npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.8 → 0.7.9 - Mend

@cyanheads/brapi-mcp-server 0.7.8 → 0.7.9

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (23) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.7.8
+**Version:** 0.7.9
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.

package/README.md CHANGED Viewed

@@ -7,7 +7,7 @@
 <div align="center">
-[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.7.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
+[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.7.9-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
 </div>
@@ -60,7 +60,7 @@
 | `brapi_dataframe_export` | _Opt-in via `BRAPI_EXPORT_DIR=<path>`, stdio-only._ Export a dataframe to disk (CSV / Parquet / JSON) under the configured directory and return the absolute path for the human to open. Optional `columns` projection or `sql` filter materializes a derived table for the export, dropped after. |
 | `brapi_build_phenotype_matrix` | Build a germplasm × trait matrix from one or more studies and materialize it as a canvas dataframe. Supports wide (pivot) or long shape with configurable per-cell aggregation. |
 | `brapi_germplasm_performance` | Per-variable performance aggregates (n, mean, median, sd, min, max, studyCount) for a single germplasm across all studies where it has observations. |
-| `brapi_export_genotype_matrix` | Export genotype calls for a variant set as a germplasm × variant canvas dataframe; also serializes to VCF-lite or PLINK `.ped`/`.map` text. |
+| `brapi_export_genotype_matrix` | Export genotype calls for a variant set as a germplasm × variant canvas dataframe; also serializes to VCF-lite or PLINK `.ped`/`.map` text. Distinct-variant columns bounded by `BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS` (default 10k, max 500k). |
 ### Write (opt-in: `BRAPI_ENABLE_WRITES=true`)
@@ -219,6 +219,7 @@ Every variable is optional.
 | `BRAPI_ALLOW_PRIVATE_IPS` | Allow RFC 1918 / loopback targets. Dev-only. | `false` |
 | `BRAPI_ENABLE_WRITES` | Opt-in for `brapi_submit_observations` registration. | `false` |
 | `BRAPI_GENOTYPE_CALLS_MAX_PULL` | Upstream row ceiling per `brapi_find_genotype_calls` invocation. Max 500,000. | `100000` |
+| `BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS` | Distinct-variant column ceiling per `brapi_export_genotype_matrix` matrix — bounds the wide dataframe, the `variantColumnLegend`, and any VCF/PLINK text (all scale with column count, independent of the row pull). A `maxColumns` input may lower it, not raise it. Max 500,000. | `10000` |
 | `BRAPI_CANVAS_DROP_ENABLED` | Opt-in for `brapi_dataframe_drop` registration. Off by default; dataframes expire via TTL when left unmanaged. | `false` |
 | `BRAPI_EXPORT_DIR` | Directory for `brapi_dataframe_export` output files. Setting a path is the opt-in (no separate enable flag); unset leaves the tool out of `tools/list`. Stdio-only — the tool stays disabled under HTTP transport regardless of this value. Bridged to the framework's `CANVAS_EXPORT_PATH` automatically. | — |
 | `BRAPI_CANVAS_MAX_ROWS` / `BRAPI_CANVAS_QUERY_TIMEOUT_MS` | Per-query response row cap and wall-clock timeout for `brapi_dataframe_query`. | `10000` / `30000` |

