@cyanheads/brapi-mcp-server 0.7.3 → 0.7.5

package/CLAUDE.md

@@ -1,8 +1,8 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.7.3
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
+**Version:** 0.7.5
+**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-0.7.3-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-0.7.5-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)
 
 </div>
 

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/changelog/0.7.x/0.7.5.md

@@ -0,0 +1,22 @@
+---
+summary: "Fix dataframe describe/query failing on an ambiguous table_name probe, and stop get_study from reporting server-wide companion counts as study-scoped"
+breaking: false
+security: false
+---
+
+# 0.7.5 — 2026-06-18
+
+## Fixed
+
+- **`brapi_dataframe_query` / `brapi_dataframe_describe`** — both failed before any user SQL ran, raising `Binder Error: Ambiguous reference to column name "table_name"`. `CanvasBridge.describe()` no longer forwards a `tableName` to the framework's describe-by-name path (which pushes an unqualified `table_name` predicate into a catalog query that LEFT JOINs `information_schema.tables` with `duckdb_tables()`, both exposing `table_name`); it lists every table via the unambiguous `table_schema`-only query and narrows by name in JS. `dataframe_query`'s internal type-probe describes its freshly-registered result by name, so this also unblocks plain queries like `SELECT 1`. Server-side reroute pending the upstream root-cause fix in [cyanheads/mcp-ts-core#235](https://github.com/cyanheads/mcp-ts-core/issues/235). ([#39](https://github.com/cyanheads/brapi-mcp-server/issues/39))
+- **`brapi_get_study`** — `observationCount` and `variableCount` reported server-wide totals when the dialect dropped the `studyDbIds` filter (`/observations`) or the server accepted but ignored it (`/variables`), silently collapsing to the global count while presented as per-study signals. Both are now omitted with a warning when the upstream can't scope the query — never reported as the server-wide total. `observationUnitCount` was already correctly scoped and is unchanged. The `brapi://study/{studyDbId}` resource delegates to the same handler and inherits the fix. ([#40](https://github.com/cyanheads/brapi-mcp-server/issues/40))
+
+## Changed
+
+- **`fetchValidatedScopedCount`** — new shared helper in `src/mcp-server/tools/shared/find-helpers.ts` consolidating the validated-count pattern (guard 1: dialect drops the scope filter; guard 2: scoped probe equals an unfiltered baseline, so the server ignored it). `brapi_get_germplasm` now uses it in place of its private `fetchValidatedStudyCount`, and `fetchTotalCount` moved to the shared module. `observationCount` / `variableCount` output `.describe()` strings note they are omitted (not zero) when the upstream can't scope the count.
+
+## Dependencies
+
+- **`@biomejs/biome`** `^2.4.16` → `^2.5.0`
+- **`vitest`** `^4.1.8` → `^4.1.9`
+- **`@duckdb/node-api`** held at `^1.5.3-r.3` (its `1.5.4-r.1` prerelease falls outside the caret) and added to the `devcheck` outdated allowlist; the bump is deferred to a maintenance pass.

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

@@ -27,26 +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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBA6J7B,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,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

@@ -98,14 +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()
@@ -115,9 +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()
@@ -136,9 +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;

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAuP5B,CAAC"}
+{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2P5B,CAAC"}

