------------------------------------------------------
+// Long-form row builder
+// ---------------------------------------------------------------------------
+function buildLongRows(obs) {
+    // Group by (germplasmDbId, observationVariableDbId, studyDbId) to assign replicate index
+    const replicateCounts = new Map();
+    return obs.map((o) => {
+        const key = `${o.germplasmDbId}|${o.observationVariableDbId}|${o.studyDbId}`;
+        const idx = replicateCounts.get(key) ?? 0;
+        replicateCounts.set(key, idx + 1);
+        return {
+            germplasmDbId: o.germplasmDbId,
+            observationVariableDbId: o.observationVariableDbId,
+            studyDbId: o.studyDbId,
+            value: o.value,
+            replicateIndex: idx,
+        };
+    });
+}
+// ---------------------------------------------------------------------------
+// Wide-form row builder
+// ---------------------------------------------------------------------------
+function buildWideRows(obs, aggregate, variableColumns, columnToVariable, warnings) {
+    if (aggregate === 'all') {
+        // Caller already redirected to long for 'all' + 'wide' — this branch should
+        // not be reached, but guard defensively.
+        return buildLongRows(obs);
+    }
+    // Group observations: germplasmDbId → variableDbId → values[]
+    const groups = new Map();
+    // Collect germplasm names (first observation per germplasm)
+    const germplasmNames = new Map();
+    for (const o of obs) {
+        if (!germplasmNames.has(o.germplasmDbId)) {
+            germplasmNames.set(o.germplasmDbId, o.germplasmName);
+        }
+        let byVar = groups.get(o.germplasmDbId);
+        if (!byVar) {
+            byVar = new Map();
+            groups.set(o.germplasmDbId, byVar);
+        }
+        const vals = byVar.get(o.observationVariableDbId) ?? [];
+        vals.push(o.value);
+        byVar.set(o.observationVariableDbId, vals);
+    }
+    const nonNumericWarned = new Set();
+    const rows = [];
+    for (const [germplasmDbId, byVar] of groups) {
+        const row = {
+            germplasmDbId,
+            germplasmName: germplasmNames.get(germplasmDbId) ?? germplasmDbId,
+        };
+        for (const col of variableColumns) {
+            const varId = columnToVariable[col];
+            const vals = varId ? byVar.get(varId) : undefined;
+            if (!vals || vals.length === 0) {
+                row[col] = null;
+                continue;
+            }
+            row[col] = aggregateValues(vals, aggregate, varId, nonNumericWarned, warnings);
+        }
+        rows.push(row);
+    }
+    return rows;
+}
+// ---------------------------------------------------------------------------
+// Aggregation
+// ---------------------------------------------------------------------------
+function aggregateValues(values, aggregate, varId, nonNumericWarned, warnings) {
+    if (aggregate === 'first') {
+        return values[0] ?? null;
+    }
+    // numeric aggregation
+    const nums = values.map((v) => Number(v)).filter((n) => !Number.isNaN(n));
+    if (nums.length === 0) {
+        if (!nonNumericWarned.has(varId)) {
+            nonNumericWarned.add(varId);
+            warnings.push(`Variable '${varId}': all values are non-numeric — cannot compute ${aggregate}. Cell set to null. Use aggregate:"first" or "all" for categorical traits.`);
+        }
+        return null;
+    }
+    if (aggregate === 'mean') {
+        return nums.reduce((a, b) => a + b, 0) / nums.length;
+    }
+    // median (nums is non-empty here — guarded above)
+    const sorted = [...nums].sort((a, b) => a - b);
+    const mid = Math.floor(sorted.length / 2);
+    const hi = sorted[mid];
+    if (hi === undefined)
+        return null;
+    if (sorted.length % 2 !== 0)
+        return hi;
+    const lo = sorted[mid - 1];
+    return lo === undefined ? hi : (lo + hi) / 2;
+}
+//# sourceMappingURL=brapi-build-phenotype-matrix.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map

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package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts

@@ -99,5 +99,5 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "Token endpoint responded but did not return an access_token";
     readonly recovery: "Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-connect.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyFvB,CAAC"}
+{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyFvB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts

@@ -38,5 +38,5 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
     readonly code: JsonRpcErrorCode.Forbidden;
     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.";
     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.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;GAkCjC,CAAC"}
+{"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts

@@ -15,5 +15,5 @@ export declare const brapiDataframeDrop: import("@cyanheads/mcp-ts-core").ToolDe
 }, z.core.$strip>, z.ZodObject<{
     dataframe: z.ZodString;
     dropped: z.ZodBoolean;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, undefined, undefined>;
 //# sourceMappingURL=brapi-dataframe-drop.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;6BAqB7B,CAAC"}
+{"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;wCAqB7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts

@@ -65,5 +65,5 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Both `columns` and `sql` were supplied";
     readonly recovery: "Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-export.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkH/B,CAAC"}
+{"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkH/B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts

@@ -42,5 +42,5 @@ export declare const brapiDataframeQuery: import("@cyanheads/mcp-ts-core").ToolD
     readonly code: 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>;
 //# sourceMappingURL=brapi-dataframe-query.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;GAmE9B,CAAC"}
+{"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;cAmE9B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts

@@ -37,5 +37,5 @@ export declare const brapiDescribeFilters: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "No filter catalog is registered for the requested endpoint";
     readonly recovery: "Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-describe-filters.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"brapi-describe-filters.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-describe-filters.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2E/B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts

@@ -0,0 +1,88 @@
+/**
+ * @fileoverview `brapi_export_genotype_matrix` — pull genotype calls for a
+ * germplasm × variant set and pivot them into a matrix in the requested format.
+ *
+ * Three output formats:
+ *
+ * - `matrix-json`: Wide germplasm × variant table registered as a canvas
+ *   dataframe (`df_<uuid>`). One row per call-set (germplasm); one column per
+ *   variant. Column names are sanitized for DuckDB (SQL-safe identifiers); a
+ *   `variantColumnLegend` maps sanitized name → original variant ID.
+ *
+ * - `vcf-lite`: Standard VCF-subset text (`#CHROM POS ID REF ALT <sample…>`),
+ *   one row per variant, returned in the `vcf` output field. CHROM/POS/REF/ALT
+ *   come from a `/variants` metadata pull; `.` when the server doesn't provide
+ *   them (common — the BrAPI test server leaves them null). The wide matrix is
+ *   also registered as a dataframe for SQL follow-up.
+ *
+ * - `plink`: `.ped` and `.map` text returned in the `ped` / `map` output fields.
+ *   `.map` carries chromosome + base-pair position from the variant pull; `.ped`
+ *   carries biallelic genotype pairs split from each call's genotype string.
+ *   Alleles are passed through verbatim (numeric 0/1 codings are not recoded to
+ *   nucleotides). The wide matrix is also registered as a dataframe.
+ *
+ * The genotype-call pull infrastructure is shared with `brapi_find_genotype_calls`
+ * via `src/mcp-server/tools/shared/genotype-calls.ts`; column sanitization is
+ * shared via `src/mcp-server/tools/shared/canvas-columns.ts`.
+ *
+ * @module mcp-server/tools/definitions/brapi-export-genotype-matrix.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const brapiExportGenotypeMatrix: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    alias: z.ZodOptional<z.ZodString>;
+    germplasmDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    variantSetDbId: z.ZodString;
+    format: z.ZodEnum<{
+        plink: "plink";
+        "vcf-lite": "vcf-lite";
+        "matrix-json": "matrix-json";
+    }>;
+    maxCalls: z.ZodOptional<z.ZodNumber>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    format: z.ZodEnum<{
+        plink: "plink";
+        "vcf-lite": "vcf-lite";
+        "matrix-json": "matrix-json";
+    }>;
+    rowCount: z.ZodNumber;
+    columnCount: z.ZodNumber;
+    variantColumnLegend: z.ZodRecord<z.ZodString, z.ZodString>;
+    callFormatting: z.ZodObject<{
+        expandHomozygotes: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
+        unknownString: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        sepPhased: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        sepUnphased: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$strip>;
+    dataframe: z.ZodObject<{
+        tableName: z.ZodString;
+        rowCount: z.ZodNumber;
+        columns: z.ZodArray<z.ZodString>;
+        createdAt: z.ZodString;
+        expiresAt: z.ZodString;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+        maxRows: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>;
+    vcf: z.ZodOptional<z.ZodString>;
+    ped: z.ZodOptional<z.ZodString>;
+    map: z.ZodOptional<z.ZodString>;
+    truncated: z.ZodBoolean;
+    warnings: z.ZodArray<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: 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: 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: 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>;
+//# sourceMappingURL=brapi-export-genotype-matrix.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map

@@ -0,0 +1 @@
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