package/changelog/0.7.x/0.7.9.md ADDED Viewed

@@ -0,0 +1,22 @@
+---
+summary: "brapi_export_genotype_matrix bounds distinct-variant columns via a new maxColumns input and BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS ceiling while keeping every germplasm row; brapi_dataframe_describe budgets its per-column listing and points overflow at brapi_dataframe_query."
+breaking: false
+security: false
+---
+# 0.7.9 — 2026-07-16
+## Added
+- **`brapi_export_genotype_matrix` `maxColumns`** — optional per-call input capping the distinct variant columns the matrix pivots into. Omit to use the deployment ceiling; a value above it clamps down. Independent of `maxCalls`, which bounds the row (call) pull. ([#46](https://github.com/cyanheads/brapi-mcp-server/issues/46))
+- **`BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS`** — deployment ceiling on distinct-variant columns per matrix; bounds the wide canvas dataframe, the `variantColumnLegend`, and any VCF/PLINK text, all of which scale with column count independently of `BRAPI_GENOTYPE_CALLS_MAX_PULL`. Default 10,000 (legend ≈ 250 KB), max 500,000. Prevents a schema-legal one-germplasm × many-variant skew from driving the column count to the full call budget and emitting a multi-megabyte legend. ([#46](https://github.com/cyanheads/brapi-mcp-server/issues/46))
+## Changed
+- **`brapi_export_genotype_matrix` `truncated`** — now set when either cap fires: the row ceiling (`BRAPI_GENOTYPE_CALLS_MAX_PULL`) or the new column ceiling; `warnings` names which. The column cap is applied inside the pivot as rows stream in, so an over-wide legend and matrix are never built then trimmed. Every germplasm still registers as a row — one whose calls all reference dropped variants renders as an all-null row, never a vanished one. ([#46](https://github.com/cyanheads/brapi-mcp-server/issues/46))
+- **`brapi_dataframe_describe` per-column listing** — bounded by the shared width-aware budget (`joinWithinBudget` / `MAX_LIST_LINE`, now exported from `find-helpers`), so a wide genotype matrix no longer emits one `content[]` line per variant. Overflow points at `brapi_dataframe_query` (`SELECT * FROM <table> LIMIT 0`); the full schema stays in `structuredContent`. ([#47](https://github.com/cyanheads/brapi-mcp-server/issues/47))
+- **`renderDataframeHandle` overflow hint** — repointed from `brapi_dataframe_describe` to `brapi_dataframe_query`, since describe's listing is now itself budgeted and pointing one capped line at another is circular. ([#47](https://github.com/cyanheads/brapi-mcp-server/issues/47))
+## Dependencies
+- **`tsc-alias` `^1.8.17 → ^1.9.1`** — dev-dependency bump.

package/dist/config/server-config.d.ts CHANGED Viewed

@@ -16,6 +16,16 @@ import { z } from '@cyanheads/mcp-ts-core';
  * advertised input range and the deployment ceiling from drifting apart.
  */
 export declare const GENOTYPE_CALLS_MAX_PULL_CEILING = 500000;
+/**
+ * Absolute upper bound on `genotypeMatrixMaxColumns`, and therefore on any
+ * caller-supplied `maxColumns` override to `brapi_export_genotype_matrix`. A
+ * matrix's distinct-variant column count can never exceed the genotype-call
+ * pull it is derived from, so it shares {@link GENOTYPE_CALLS_MAX_PULL_CEILING}'s
+ * absolute ceiling; the tool input schema bounds against this constant rather
+ * than restating the literal, keeping the advertised input range and the
+ * deployment ceiling from drifting apart.
+ */
+export declare const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500000;
 export declare const ServerConfigSchema: z.ZodObject<{
     defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
     defaultUsername: z.ZodOptional<z.ZodString>;
@@ -38,6 +48,7 @@ export declare const ServerConfigSchema: z.ZodObject<{
     allowPrivateIps: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     enableWrites: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     genotypeCallsMaxPull: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    genotypeMatrixMaxColumns: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     canvasDropEnabled: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     exportDir: z.ZodOptional<z.ZodString>;
     canvasMaxRows: z.ZodDefault<z.ZodCoercedNumber<unknown>>;

package/dist/config/server-config.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/config/server-config.js CHANGED Viewed