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

@@ -11,7 +11,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, dedupSynonymsByIdentity, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, collectPassthroughParts, dedupSynonymsByIdentity, fetchTotalCount, fetchValidatedScopedCount, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
 const GermplasmSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -162,12 +162,16 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
                 ? fetchAttributes(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'attributes lookup failed', err))
                 : Promise.resolve(undefined),
             supportsStudies && dialect
-                ? fetchValidatedStudyCount({
+                ? fetchValidatedScopedCount({
                     client,
                     connection,
-                    germplasmDbId: input.germplasmDbId,
-                    dialect,
                     ctx,
+                    dialect,
+                    label: 'studyCount',
+                    path: '/studies',
+                    scopeDescription: 'germplasm filter',
+                    scopeFilter: { germplasmDbIds: [input.germplasmDbId] },
+                    service: 'studies',
                     warnings,
                 }).catch((err) => recordWarning(warnings, 'study count probe failed', err))
                 : Promise.resolve(undefined),
@@ -343,49 +347,4 @@ async function fetchAttributes(client, baseUrl, id, ctx, options) {
             : [];
     return rows.filter((r) => typeof r === 'object' && r !== null);
 }
-async function fetchTotalCount(client, baseUrl, path, ctx, options) {
-    const env = await client.get(baseUrl, path, ctx, options);
-    const total = env.metadata?.pagination?.totalCount;
-    return typeof total === 'number' ? total : undefined;
-}
-/**
- * Probe `/studies?germplasmDbIds=X` and a parallel unfiltered baseline.
- * Some servers (notably the SGN family) silently drop the germplasm filter on
- * `/studies` and return the global studies total — which would be wildly
- * misleading as a per-germplasm `studyCount`. The cross-check catches that:
- * if the filtered total matches the unfiltered baseline, the filter was
- * ignored and we drop the count rather than report a misleading global.
- *
- * Routes the filtered probe through the dialect adapter so any per-server
- * key translation (or filter drop) takes effect, and surfaces the dialect's
- * own warnings so the agent sees why a count is missing.
- */
-async function fetchValidatedStudyCount(input) {
-    const { client, connection, ctx, dialect, germplasmDbId, warnings } = input;
-    const adapted = dialect.adaptGetFilters('studies', {
-        germplasmDbIds: [germplasmDbId],
-    });
-    warnings.push(...adapted.warnings);
-    // If the dialect dropped the filter entirely, the count would be the
-    // global studies total — useless. Skip and let the caller render `—`.
-    if (Object.keys(adapted.filters).length === 0) {
-        warnings.push('studyCount probe skipped: the active dialect dropped the germplasm filter for /studies (server does not honor it).');
-        return;
-    }
-    const filteredParams = {
-        ...adapted.filters,
-        pageSize: 1,
-    };
-    const [filtered, baseline] = await Promise.all([
-        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, filteredParams)),
-        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, { pageSize: 1 })).catch(() => undefined),
-    ]);
-    if (typeof filtered !== 'number')
-        return;
-    if (typeof baseline === 'number' && baseline > 0 && filtered === baseline) {
-        warnings.push(`studyCount omitted: /studies returned the same total (${baseline}) for both the germplasm-filtered probe and an unfiltered baseline — the upstream silently ignored the germplasm filter, so a per-germplasm count cannot be trusted.`);
-        return;
-    }
-    return filtered;
-}
 //# sourceMappingURL=brapi-get-germplasm.tool.js.map

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

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAqQxB,CAAC"}
+{"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmJjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA8QxB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js

