@cyanheads/brapi-mcp-server 0.7.2 → 0.7.4

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.7.2
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+**Version:** 0.7.4
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.6`
 
 > **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

@@ -37,10 +37,12 @@ WORKDIR /usr/src/app
 ENV NODE_ENV=production
 
 # OCI image metadata (https://github.com/opencontainers/image-spec/blob/main/annotations.md)
+ARG APP_VERSION=dev
 LABEL org.opencontainers.image.title="@cyanheads/brapi-mcp-server"
 LABEL org.opencontainers.image.description="BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees across Breedbase, T3, Sweetpotatobase, and any BrAPI-compliant server."
 LABEL org.opencontainers.image.source="https://github.com/cyanheads/brapi-mcp-server"
 LABEL org.opencontainers.image.licenses="Apache-2.0"
+LABEL org.opencontainers.image.version="${APP_VERSION}"
 
 # Copy dependency manifests
 COPY package.json bun.lock ./
@@ -104,5 +106,9 @@ 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
+HEALTHCHECK --interval=30s --timeout=10s --start-period=10s --retries=3 \
+  CMD curl -f http://localhost:${MCP_HTTP_PORT}/healthz || 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-0.7.2-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-0.7.4-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)
 
 </div>
 
@@ -207,7 +207,8 @@ Every variable is optional.
 | `BRAPI_DEFAULT_OAUTH_CLIENT_ID` / `_OAUTH_CLIENT_SECRET` | OAuth2 client-credentials for the default connection. | — |
 | `BRAPI_DEFAULT_API_KEY` / `_API_KEY_HEADER` | Static API key for the default connection. | header `Authorization` |
 | `BRAPI_BUILTIN_ALIASES_DISABLED` | Comma-separated alias names (case-insensitive) to remove from the built-in registry. | — |
-| `BRAPI_LOAD_LIMIT` | In-context row cap before `find_*` spills to a canvas dataframe; also doubles as the upstream pageSize during spillover walks (`loadLimit × 50` is the dataframe ceiling). | `1000` |
+| `BRAPI_LOAD_LIMIT` | In-context row cap returned by `find_*` tools before spilling to a canvas dataframe. | `1000` |
+| `BRAPI_PAGE_SIZE` | Upstream `pageSize` used during canvas spillover walks (decoupled from `BRAPI_LOAD_LIMIT`). Dataframe ceiling = `pageSize × 50`. | `1000` |
 | `BRAPI_MAX_CONCURRENT_REQUESTS` | Per-connection concurrency cap. | `4` |
 | `BRAPI_RETRY_MAX_ATTEMPTS` / `BRAPI_RETRY_BASE_DELAY_MS` | Retry policy for 429/5xx with exponential backoff. | `3` / `500` |
 | `BRAPI_REQUEST_TIMEOUT_MS` | Per-request HTTP timeout. | `30000` |

package/changelog/0.7.x/0.7.3.md

@@ -0,0 +1,22 @@
+---
+summary: "Decouple spillover pageSize from loadLimit via BRAPI_PAGE_SIZE — fixes spillover timeout when agents request a small inline preview"
+breaking: false
+security: false
+---
+
+# 0.7.3 — 2026-06-08
+
+## Added
+
+- **`BRAPI_PAGE_SIZE`** — new env var (default `1000`) controls the upstream `pageSize` used during canvas spillover walks, decoupled from `BRAPI_LOAD_LIMIT`. Previously `loadLimit` doubled as the upstream pageSize, so `loadLimit=5` triggered a 245-page walk against sweetpotatobase (1221 rows ÷ 5) instead of 2 pages. Now the walk always uses `pageSize` regardless of the agent's inline-preview cap ([#26](https://github.com/cyanheads/brapi-mcp-server/issues/26)).
+- **Distributions truncation caveat** — when a `find_*` result dataframe is truncated (upstream total > dataframe rowCount), `renderDistributions` prefixes the block with `_Computed over N of M upstream rows — narrow filters or raise loadLimit for a representative sample._` ([#26](https://github.com/cyanheads/brapi-mcp-server/issues/26)).
+- **Page-offset alignment** — `spillToCanvas` re-fetches from page 0 when `loadLimit !== pageSize` to keep page offsets consistent with the spillover walk.
+
+## Changed
+
+- **`LoadLimitInput.describe()`** — rewritten to drop the dual-role footgun warning; now reads "Cap on rows returned inline. Rows beyond the cap land in a dataframe; query with `brapi_dataframe_query` (SQL)."
+- **`@types/node`** — added to `devcheck.config.json` outdated allowlist (patch behind, held per framework hold convention).
+
+## Fixed
+
+- **Spillover timeout on small `loadLimit`** — resolved as a side effect of the `BRAPI_PAGE_SIZE` decoupling: agents requesting a narrow inline preview no longer silently shrink the upstream pageSize and trigger excessive page counts ([#21](https://github.com/cyanheads/brapi-mcp-server/issues/21)). Live re-test on sweetpotatobase study 1131: ~14s elapsed (2 pages at `pageSize=1000`) versus the prior ~200+ pages at `loadLimit=5`.