@@ -17,6 +17,16 @@ import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
  * advertised input range and the deployment ceiling from drifting apart.
  */
 export const GENOTYPE_CALLS_MAX_PULL_CEILING = 500_000;
+/**
+ * Absolute upper bound on `genotypeMatrixMaxColumns`, and therefore on any
+ * caller-supplied `maxColumns` override to `brapi_export_genotype_matrix`. A
+ * matrix's distinct-variant column count can never exceed the genotype-call
+ * pull it is derived from, so it shares {@link GENOTYPE_CALLS_MAX_PULL_CEILING}'s
+ * absolute ceiling; the tool input schema bounds against this constant rather
+ * than restating the literal, keeping the advertised input range and the
+ * deployment ceiling from drifting apart.
+ */
+export const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500_000;
 export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
         .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
@@ -120,6 +130,13 @@ export const ServerConfigSchema = z.object({
         .max(GENOTYPE_CALLS_MAX_PULL_CEILING)
         .default(100_000)
         .describe('Hard ceiling on rows pulled from the upstream BrAPI server in a single brapi_find_genotype_calls or brapi_export_genotype_matrix invocation. Bounds total page count per query — protects the upstream from unbounded pagination loops. brapi_export_genotype_matrix accepts a maxCalls override but clamps it to this value, so the ceiling holds regardless of caller input. Default 100,000 (≈10 pages at the standard pageSize=10,000); maximum 500,000 (≈50 pages, matching the per-query budget of other find_* tools).'),
+    genotypeMatrixMaxColumns: z.coerce
+        .number()
+        .int()
+        .positive()
+        .max(GENOTYPE_MATRIX_MAX_COLUMNS_CEILING)
+        .default(10_000)
+        .describe('Hard ceiling on the number of distinct variant columns brapi_export_genotype_matrix pivots into a single germplasm × variant matrix. Bounds the wide canvas dataframe, the variantColumnLegend, and any VCF/PLINK serialization — all of which scale with column count independently of the row (call) pull cap. A schema-legal skew (one germplasm × many variants) can otherwise drive the column count to the full genotypeCallsMaxPull budget and emit a multi-megabyte legend. brapi_export_genotype_matrix accepts a maxColumns override but clamps it to this value, so the ceiling holds regardless of caller input. Default 10,000 (legend ≈ 250 KB) — an order of magnitude below genotypeCallsMaxPull; maximum 500,000. Raise it only when a wide panel genuinely needs more variant columns inline.'),
     canvasDropEnabled: z
         .stringbool()
         .default(false)
@@ -169,6 +186,7 @@ export function getServerConfig() {
         allowPrivateIps: 'BRAPI_ALLOW_PRIVATE_IPS',
         enableWrites: 'BRAPI_ENABLE_WRITES',
         genotypeCallsMaxPull: 'BRAPI_GENOTYPE_CALLS_MAX_PULL',
+        genotypeMatrixMaxColumns: 'BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS',
         canvasDropEnabled: 'BRAPI_CANVAS_DROP_ENABLED',
         exportDir: 'BRAPI_EXPORT_DIR',
         canvasMaxRows: 'BRAPI_CANVAS_MAX_ROWS',

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

	@@ -1 +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;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC,CAAC"}
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;AA8CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js CHANGED Viewed

@@ -15,6 +15,7 @@ import { tool, z } from '@cyanheads/mcp-ts-core';
 import { config } from '@cyanheads/mcp-ts-core/config';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
+import { joinWithinBudget, MAX_LIST_LINE } from '../shared/find-helpers.js';
 const ColumnSchema = z.object({
     name: z.string().describe('Column name.'),
     type: z.string().describe('SQL column type (VARCHAR, INTEGER, DOUBLE, BOOLEAN, etc.).'),
@@ -96,10 +97,22 @@ function renderDescribe(tables) {
             lines.push(`- approxSizeBytes: ${table.approxSizeBytes}`);
         }
         lines.push(`- columns: ${table.columns.length}`);
-        for (const col of table.columns) {
+        // Width-aware budget on the per-column listing: a normal find_* dataframe
+        // (~18 columns) renders every column with its type, while a wide genotype
+        // matrix (one column per variant, up to hundreds of thousands) caps instead
+        // of emitting a line per variant into content[]. Safe to omit here because
+        // the full column set stays retrievable — brapi_dataframe_query renders it
+        // uncapped via `SELECT * FROM <table> LIMIT 0`, and the complete schema is
+        // in structuredContent.tables[].columns regardless of what this renders.
+        const { omitted } = joinWithinBudget(table.columns.map((col) => col.name), MAX_LIST_LINE);
+        const shownCount = table.columns.length - omitted;
+        for (const col of table.columns.slice(0, shownCount)) {
             const nullable = col.nullable === undefined ? '' : ` (nullable: ${col.nullable})`;
             lines.push(`  - ${col.name}: ${col.type}${nullable}`);
         }
+        if (omitted > 0) {
+            lines.push(`  - …+${omitted} more column(s) not shown — list all columns via brapi_dataframe_query: \`SELECT * FROM ${table.name} LIMIT 0\``);
+        }
         if (table.provenance) {
             lines.push('- provenance:');
             lines.push(`  - source: ${table.provenance.source}`);

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts CHANGED Viewed

@@ -39,6 +39,7 @@ export declare const brapiExportGenotypeMatrix: import("@cyanheads/mcp-ts-core")
         "matrix-json": "matrix-json";
     }>;
     maxCalls: z.ZodOptional<z.ZodNumber>;
+    maxColumns: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;
     format: z.ZodEnum<{

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-export-genotype-matrix.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA2GjE~~,eAAO,MAAM,yBAAyB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmPpC~~,CAAC"}
1	+ {"version":3,"file":"brapi-export-genotype-matrix.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4BG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiHjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyRpC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js CHANGED Viewed

@@ -29,7 +29,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { GENOTYPE_CALLS_MAX_PULL_CEILING, getServerConfig } from '../../../config/server-config.js';
+import { GENOTYPE_CALLS_MAX_PULL_CEILING, GENOTYPE_MATRIX_MAX_COLUMNS_CEILING, 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';
@@ -86,7 +86,7 @@ const OutputSchema = z.object({
         .describe('PLINK .map text — chromosome, variant-id, genetic-distance (0 placeholder), base-pair position, one row per variant. Present only when format="plink". Chromosome/position come from /variants metadata; `0` when absent.'),
     truncated: z
         .boolean()
-        .describe('True when the call pull was capped before exhausting upstream data.'),
+        .describe('True when the matrix is not the complete upstream result — either the call pull hit the row ceiling (BRAPI_GENOTYPE_CALLS_MAX_PULL) or the distinct-variant count hit the column ceiling (BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS). `warnings` names which ceiling fired.'),
     warnings: z.array(z.string()).describe('Advisory messages (truncation, missing fields, etc.).'),
 });
 // ---------------------------------------------------------------------------
@@ -132,6 +132,13 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             .max(GENOTYPE_CALLS_MAX_PULL_CEILING)
             .optional()
             .describe('Lower the pull cap for this call. Omit to use the deployment ceiling (BRAPI_GENOTYPE_CALLS_MAX_PULL). Cannot raise it: a value above the deployment ceiling is clamped down to it and the effective cap is reported in `warnings`.'),
+        maxColumns: z
+            .number()
+            .int()
+            .positive()
+            .max(GENOTYPE_MATRIX_MAX_COLUMNS_CEILING)
+            .optional()
+            .describe('Lower the distinct-variant column cap for this call. Omit to use the deployment ceiling (BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS). Cannot raise it: a value above the deployment ceiling is clamped down to it. When the variant set resolves more distinct variants than the effective cap, the matrix is capped at that many variant columns, `truncated` is set, and the effective cap is reported in `warnings`. Independent of `maxCalls`, which bounds the row (call) pull.'),
     }),
     output: OutputSchema,
     async handler(input, ctx) {
@@ -160,6 +167,17 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
         if (maxCalls < requestedMaxCalls) {
             warnings.push(`maxCalls=${requestedMaxCalls} exceeds this deployment's genotype-call ceiling (BRAPI_GENOTYPE_CALLS_MAX_PULL=${config.genotypeCallsMaxPull}); the pull was capped at ${maxCalls} calls. Results may be truncated — see \`truncated\`.`);
         }
+        // Same deployment-ceiling-wins shape as `maxCalls`, on the orthogonal axis:
+        // `maxCalls` bounds the rows pulled, `maxColumns` bounds the distinct-variant
+        // columns those rows pivot into. Nothing constrains the germplasm-to-variant
+        // ratio, so a schema-legal skew (one germplasm × `maxCalls` variants) would
+        // otherwise drive `columnCount` — and the variantColumnLegend, the wide
+        // dataframe, and the vcf/ped/map text with it — to the full call budget.
+        const requestedMaxColumns = input.maxColumns ?? config.genotypeMatrixMaxColumns;
+        const maxColumns = Math.min(requestedMaxColumns, config.genotypeMatrixMaxColumns);
+        if (maxColumns < requestedMaxColumns) {
+            warnings.push(`maxColumns=${requestedMaxColumns} exceeds this deployment's genotype-matrix column ceiling (BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS=${config.genotypeMatrixMaxColumns}); the matrix is capped at ${maxColumns} variant columns. See \`truncated\`.`);
+        }
         const searchOpts = {
             variantSetDbId: input.variantSetDbId,
         };
@@ -178,7 +196,14 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             warnings,
         });
         // Build the pivot matrix plus the structured data the text encoders need.
-        const matrix = buildMatrix(collected.rows, collected.callFormatting);
+        // The column cap is applied *inside* the pivot loop (net-new variants past
+        // `maxColumns` are skipped as rows stream in), so the over-wide legend and
+        // matrix are never materialized then trimmed — a true resource bound, not
+        // post-hoc waste.
+        const matrix = buildMatrix(collected.rows, collected.callFormatting, maxColumns);
+        if (matrix.columnsTruncated) {
+            warnings.push(`The variant set resolved more than ${maxColumns} distinct variants; the matrix was capped at ${maxColumns} variant columns (BRAPI_GENOTYPE_MATRIX_MAX_COLUMNS) and the remaining variants were dropped. Every germplasm is still present — one whose calls all fall in the dropped variants appears as an all-null row. Narrow germplasmDbIds or the variant set and re-pull to capture the rest.`);
+        }
         // Register the wide matrix as a canvas dataframe (used by all three formats).
         const registerInput = {
             source: 'export_genotype_matrix',
@@ -186,8 +211,14 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             query: searchBody,
             rows: matrix.matrixRows,
         };
-        if (collected.truncated) {
+        // A column cap leaves the dataframe incomplete too — flag it so a reader who
+        // inspects the handle without reading `warnings` doesn't take the matrix as
+        // whole. `maxRows` stays row-scoped: it's set only when the call pull hit the
+        // row ceiling, never for a pure column cap (which doesn't reduce row count).
+        if (collected.truncated || matrix.columnsTruncated) {
             registerInput.truncated = true;
+        }
+        if (collected.truncated) {
             registerInput.maxRows = maxCalls;
         }
         const dfResult = await bridge.registerDataframe(ctx, registerInput);
@@ -223,7 +254,7 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             variantColumnLegend: matrix.variantColumnLegend,
             callFormatting: collected.callFormatting,
             dataframe: dataframeHandle,
-            truncated: collected.truncated,
+            truncated: collected.truncated || matrix.columnsTruncated,
             warnings,
         };
         if (vcf !== undefined)
@@ -238,7 +269,7 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
         const lines = [];
         lines.push(`# Genotype matrix — ${result.format} — ${result.rowCount} germplasm × ${result.columnCount} variants — \`${result.alias}\``);
         if (result.truncated)
-            lines.push('> **Truncated** at pull cap. See `warnings` for details.');
+            lines.push('> **Truncated.** See `warnings` for which cap fired.');
         lines.push('');
         lines.push('## Dataframe');
         lines.push(...renderDataframeHandle(result.dataframe));
@@ -323,26 +354,48 @@ function renderTextPreview(opts) {
  *
  * Row identity: `callSetDbId` (preferred) or `callSetName`, else `'unknown'`.
  * Variant identity: `variantDbId` (preferred) or `variantName`.
+ *
+ * `maxColumns` bounds the distinct-variant column count only — never the
+ * germplasm rows. Every germplasm seen in any row is registered as a matrix
+ * row; the cap drops variant *columns*, not rows. The cap is enforced as rows
+ * stream in: once `maxColumns` distinct variants have been seen, a row
+ * introducing a *net-new* variant contributes no column and no stored genotype,
+ * but its germplasm is still registered first. A germplasm whose calls all
+ * reference beyond-cap variants therefore renders as an honest all-null row —
+ * present, empty in the kept columns — never a vanished row. This stays a
+ * resource bound: the over-wide legend and per-column genotype cells are never
+ * built, not built-then-trimmed.
  */
-function buildMatrix(rows, callFormatting) {
+function buildMatrix(rows, callFormatting, maxColumns) {
     const variantSeen = new Set();
     const variantIdOrder = [];
     const sampleSeen = new Set();
     const sampleOrder = [];
     const sampleLabels = {};
     const genotypeAt = new Map();
+    let columnsTruncated = false;
     for (const row of rows) {
         const vid = row.variantDbId ?? row.variantName ?? 'unknown_variant';
-        if (!variantSeen.has(vid)) {
-            variantSeen.add(vid);
-            variantIdOrder.push(vid);
-        }
+        // Register the germplasm (sample) on its first appearance, BEFORE the
+        // variant-cap check below. Gating registration on a kept variant would drop
+        // the entire row of any germplasm whose calls all reference beyond-cap
+        // variants — silent row loss under germplasm-major, disjoint coverage (the
+        // common Breedbase /search/calls shape). It must still appear, empty in the
+        // kept columns.
         const sampleKey = row.callSetDbId ?? row.callSetName ?? 'unknown';
         if (!sampleSeen.has(sampleKey)) {
             sampleSeen.add(sampleKey);
             sampleOrder.push(sampleKey);
             sampleLabels[sampleKey] = row.callSetName ?? sampleKey;
         }
+        if (!variantSeen.has(vid)) {
+            if (variantIdOrder.length >= maxColumns) {
+                columnsTruncated = true;
+                continue;
+            }
+            variantSeen.add(vid);
+            variantIdOrder.push(vid);
+        }
         const gt = renderGenotypeString(row, callFormatting);
         let byVariant = genotypeAt.get(sampleKey);
         if (!byVariant) {
@@ -365,6 +418,7 @@ function buildMatrix(rows, callFormatting) {
         matrixRows,
         variantColumnLegend,
         columnCount: variantIdOrder.length,
+        columnsTruncated,
         variantIdOrder,
         sampleOrder,
         sampleLabels,

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED Viewed

@@ -434,6 +434,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         "matrix-json": "matrix-json";
     }>;
     maxCalls: import("zod").ZodOptional<import("zod").ZodNumber>;
+    maxColumns: import("zod").ZodOptional<import("zod").ZodNumber>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     alias: import("zod").ZodString;
     format: import("zod").ZodEnum<{

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

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

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

@@ -195,6 +195,35 @@ export declare function renderFindHeader(opts: {
  * surfaces in the warnings produced by `checkFilterMatchRates`.
  */
 export declare function renderAppliedFilters(filters: Record<string, unknown>, serverToUser?: Record<string, string>): string;
+/**
+ * Character budget for one rendered comma-joined list line before it caps.
+ *
+ * Sized by rendered width rather than a fixed entry count so a line adapts to
+ * its data: the common case (a distribution over a 26-study server, a `find_*`
+ * dataframe's ~18 columns) renders complete, while a pathological one (a
+ * spilled set whose `fullRows` reach {@link MAX_SPILLOVER_ROWS}; a genotype
+ * matrix's 500,000 variant columns) caps instead of emitting megabytes into
+ * `content[]`. Mirrors {@link MAX_INLINE_JSON}'s size-aware philosophy; a
+ * hardcoded top-N did neither job well.
+ *
+ * Applied only to lines whose omitted entries stay retrievable elsewhere —
+ * never to a line that is the sole carrier of a mapping (see
+ * `renderDataframeHandle`'s `renamedColumns`).
+ *
+ * Exported so `brapi_dataframe_describe` can bound its own per-column listing
+ * with the same width-aware budget rather than reimplementing an equivalent.
+ */
+export declare const MAX_LIST_LINE = 400;
+/**
+ * Join `parts` with `, ` until `budget` characters are consumed. Always emits
+ * at least one part — a line naming no value carries less than one that
+ * overruns the budget slightly. Returns the rendered prefix plus how many parts
+ * were left out, so callers can append their own recovery hint.
+ */
+export declare function joinWithinBudget(parts: readonly string[], budget: number): {
+    omitted: number;
+    text: string;
+};
 /**
  * Render a distributions block in markdown. Pass the `find_*` result's
  * dataframe handle (when it spilled): a truncation caveat is prepended when the
@@ -308,9 +337,12 @@ export type DataframeHandle = z.infer<typeof DataframeHandleSchema>;
  *
  * This is a *summary* surface — it is not the authoritative carrier of the
  * schema, so `columns` is budgeted: it costs megabytes on a wide pivot (a
- * genotype matrix reaches 500,000 variant columns) while
- * `brapi_dataframe_describe` lists the full schema on demand, uncapped, from
- * `content[]`. `renamedColumns` is deliberately NOT budgeted — it is the only
+ * genotype matrix reaches 500,000 variant columns). The omission notice points
+ * at `brapi_dataframe_query` (`SELECT * FROM <table> LIMIT 0` renders the full
+ * column list, uncapped, in `content[]`) rather than at
+ * `brapi_dataframe_describe`, whose own per-column listing is now budgeted the
+ * same way — pointing a capped line at another capped line is circular.
+ * `renamedColumns` is deliberately NOT budgeted — it is the only
  * mapping from a sanitized column back to its upstream key, with no describe
  * or re-call path behind it, and capping the sole decoder is the same defect as
  * capping the tool-level variant legend. It stays bounded in practice anyway:

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

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

@@ -358,15 +358,18 @@ export function renderAppliedFilters(filters, serverToUser = {}) {
  * Applied only to lines whose omitted entries stay retrievable elsewhere —
  * never to a line that is the sole carrier of a mapping (see
  * `renderDataframeHandle`'s `renamedColumns`).
+ *
+ * Exported so `brapi_dataframe_describe` can bound its own per-column listing
+ * with the same width-aware budget rather than reimplementing an equivalent.
  */
-const MAX_LIST_LINE = 400;
+export const MAX_LIST_LINE = 400;
 /**
  * Join `parts` with `, ` until `budget` characters are consumed. Always emits
  * at least one part — a line naming no value carries less than one that
  * overruns the budget slightly. Returns the rendered prefix plus how many parts
  * were left out, so callers can append their own recovery hint.
  */
-function joinWithinBudget(parts, budget) {
+export function joinWithinBudget(parts, budget) {
     const shown = [];
     let remaining = budget;
     for (const part of parts) {
@@ -525,9 +528,12 @@ export const DataframeHandleSchema = z.object({
  *
  * This is a *summary* surface — it is not the authoritative carrier of the
  * schema, so `columns` is budgeted: it costs megabytes on a wide pivot (a
- * genotype matrix reaches 500,000 variant columns) while
- * `brapi_dataframe_describe` lists the full schema on demand, uncapped, from
- * `content[]`. `renamedColumns` is deliberately NOT budgeted — it is the only
+ * genotype matrix reaches 500,000 variant columns). The omission notice points
+ * at `brapi_dataframe_query` (`SELECT * FROM <table> LIMIT 0` renders the full
+ * column list, uncapped, in `content[]`) rather than at
+ * `brapi_dataframe_describe`, whose own per-column listing is now budgeted the
+ * same way — pointing a capped line at another capped line is circular.
+ * `renamedColumns` is deliberately NOT budgeted — it is the only
  * mapping from a sanitized column back to its upstream key, with no describe
  * or re-call path behind it, and capping the sole decoder is the same defect as
  * capping the tool-level variant legend. It stays bounded in practice anyway:
@@ -537,7 +543,9 @@ export const DataframeHandleSchema = z.object({
  */
 export function renderDataframeHandle(handle) {
     const { text: columns, omitted } = joinWithinBudget(handle.columns, MAX_LIST_LINE);
-    const columnsSuffix = omitted > 0 ? `, …+${omitted} more — brapi_dataframe_describe lists the full schema` : '';
+    const columnsSuffix = omitted > 0
+        ? `, …+${omitted} more — list all columns via brapi_dataframe_query: \`SELECT * FROM ${handle.tableName} LIMIT 0\``
+        : '';
     const lines = [
         `- tableName: \`${handle.tableName}\` (query via brapi_dataframe_query)`,
         `- rowCount: ${handle.rowCount}`,

package/dist/mcp-server/tools/shared/find-helpers.js.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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package/manifest.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "brapi-mcp-server",
-  "version": "0.7.8",
+  "version": "0.7.9",
   "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
   "author": {
     "name": "cyanheads"

package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.7.8",
+  "version": "0.7.9",
   "description": "A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, & more - across Breedbase, T3, Sweetpotatobase, & any BrAPI v2-compliant server.",
   "author": "Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)",
   "type": "module",
@@ -92,7 +92,7 @@
     "@types/node": "^26.1.1",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.6",
-    "tsc-alias": "^1.8.17",
+    "tsc-alias": "^1.9.1",
     "typescript": "^6.0.3",
     "vitest": "^4.1.10"
   }

package/server.json CHANGED Viewed

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.7.8",
+  "version": "0.7.9",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.8",
+      "version": "0.7.9",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -56,7 +56,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.8",
+      "version": "0.7.9",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }