npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.5.1 → 0.5.2 - Mend

@cyanheads/brapi-mcp-server 0.5.1 → 0.5.2

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package/README.md CHANGED Viewed

@@ -1,13 +1,13 @@
 <div align="center">
   <h1>@cyanheads/brapi-mcp-server</h1>
-  <p><b>BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees across Breedbase, T3, Sweetpotatobase, and any BrAPI-compliant server.</b>
-  <div>22 Tools • 5 Resources • 2 Prompts</div>
+  <p><b>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.</b>
+  <div>22 Tools • 5 Resources • 2 Prompts • Multi-agent collaboration</div>
   </p>
 </div>
 <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-0.5.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![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-0.5.2-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![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)
@@ -17,7 +17,7 @@
 ## Tools
-22 tools grouped by shape — connection tools bootstrap a session, `find_*` tools return a summarized page plus distributions and spill overflow rows into a canvas dataframe, `get_*` tools fetch a single record with companion counts, plus pedigree walking, an embedded SQL workspace over spilled rows (DuckDB-backed), file export for human handoff, an additive write surface for observations, and raw passthrough escape hatches.
+22 tools grouped by shape — connection tools bootstrap a session, `find_*` tools return a summarized page plus distributions and spill overflow rows into a canvas dataframe that any agent can query or hand off by ID, `get_*` tools fetch a single record with companion counts, plus pedigree walking, an embedded SQL workspace over spilled rows (DuckDB-backed), file export for human handoff, an additive write surface for observations, and raw passthrough escape hatches.
 ### Orient
@@ -95,12 +95,34 @@ Multi-step BrAPI workflow templates — pure user-message generators, no side ef
 ---
+## Multi-agent workflows
+The server has two layers, both tenant-scoped:
+| Layer | Scope | Why |
+|:------|:------|:----|
+| **Connection state** (aliases, exchanged tokens, capability cache) | Per-tenant via `ctx.state` | Holds credentials. Tenant keys never cross. |
+| **Dataframes** (`df_<uuid>` tables) | Per-tenant via the framework's canvas registry | Within one tenant, agents share by `df_<uuid>` name — possession grants full read/write/drop, auto-expires in 24h, provenance recorded. The underlying canvas is tenant-gated by the framework, so names from one tenant don't resolve in another. |
+Within one tenant, dataframes act as a self-cleaning shared notebook: hand the `df_<uuid>` name between parallel agents, persist it across a multi-step workflow, query / project / aggregate / join from any position. Address-by-name, time-bounded, scoped to one tenant.
+**Concrete patterns:**
+1. **Parallel agents, same researcher** — a planning agent, an analysis agent, and a writeup agent all reference the same `df_<uuid>` without re-pulling from the upstream BrAPI server. Works in every deployment shape.
+2. **Pipeline accumulation** — `find_studies` → `find_observations` → `find_variables` builds up multiple dataframes in one workspace; SQL joins them; export materializes the result. Works in every deployment shape.
+3. **Cross-server analysis** — pull germplasm from Breedbase and trait data from Triticeae Toolbox in one session; join in DuckDB; no copy-paste. Works in every deployment shape.
+4. **Cross-user handoff** — under `MCP_AUTH_MODE=none` (shared trust), every client resolves to one tenant and shares the dataframe namespace. Under `jwt` / `oauth`, each user has their own tenant and dataframe names don't cross — see [Deployment shapes](#deployment-shapes).
+**On privileged data.** The `df_<uuid>` name is a capability token within a canvas, scoped per tenant — not row-level access control. Each tenant gets one default canvas; under `auth=none` HTTP every caller resolves to `tenantId='default'` and shares it, while under `jwt` / `oauth` each user carves their own. Once rows from a privileged upstream session land in a dataframe, anyone in the same tenant with the name can read them. Treat dataframe names like authenticated share links — share within the team, not externally. The 24h TTL caps blast radius; the provenance trail (originating tool, baseUrl, query) supports audit. To isolate dataframes between users on a shared host, run under `MCP_AUTH_MODE=jwt` or `oauth` so each caller carves their own tenant; under shared-trust HTTP, `brapi_dataframe_describe` is gated against list-all enumeration, and `brapi_dataframe_query` rejects system-catalog reads (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*`) — so a caller without a known `df_<uuid>` name can't fish through either surface.