package/changelog/0.7.x/0.7.4.md

@@ -0,0 +1,27 @@
+---
+summary: "Adopt @cyanheads/mcp-ts-core ^0.10.6, migrate boolean env flags to z.stringbool(), set explicit createApp identity, and harden MCPB bundle packaging"
+breaking: false
+security: false
+---
+
+# 0.7.4 — 2026-06-12
+
+## Added
+
+- **`createApp` identity** — `name` and `title` are now passed explicitly as `'brapi-mcp-server'` so the served `server_name` and display title are the unscoped machine name rather than the scoped npm package name.
+- **`scripts/clean-mcpb.ts`** — post-pack bundle cleaner wired into the `bundle` script: runs `mcpb clean` (dev-dependency prune + manifest validation) then strips dependency-shipped agent-doc entries (`node_modules/**/skills/`, `.claude/`, `.agents/`, `SKILL.md`) that root-anchored `.mcpbignore` patterns cannot reach.
+- **`lint-packaging` checks 5–9** — bundle-content guards (root dev dirs excluded, no unanchored `.mcpbignore` patterns stripping `node_modules/**` runtime paths, no critical runtime path stripped), a post-bundle scan asserting zero `node_modules` agent-doc entries in a built `.mcpb`, and an identity check that `createApp`/`createWorkerHandler` `name`/`title` and manifest `display_name` equal the unscoped package name.
+- **`check-framework-antipatterns` rule 4** — flags `z.coerce.boolean()` on env flags (it can't be disabled via the environment, since `Boolean("false") === true`); comment lines are skipped so documenting the pattern doesn't self-trigger.
+- **Dockerfile `APP_VERSION` + `HEALTHCHECK`** — build arg feeds `org.opencontainers.image.version`; a `HEALTHCHECK` polls the framework `/healthz` endpoint.
+
+## Changed
+
+- **Boolean env config** — `allowPrivateIps`, `enableWrites`, `canvasDropEnabled`, and `sessionIsolation` migrate from `z.enum(['true','false']).transform(...)` to `z.stringbool()`, which parses `true/false/1/0/yes/no/on/off` and rejects other values.
+- **`.mcpbignore`** — root dev-dir patterns anchored with a leading `/` (`/.claude/`, `/skills/`, `/Dockerfile`, …) so they no longer also strip nested `node_modules/**` runtime paths; adds `/.agents/` and `/skills/`.
+- **`.codex-plugin/plugin.json`** — `interface.displayName` set to the unscoped `brapi-mcp-server`; both plugin manifests resynced to the current package version.
+
+## Dependencies
+
+- **`@cyanheads/mcp-ts-core`** `^0.9.21` → `^0.10.6`
+- **`@types/node`** `^25.9.1` → `^25.9.3`
+- Transitive: `hono` `4.12.23` → `4.12.25`, `@modelcontextprotocol/ext-apps` `1.7.3` → `1.7.4`

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

@@ -18,6 +18,7 @@ export declare const ServerConfigSchema: z.ZodObject<{
     defaultApiKeyHeader: z.ZodDefault<z.ZodString>;
     datasetTtlSeconds: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     loadLimit: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    pageSize: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     maxConcurrentRequests: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     retryMaxAttempts: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     retryBaseDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
@@ -26,26 +27,14 @@ export declare const ServerConfigSchema: z.ZodObject<{
     companionTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     searchPollTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     searchPollIntervalMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    allowPrivateIps: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
-        true: "true";
-        false: "false";
-    }>>, z.ZodTransform<boolean, "true" | "false">>;
-    enableWrites: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
-        true: "true";
-        false: "false";
-    }>>, z.ZodTransform<boolean, "true" | "false">>;
+    allowPrivateIps: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
+    enableWrites: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     genotypeCallsMaxPull: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    canvasDropEnabled: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
-        true: "true";
-        false: "false";
-    }>>, z.ZodTransform<boolean, "true" | "false">>;
+    canvasDropEnabled: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
     exportDir: z.ZodOptional<z.ZodString>;
     canvasMaxRows: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     canvasQueryTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
-    sessionIsolation: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
-        true: "true";
-        false: "false";
-    }>>, z.ZodTransform<boolean, "true" | "false">>;
+    sessionIsolation: z.ZodDefault<z.ZodCodec<z.ZodString, z.ZodBoolean>>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;
 export declare function getServerConfig(): ServerConfig;

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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAqJ7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA6B9C;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,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

@@ -42,7 +42,13 @@ export const ServerConfigSchema = z.object({
         .int()
         .positive()
         .default(1_000)
-        .describe('Default row cap returned in-context before spilling to a canvas dataframe. Also doubles as the upstream `pageSize` used during spillover walks — the dataframe ceiling is `loadLimit × MAX_SPILLOVER_PAGES (50)`, so the 1,000 default lines up with the documented 50,000-row spillover cap. Operators on small/test BrAPI servers can lower it; raising it above 1,000 is rarely useful because most BrAPI servers cap server-side pageSize at 1,000.'),
+        .describe('Default in-context row cap returned by find_* tools before spilling to a canvas dataframe. Rows beyond this cap land in the dataframe; query with brapi_dataframe_query (SQL).'),
+    pageSize: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(1_000)
+        .describe('Upstream pageSize used during canvas spillover walks. Decoupled from loadLimit so lowering the inline preview cap no longer shrinks the dataframe ceiling. Most BrAPI servers cap pageSize at 1,000; the dataframe ceiling is pageSize × MAX_SPILLOVER_PAGES (50).'),
     maxConcurrentRequests: z.coerce
         .number()
         .int()
@@ -92,14 +98,12 @@ export const ServerConfigSchema = z.object({
         .default(1_000)
         .describe('Poll interval between async-search status checks.'),
     allowPrivateIps: z
-        .enum(['true', 'false'])
-        .default('false')
-        .transform((v) => v === 'true')
+        .stringbool()
+        .default(false)
         .describe('Allow connecting to RFC 1918 / loopback targets. Dev-only.'),
     enableWrites: z
-        .enum(['true', 'false'])
-        .default('false')
-        .transform((v) => v === 'true')
+        .stringbool()
+        .default(false)
         .describe('Opt-in flag for the write surface (`brapi_submit_observations`). Off by default — the tool is omitted from `tools/list` unless the operator opts in for this deployment.'),
     genotypeCallsMaxPull: z.coerce
         .number()
@@ -109,9 +113,8 @@ export const ServerConfigSchema = z.object({
         .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).'),
     canvasDropEnabled: z
-        .enum(['true', 'false'])
-        .default('false')
-        .transform((v) => v === 'true')
+        .stringbool()
+        .default(false)
         .describe('Opt-in flag for `brapi_dataframe_drop`. Off by default — the tool is omitted from `tools/list` unless the operator opts in. Dataframes still expire via TTL when left unmanaged.'),
     exportDir: z
         .string()
@@ -130,9 +133,8 @@ export const ServerConfigSchema = z.object({
         .default(30_000)
         .describe('Per-query wall-clock timeout for brapi_dataframe_query.'),
     sessionIsolation: z
-        .enum(['true', 'false'])
-        .default('true')
-        .transform((v) => v === 'true')
+        .stringbool()
+        .default(true)
         .describe('When true (default) and an MCP session ID is present (HTTP stateful/auto), scope ServerRegistry connection state and the CanvasBridge default canvas to the session. Concurrent HTTP callers under MCP_AUTH_MODE=none then operate in isolated workspaces — registered aliases, exchanged tokens, and df_<uuid> namespaces do not cross sessions. Set to false to share state across sessions in one tenant (the pre-0.6 multi-agent collaboration model). No effect on stdio (no session) or HTTP stateless without exposeStatelessSessionId; both fall back to per-tenant keying. Under MCP_AUTH_MODE=jwt|oauth, tenants already isolate — sessions add a sub-scope inside each tenant.'),
 });
 let _config;
@@ -147,6 +149,7 @@ export function getServerConfig() {
         defaultApiKeyHeader: 'BRAPI_DEFAULT_API_KEY_HEADER',
         datasetTtlSeconds: 'BRAPI_DATASET_TTL_SECONDS',
         loadLimit: 'BRAPI_LOAD_LIMIT',
+        pageSize: 'BRAPI_PAGE_SIZE',
         maxConcurrentRequests: 'BRAPI_MAX_CONCURRENT_REQUESTS',
         retryMaxAttempts: 'BRAPI_RETRY_MAX_ATTEMPTS',
         retryBaseDelayMs: 'BRAPI_RETRY_BASE_DELAY_MS',

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

@@ -1 +1 @@
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package/dist/index.js

@@ -95,6 +95,8 @@ const tools = [
     ...writeToolDefinitions.map((d) => serverConfig.enableWrites ? d : disabledTool(d, writesDisabled)),
 ];
 await createApp({
+    name: 'brapi-mcp-server',
+    title: 'brapi-mcp-server',
     tools,
     resources: [
         brapiServerInfoResource,

package/dist/index.js.map

@@ -1 +1 @@
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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;;GAMG;AAEH,0EAA0E;AAC1E,yEAAyE;AACzE,qEAAqE;AACrE,uEAAuE;AACvE,0BAA0B;AAC1B,EAAE;AACF,2EAA2E;AAC3E,uEAAuE;AACvE,0EAA0E;AAC1E,gEAAgE;AAChE,wDAAwD;AACxD,OAAO,CAAC,GAAG,CAAC,oBAAoB,KAAK,QAAQ,CAAC;AAE9C,6EAA6E;AAC7E,wEAAwE;AACxE,4EAA4E;AAC5E,yEAAyE;AACzE,wEAAwE;AACxE,yEAAyE;AACzE,kBAAkB;AAClB,IAAI,OAAO,CAAC,GAAG,CAAC,gBAAgB,EAAE,CAAC;IACjC,OAAO,CAAC,GAAG,CAAC,kBAAkB,KAAK,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC;AAClE,CAAC;AAED,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AACnE,OAAO,EAAE,wBAAwB,EAAE,MAAM,mCAAmC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,mCAAmC,CAAC;AACrE,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,uCAAuC,CAAC;AAC7E,OAAO,EAAE,sBAAsB,EAAE,MAAM,0CAA0C,CAAC;AAClF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qCAAqC,CAAC;AACzE,OAAO,EAAE,aAAa,EAAE,MAAM,4DAA4D,CAAC;AAC3F,OAAO,EAAE,iBAAiB,EAAE,MAAM,gEAAgE,CAAC;AACnG,OAAO,EAAE,kBAAkB,EAAE,MAAM,4DAA4D,CAAC;AAChG,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,sBAAsB,EAAE,MAAM,gEAAgE,CAAC;AACxG,OAAO,EAAE,uBAAuB,EAAE,MAAM,kEAAkE,CAAC;AAC3G,OAAO,EAAE,kBAAkB,EAAE,MAAM,4DAA4D,CAAC;AAChG,OAAO,EAAE,qBAAqB,EAAE,MAAM,+DAA+D,CAAC;AACtG,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,uBAAuB,EACvB,oBAAoB,GACrB,MAAM,yCAAyC,CAAC;AAEjD,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;AAEvC;;;;GAIG;AACH,MAAM,YAAY,GAAG;IACnB,MAAM,EAAE,gEAAgE;IACxE,IAAI,EAAE,iHAAiH;CACxH,CAAC;AAEF,MAAM,cAAc,GAAG;IACrB,MAAM,EAAE,kDAAkD;IAC1D,IAAI,EAAE,gEAAgE;CACvE,CAAC;AAEF;;;;;;;;GAQG;AACH,SAAS,iBAAiB;IACxB,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,OAAO,CAAC;IAChE,IAAI,aAAa,KAAK,OAAO,EAAE,CAAC;QAC9B,OAAO;YACL,MAAM,EAAE,4CAA4C;YACpD,IAAI,EAAE,mHAAmH;SAC1H,CAAC;IACJ,CAAC;IACD,IAAI,CAAC,YAAY,CAAC,SAAS,EAAE,CAAC;QAC5B,OAAO;YACL,MAAM,EAAE,4DAA4D;YACpE,IAAI,EAAE,wFAAwF;SAC/F,CAAC;IACJ,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,cAAc,GAAG,iBAAiB,EAAE,CAAC;AAE3C,MAAM,KAAK,GAAG;IACZ,GAAG,uBAAuB;IAC1B,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAC/B,YAAY,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,YAAY,CAAC,CACnE;IACD,GAAG,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC3F,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAChC,YAAY,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,cAAc,CAAC,CAChE;CACF,CAAC;AAEF,MAAM,SAAS,CAAC;IACd,IAAI,EAAE,kBAAkB;IACxB,KAAK,EAAE,kBAAkB;IACzB,KAAK;IACL,SAAS,EAAE;QACT,uBAAuB;QACvB,kBAAkB;QAClB,kBAAkB;QAClB,sBAAsB;QACtB,qBAAqB;QACrB,oBAAoB;KACrB;IACD,OAAO,EAAE,CAAC,aAAa,EAAE,iBAAiB,CAAC;IAC3C,+EAA+E;IAC/E,6EAA6E;IAC7E,+EAA+E;IAC/E,OAAO,EAAE,EAAE,WAAW,EAAE,KAAK,EAAE;IAC/B,YAAY,EACV,onBAAonB;IACtnB,KAAK,CAAC,IAAI;QACR,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,MAAM,kBAAkB,CACtB,kLAAkL,EAClL,EAAE,kBAAkB,EAAE,OAAO,CAAC,GAAG,CAAC,oBAAoB,IAAI,QAAQ,EAAE,CACrE,CAAC;QACJ,CAAC;QACD,gBAAgB,CAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC;QAC5C,eAAe,CAAC,YAAY,CAAC,CAAC;QAC9B,sBAAsB,CAAC,YAAY,CAAC,CAAC;QACrC,wBAAwB,EAAE,CAAC;QAC3B,sBAAsB,CAAC,YAAY,CAAC,CAAC;QACrC,kBAAkB,CAAC,YAAY,CAAC,CAAC;QACjC,oBAAoB,EAAE,CAAC;IACzB,CAAC;CACF,CAAC,CAAC"}

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

@@ -61,6 +61,7 @@ export declare const brapiBuildPhenotypeMatrix: import("@cyanheads/mcp-ts-core")
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-build-phenotype-matrix.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAgPpC,CAAC"}
+{"version":3,"file":"brapi-build-phenotype-matrix.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAgPpC,CAAC"}

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

@@ -64,6 +64,7 @@ export declare const brapiExportGenotypeMatrix: import("@cyanheads/mcp-ts-core")
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>;
     vcf: z.ZodOptional<z.ZodString>;
     ped: z.ZodOptional<z.ZodString>;

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

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyNpC,CAAC"}
+{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyNpC,CAAC"}

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

@@ -62,6 +62,7 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     truncated: z.ZodBoolean;
 }, z.core.$strip>, readonly [{

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

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

@@ -63,6 +63,7 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW7B,CAAC"}
+{"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2W7B,CAAC"}

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

@@ -13,7 +13,7 @@ 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, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, truncationMeta, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -355,7 +355,8 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push('');
         }
         lines.push('## Distributions');
-        lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
+        lines.push(renderDistributions(result.distributions, truncationMeta(result.dataframe)) ||
+            '_No values to summarize._');
         lines.push('');
         lines.push('## Germplasm');
         if (result.results.length === 0) {

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

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

@@ -56,6 +56,7 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAgS1B,CAAC"}
+{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmS1B,CAAC"}

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

@@ -13,7 +13,7 @@ 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, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, truncationMeta, } from '../shared/find-helpers.js';
 const ImageRowSchema = z
     .object({
     imageDbId: z.string().describe('Server-side identifier for the image.'),
@@ -298,7 +298,8 @@ export const brapiFindImages = tool('brapi_find_images', {
             lines.push('');
         }
         lines.push('## Distributions');
-        lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
+        lines.push(renderDistributions(result.distributions, truncationMeta(result.dataframe)) ||
+            '_No values to summarize._');
         lines.push('');
         lines.push('## Images');
         if (result.results.length === 0) {