@@ -13,7 +13,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getReferenceDataCache } from '../../../services/reference-data-cache/index.js';
-import { AliasInput, appendPassthroughLines, asStringArray, buildRequestOptions, companionRequestOptions, extractCoordinates, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, asStringArray, buildRequestOptions, companionRequestOptions, extractCoordinates, fetchTotalCount, fetchValidatedScopedCount, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
 const StudySchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -102,7 +102,7 @@ const OutputSchema = z.object({
         .int()
         .nonnegative()
         .optional()
-        .describe('Total observations recorded against this study.'),
+        .describe('Total observations recorded against this study. Omitted (with a warning) when the upstream server cannot scope the count to the study — never reported as the server-wide total.'),
     observationUnitCount: z
         .number()
         .int()
@@ -114,7 +114,7 @@ const OutputSchema = z.object({
         .int()
         .nonnegative()
         .optional()
-        .describe('Total observation variables (traits) measured in this study.'),
+        .describe('Total observation variables (traits) measured in this study. Omitted (with a warning) when the upstream server cannot scope the count to the study — never reported as the server-wide total.'),
     warnings: z.array(z.string()).describe('Advisory messages — failed FK lookups, missing counts.'),
 });
 export const brapiGetStudy = tool('brapi_get_study', {
@@ -200,11 +200,23 @@ export const brapiGetStudy = tool('brapi_get_study', {
                     .catch((err) => recordWarning(warnings, 'location FK lookup failed', err))
                 : Promise.resolve(undefined),
             supportsObservations
-                ? fetchTotalCount(client, connection.baseUrl, '/observations', ctx, companionRequestOptions(connection, dialect, config, warnings, {
-                    studyDbIds: [input.studyDbId],
-                    pageSize: 1,
-                })).catch((err) => recordWarning(warnings, 'observation count probe failed', err))
+                ? fetchValidatedScopedCount({
+                    client,
+                    connection,
+                    ctx,
+                    dialect,
+                    label: 'observationCount',
+                    path: '/observations',
+                    scopeDescription: 'study filter',
+                    scopeFilter: { studyDbIds: [input.studyDbId] },
+                    service: 'observations',
+                    warnings,
+                }).catch((err) => recordWarning(warnings, 'observation count probe failed', err))
                 : Promise.resolve(undefined),
+            // observationUnitCount stays a plain probe — the test server (and the
+            // SGN family) honor studyDbId on /observationunits, so it's reliably
+            // study-scoped. The dialect is threaded through the client here so the
+            // plural→singular translation happens at the wire edge.
             supportsObservationUnits
                 ? fetchTotalCount(client, connection.baseUrl, '/observationunits', ctx, companionRequestOptions(connection, dialect, config, warnings, {
                     studyDbIds: [input.studyDbId],
@@ -212,14 +224,23 @@ export const brapiGetStudy = tool('brapi_get_study', {
                 })).catch((err) => recordWarning(warnings, 'observation-unit count probe failed', err))
                 : Promise.resolve(undefined),
             supportsVariables
-                ? fetchTotalCount(client, connection.baseUrl, '/variables', ctx, companionRequestOptions(connection, dialect, config, warnings, {
-                    // /variables historically responded to singular `studyDbId` on
-                    // SGN deployments — keep the singular here so the dialect (which
-                    // doesn't carry a `variables.studyDbIds → studyDbId` entry) is a
-                    // pass-through, not a silent translation that breaks the probe.
-                    studyDbId: input.studyDbId,
-                    pageSize: 1,
-                })).catch((err) => recordWarning(warnings, 'variable count probe failed', err))
+                ? fetchValidatedScopedCount({
+                    client,
+                    connection,
+                    ctx,
+                    dialect,
+                    label: 'variableCount',
+                    path: '/variables',
+                    scopeDescription: 'study filter',
+                    // /variables historically responded to singular `studyDbId` on SGN
+                    // deployments — keep the singular key so the dialect (which carries
+                    // no `variables.studyDbIds → studyDbId` entry) passes it through
+                    // rather than dropping it; the baseline cross-check still catches
+                    // servers (e.g. the BrAPI test server) that accept but ignore it.
+                    scopeFilter: { studyDbId: input.studyDbId },
+                    service: 'variables',
+                    warnings,
+                }).catch((err) => recordWarning(warnings, 'variable count probe failed', err))
                 : Promise.resolve(undefined),
         ]);
         const result = {
@@ -354,11 +375,6 @@ function recordWarning(warnings, label, err) {
     warnings.push(`${label}: ${err instanceof Error ? err.message : String(err)}`);
     return;
 }
-async function fetchTotalCount(client, baseUrl, path, ctx, options) {
-    const env = await client.get(baseUrl, path, ctx, options);
-    const total = env.metadata?.pagination?.totalCount;
-    return typeof total === 'number' ? total : undefined;
-}
 function renderKeyValues(lines, record) {
     for (const [key, value] of Object.entries(record)) {
         if (value === undefined || value === null)