+---
 ## BrAPI-specific features
+- **Dataframe spillover** — `find_*` tools cap in-context rows at `loadLimit` and materialize larger unions (up to 50k rows / 50 pages) as DuckDB-backed `df_<uuid>` canvas dataframes. Discover with `brapi_dataframe_describe`, query with `brapi_dataframe_query` (SQL paging via `LIMIT/OFFSET`, projection, aggregation). Read-only enforcement at the SQL gate; tenant-scoped — agents in the same tenant share by `df_<uuid>` name (see [Multi-agent workflows](#multi-agent-workflows)).
 - **Multi-server session** — `ServerRegistry` maps aliases to live BrAPI connections; one session can span Breedbase, T3, and Sweetpotatobase in parallel.
-- **Capability-aware calls** — `CapabilityRegistry` caches `/serverinfo` per connection and guards every tool call against unsupported endpoints. Falls back to `/calls` when `/serverinfo` is sparse.
 - **Built-in known-server registry** — `bti-cassava`, `bti-sweetpotato`, `bti-breedbase-demo`, `t3-wheat`, `t3-oat`, `t3-barley` resolve out-of-the-box without env vars; orientation envelope carries CC-BY attribution.
-- **Dataframe spillover** — `find_*` tools cap in-context rows at `loadLimit` and materialize larger unions (up to 50k rows / 50 pages) as DuckDB-backed `df_<uuid>` canvas dataframes. Discover with `brapi_dataframe_describe`, query with `brapi_dataframe_query` (SQL paging via `LIMIT/OFFSET`, projection, aggregation). Read-only enforcement at the SQL gate; per-tenant workspace.
+- **Capability-aware calls** — `CapabilityRegistry` caches `/serverinfo` per connection and guards every tool call against unsupported endpoints. Falls back to `/calls` when `/serverinfo` is sparse.
 - **DuckDB required** — `@duckdb/node-api` is a regular dependency; startup fails closed when the framework canvas is unavailable. Not supported on Cloudflare Workers (no native binary in that runtime).
 - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern automatically.
 - **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call).
@@ -113,10 +135,12 @@ Built on [`@cyanheads/mcp-ts-core`](https://www.npmjs.com/package/@cyanheads/mcp
 ---
-## Working with large results
+## Working with dataframes
 When a `find_*` tool's upstream total exceeds `loadLimit`, the full union materializes as a canvas dataframe and the response carries an inline `dataframe` handle (`{ tableName, rowCount, columns, createdAt, expiresAt, … }`). SQL is the paging idiom — use `LIMIT/OFFSET` to walk pages, projection (`SELECT col1, col2`) to trim columns, and aggregation (`COUNT`, `GROUP BY`, `AVG`) to summarize without materializing every row.
+Dataframe names are tenant-scoped capability tokens — pass `tableName` to any sibling agent in the same tenant (or a downstream step in the same workflow) and they query the same workspace by name without re-pulling from the upstream. See [Multi-agent workflows](#multi-agent-workflows) for cross-user / cross-tenant rules.
 ```text
 1. brapi_find_observations { studies: ["s-422"] }
    → first-page rows inline + dataframe.tableName = "df_<uuid>" (when totalCount > loadLimit)
@@ -275,17 +299,20 @@ docker run --rm -p 3010:3010 brapi-mcp-server
 Defaults to HTTP transport, stateless session mode, logs to `/var/log/brapi-mcp-server`. OTel peer deps are installed by default — `--build-arg OTEL_ENABLED=false` to omit.
-### Multi-user HTTP deployments
+### Deployment shapes
+`brapi-mcp-server` runs in two shapes — pick the one that matches your trust domain.
