npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.5 → 0.7.7 - Mend

@cyanheads/brapi-mcp-server 0.7.5 → 0.7.7

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 (44) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,8 +1,8 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.7.5
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.6`
+**Version:** 0.7.7
+**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 CHANGED Viewed

@@ -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 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-0.7.5-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-0.7.7-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)
 </div>

package/changelog/0.7.x/0.7.6.md ADDED Viewed

@@ -0,0 +1,24 @@
+---
+summary: "mcp-ts-core ^0.10.6 → ^0.10.9 — ctx.content media collector, two new devcheck guards (dependency specifiers, plugin marketplace manifests), sharper canvas SQL error classification; @duckdb/node-api and @types/node bumps; eight skills re-synced"
+breaking: false
+security: false
+---
+# 0.7.6 — 2026-06-20
+## Added
+- **`check-dependency-specifiers` devcheck step** — re-synced `scripts/check-dependency-specifiers.ts` (registered in `ALL_CHECKS`, flag `--no-dep-specifiers`) hard-fails on floating specifiers (`latest`, `*`, pre-release dist-tags) in `package.json` dependency sections and `bun.lock`'s `workspaces` map. Catches a `bun update --latest` writing a `latest` dist-tag into the lock that would let the next `bun install` re-resolve past an intentional hold. ([cyanheads/mcp-ts-core#246](https://github.com/cyanheads/mcp-ts-core/issues/246))
+- **Plugin marketplace manifest checks** — `lint:packaging` gains a check validating `.claude-plugin/plugin.json` and `.codex-plugin/plugin.json` (+ `.codex-plugin/mcp.json`): non-empty descriptions, unscoped machine name in display fields, and the full `package.json` name in the `npx -y` install arg. Enabled by the new `devcheck.config.json` `packaging.pluginManifests: true` flag. ([cyanheads/mcp-ts-core#240](https://github.com/cyanheads/mcp-ts-core/issues/240))
+## Changed
+- **`@cyanheads/mcp-ts-core`** `^0.10.6` → `^0.10.9`. Picks up: `ctx.content` — an always-present collector for image/audio content blocks that ride `content[]` only (never `structuredContent`); canvas SQL gate now classifies a `SELECT`-shaped statement that fails to prepare (bad column, unknown function) as `ValidationError` `data.reason: 'invalid_sql'` with the DuckDB binder detail, instead of the misleading `non_select_statement`; corrected `OTEL_SERVICE_NAME` seeding docs (`createApp({ name })` seeds it only when unset). ([cyanheads/mcp-ts-core#239](https://github.com/cyanheads/mcp-ts-core/issues/239), [#236](https://github.com/cyanheads/mcp-ts-core/issues/236), [#233](https://github.com/cyanheads/mcp-ts-core/issues/233))
+- **`.codex-plugin/plugin.json`** — filled the empty `interface.longDescription` so the Codex marketplace manifest passes the new packaging check.
+- **Eight `skills/<name>/SKILL.md` re-synced** from the framework — `add-tool` 2.14→2.15, `api-canvas` 1.6→1.7, `api-config` 1.7→1.8, `api-context` 1.8→1.9, `api-telemetry` 1.1→1.2, `git-wrapup` 1.2→1.4, `orchestrations` 1.3→1.4, `polish-docs-meta` 2.7→2.9 — mirrored into `.claude/skills/` and `.agents/skills/`.
+## Dependencies
+- **`@cyanheads/mcp-ts-core`** `^0.10.6` → `^0.10.9`
+- **`@duckdb/node-api`** `^1.5.3-r.3` → `^1.5.4-r.1` (the bump deferred from 0.7.5 — now inside the caret)
+- **`@types/node`** `^25.9.3` → `^26.0.0`

package/changelog/0.7.x/0.7.7.md ADDED Viewed

@@ -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/template.md CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

	@@ -1 +1 @@
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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"}

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 { 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 CHANGED Viewed

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

	@@ -1 +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"}
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;AAgHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAyQjC,CAAC"}

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

@@ -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 CHANGED Viewed

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

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