@cyanheads/brapi-mcp-server 0.5.3 → 0.5.5

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Files changed (27) hide show
  1. package/CLAUDE.md +12 -4
  2. package/Dockerfile +2 -2
  3. package/README.md +9 -9
  4. package/changelog/0.5.x/0.5.4.md +25 -0
  5. package/changelog/0.5.x/0.5.5.md +25 -0
  6. package/changelog/template.md +67 -25
  7. package/dist/index.js +1 -0
  8. package/dist/index.js.map +1 -1
  9. package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map +1 -1
  10. package/dist/mcp-server/tools/definitions/brapi-connect.tool.js +1 -2
  11. package/dist/mcp-server/tools/definitions/brapi-connect.tool.js.map +1 -1
  12. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts +3 -3
  13. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map +1 -1
  14. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js +4 -2
  15. package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map +1 -1
  16. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts +1 -1
  17. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map +1 -1
  18. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js +2 -1
  19. package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map +1 -1
  20. package/dist/mcp-server/tools/definitions/index.d.ts +4 -4
  21. package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map +1 -1
  22. package/dist/mcp-server/tools/shared/connect-auth-schema.js +1 -2
  23. package/dist/mcp-server/tools/shared/connect-auth-schema.js.map +1 -1
  24. package/dist/services/canvas-bridge/canvas-bridge.d.ts +1 -1
  25. package/dist/services/canvas-bridge/canvas-bridge.js +4 -4
  26. package/package.json +7 -7
  27. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,7 +1,7 @@
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  # Agent Protocol
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  **Server:** brapi-mcp-server
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- **Version:** 0.5.3
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+ **Version:** 0.5.5
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  **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
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  > **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.
@@ -306,20 +306,25 @@ Available skills:
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  | `add-service` | Scaffold a new service integration |
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  | `add-test` | Scaffold test file for a tool, resource, or service |
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  | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
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+ | `tool-defs-analysis` | Read-only audit of MCP definition language across the surface (12 categories) |
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  | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
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  | `devcheck` | Lint, format, typecheck, audit |
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  | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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+ | `release-and-publish` | Post-wrapup ship workflow: verification gate, push, publish to npm / MCP Registry / GHCR |
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+ | `migrate-mcp-ts-template` | Migrate legacy `mcp-ts-template` fork to package dependency |
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  | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
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  | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
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  | `api-auth` | Auth modes, scopes, JWT/OAuth |
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+ | `api-linter` | Definition lint rule reference (`format-parity`, `schema-*`, `name-*`, `server-json-*`, …) |
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  | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
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  | `api-config` | AppConfig, parseConfig, env vars |
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  | `api-context` | Context interface, logger, state, progress |
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  | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
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  | `api-services` | LLM, Speech, Graph services |
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+ | `api-telemetry` | OTel catalog: spans, metrics, completion logs, env config, cardinality rules |
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  | `api-testing` | createMockContext, test patterns |
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- | `api-utils` | Formatting, parsing, security, pagination, scheduling |
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+ | `api-utils` | Formatting, parsing, security, pagination, scheduling, telemetry helpers |
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  | `api-workers` | Cloudflare Workers runtime |
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  When you complete a skill's checklist, check the boxes and add a completion timestamp at the end (e.g., `Completed: 2026-03-11`).
@@ -356,15 +361,18 @@ Each per-version file opens with YAML frontmatter:
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  ```markdown
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  ---
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- summary: One-line headline, ≤250 chars # required — powers the rollup index
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+ summary: One-line headline, ≤350 chars # required — powers the rollup index
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  breaking: false # optional — true flags breaking changes
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+ security: false # optional — true flags security fixes
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  ---
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  # 0.1.0 — YYYY-MM-DD
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  ...
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  ```
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- `breaking: true` renders a `· ⚠️ Breaking` badge in the rollup — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames).
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+ `breaking: true` renders a `· ⚠️ Breaking` badge — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames). `security: true` renders a `· 🛡️ Security` badge and pairs with a `## Security` body section. When both are set, badges render `· ⚠️ Breaking · 🛡️ Security`.