+| Shape | Auth | Connection state | Dataframes | Best for |
+|:------|:-----|:-----------------|:-----------|:---------|
+| **Shared trust** | `MCP_AUTH_MODE=none` | One bucket — all callers share aliases and cached upstream tokens | One shared workspace — every caller can query any `df_<uuid>` name they hold | Solo, lab, or hosting where users share upstream credentials |
+| **Per-user credentials** | `MCP_AUTH_MODE=jwt` or `oauth` | JWT `tid` claim scopes per user | Per-tenant — names don't resolve across users (framework gates the canvas by tenant) | One institution, multi-user, separate upstream identities |
-`ctx.state` (where `ServerRegistry`, `CanvasBridge`, and `CapabilityRegistry` live) is **scoped by `tenantId`, not session id**:
+The differentiator is whether **connection state** (registered aliases, cached upstream tokens) is isolated per user. **Shared trust** is right when your users share BrAPI credentials anyway — dataframes accumulate in one workspace. **Per-user credentials** is right when each user authenticates separately to upstream BrAPI servers — each gets their own workspace and dataframe names don't cross.
-| Mode | `tenantId` |
-|:-----|:-----------|
-| `MCP_TRANSPORT_TYPE=stdio` (any auth) | `default` |
-| `http` + `MCP_AUTH_MODE=none` | `default` for every client — **shared bucket** |
-| `http` + `jwt` or `oauth` | JWT `tid` claim, fail-closed if absent |
+Under shared-trust HTTP, `brapi_dataframe_describe` requires an explicit `dataframe` name — list-all is gated so a caller without a known name can't enumerate other concurrent clients' workspaces. The dataframe name is the capability token; possession proves it.
-For shared HTTP deployments, set `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`) so each caller's `tid` carves its own state. Otherwise registered aliases — including SGN-exchanged bearer tokens — leak across users.
+For HTTP, set `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`) so each caller's `tid` carves its own connection state. Without this, all callers resolve to `tenantId='default'` and registered aliases — including SGN-exchanged bearer tokens — share one bucket.
 ---

package/changelog/0.5.x/0.5.2.md ADDED Viewed

@@ -0,0 +1,25 @@
+---
+summary: "Tenant-isolation hardening on the dataframe surface — gate brapi_dataframe_describe list-all under shared-trust HTTP, reject system-catalog reads in brapi_dataframe_query, and forward gate context on rejection."
+breaking: false
+---
+# 0.5.2 — 2026-05-05
+Closes two enumeration paths through the dataframe surface that would have let a caller without a known `df_<uuid>` name fish through other concurrent clients' workspaces under shared-trust HTTP. Possession of a dataframe name is the capability gate; these fixes make that gate stand on its own. Also forwards structured gate context (catalog, operators, statementType) on SQL rejection so structured-only consumers see which specific element matched without parsing the message text.
+## Added
+- **System-catalog SQL gate in `CanvasBridge.query()`.** Rejects queries that reference DuckDB's metadata views and introspection functions: `information_schema.*`, `pg_catalog.*`, `sqlite_master`, `sqlite_temp_master`, and 30+ `duckdb_*(…)` functions (`duckdb_tables`, `duckdb_columns`, `duckdb_views`, `duckdb_databases`, `duckdb_schemas`, `duckdb_functions`, etc.). Without this gate, `SELECT * FROM information_schema.tables` would leak the full `df_<uuid>` namespace on a shared canvas, bypassing `brapi_dataframe_describe`'s possession-required list-all gate. Throws `validationError` with `data.reason = 'system_catalog_access'` and a `catalog` label naming which family matched. Comments and string literals are stripped before matching so a column named `information_schema_id` or a literal value `'information_schema.tables'` doesn't false-positive. `SYSTEM_CATALOG_ACCESS_REASON` is exported from `@/services/canvas-bridge` so the dataframe-query tool's contract translator routes it through `sql_rejected` alongside the framework's `SQL_GATE_REASONS`.
+- **Typed error contract on `brapi_dataframe_describe`: `list_all_disabled_on_shared_http`.** Calling the tool without a `dataframe` argument under `MCP_AUTH_MODE=none` on HTTP transport (where every caller resolves to `tenantId='default'` and shares the canvas) now throws `Forbidden` with structured recovery: pass `dataframe` with a name from a prior `find_*` spillover (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Stdio is unaffected (only the operator runs there); JWT/OAuth is unaffected (each caller carves their own tenant). Tool description now flags this gate inline so an LLM client doesn't burn a call discovering the policy.
+- **`tests/config/server-config.test.ts`.** New unit suite covering `getServerConfig` env-var mapping, defaults, type coercion, and validation errors. Required exporting `ServerConfigSchema` from `src/config/server-config.ts` for testability — purely additive, no runtime change.
+## Changed
+- **`brapi_dataframe_query` forwards gate context on rejection.** When `bridge.query()` rethrows a gate `validationError`, the handler's `sql_rejected` translator now spreads the original error's structured fields (other than `reason` and `recovery`) into `data` — so structured-only consumers see `data.catalog` for system-catalog rejections, `data.operators` for plan-operator rejections, `data.statementType` for non-SELECT rejections, etc. — without parsing the human message text. New `extractGateContext` helper isolates the forwarding logic. Recovery hint and `gateReason` keys still come from the contract / framework.
+- **`brapi_dataframe_describe` and `brapi_dataframe_query` descriptions emphasize the inline-name flow.** Both tools now state explicitly that the dataframe name appears on every `find_*` response that spilled (`result.dataframe.tableName`), so the typical flow is `find_*` → read the name → query / describe by name. Reduces wasted "list everything first" calls — and aligns with the new shared-trust HTTP policy where listing requires possession.
+- **README rewritten around multi-agent collaboration as the headline value.** New top-of-file framing ("A collaborative BrAPI v2.1 workspace for multi-agent research via MCP"), new **Multi-agent workflows** section explaining the connection-state vs dataframe-state split (both tenant-scoped, dataframe `df_<uuid>` names act as in-tenant capability tokens, 24h TTL caps blast radius, provenance trail supports audit), and new **Deployment shapes** section replacing the older **Multi-user HTTP deployments** table with a clearer shared-trust vs per-user-credentials axis. Documents the two new gates inline.
+- **Server descriptions refreshed across `package.json`, `server.json`, README h1, and the GitHub repo metadata** to lead with multi-agent collaboration. `server.json` carries a condensed variant to fit the MCP Registry's 100-character cap.
+## Dependencies
+- **`@cyanheads/mcp-ts-core` ^0.8.15 → ^0.8.16.** Picks up the upstream gate context (catalog / operators / statementType structured fields) that the dataframe-query handler now forwards.

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

@@ -8,7 +8,7 @@
  * @module config/server-config
  */
 import { z } from '@cyanheads/mcp-ts-core';
-declare const ServerConfigSchema: z.ZodObject<{
+export declare const ServerConfigSchema: z.ZodObject<{
     defaultBaseUrl: z.ZodOptional<z.ZodString>;
     defaultUsername: z.ZodOptional<z.ZodString>;
     defaultPassword: z.ZodOptional<z.ZodString>;
@@ -47,5 +47,4 @@ export type ServerConfig = z.infer<typeof ServerConfigSchema>;
 export declare function getServerConfig(): ServerConfig;
 /** Test-only — reset the lazy cache between suites. */
 export declare function resetServerConfig(): void;
-export {};
 //# sourceMappingURL=server-config.d.ts.map

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

	@@ -1 +1 @@
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package/dist/config/server-config.js CHANGED Viewed

@@ -9,7 +9,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
-const ServerConfigSchema = z.object({
+export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
         .string()
         .url()

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts CHANGED Viewed

@@ -12,6 +12,7 @@
  * @module mcp-server/tools/definitions/brapi-dataframe-describe.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     dataframe: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{
@@ -32,5 +33,10 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
             expiresAt: z.ZodString;
         }, z.core.$strip>>;
     }, z.core.$strip>>;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "list_all_disabled_on_shared_http";
+    readonly code: JsonRpcErrorCode.Forbidden;
+    readonly when: "Running under MCP_AUTH_MODE=none on HTTP transport — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
+    readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available.";
+}]>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA6CjD~~,eAAO,MAAM,sBAAsB~~;;;;;;;;;;;;;;;;;;;;6BAgBjC~~,CAAC"}
1	+ {"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;GAkCjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js CHANGED Viewed

@@ -12,6 +12,8 @@
  * @module mcp-server/tools/definitions/brapi-dataframe-describe.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { config } from '@cyanheads/mcp-ts-core/config';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 const ColumnSchema = z.object({
     name: z.string().describe('Column name.'),
@@ -49,11 +51,26 @@ const InputSchema = z.object({
         .describe('When set, return only the named dataframe. Omit to list all dataframes.'),
 });
 export const brapiDataframeDescribe = tool('brapi_dataframe_describe', {
-    description: 'Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The schema and provenance answer "what tool produced this and what filters were used" before you write the first brapi_dataframe_query.',
+    description: 'Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writing the first brapi_dataframe_query. Listing without a name is gated under shared-tenant HTTP (`MCP_AUTH_MODE=none`); pass a known name instead.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: false },
+    errors: [
+        {
+            reason: 'list_all_disabled_on_shared_http',
+            code: JsonRpcErrorCode.Forbidden,
+            when: "Running under MCP_AUTH_MODE=none on HTTP transport — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.",
+            recovery: 'Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available.',
+        },
+    ],
     input: InputSchema,
     output: OutputSchema,
     async handler(input, ctx) {
+        if (input.dataframe === undefined &&
+            ctx.tenantId === 'default' &&
+            config.mcpTransportType === 'http') {
+            throw ctx.fail('list_all_disabled_on_shared_http', undefined, {
+                ...ctx.recoveryFor('list_all_disabled_on_shared_http'),
+            });
+        }
         const bridge = getCanvasBridge();
         const describeOpts = {};
         if (input.dataframe !== undefined)

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.js.map CHANGED Viewed

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js CHANGED Viewed

@@ -25,15 +25,11 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { inferSchemaFromRows, SQL_GATE_REASONS, } from '@cyanheads/mcp-ts-core/canvas';
 import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
-import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
-/**
- * Single source of truth for the SQL gate reason strings — re-exported from
- * the framework's `sqlGate` module. When the bridge's `query()` rethrows a
- * gate `validationError`, the handler translates it into the typed
- * `sql_rejected` contract reason while preserving the granular gate reason
- * on `data.gateReason`.
- */
-const KNOWN_GATE_REASONS = new Set(Object.values(SQL_GATE_REASONS));
+import { getCanvasBridge, SYSTEM_CATALOG_ACCESS_REASON, } from '../../../services/canvas-bridge/index.js';
+const KNOWN_GATE_REASONS = new Set([
+    ...Object.values(SQL_GATE_REASONS),
+    SYSTEM_CATALOG_ACCESS_REASON,
+]);
 function extractSqlGateReason(err) {
     if (!(err instanceof McpError))
         return;
@@ -44,6 +40,23 @@ function extractSqlGateReason(err) {
         ? reason
         : undefined;
 }
+/**
+ * Forward the gate's structured context (e.g. `catalog` for system_catalog_access,
+ * `operators` for plan_operator_not_allowed, `statementType` for non_select_statement)
+ * so structured-only consumers see which specific element matched without parsing
+ * the message text. `reason` becomes `gateReason` upstream; `recovery` is
+ * overridden by the contract recovery hint.
+ */
+function extractGateContext(err) {
+    if (!(err instanceof McpError) || err.data === null || typeof err.data !== 'object')
+        return {};
+    const out = {};
+    for (const [k, v] of Object.entries(err.data)) {
+        if (k !== 'reason' && k !== 'recovery')
+            out[k] = v;
+    }
+    return out;
+}
 const InputSchema = z.object({
     sql: z
         .string()
@@ -94,7 +107,7 @@ const OutputSchema = z.object({
         .describe('Name of the dataframe holding the full result, populated when `registerAs` was supplied. Reference this name in follow-up queries.'),
 });
 export const brapiDataframeQuery = tool('brapi_dataframe_query', {
-    description: 'Run SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`); list them via brapi_dataframe_describe. SELECT only — writes/DDL/COPY/PRAGMA/ATTACH/file-reads are rejected. Use SQL as the paging idiom: `LIMIT/OFFSET` to walk results, projection to trim columns, aggregation to summarize. Use `registerAs` to chain — the result lands as a new dataframe.',
+    description: 'Run SQL across in-memory dataframes. Dataframes auto-populate when find_* tools spill (named `df_<uuid>`) — the dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`), so the typical flow is find_* → read the name → query here. Use brapi_dataframe_describe to inspect schema and provenance for a known name. SELECT only — writes/DDL/COPY/PRAGMA/ATTACH/file-reads are rejected. Use SQL as the paging idiom: `LIMIT/OFFSET` to walk results, projection to trim columns, aggregation to summarize. Use `registerAs` to chain — the result lands as a new dataframe.',
     annotations: { readOnlyHint: false, idempotentHint: false, openWorldHint: false },
     errors: [
         {
@@ -126,7 +139,7 @@ export const brapiDataframeQuery = tool('brapi_dataframe_query', {
             if (gateReason === undefined)
                 throw err;
             const message = err instanceof Error ? err.message : 'Query rejected.';
-            throw ctx.fail('sql_rejected', message, { gateReason, ...ctx.recoveryFor('sql_rejected') }, { cause: err });
+            throw ctx.fail('sql_rejected', message, { gateReason, ...extractGateContext(err), ...ctx.recoveryFor('sql_rejected') }, { cause: err });
         }
         let typedColumns;
         try {

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED Viewed

@@ -321,7 +321,12 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
             expiresAt: import("zod").ZodString;
         }, import("zod/v4/core").$strip>>;
     }, import("zod/v4/core").$strip>>;
-}, import("zod/v4/core").$strip>, undefined> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
+}, import("zod/v4/core").$strip>, readonly [{
+    readonly reason: "list_all_disabled_on_shared_http";
+    readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.Forbidden;
+    readonly when: "Running under MCP_AUTH_MODE=none on HTTP transport — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
+    readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available.";
+}]> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     sql: import("zod").ZodString;
     registerAs: import("zod").ZodOptional<import("zod").ZodString>;
     preview: import("zod").ZodOptional<import("zod").ZodNumber>;

package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAyBH;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;+CAoBnC,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;;8CAAuB,CAAC;AAExD;;;;GAIG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAAyB,CAAC;AAE5D,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAA4B,CAAC"}
1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/index.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAyBH;;;;GAIG;AACH,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;+CAoBnC,CAAC;AAEF;;;;;GAKG;AACH,eAAO,MAAM,mBAAmB;;;;;8CAAuB,CAAC;AAExD;;;;GAIG;AACH,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAAyB,CAAC;AAE5D,qEAAqE;AACrE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;KAA4B,CAAC"}

package/dist/services/canvas-bridge/canvas-bridge.d.ts CHANGED Viewed

@@ -66,6 +66,13 @@ export declare class CanvasBridge {
      * `BRAPI_CANVAS_MAX_ROWS` so a missing/excessive caller value can't bypass
      * the response-size budget. Cancellation flows through `ctx.signal`; the
      * timeout wraps the AbortSignal with a wall-clock cap.
+     *
+     * Pre-gate: rejects SQL that reaches into DuckDB's system catalogs
+     * (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*` metadata
+     * functions). Under shared-tenant deployments the canvas hosts every
+     * caller's dataframes; without this gate, `SELECT * FROM information_schema.tables`
+     * leaks the full df_<uuid> namespace and bypasses brapi_dataframe_describe's
+     * possession-required policy.
      */
     query(ctx: Context, sql: string, options?: {
         preview?: number;
@@ -113,6 +120,13 @@ export declare class CanvasBridge {
     }): Promise<DescribedTable[]>;
     private augmentTableInfo;
 }
+/**
+ * Reason string set on `validationError.data.reason` when a query is rejected
+ * for reaching into DuckDB's system catalogs. Exported so the dataframe-query
+ * tool can recognize it alongside the framework's `SQL_GATE_REASONS` and route
+ * it through the typed `sql_rejected` contract.
+ */
+export declare const SYSTEM_CATALOG_ACCESS_REASON: "system_catalog_access";
 /**
  * Initialize the singleton bridge. The framework canvas is mandatory — the
  * caller is responsible for ensuring `core.canvas` is defined before this

package/dist/services/canvas-bridge/canvas-bridge.d.ts.map CHANGED Viewed

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

@@ -13,7 +13,7 @@
  * @module services/canvas-bridge/canvas-bridge
  */
 import { unlink } from 'node:fs/promises';
-import { JsonRpcErrorCode, McpError } from '@cyanheads/mcp-ts-core/errors';
+import { JsonRpcErrorCode, McpError, validationError } from '@cyanheads/mcp-ts-core/errors';
 /**
  * Construct a `RequestContext` slice from the handler `Context`. The
  * framework's `RequestContext` carries an `[key: string]: unknown` index
@@ -137,8 +137,16 @@ export class CanvasBridge {
      * `BRAPI_CANVAS_MAX_ROWS` so a missing/excessive caller value can't bypass
      * the response-size budget. Cancellation flows through `ctx.signal`; the
      * timeout wraps the AbortSignal with a wall-clock cap.
+     *
+     * Pre-gate: rejects SQL that reaches into DuckDB's system catalogs
+     * (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*` metadata
+     * functions). Under shared-tenant deployments the canvas hosts every
+     * caller's dataframes; without this gate, `SELECT * FROM information_schema.tables`
+     * leaks the full df_<uuid> namespace and bypasses brapi_dataframe_describe's
+     * possession-required policy.
      */
     async query(ctx, sql, options = {}) {
+        assertNoSystemCatalogAccess(sql);
         const instance = await this.getInstance(ctx);
         const cap = this.serverConfig.canvasMaxRows;
         const rowLimit = Math.min(options.rowLimit ?? cap, cap);
@@ -268,6 +276,60 @@ export class CanvasBridge {
 function generateDataframeName() {
     return `${DATAFRAME_TABLE_PREFIX}${crypto.randomUUID().replace(/-/g, '_')}`;
 }
+/**
+ * Reason string set on `validationError.data.reason` when a query is rejected
+ * for reaching into DuckDB's system catalogs. Exported so the dataframe-query
+ * tool can recognize it alongside the framework's `SQL_GATE_REASONS` and route
+ * it through the typed `sql_rejected` contract.
+ */
+export const SYSTEM_CATALOG_ACCESS_REASON = 'system_catalog_access';
+/**
+ * DuckDB metadata views and functions that enumerate the canvas. Catalog
+ * schemas are matched as qualified references (`schema.thing`) so legitimate
+ * column names like `information_schema_id` don't false-positive. DuckDB's
+ * `duckdb_*` introspection functions are matched at the call site (`name(`)
+ * so columns or projected literals carrying the same prefix don't trigger.
+ */
+const SYSTEM_CATALOG_PATTERNS = [
+    { regex: /\binformation_schema\s*\.\s*\w+/i, label: 'information_schema' },
+    { regex: /\bpg_catalog\s*\.\s*\w+/i, label: 'pg_catalog' },
+    { regex: /\bsqlite_master\b/i, label: 'sqlite_master' },
+    { regex: /\bsqlite_temp_master\b/i, label: 'sqlite_temp_master' },
+    {
+        regex: /\bduckdb_(?:tables|columns|views|databases|schemas|functions|types|secrets|extensions|settings|temporary_files|memory|approx_database_size|optimizers|prepared_statements|sequences|indexes|constraints|keywords|dependencies|log_contexts|logs|temp_files|temp_relations|sql_keywords|lib_versions)\s*\(/i,
+        label: 'duckdb_*',
+    },
+];
+/** Strip SQL block and line comments — mirror of the framework gate's helper. */
+function stripSqlComments(sql) {
+    return sql.replace(/\/\*[\s\S]*?\*\//g, ' ').replace(/--[^\n]*/g, '');
+}
+/**
+ * Strip standard SQL string literals so values that happen to mention catalog
+ * names (e.g. `WHERE col = 'information_schema.tables'`) don't trigger the
+ * deny. Matches single-quoted strings with `''` escape; mirror of the
+ * framework gate's helper.
+ */
+function stripSqlStringLiterals(sql) {
+    return sql.replace(/'(?:[^']|'')*'/g, "''");
+}
+/**
+ * Reject SQL that reaches into DuckDB's system catalogs (information_schema,
+ * pg_catalog, sqlite_master, duckdb_* introspection functions). Possession of
+ * a `df_<uuid>` name is the capability gate for direct queries; system catalogs
+ * would let any caller list every name on the shared canvas, bypassing that
+ * gate. Throws `validationError` with `data.reason = 'system_catalog_access'`
+ * so the dataframe-query tool's contract translator routes it through
+ * `sql_rejected`.
+ */
+function assertNoSystemCatalogAccess(sql) {
+    const stripped = stripSqlStringLiterals(stripSqlComments(sql));
+    for (const { regex, label } of SYSTEM_CATALOG_PATTERNS) {
+        if (regex.test(stripped)) {
+            throw validationError(`Canvas query references a system catalog (${label}). System tables and metadata views are not accessible — use brapi_dataframe_describe with a specific dataframe name to inspect schema.`, { reason: SYSTEM_CATALOG_ACCESS_REASON, catalog: label });
+        }
+    }
+}
 function tableMetaKey(tableName) {
     return `${TABLE_META_PREFIX}${tableName}`;
 }

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

	@@ -1 +1 @@
1	- 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package/dist/services/canvas-bridge/index.d.ts CHANGED Viewed

@@ -3,6 +3,6 @@
  *
  * @module services/canvas-bridge
  */
-export { CanvasBridge, getCanvasBridge, initCanvasBridge, type RegisterDataframeInput, type RegisterDataframeResult, resetCanvasBridge, } from './canvas-bridge.js';
+export { CanvasBridge, getCanvasBridge, initCanvasBridge, type RegisterDataframeInput, type RegisterDataframeResult, resetCanvasBridge, SYSTEM_CATALOG_ACCESS_REASON, } from './canvas-bridge.js';
 export type { CanvasTableMeta, DescribedTable } from './types.js';
 //# sourceMappingURL=index.d.ts.map

package/dist/services/canvas-bridge/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../../src/services/canvas-bridge/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACL,YAAY,EACZ,eAAe,EACf,gBAAgB,EAChB,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,iBAAiB,EACjB,4BAA4B,GAC7B,MAAM,oBAAoB,CAAC;AAC5B,YAAY,EAAE,eAAe,EAAE,cAAc,EAAE,MAAM,YAAY,CAAC"}

package/dist/services/canvas-bridge/index.js CHANGED Viewed

@@ -3,5 +3,5 @@
  *
  * @module services/canvas-bridge
  */
-export { CanvasBridge, getCanvasBridge, initCanvasBridge, resetCanvasBridge, } from './canvas-bridge.js';
+export { CanvasBridge, getCanvasBridge, initCanvasBridge, resetCanvasBridge, SYSTEM_CATALOG_ACCESS_REASON, } from './canvas-bridge.js';
 //# sourceMappingURL=index.js.map

package/dist/services/canvas-bridge/index.js.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../src/services/canvas-bridge/index.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,EACL,YAAY,EACZ,eAAe,EACf,gBAAgB,EAGhB,iBAAiB,EACjB,4BAA4B,GAC7B,MAAM,oBAAoB,CAAC"}

package/package.json CHANGED Viewed

@@ -1,8 +1,8 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.5.1",
-  "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
+  "version": "0.5.2",
+  "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",
   "main": "dist/index.js",
@@ -71,7 +71,7 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.8.15",
+    "@cyanheads/mcp-ts-core": "^0.8.16",
     "@duckdb/node-api": "^1.5.2-r.1",
     "pino-pretty": "^13.1.3"
   },

package/server.json CHANGED Viewed

@@ -1,19 +1,19 @@
 {
   "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
   "name": "io.github.cyanheads/brapi-mcp-server",
-  "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
+  "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
   "repository": {
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.5.1",
+  "version": "0.5.2",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.5.1",
+      "version": "0.5.2",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.5.1",
+      "version": "0.5.2",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }