@cyanheads/brapi-mcp-server 0.7.6 → 0.7.8

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.7.6
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.9`
+**Version:** 0.7.8
+**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/Dockerfile

@@ -4,15 +4,20 @@
 # This stage installs all dependencies (including dev), builds the TypeScript
 # source code into JavaScript, and prepares the production assets.
 # ==============================================================================
-FROM oven/bun:1.3 AS build
+FROM oven/bun:1.3.14 AS build
 
 WORKDIR /usr/src/app
 
 # Copy dependency manifests for optimized layer caching
 COPY package.json bun.lock ./
 
-# Install all dependencies (including dev dependencies for building)
-RUN bun install --frozen-lockfile
+# Install all dependencies (including dev dependencies for building).
+# The BuildKit cache mount persists Bun's global package cache across builds.
+# --ignore-scripts: the build only runs tsc, which needs type declarations, not
+# compiled bindings. DuckDB ships prebuilt os/cpu-gated binding packages, so no
+# native postinstall is needed here.
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --frozen-lockfile --ignore-scripts
 
 # Copy the rest of the source code
 COPY . .
@@ -28,7 +33,7 @@ RUN bun run build
 # application. It uses a slim base image and only includes production
 # dependencies and build artifacts.
 # ==============================================================================
-FROM oven/bun:1.3-slim AS production
+FROM oven/bun:1.3.14-slim AS production
 
 WORKDIR /usr/src/app
 
@@ -49,13 +54,15 @@ COPY package.json bun.lock ./
 
 # Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
 # that are not needed in the final production image.
-RUN bun install --production --frozen-lockfile --ignore-scripts
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    bun install --production --frozen-lockfile --ignore-scripts
 
 # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
 # These are not bundled by default to keep the base image lean. Enable at build time
 # with: docker build --build-arg OTEL_ENABLED=true
 ARG OTEL_ENABLED=true
-RUN if [ "$OTEL_ENABLED" = "true" ]; then \
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    if [ "$OTEL_ENABLED" = "true" ]; then \
       bun add @hono/otel \
         @opentelemetry/instrumentation-http \
         @opentelemetry/exporter-metrics-otlp-http \
@@ -73,7 +80,8 @@ RUN if [ "$OTEL_ENABLED" = "true" ]; then \
 # CANVAS_PROVIDER_TYPE=duckdb. Disable for size-sensitive self-builds with:
 #   docker build --build-arg CANVAS_ENABLED=false
 ARG CANVAS_ENABLED=true
-RUN if [ "$CANVAS_ENABLED" = "true" ]; then \
+RUN --mount=type=cache,target=/root/.bun/install/cache \
+    if [ "$CANVAS_ENABLED" = "true" ]; then \
       bun add @duckdb/node-api; \
     fi
 
@@ -106,9 +114,10 @@ ENV MCP_FORCE_CONSOLE_LOGGING="true"
 # Expose the port the server listens on
 EXPOSE ${MCP_HTTP_PORT}
 
-# Health check — hits the framework's /healthz endpoint
+# Health check — hits the framework's /healthz endpoint using a bun-native
+# fetch (the slim image ships no curl/wget).
 HEALTHCHECK --interval=30s --timeout=10s --start-period=10s --retries=3 \
-  CMD curl -f http://localhost:${MCP_HTTP_PORT}/healthz || exit 1
+  CMD bun -e "fetch('http://localhost:'+(process.env.MCP_HTTP_PORT??'3010')+'/healthz').then((r)=>process.exit(r.ok?0:1)).catch(()=>process.exit(1))"
 
 # The command to start the server
 CMD ["bun", "run", "dist/index.js"]

package/README.md

@@ -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-0.7.6-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-v1.3.11-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-0.7.8-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)
 
 </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). |
 
@@ -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).

package/changelog/0.7.x/0.7.7.md

@@ -0,0 +1,43 @@
+---
+summary: "mcp-ts-core ^0.10.9 → ^0.10.14, adopting the supply-chain install guard (bunfig minimumReleaseAge, Socket scanner) and a bun-native Docker HEALTHCHECK the slim image can actually run; capped find_* renders and the genotype-matrix preview now name the dataframe holding the rest; export_genotype_matrix clamps maxCalls to the deployment ceiling"
+breaking: false
+security: false
+---
+
+# 0.7.7 — 2026-07-15
+
+## Added
+
+- **`GENOTYPE_CALLS_MAX_PULL_CEILING`** — exported from `src/config/server-config.ts` (500,000). Bounds both the `genotypeCallsMaxPull` config max and `brapi_export_genotype_matrix`'s `maxCalls` input, so the advertised input range and the deployment ceiling cannot drift apart. ([#45](https://github.com/cyanheads/brapi-mcp-server/issues/45))
+- **Supply-chain install guard** — `bunfig.toml` gains `minimumReleaseAge = 259200` (a 3-day hold on freshly published versions; existing `bun.lock` entries are unaffected) with `minimumReleaseAgeExcludes = ["@cyanheads/mcp-ts-core"]`, plus `[install.security] scanner = "@socketsecurity/bun-security-scanner"`. Configuring a scanner disables Bun's auto-install.
+- **`.github/SECURITY.md`, `.github/FUNDING.yml`, `.gitattributes`** — disclosure policy, funding metadata, and LF normalization with `linguist-generated` markers on `bun.lock`, `CHANGELOG.md`, and `docs/tree.md`.
+
+## Changed
+
+- **`@cyanheads/mcp-ts-core`** `^0.10.9` → `^0.10.14`. Picks up the supply-chain guard and `oven/bun:1.3.14` Dockerfile pin with BuildKit install-cache mounts ([0.10.13](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.10.x/0.10.13.md)); the Docker build stage's `--ignore-scripts`, a definition-linter null guard, and canvas `importFrom` carrying `reason: 'missing_table'` ([0.10.14](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.10.x/0.10.14.md)); canvas not-found errors carrying `reason: 'canvas_not_found'` plus a recovery hint ([0.10.12](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.10.x/0.10.12.md)); the changelog `security` flag scoped to source-code fixes ([0.10.11](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.10.x/0.10.11.md)); and the js-yaml v4 → v5 migration ([0.10.10](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.10.x/0.10.10.md)).
+- **`renderDistributions`** — takes the caller's `DataframeHandle` directly instead of a projected `{ truncated, rowCount, totalCount }` object, so a capped line can name the dataframe holding the omitted entries.
+- **`collectPassthroughParts`** — accepts an optional trailing `DataframeHandle`. The `get_*` detail tools pass nothing: their records are not in a dataframe.
+- **`devcheck` Outdated gate** — a row bun reports as held by `minimumReleaseAge` (Update equal to Current, marked `*`) is no longer a finding; a genuine update still fails the gate. `typescript` added to the outdated allowlist.
+- **Twelve `skills/<name>/SKILL.md` re-synced** from the framework — `add-tool` 2.15→2.16, `api-canvas` 1.7→1.9, `api-linter` 1.7→1.8, `api-utils` 2.3→2.4, `api-workers` 1.5→1.6, `code-simplifier` 1.1→1.2, `design-mcp-server` 2.18→2.20, `git-wrapup` 1.4→1.7, `orchestrations` 1.4→1.6, `polish-docs-meta` 2.9→2.11, `release-and-publish` 2.9→2.11, `techniques` 0.1→0.2 — mirrored into `.claude/skills/` and `.agents/skills/`.
+- **`package.json` packaging** — `author` set to `Casey Hand <casey@caseyjhand.com> (https://caseyjhand.com)`; `packageManager` bun@1.3.11 → bun@1.3.14.
+
+## Removed
+
+- **`truncationMeta`** — dropped from `find-helpers.ts`; `renderDistributions` now reads the handle's `truncated`/`rowCount`/`totalCount` itself.
+
+## Fixed
+
+- **Capped `find_*` renders pointed content-only clients at `structuredContent`** — a surface those clients cannot read. Oversized passthrough values and capped distributions now name the spilled dataframe and `brapi_dataframe_query` as the retrieval path, falling back to `structuredContent` only when no dataframe exists. `renderDistributions`'s hardcoded top-5 cap is replaced by a 400-character line budget, so a distribution that fits renders complete instead of dropping values at a scale that cost nothing to show. ([#41](https://github.com/cyanheads/brapi-mcp-server/issues/41))
+- **`brapi_export_genotype_matrix` honored a caller `maxCalls` above the deployment ceiling** — the pull is now clamped to `min(maxCalls, genotypeCallsMaxPull)` with the effective cap reported in `warnings`, and the input schema rejects anything above `GENOTYPE_CALLS_MAX_PULL_CEILING`. `maxCalls` bounds the generated matrix, so an unclamped override also sized the `vcf`/`ped`/`map` text and the canvas table. ([#45](https://github.com/cyanheads/brapi-mcp-server/issues/45))
+- **`brapi_export_genotype_matrix` truncated the variant column legend at 20 entries** — the legend is the only decoder from a sanitized column name back to its variant ID and has no describe or re-call path behind it, so it now renders complete. The VCF/PLINK preview notice names the matrix dataframe as a content-visible path to the genotypes, disclosing that it carries no CHROM/POS/REF/ALT coordinates, and now renders outside the fenced block rather than inside it. The preview cap itself stays: a skewed input can drive one serialization to ~16MB. Partially resolves [#42](https://github.com/cyanheads/brapi-mcp-server/issues/42) — the render-side loss is closed; the unbounded `columnCount` behind it is tracked in [#46](https://github.com/cyanheads/brapi-mcp-server/issues/46).
+- **Docker `HEALTHCHECK` probed with `curl`, which `oven/bun:*-slim` does not ship** — a container reported `unhealthy` for its whole lifetime while serving correctly, failing any orchestrator gating on container health. Replaced with a bun-native `fetch` probe. ([#44](https://github.com/cyanheads/brapi-mcp-server/issues/44))
+- **`renderDataframeHandle`** — the `columns` list is budgeted to one line and points at `brapi_dataframe_describe` for the full schema, bounding a wide genotype-matrix pivot. `renamedColumns` stays uncapped: it is the sole decoder for its mapping.
+- **`brapi_submit_observations` apply mode returned `elicit_unavailable` on every client** — `ctx.elicit` was undefined at runtime, so the confirmation gate failed closed even for elicitation-capable clients and steered callers toward `force: true`. Fixed upstream in mcp-ts-core 0.10.3 ([cyanheads/mcp-ts-core#211](https://github.com/cyanheads/mcp-ts-core/issues/211)) and settled here by the `^0.10.14` adoption — no change to this server's code. ([#38](https://github.com/cyanheads/brapi-mcp-server/issues/38))
+
+## Dependencies
+
+- **`@cyanheads/mcp-ts-core`** `^0.10.9` → `^0.10.14`
+- **`@socketsecurity/bun-security-scanner`** — new devDependency at `^1.1.2` (Bun install scanner)
+- **`@types/node`** `^26.0.0` → `^26.1.1`
+- **`ignore`** `^7.0.5` → `^7.0.6`
+- **`vitest`** `^4.1.9` → `^4.1.10`

package/changelog/0.7.x/0.7.8.md

@@ -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/template.md

@@ -15,9 +15,11 @@ summary: ""
 # usage. Flagged as `Breaking` in the rollup.
 breaking: false
 
-# Set `true` if this release contains any security fix. Pairs with the
-# `## Security` section below. Flagged as `Security` in the rollup so
-# users can triage upgrade urgency at a glance.
+# Set `true` ONLY for a security fix in THIS project's own source code — a
+# vulnerability or hardening in code you ship. A dependency or transitive CVE
+# bump is routine maintenance, NOT a security release: record it under
+# `## Dependencies` (with the advisory ID) and leave this `false`. When true,
+# pairs with the `## Security` section below and flags `Security` in the rollup.
 security: false
 
 # Optional free-form notes for maintenance agents processing this release.

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

@@ -8,6 +8,14 @@
  * @module config/server-config
  */
 import { z } from '@cyanheads/mcp-ts-core';
+/**
+ * Absolute upper bound on `genotypeCallsMaxPull`, and therefore on any
+ * caller-supplied `maxCalls` override. No deployment can configure a ceiling
+ * above this, so a tool input above it can never be honored — the input schemas
+ * bound against this constant rather than restating the literal, keeping the
+ * advertised input range and the deployment ceiling from drifting apart.
+ */
+export declare const GENOTYPE_CALLS_MAX_PULL_CEILING = 500000;
 export declare const ServerConfigSchema: z.ZodObject<{
     defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
     defaultUsername: z.ZodOptional<z.ZodString>;

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

@@ -1 +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,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAyJ7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA8B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}
+{"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,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAyJ7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA8B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

package/dist/config/server-config.js

@@ -9,6 +9,14 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+/**
+ * Absolute upper bound on `genotypeCallsMaxPull`, and therefore on any
+ * caller-supplied `maxCalls` override. No deployment can configure a ceiling
+ * above this, so a tool input above it can never be honored — the input schemas
+ * bound against this constant rather than restating the literal, keeping the
+ * advertised input range and the deployment ceiling from drifting apart.
+ */
+export const GENOTYPE_CALLS_MAX_PULL_CEILING = 500_000;
 export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
         .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
@@ -109,9 +117,9 @@ export const ServerConfigSchema = z.object({
         .number()
         .int()
         .positive()
-        .max(500_000)
+        .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 invocation. Bounds total page count per query — protects the upstream from unbounded pagination loops. 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).'),
+        .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).'),
     canvasDropEnabled: z
         .stringbool()
         .default(false)

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

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

@@ -1 +1 @@
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+{"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"}

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

@@ -29,7 +29,7 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
-import { getServerConfig } from '../../../config/server-config.js';
+import { GENOTYPE_CALLS_MAX_PULL_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';
@@ -40,7 +40,7 @@ import { buildCallsSearchBody, collectCalls, renderGenotypeString, } from '../sh
 /** Max variant records scanned when pulling coordinate metadata for vcf/plink. */
 const MAX_VARIANT_METADATA_ROWS = 50_000;
 const VARIANT_METADATA_PAGE_SIZE = 1_000;
-/** Lines of format text shown inline in content[]; full text lives in structuredContent. */
+/** Lines of format text shown inline in content[] before the preview notice fires. */
 const FORMAT_PREVIEW_LINES = 25;
 // ---------------------------------------------------------------------------
 // Output schema
@@ -129,8 +129,9 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             .number()
             .int()
             .positive()
+            .max(GENOTYPE_CALLS_MAX_PULL_CEILING)
             .optional()
-            .describe('Override the deployment-level pull cap (BRAPI_GENOTYPE_CALLS_MAX_PULL). Useful for large panels where the default is too low.'),
+            .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`.'),
     }),
     output: OutputSchema,
     async handler(input, ctx) {
@@ -147,7 +148,18 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
             throw ctx.fail('search_endpoint_disabled', `Dialect '${dialect.id}' marks POST /search/calls as known-dead on this server. Genotype-call workflows are not viable here.`, { dialectId: dialect.id, ...ctx.recoveryFor('search_endpoint_disabled') });
         }
         const config = getServerConfig();
-        const maxCalls = input.maxCalls ?? config.genotypeCallsMaxPull;
+        const warnings = [];
+        // The deployment ceiling wins: `maxCalls` may lower the pull for this call
+        // but never raise it past what the operator configured. `maxCalls` is the
+        // only bound on the generated matrix — and therefore on the vcf/ped/map
+        // text and the canvas table — so an unclamped override would let a single
+        // call page far past the operator's limit and generate an artifact sized
+        // to match.
+        const requestedMaxCalls = input.maxCalls ?? config.genotypeCallsMaxPull;
+        const maxCalls = Math.min(requestedMaxCalls, config.genotypeCallsMaxPull);
+        if (maxCalls < requestedMaxCalls) {
+            warnings.push(`maxCalls=${requestedMaxCalls} exceeds this deployment's genotype-call ceiling (BRAPI_GENOTYPE_CALLS_MAX_PULL=${config.genotypeCallsMaxPull}); the pull was capped at ${maxCalls} calls. Results may be truncated — see \`truncated\`.`);
+        }
         const searchOpts = {
             variantSetDbId: input.variantSetDbId,
         };
@@ -157,7 +169,6 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
         if (!searchBody.variantSetDbIds) {
             throw ctx.fail('no_filters', 'variantSetDbId is required — unfiltered genotype-call pulls are prohibitively expensive.', { ...ctx.recoveryFor('no_filters') });
         }
-        const warnings = [];
         const collected = await collectCalls({
             client,
             connection,
@@ -243,24 +254,29 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
         if (legendEntries.length > 0) {
             const remapped = legendEntries.filter(([col, orig]) => col !== orig);
             if (remapped.length > 0) {
+                // Rendered in full: this legend is the only thing that decodes the
+                // sanitized column names back to variant IDs, and it has no dataframe
+                // or re-call path to fall back on — a cap here silently drops the
+                // decoding for columns the `## Dataframe` section above already names.
                 lines.push('## Column name remappings (sanitized → original)');
-                for (const [col, orig] of remapped.slice(0, 20)) {
+                for (const [col, orig] of remapped) {
                     lines.push(`- \`${col}\` → \`${orig}\``);
                 }
-                if (remapped.length > 20)
-                    lines.push(`- …and ${remapped.length - 20} more`);
                 lines.push('');
             }
         }
-        // Render the format text (preview-capped; full text is in structuredContent).
+        // Independent `if`s, never an if/else chain on `format`: the parity linter
+        // populates every output field at once, so an untaken branch would render
+        // nothing and fail the check. Render on field presence.
+        const tableName = result.dataframe.tableName;
         if (result.vcf !== undefined) {
-            lines.push(...renderTextPreview('VCF-lite', 'vcf', result.vcf));
+            lines.push(...renderTextPreview({ label: 'VCF-lite', field: 'vcf', text: result.vcf, tableName }));
         }
         if (result.map !== undefined) {
-            lines.push(...renderTextPreview('PLINK .map', 'map', result.map));
+            lines.push(...renderTextPreview({ label: 'PLINK .map', field: 'map', text: result.map, tableName }));
         }
         if (result.ped !== undefined) {
-            lines.push(...renderTextPreview('PLINK .ped', 'ped', result.ped));
+            lines.push(...renderTextPreview({ label: 'PLINK .ped', field: 'ped', text: result.ped, tableName }));
         }
         if (result.warnings.length > 0) {
             lines.push('## Warnings');
@@ -274,14 +290,31 @@ export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
 // ---------------------------------------------------------------------------
 // content[] text preview
 // ---------------------------------------------------------------------------
-function renderTextPreview(label, field, text) {
-    const allLines = text.split('\n');
+/**
+ * Render a format text field as a capped preview plus a notice naming where the
+ * rest can actually be read.
+ *
+ * The text is not rendered complete on purpose: `maxCalls` bounds
+ * `rowCount × columnCount`, but nothing constrains the germplasm-to-variant
+ * ratio, so a schema-legal skew (one germplasm × `maxCalls` variants) drives a
+ * single `vcf` or `map` string to ~16MB at the 500,000 ceiling — and
+ * `content[]` would carry it a second time on top of `structuredContent`.
+ *
+ * The notice names the dataframe rather than only `structuredContent`, which
+ * content-only clients cannot read. It is registered for every format, so it
+ * always exists by the time this runs. The coordinate caveat is not hedging:
+ * the dataframe holds `{germplasmDbId, <variant columns>: genotype}` and none
+ * of the CHROM/POS/REF/ALT metadata pulled separately from `/variants`, so
+ * presenting it as a complete substitute for the text would be false.
+ */
+function renderTextPreview(opts) {
+    const allLines = opts.text.split('\n');
     const preview = allLines.slice(0, FORMAT_PREVIEW_LINES);
-    const out = [`## ${label}`, '```', ...preview];
+    const out = [`## ${opts.label}`, '```', ...preview, '```'];
     if (allLines.length > FORMAT_PREVIEW_LINES) {
-        out.push(`… ${allLines.length - FORMAT_PREVIEW_LINES} more line(s) — full text in structuredContent.${field}`);
+        out.push(`… ${allLines.length - FORMAT_PREVIEW_LINES} more line(s) not shown. Complete text: \`structuredContent.${opts.field}\`. Every germplasm × variant genotype is also in dataframe \`${opts.tableName}\` — query it with brapi_dataframe_query; it carries genotypes only, not the CHROM/POS/REF/ALT coordinates shown above.`);
     }
-    out.push('```', '');
+    out.push('');
     return out;
 }
 /**

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwQjC,CAAC"}
+{"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyQjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js

@@ -18,7 +18,7 @@ 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 { AliasInput, asString, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, toDataframeHandle, truncationMeta, } from '../shared/find-helpers.js';
+import { AliasInput, asString, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
 import { buildCallsSearchBody, collectCalls } from '../shared/genotype-calls.js';
 const CallRowSchema = z
     .object({
@@ -277,8 +277,7 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
         lines.push(`- sepUnphased: ${f.sepUnphased ?? '—'}`);
         lines.push('');
         lines.push('## Distributions');
-        lines.push(renderDistributions(result.distributions, truncationMeta(result.dataframe)) ||
-            '_No values to summarize._');
+        lines.push(renderDistributions(result.distributions, result.dataframe) || '_No values to summarize._');
         lines.push('');
         lines.push('## Calls');
         if (result.results.length === 0) {
@@ -311,7 +310,7 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
                     parts.push(`genotypeValue=${call.genotypeValue}`);
                 if (call.phaseSet)
                     parts.push(`phaseSet=${call.phaseSet}`);
-                parts.push(...collectPassthroughParts(call, RENDERED));
+                parts.push(...collectPassthroughParts(call, RENDERED, result.dataframe));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.d.ts.map

@@ -1 +1 @@
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