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map

@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.d.ts

@@ -114,6 +114,54 @@ export declare function buildRequestOptions(connection: RegisteredServer, params
  * downcasts) flow into the same array the tool surfaces in its envelope.
  */
 export declare function companionRequestOptions(connection: RegisteredServer, dialect: BrapiDialect, config: ServerConfig, warnings: string[], params?: BrapiRequestOptions['params']): BrapiRequestOptions;
+/**
+ * Read `metadata.pagination.totalCount` from a BrAPI list endpoint with a
+ * `pageSize: 1` probe. Returns `undefined` when the server omits the count.
+ * Shared by the companion-count probes on the `get_*` tools.
+ */
+export declare function fetchTotalCount(client: BrapiClient, baseUrl: string, path: string, ctx: Context, options: BrapiRequestOptions): Promise<number | undefined>;
+/** Input to {@link fetchValidatedScopedCount}. */
+export interface ValidatedScopedCountInput {
+    client: BrapiClient;
+    connection: RegisteredServer;
+    ctx: Context;
+    dialect: BrapiDialect;
+    /** Output-field name used in the omission warning (e.g. `observationCount`). */
+    label: string;
+    /** Endpoint path to count against (e.g. `/observations`). */
+    path: string;
+    /** Human label for the scope in warnings (e.g. `study filter`). */
+    scopeDescription: string;
+    /** The scoping filter to apply (e.g. `{ studyDbIds: [studyDbId] }`). */
+    scopeFilter: Record<string, unknown>;
+    /** Dialect resource segment for filter adaptation (e.g. `observations`). */
+    service: string;
+    warnings: string[];
+}
+/**
+ * Fetch a study/germplasm-scoped total count, omitting it when the upstream
+ * can't actually scope the query — so a per-entity count is never silently
+ * reported as the server-wide total. Two guards, in order:
+ *
+ *   1. **Dropped filter** — if the dialect drops the scope filter entirely
+ *      (the server doesn't honor it), the count would be the global total;
+ *      skip the probe and warn.
+ *   2. **Ignored filter** — run the scoped probe and an unfiltered baseline in
+ *      parallel; if the totals match, the upstream silently ignored the filter
+ *      (accepted it on the wire but returned the unfiltered set), so the
+ *      "scoped" count is really the global total. Drop it and warn.
+ *
+ * Returns the trustworthy scoped total, or `undefined` (with a warning pushed
+ * onto `warnings`) when neither guard can vouch for it. Both probes run at
+ * `pageSize: 1` under the companion budget (tight timeout, no retries) — these
+ * counts decorate a response, never gate it, so a slow or non-conforming
+ * upstream surfaces as one missing count rather than a wrong one or a stall.
+ *
+ * The scope filter is adapted through the dialect here (so per-server key
+ * translation / drops take effect) and sent with `buildRequestOptions` — never
+ * re-threaded through the client, which would double-apply the dialect.
+ */
+export declare function fetchValidatedScopedCount(input: ValidatedScopedCountInput): Promise<number | undefined>;
 /**
  * Compute a frequency distribution for one field across a result set.
  * Accepts a field accessor that may return a scalar or array; arrays are

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

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

@@ -216,6 +216,73 @@ export function companionRequestOptions(connection, dialect, config, warnings, p
         opts.params = params;
     return opts;
 }
+/**
+ * Read `metadata.pagination.totalCount` from a BrAPI list endpoint with a
+ * `pageSize: 1` probe. Returns `undefined` when the server omits the count.
+ * Shared by the companion-count probes on the `get_*` tools.
+ */
+export async function fetchTotalCount(client, baseUrl, path, ctx, options) {
+    const env = await client.get(baseUrl, path, ctx, options);
+    const total = env.metadata?.pagination?.totalCount;
+    return typeof total === 'number' ? total : undefined;
+}
+/**
+ * Fetch a study/germplasm-scoped total count, omitting it when the upstream
+ * can't actually scope the query — so a per-entity count is never silently
+ * reported as the server-wide total. Two guards, in order:
+ *
+ *   1. **Dropped filter** — if the dialect drops the scope filter entirely
+ *      (the server doesn't honor it), the count would be the global total;
+ *      skip the probe and warn.
+ *   2. **Ignored filter** — run the scoped probe and an unfiltered baseline in
+ *      parallel; if the totals match, the upstream silently ignored the filter
+ *      (accepted it on the wire but returned the unfiltered set), so the
+ *      "scoped" count is really the global total. Drop it and warn.
+ *
+ * Returns the trustworthy scoped total, or `undefined` (with a warning pushed
+ * onto `warnings`) when neither guard can vouch for it. Both probes run at
+ * `pageSize: 1` under the companion budget (tight timeout, no retries) — these
+ * counts decorate a response, never gate it, so a slow or non-conforming
+ * upstream surfaces as one missing count rather than a wrong one or a stall.
+ *
+ * The scope filter is adapted through the dialect here (so per-server key
+ * translation / drops take effect) and sent with `buildRequestOptions` — never
+ * re-threaded through the client, which would double-apply the dialect.
+ */
+export async function fetchValidatedScopedCount(input) {
+    const { client, connection, ctx, dialect, label, path, scopeDescription, scopeFilter, service, warnings, } = input;
+    const config = getServerConfig();
+    const companion = (params) => buildRequestOptions(connection, params, {
+        timeoutMs: config.companionTimeoutMs,
+        retryMaxAttempts: 0,
+    });
+    const adapted = dialect.adaptGetFilters(service, scopeFilter);
+    warnings.push(...adapted.warnings);
+    // Guard 1: the dialect dropped the scope filter — the server doesn't honor
+    // it, so any count we got back would be the global total.
+    if (Object.keys(adapted.filters).length === 0) {
+        warnings.push(`${label} omitted: the '${dialect.id}' dialect drops the ${scopeDescription} for ${path}, so a scoped count can't be computed (the server does not honor it).`);
+        return;
+    }
+    const filteredParams = {
+        ...adapted.filters,
+        pageSize: 1,
+    };
+    const [filtered, baseline] = await Promise.all([
+        fetchTotalCount(client, connection.baseUrl, path, ctx, companion(filteredParams)),
+        fetchTotalCount(client, connection.baseUrl, path, ctx, companion({ pageSize: 1 })).catch(() => undefined),
+    ]);
+    if (typeof filtered !== 'number')
+        return;
+    // Guard 2: the scoped probe and the unfiltered baseline returned the same
+    // total — the upstream silently ignored the filter, so this is the global
+    // count wearing a per-entity label.
+    if (typeof baseline === 'number' && baseline > 0 && filtered === baseline) {
+        warnings.push(`${label} omitted: ${path} returned the same total (${baseline}) for both the scoped probe and an unfiltered baseline — the upstream silently ignored the ${scopeDescription}, so a scoped count can't be trusted.`);
+        return;
+    }
+    return filtered;
+}
 /**
  * Compute a frequency distribution for one field across a result set.
  * Accepts a field accessor that may return a scalar or array; arrays are

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

@@ -1 +1 @@
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package/dist/services/canvas-bridge/canvas-bridge.d.ts.map

@@ -1 +1 @@
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package/dist/services/canvas-bridge/canvas-bridge.js

@@ -271,11 +271,20 @@ export class CanvasBridge {
      */
     async describe(ctx, options = {}) {
         const instance = await this.getInstance(ctx);
-        const describeOpts = {};
-        if (options.tableName !== undefined)
-            describeOpts.tableName = options.tableName;
-        const tables = await instance.describe(describeOpts);
-        return Promise.all(tables.map((t) => this.augmentTableInfo(ctx, t)));
+        // Always list every table and narrow by name in JS rather than forwarding a
+        // `tableName` to the framework's describe-by-name path. That path pushes an
+        // unqualified `table_name` predicate into a catalog query that LEFT JOINs
+        // `information_schema.tables` with `duckdb_tables()` — both expose
+        // `table_name`, so DuckDB rejects it as ambiguous. Forwarding a name breaks
+        // every describe-by-name AND every dataframe_query (its internal type-probe
+        // describes the freshly-registered result by name, so even `SELECT 1`
+        // fails). The list-all query filters on the unambiguous `table_schema`
+        // alone, so it stays safe; we select the requested table here. Bounded by
+        // the per-session dataframe count. Tracked upstream for a root-cause fix in
+        // the mcp-ts-core DuckDB provider.
+        const tables = await instance.describe({});
+        const selected = options.tableName === undefined ? tables : tables.filter((t) => t.name === options.tableName);
+        return Promise.all(selected.map((t) => this.augmentTableInfo(ctx, t)));
     }
     async augmentTableInfo(ctx, table) {
         const out = {

package/dist/services/canvas-bridge/canvas-bridge.js.map

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package/manifest.json

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "brapi-mcp-server",
-  "version": "0.7.3",
+  "version": "0.7.5",
   "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
   "author": {
     "name": "cyanheads"

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.7.3",
+  "version": "0.7.5",
   "description": "A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, & more - across Breedbase, T3, Sweetpotatobase, & any BrAPI v2-compliant server.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -31,7 +31,7 @@
     "lint:mcp": "bun run scripts/lint-mcp.ts",
     "lint:packaging": "bun run scripts/lint-packaging.ts",
     "list-skills": "bun run scripts/list-skills.ts",
-    "bundle": "bun run build && bunx -y @anthropic-ai/mcpb pack . dist/brapi-mcp-server.mcpb",
+    "bundle": "bun run build && bunx -y @anthropic-ai/mcpb pack . dist/brapi-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/brapi-mcp-server.mcpb",
     "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "changelog:build": "bun run scripts/build-changelog.ts",
     "changelog:check": "bun run scripts/build-changelog.ts --check",
@@ -81,18 +81,18 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.21",
+    "@cyanheads/mcp-ts-core": "^0.10.6",
     "@duckdb/node-api": "^1.5.3-r.3",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.16",
-    "@types/node": "^25.9.1",
+    "@biomejs/biome": "^2.5.0",
+    "@types/node": "^25.9.3",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.8"
+    "vitest": "^4.1.9"
   }
 }

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.7.3",
+  "version": "0.7.5",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.3",
+      "version": "0.7.5",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -56,7 +56,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.7.3",
+      "version": "0.7.5",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }