npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.7 → 0.7.9 - Mend

@cyanheads/brapi-mcp-server 0.7.7 → 0.7.9

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Files changed (55) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.7.7
+**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-0.7.7-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>
@@ -46,7 +46,7 @@
 | `brapi_find_observations` | Pull observation records by study / germplasm / variable / season / unit / timestamp. Dataframe spillover. |
 | `brapi_find_images` | Filter image metadata by unit / study / ontology / MIME type. Bytes via `brapi_get_image`. |
 | `brapi_get_image` | Fetch image bytes for up to 5 imageDbIds inline as `type: image` blocks. Prefers `/imagecontent`, falls back to `imageURL`. |
-| `brapi_find_locations` | Find research stations by country / type / abbreviation, with optional client-side bbox filter. |
+| `brapi_find_locations` | Find research stations by country (ISO alpha-3 code, or English country name resolved client-side) / type / abbreviation, with optional client-side bbox filter. |
 | `brapi_find_variants` | Find variant records by variant set, reference, or genomic region (1-based inclusive / exclusive). |
 | `brapi_find_genotype_calls` | Pull genotype calls via async-search polling. Upstream pull bounded by `BRAPI_GENOTYPE_CALLS_MAX_PULL` (default 100k, max 500k). |
@@ -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`)
@@ -133,7 +133,7 @@ Within one (tenant, session), dataframes act as a self-cleaning shared notebook:
 - **Dialect adaptation** — `spec` / `brapi-test` / `breedbase` / `cassavabase` / `bms` dialects translate v2.1 plural filter keys to the singular form each server family honors, drop filters known to be broken, normalize sparse-shape encodings, and escalate to POST `/search/{noun}` when GET would silently downcast multi-value filters. Detected from `/serverinfo` (server-name / organization-name); pin per-alias via `BRAPI_<ALIAS>_DIALECT`. Verified-vs-inferred mapping counts surface on the orientation envelope so agents see the confidence floor at a glance.
 - **DuckDB required** — `@duckdb/node-api` is a regular dependency; startup fails closed when the framework canvas is unavailable. Not supported on Cloudflare Workers (no native binary in that runtime).
 - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern automatically.
-- **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call); a 1,000-node safety cap bounds the walk and sets `truncated` when reached.
+- **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call); a 1,000-node safety cap bounds the walk and sets `truncated` when reached. Walks larger than `loadLimit` spill their node and edge sets to two JOINable canvas dataframes and return a bounded inline preview.
 - **Image content** — `brapi_get_image` fetches bytes inline as MCP `type: image` blocks, preferring `/images/{id}/imagecontent` with `imageURL` fallback.
 - **Free-text variable ranking** — `OntologyResolver` scores variables against a query (PUI / name / synonym / trait-class) so `find_variables text:"..."` returns ranked candidates even without `/ontologies`.
 - **Auth variants in one schema** — tagged-union covers `none` / `bearer` / `api_key` / `sgn` (session-token exchange) / `oauth2` (client-credentials).
@@ -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/0.7.8.md ADDED Viewed

@@ -0,0 +1,14 @@
+---
+summary: "brapi_germplasm_performance gains an optional studyDbIds bypass for its study-discovery cap; brapi_walk_pedigree spills node and edge sets exceeding loadLimit to two JOINable canvas dataframes; brapi_find_locations resolves free-form country names to ISO 3166-1 alpha-3 codes via a new iso-country service"
+breaking: false
+security: false
+---
+# 0.7.8 — 2026-07-16
+## Added
+- **`brapi_germplasm_performance` `studyDbIds`** — optional input that bypasses automatic study discovery (and its 200-study `STUDY_DISCOVERY_CAP`) entirely. Pass a specific set — e.g. the full germplasm-scoped list retrieved via `brapi_find_studies` with `extraFilters.germplasmDbIds` — to aggregate a slice discovery would otherwise cap. ([#43](https://github.com/cyanheads/brapi-mcp-server/issues/43))
+- **`germplasmDbIds`** — added to the `/studies` filter catalog (`brapi_describe_filters`); the capped-discovery warning on `brapi_germplasm_performance` now names this `brapi_find_studies` retrieval path alongside the `studyDbIds` input above. ([#43](https://github.com/cyanheads/brapi-mcp-server/issues/43))
+- **`brapi_walk_pedigree` dataframe spillover** — new `loadLimit` input; when the node or edge set exceeds it, both spill to two canvas dataframes (`nodesDataframe` / `edgesDataframe`, JOINable on `germplasmDbId`) with a bounded inline preview. Completes [#17](https://github.com/cyanheads/brapi-mcp-server/issues/17) — Part B of the walk's cap handling; the 1,000-node safety cap and truncation warning (Part A) shipped in [0.7.1](https://github.com/cyanheads/brapi-mcp-server/blob/main/changelog/0.7.x/0.7.1.md).
+- **`brapi_find_locations` `countryNames`** — free-form English country names and aliases (e.g. "Uganda", "USA") resolved client-side to ISO 3166-1 alpha-3 codes and merged into `countryCodes`; unresolved names surface as a warning. New `src/services/iso-country/` service backs the resolution — 249 countries, case- and diacritic-insensitive, accepts alpha-2/alpha-3 codes directly. ([#19](https://github.com/cyanheads/brapi-mcp-server/issues/19))

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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1	+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C;;;;;;GAMG;AACH,eAAO,MAAM,+BAA+B,SAAU,CAAC;AAEvD;;;;;;;;GAQG;AACH,eAAO,MAAM,mCAAmC,SAAU,CAAC;AAE3D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAkK7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA+B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

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',

package/dist/config/server-config.js.map CHANGED Viewed

	@@ -1 +1 @@
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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/brapi-find-locations.tool.d.ts CHANGED Viewed

@@ -14,6 +14,7 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
     locations: z.ZodOptional<z.ZodArray<z.ZodString>>;
     locationNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
     countryCodes: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    countryNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
     locationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
     abbreviations: z.ZodOptional<z.ZodArray<z.ZodString>>;
     bbox: z.ZodOptional<z.ZodObject<{

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAiHjE~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAkX7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmY7B,CAAC"}