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+
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+ **Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
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  ---
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package/Dockerfile CHANGED
@@ -4,7 +4,7 @@
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  # This stage installs all dependencies (including dev), builds the TypeScript
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  # source code into JavaScript, and prepares the production assets.
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  # ==============================================================================
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- FROM oven/bun:1 AS build
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+ FROM oven/bun:1.3 AS build
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  WORKDIR /usr/src/app
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@@ -28,7 +28,7 @@ RUN bun run build
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  # application. It uses a slim base image and only includes production
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  # dependencies and build artifacts.
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  # ==============================================================================
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- FROM oven/bun:1-slim AS production
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+ FROM oven/bun:1.3-slim AS production
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  WORKDIR /usr/src/app
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package/README.md CHANGED
@@ -7,7 +7,7 @@
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  <div align="center">
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- [![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-0.5.3-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/)
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+ [![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-0.5.5-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/)
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  [![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)
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@@ -17,7 +17,7 @@
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  ## Tools
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- 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.
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+ 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 agents on the same session 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.
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  ### Orient
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@@ -108,7 +108,7 @@ Within one (tenant, session), dataframes act as a self-cleaning shared notebook:
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  **Default (isolated) shape.** Under `MCP_AUTH_MODE=none` + HTTP stateful (the default), each MCP session carves its own connection state and its own canvas. Two researchers connected to the same host don't see each other's `brapi_connect` aliases, exchanged SGN/OAuth tokens, or spilled `df_<uuid>` rows. Stdio always behaves as one session (single-process, no concurrency).
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- **Legacy shared-workspace shape.** Set `BRAPI_SESSION_ISOLATION=false` for cross-session collaboration in one tenant — multiple MCP sessions then share connection state and one default canvas, the way pre-0.6 deployments behaved. Useful when planning, analysis, and writeup agents run as separate MCP clients but operate as one researcher on shared upstream credentials.
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+ **Shared-workspace shape.** Set `BRAPI_SESSION_ISOLATION=false` for cross-session collaboration in one tenant — multiple MCP sessions then share connection state and one default canvas, the way pre-0.5.3 deployments behaved. Useful when planning, analysis, and writeup agents run as separate MCP clients but operate as one researcher on shared upstream credentials.
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  **On privileged data.** The `df_<uuid>` name is a capability token within a canvas — not row-level access control. Anyone holding the name within the same (tenant, session) bucket can read its rows. Under default isolation, that bucket is one MCP session. Under `BRAPI_SESSION_ISOLATION=false`, the bucket widens to the whole tenant (all callers under `auth=none`, or one user's sessions under `jwt`/`oauth`). Treat dataframe names like authenticated share links — pass within the bucket, not externally. The 24h TTL caps blast radius; the provenance trail (originating tool, baseUrl, query) supports audit. Belt-and-braces: `brapi_dataframe_describe` requires an explicit `dataframe` name on shared-trust HTTP (no 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.
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@@ -181,7 +181,7 @@ MCP_TRANSPORT_TYPE=http MCP_HTTP_PORT=3010 bun run start:http
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  No env vars are required — the six built-in aliases (`bti-cassava`, `bti-sweetpotato`, `bti-breedbase-demo`, `t3-wheat`, `t3-oat`, `t3-barley`) resolve out-of-the-box, and agents can connect to any other BrAPI v2 URL at runtime via `brapi_connect`. **For credentialed servers, prefer env vars over agent input** so passwords / tokens / API keys stay out of the LLM context — see [Per-alias credentials](#per-alias-credentials).
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- **Prerequisites:** [Bun v1.3.11+](https://bun.sh/) or Node.js v22+. [`@duckdb/node-api`](https://www.npmjs.com/package/@duckdb/node-api) is a required dependency — supported on Linux/macOS/Windows × x64 plus Linux/macOS arm64 (no Windows arm64; no Cloudflare Workers).
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+ **Prerequisites:** [Bun v1.3.11+](https://bun.sh/) or Node.js v24+. [`@duckdb/node-api`](https://www.npmjs.com/package/@duckdb/node-api) is a required dependency — supported on Linux/macOS/Windows × x64 plus Linux/macOS arm64 (no Windows arm64; no Cloudflare Workers).
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  ---
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@@ -212,7 +212,7 @@ Every variable is optional.
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  | `BRAPI_CANVAS_MAX_ROWS` / `BRAPI_CANVAS_QUERY_TIMEOUT_MS` | Per-query response row cap and wall-clock timeout for `brapi_dataframe_query`. | `10000` / `30000` |
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  | `MCP_TRANSPORT_TYPE` / `MCP_HTTP_PORT` / `MCP_SESSION_MODE` | Transport (`stdio` \| `http`), HTTP port, session mode (`stateful` \| `stateless` \| `auto`). | `stdio` / `3010` / `auto` |
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  | `MCP_AUTH_MODE` / `MCP_LOG_LEVEL` / `STORAGE_PROVIDER_TYPE` / `OTEL_ENABLED` | Auth mode (`none` \| `jwt` \| `oauth`), log level, storage backend, OpenTelemetry. | `none` / `info` / `in-memory` / `false` |
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- | `BRAPI_SESSION_ISOLATION` | When `true`, scope ServerRegistry connection state and the CanvasBridge default canvas to `ctx.sessionId` (HTTP stateful/auto). Concurrent callers under `MCP_AUTH_MODE=none` operate in isolated workspaces. Set `false` for the legacy shared-workspace collaboration model. No effect on stdio. | `true` |
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+ | `BRAPI_SESSION_ISOLATION` | When `true`, scope ServerRegistry connection state and the CanvasBridge default canvas to `ctx.sessionId` (HTTP stateful/auto). Concurrent callers under `MCP_AUTH_MODE=none` operate in isolated workspaces. Set `false` for the shared-workspace collaboration model. No effect on stdio. | `true` |
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  Per-alias overrides follow the `BRAPI_<ALIAS>_*` pattern — see [`.env.example`](./.env.example) for every override and inline comments.
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@@ -295,7 +295,7 @@ docker build -t brapi-mcp-server .
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  docker run --rm -p 3010:3010 brapi-mcp-server
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  ```
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- Defaults to HTTP transport, stateful session mode (engages `mcp-session-id` lifecycle and hijack protection), logs to `/var/log/brapi-mcp-server`. OTel peer deps are installed by default — `--build-arg OTEL_ENABLED=false` to omit.
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+ Defaults to HTTP transport, stateful session mode (engages the `mcp-session-id` lifecycle — precondition for `BRAPI_SESSION_ISOLATION=true`; hijack protection requires layering `MCP_AUTH_MODE=jwt|oauth` on top), logs to `/var/log/brapi-mcp-server`. OTel peer deps are installed by default — `--build-arg OTEL_ENABLED=false` to omit.
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  ### Deployment shapes
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@@ -305,13 +305,13 @@ Defaults to HTTP transport, stateful session mode (engages `mcp-session-id` life
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  |:------|:---------|:----------|:---------|
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  | **Per-session (default)** | `MCP_AUTH_MODE=none` + HTTP stateful + `BRAPI_SESSION_ISOLATION=true` | Each MCP session carves its own connection state and canvas. Concurrent HTTP callers don't see each other's aliases, exchanged tokens, or `df_<uuid>` rows. | Multi-user host without SSO. Default for institutional / public deployment under shared-trust auth. |
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  | **Per-user credentials** | `MCP_AUTH_MODE=jwt` or `oauth` (+ HTTP stateful) | Each user's JWT `tid` claim carves a tenant. Sessions sub-scope inside each tenant when isolation is on. Cross-user spillover impossible at the framework level. | Multi-user host with institutional SSO (Shibboleth, Okta, etc.) — strongest separation. |
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- | **Shared workspace (legacy)** | `MCP_AUTH_MODE=none` + `BRAPI_SESSION_ISOLATION=false` | All callers in one tenant share connection state and one canvas. Possession of a `df_<uuid>` name = full read/write across the workspace. | Solo, lab, or hosting where every caller is one researcher running parallel agents on shared upstream credentials. |
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+ | **Shared workspace** | `MCP_AUTH_MODE=none` + `BRAPI_SESSION_ISOLATION=false` | All callers in one tenant share connection state and one canvas. Possession of a `df_<uuid>` name = full read/write across the workspace. | Solo, lab, or hosting where every caller is one researcher running parallel agents on shared upstream credentials. |
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  **Shape selection guide:**
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  - **Multi-user public/institutional HTTP, no SSO.** Use the per-session default. Each researcher's stateful HTTP session is isolated even though they all resolve to `tenantId='default'`.
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- - **Multi-user with institutional SSO.** Layer JWT or OAuth on top of per-session: `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`). Each user's `tid` carves a tenant; `BRAPI_SESSION_ISOLATION=true` then sub-scopes inside it for users running parallel sessions.
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- - **One researcher, parallel agents.** If multiple agents (planner, analyst, writeup) connect as separate MCP clients but should share one workspace, set `BRAPI_SESSION_ISOLATION=false` and rely on shared trust. This is the legacy shape.
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+ - **Multi-user with institutional SSO.** `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`). Each user's `tid` claim carves a tenant — the outer scope. `BRAPI_SESSION_ISOLATION=true` (default) then sub-scopes inside each tenant for users running parallel sessions, and JWT/OAuth identity binding gives real session-hijack protection on top.
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+ - **One researcher, parallel agents.** If multiple agents (planner, analyst, writeup) connect as separate MCP clients but should share one workspace, set `BRAPI_SESSION_ISOLATION=false` and rely on shared trust. This is the shared-workspace shape.
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  - **Stdio.** Always one session; isolation is moot. The flag has no effect.
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  **Belt-and-braces under shared trust.** Even with `BRAPI_SESSION_ISOLATION=false`, `brapi_dataframe_describe` requires an explicit `dataframe` name on HTTP (no list-all enumeration), and `brapi_dataframe_query` rejects system-catalog reads (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*`). The dataframe name is the capability token; possession proves it.
package/changelog/0.5.x/0.5.4.md ADDED
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+ ---
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+ summary: "Patch maintenance — drop misleading 'legacy' label from the shared-workspace shape; adopt framework 0.8.19 (engines bump, Docker base 1.3, api-telemetry skill)."
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+ breaking: false
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+ ---
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+
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+ # 0.5.4 — 2026-05-08
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+
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+ ## Changed
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+ - **Engines bumped:** `node >=22.0.0 → >=24.0.0`, `bun >=1.2.0 → >=1.3.0` — tracks the `@cyanheads/mcp-ts-core` 0.8.19 floor.
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+ - **Dockerfile base:** `oven/bun:1 → oven/bun:1.3` (build and slim-runtime stages).
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+ - **README prerequisite line:** Node.js v22+ → v24+.
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+ - **`scripts/build-changelog.ts` synced** — adds optional `security: boolean` frontmatter; pairs with the `## Security` body section to render a `🛡️ Security` badge in the rollup. Existing per-version files stay valid (the field defaults to `false`).
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+ - **`changelog/template.md` synced** (pristine reference) — bold-the-symbol bullet style, Keep-a-Changelog section order, scaffolded Deprecated / Removed / Security sections (commented out by default).
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+ - **`CLAUDE.md` / `AGENTS.md` skill table** — added `api-telemetry`; `api-utils` description now mentions telemetry helpers.
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+ - **Skills resynced from `@cyanheads/mcp-ts-core@0.8.19`** — `api-telemetry` (NEW v1.0; full OTel catalog of spans, metrics, completion-log fields, env config, cardinality rules), `api-utils` 2.1 → 2.2, `maintenance` 2.0 → 2.1 (Phase C now also resyncs pristine reference files), `report-issue-framework` 1.5 → 1.6, `report-issue-local` 1.4 → 1.5, `setup` 1.6 → 1.7. Phase B mirrored into `.claude/skills/` and `.agents/skills/`.
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+ ## Fixed
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+
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+ - **Dropped misleading "legacy" label from the shared-workspace deployment shape** — `README.md` table row + env-var description + multi-agent workflows section, `src/services/canvas-bridge/canvas-bridge.ts` comments, `tests/services/server-registry.test.ts` test comment. The shape (`MCP_AUTH_MODE=none + BRAPI_SESSION_ISOLATION=false`) remains a first-class supported deployment mode — only non-default since 0.5.3.
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+ ## Dependencies
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+
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+ - **`@cyanheads/mcp-ts-core` `^0.8.17 → ^0.8.19`** — `ctx.auth.token` reaches handlers ([#121](https://github.com/cyanheads/mcp-ts-core/issues/121); not used by this server), new `api-telemetry` skill, `security: boolean` changelog frontmatter, hono `^4.12.18` security floor, OTel SDK `^0.217.0`, engines + Docker base bumps.
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+ - **`@types/node` `^25.6.0 → ^25.6.2`**.
package/changelog/0.5.x/0.5.5.md ADDED
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+ ---
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+ summary: "Adopt framework 0.9.1 — wire `instructions` field for server-level orientation, port two raw schemas off `z.url()` and three off `.nullish()` unions to clear the new cross-vendor portability lint family (`schema-format-portability`, `schema-anyof-needs-type`)."
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+ breaking: false
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+ security: false
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+ ---
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+ # 0.5.5 — 2026-05-16
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+ ## Added
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+ - **Server-level `instructions` on `createApp()`** — agents now receive a one-paragraph orientation on `initialize` describing the connect-first handshake, the `find_*` / `get_*` / `raw_*` tool families, the spillover-to-canvas flow, and which tools to prefer. Spec-compliant clients forward it as session-level system context, so the same guidance reaches the model without bloating individual tool descriptions. ([@cyanheads/mcp-ts-core#91](https://github.com/cyanheads/mcp-ts-core/issues/91))
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+ ## Changed
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+ - **`brapi_connect` and OAuth2 auth schemas dropped `z.url()`** ([`src/mcp-server/tools/definitions/brapi-connect.tool.ts`](./src/mcp-server/tools/definitions/brapi-connect.tool.ts), [`src/mcp-server/tools/shared/connect-auth-schema.ts`](./src/mcp-server/tools/shared/connect-auth-schema.ts)) — `z.url()` emits `format: "uri"` which OpenAI's tool validator hard-rejects, so `gpt-5-codex` was silently dropping the tools. Replaced with `z.string()` and moved the "absolute URL" constraint into `.describe()` text where the model actually reads it; clears the new default-on `schema-format-portability` lint rule. ([@cyanheads/mcp-ts-core#132](https://github.com/cyanheads/mcp-ts-core/issues/132), field report: [cyanheads/git-mcp-server#47](https://github.com/cyanheads/git-mcp-server/issues/47))
16
+ - **`find_observations` season + season.year and `find_variants` variantSetDbId unions ported off `.nullish()`** ([`src/mcp-server/tools/definitions/brapi-find-observations.tool.ts`](./src/mcp-server/tools/definitions/brapi-find-observations.tool.ts), [`src/mcp-server/tools/definitions/brapi-find-variants.tool.ts`](./src/mcp-server/tools/definitions/brapi-find-variants.tool.ts)) — `.nullish()` on a `z.union([...])` emits a typeless `anyOf` branch that Gemini rejects with `400: reference to undefined schema`. Switched to `.optional()` + explicit `z.null()` in the union so every branch carries a top-level `type`; clears the new default-on `schema-anyof-needs-type` lint rule.
17
+ - **`scripts/devcheck.ts` `bun outdated` parser fixed** — `bun outdated` emits markdown-style rows (`| pkg | … |`) with an empty leading cell, so `split('|')[0]` was always empty and the allowlist never matched. Now reads index `[1]` and strips the trailing `(dev|peer|prod|optional)` workspace marker so bare package names match. Synced from framework 0.9.1.
18
+ - **Changelog summary cap raised 250 → 350 chars** — `SUMMARY_MAX_LENGTH` in `scripts/build-changelog.ts`, `changelog/template.md`, and the AGENTS.md / CLAUDE.md changelog section. Synced from framework 0.9.0 — 250 was forcing operator-relevant context out of recent summaries. ([@cyanheads/mcp-ts-core#129](https://github.com/cyanheads/mcp-ts-core/issues/129))
19
+ - **AGENTS.md / CLAUDE.md skill table** — added rows for `tool-defs-analysis`, `release-and-publish`, `migrate-mcp-ts-template`, and `api-linter`; refreshed the changelog frontmatter section with the `security: boolean` flag and Keep-a-Changelog section-order guidance.
20
+ - **Skills resynced from `@cyanheads/mcp-ts-core@0.9.1`** — `api-auth` 1.0 → 1.1 (`mcp_tool_scopes` union claim, Authentik/Keycloak/Zitadel operator setup, `MCP_AUTH_DISABLE_SCOPE_CHECKS` bypass), `api-linter` 1.2 → 1.3 (new portability rule family), `api-workers` 1.3 → 1.4 (`instructions` resolver form documented), `polish-docs-meta` 1.7 → 1.8 (350-char summary cap), `add-tool`, `api-config`, `api-errors`, `design-mcp-server`, `field-test`, `security-pass`, `tool-defs-analysis`. Phase B mirrored into `.claude/skills/` and `.agents/skills/`.
21
+
22
+ ## Dependencies
23
+
24
+ - **`@cyanheads/mcp-ts-core` `^0.8.19 → ^0.9.1`** — Workers boot under `nodejs_compat` ([#124](https://github.com/cyanheads/mcp-ts-core/issues/124); not used by this server but unblocks anyone bridging to Workers), `instructions` field on `createApp` ([#91](https://github.com/cyanheads/mcp-ts-core/issues/91)), cross-vendor JSON Schema portability lint family ([#132](https://github.com/cyanheads/mcp-ts-core/issues/132)), build-time-only definition linting (no longer gates `createApp()` startup), RFC 8414 §3 path-suffixed well-known mount, SSRF DNS validation now enforced in Workers, IPv6-mapped/unique-local/link-local SSRF blocklist, FileSystemProvider tenant-id boundary check, rate-limit metric cardinality bound. ⚠️ Breaking: `schema-format-portability` is default-on `error` — the two `z.url()` migrations above are this server's response. ([changelog](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.9.x/0.9.0.md))
25
+ - **`@biomejs/biome` `^2.4.14 → ^2.4.15`**, **`@types/node` `^25.6.2 → ^25.8.0`**, **`vitest` `^4.1.5 → ^4.1.6`** — patch refreshes.
package/changelog/template.md CHANGED
@@ -1,41 +1,71 @@
1
1
  ---
2
- # FORMAT REFERENCE — this file is never edited, never moved, never renamed.
3
- #
4
- # At release time, author a new per-version file at:
5
- # changelog/<major.minor>.x/<version>.md (e.g. changelog/0.1.x/0.1.0.md)
6
- # using this file's frontmatter and section layout as the starting point.
7
- # Set that new file's H1 to `# <version> — YYYY-MM-DD` with a concrete date.
8
-
9
- # Required. One-line headline describing the release. Max 250 chars. No markdown.
10
- # This line is what the CHANGELOG.md rollup shows — write it like a GitHub Release title.
2
+ # FORMAT REFERENCE — do not edit. Copy this file to
3
+ # `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.8.x/0.8.6.md`)
4
+ # to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
5
+ # with a concrete date.
6
+
7
+ # Required. One-line GitHub Release-style headline. 350 character cap.
8
+ # Default short and scannable. Don't pad, don't stitch unrelated changes with
9
+ # semicolons — pick the headline. Quotes required: unquoted YAML treats `: `
10
+ # inside the value as a key separator and fails GitHub's strict parser.
11
11
  summary: ""
12
12
 
13
- # Set to `true` only if this release has breaking changes (API removals, signature
14
- # changes, config renames, anything that requires consumer code changes on update).
15
- # Flagged as ⚠️ Breaking in the rollup.
13
+ # Set `true` when consumers must change code to upgrade: API removals,
14
+ # signature changes, config renames, behavior changes that break existing
15
+ # usage. Flagged as `Breaking` in the rollup.
16
16
  breaking: false
17
+
18
+ # Set `true` if this release contains any security fix. Pairs with the
19
+ # `## Security` section below. Flagged as `Security` in the rollup so
20
+ # users can triage upgrade urgency at a glance.
21
+ security: false
17
22
  ---
18
23
 
19
24
  # <version> — YYYY-MM-DD
20
25
 
21
26
  <!--
22
- FORMAT REFERENCE — do not edit this file. It exists so the per-version file
23
- structure has a single copy-source. Create new release notes at
24
- `changelog/<major.minor>.x/<version>.md` using this layout.
27
+ AUTHORING GUIDE — applies to the new per-version file you create from this
28
+ template.
29
+
30
+ Audience: someone scanning release notes to decide what affects them. Lead
31
+ each bullet with the symbol or concept name in **bold** so they can skip
32
+ what's irrelevant and zoom in on what's not.
33
+
34
+ Tone: terse, fact-dense, not verbose. Default to one sentence per bullet —
35
+ name the symbol, state what changed, stop. Use a second sentence only when
36
+ it carries weight. If a bullet feels long, it is.
37
+
38
+ Cut: mechanism walkthroughs (those belong in JSDoc, AGENTS.md, or the
39
+ relevant skill), ceremonial framings ("This release introduces…",
40
+ backwards-compat paragraphs), file-by-file test enumerations, internal
41
+ implementation notes. Prefer code/symbol names over English re-explanations.
42
+
43
+ Narrative intro: skip by default. Add one short sentence only when the
44
+ release theme genuinely needs framing the bullets can't carry.
45
+
46
+ Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
47
+ Fixed, Security. Include only sections with entries; delete the rest
48
+ (including the commented-out scaffolding below). Don't ship empty headers.
25
49
 
26
- Optional narrative intro — 1-3 sentences framing the release theme. Delete if not needed.
50
+ Include: every distinct fact a reader needs to adopt or audit the release —
51
+ new exports, signatures, lint rule IDs, env vars, breaking changes, version
52
+ bumps on shipped skills. Nothing more.
27
53
 
28
- Linking issues/PRs: use full URLs so the link works everywhere (GitHub web UI,
29
- npm/node_modules reads, local editors). GitHub's bare `#NN` auto-link only
30
- resolves inside its own UI.
54
+ Links: link issues, PRs, docs, or skills where they help a reader jump to
55
+ context. Once per item per entry — don't re-link the same issue in summary,
56
+ narrative, and bullet. Skip links for inline symbol names; code spans speak
57
+ for themselves.
31
58
 
32
- [#12](https://github.com/<owner>/<repo>/issues/12) ← issue
33
- [#17](https://github.com/<owner>/<repo>/pull/17) ← PR
59
+ Issue/PR URLs: use full URLs. GitHub's bare `#NN` auto-link only resolves
60
+ inside its own UI, not in npm reads or local editors.
34
61
 
35
- Only link numbers you've verified exist (via `gh issue view NN` or
36
- `gh pr view NN`). Never speculate on a future number — `#17` for "my
37
- upcoming PR" will quietly resolve to whatever real item already owns 17,
38
- and GitHub timeline previews will pull in that unrelated item's title.
62
+ [#38](https://github.com/cyanheads/mcp-ts-core/issues/38) ← issue
63
+ [#42](https://github.com/cyanheads/mcp-ts-core/pull/42) ← PR
64
+
65
+ Verify numbers exist before linking (`gh issue view NN`, `gh pr view NN`).
66
+ Never speculate on a future number — `#42` for an upcoming PR silently
67
+ resolves to whatever real item already owns 42, and timeline previews pull
68
+ in that unrelated item's metadata.
39
69
  -->
40
70
 
41
71
  ## Added
@@ -46,6 +76,18 @@ breaking: false
46
76
 
47
77
  -
48
78
 
79
+ <!-- ## Deprecated
80
+
81
+ - -->
82
+
83
+ <!-- ## Removed
84
+
85
+ - -->
86
+
49
87
  ## Fixed
50
88
 
51
89
  -
90
+
91
+ <!-- ## Security
92
+
93
+ - -->
package/dist/index.js CHANGED
@@ -103,6 +103,7 @@ await createApp({
103
103
  brapiFiltersResource,
104
104
  ],
105
105
  prompts: [brapiEdaStudy, brapiMetaAnalysis],
106
+ instructions: 'Bridges BrAPI v2 servers (Breeding API for plant/crop research). Call `brapi_connect` first to register a server under an alias and return the orientation envelope (capabilities, dialect, sample IDs). `brapi_find_*` tools page filtered lookups across studies, germplasm, observations, variables, locations, images, variants, and genotype calls; rows beyond the per-call cap spill to a canvas dataframe — query with `brapi_dataframe_query` (SELECT-only SQL). `brapi_get_*` fetch single records by `*DbId`. Use `brapi_raw_get` / `brapi_raw_search` only when no curated tool fits — responses route back to the right curated tool.',
106
107
  setup(core) {
107
108
  if (!core.canvas) {
108
109
  throw configurationError('brapi-mcp-server requires the framework canvas service (DuckDB) for dataframe spillover. Set CANVAS_PROVIDER_TYPE=duckdb (the default) and ensure @duckdb/node-api is installed.', { canvasProviderType: process.env.CANVAS_PROVIDER_TYPE ?? 'duckdb' });
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package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0FvB,CAAC"}
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+ {"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyFvB,CAAC"}
package/dist/mcp-server/tools/definitions/brapi-connect.tool.js CHANGED
@@ -43,9 +43,8 @@ export const brapiConnect = tool('brapi_connect', {
43
43
  input: z.object({
44
44
  baseUrl: z
45
45
  .string()
46
- .url()
47
46
  .optional()
48
- .describe('BrAPI v2 base URL including any path prefix — e.g. https://test-server.brapi.org/brapi/v2. Omit to use the configured default for this alias.'),
47
+ .describe('BrAPI v2 base URL (absolute URL) including any path prefix — e.g. https://test-server.brapi.org/brapi/v2. Omit to use the configured default for this alias.'),
49
48
  auth: ConnectAuthSchema.optional().describe('Auth payload. Omit to use credentials configured server-side for this alias (or no auth when none are configured).'),
50
49
  alias: z
51
50
  .string()
package/dist/mcp-server/tools/definitions/brapi-connect.tool.js.map CHANGED
@@ -1 +1 @@
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+ {"version":3,"file":"brapi-connect.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EACL,yBAAyB,EACzB,2BAA2B,EAC3B,mBAAmB,GACpB,MAAM,+BAA+B,CAAC;AACvC,OAAO,EAAE,cAAc,EAAE,MAAM,kCAAkC,CAAC;AAClE,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAChF,OAAO,EAAE,iBAAiB,EAAE,MAAM,qCAAqC,CAAC;AACxE,OAAO,EAAE,iBAAiB,EAAE,MAAM,kCAAkC,CAAC;AACrE,OAAO,EACL,wBAAwB,EACxB,yBAAyB,EACzB,yBAAyB,GAC1B,MAAM,mCAAmC,CAAC;AAE3C,MAAM,gBAAgB,GACpB,uUAAuU,CAAC;AAE1U,MAAM,uBAAuB,GAAG,2BAA2B,CAAC,yBAAyB,EAAE,CAAC,CAAC;AAEzF,MAAM,CAAC,MAAM,YAAY,GAAG,IAAI,CAAC,eAAe,EAAE;IAChD,WAAW,EAAE,uBAAuB;QAClC,CAAC,CAAC,GAAG,gBAAgB,IAAI,uBAAuB,EAAE;QAClD,CAAC,CAAC,gBAAgB;IACpB,WAAW,EAAE;QACX,aAAa,EAAE,IAAI;QACnB,YAAY,EAAE,KAAK;QACnB,cAAc,EAAE,IAAI;KACrB;IACD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,4BAA4B;YACpC,IAAI,EAAE,gBAAgB,CAAC,SAAS;YAChC,IAAI,EAAE,sEAAsE;YAC5E,QAAQ,EAAE,4EAA4E;SACvF;QACD;YACE,MAAM,EAAE,sBAAsB;YAC9B,IAAI,EAAE,gBAAgB,CAAC,SAAS;YAChC,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EACN,6FAA6F;SAChG;KACO;IACV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,OAAO,EAAE,CAAC;aACP,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,8JAA8J,CAC/J;QACH,IAAI,EAAE,iBAAiB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CACzC,oHAAoH,CACrH;QACD,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,KAAK,CAAC,kBAAkB,CAAC;aACzB,OAAO,CAAC,SAAS,CAAC;aAClB,QAAQ,CACP,oGAAoG,CACrG;KACJ,CAAC;IACF,MAAM,EAAE,yBAAyB;IAEjC,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,QAAQ,GAAG,iBAAiB,EAAE,CAAC;QACrC,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;QAC7C,MAAM,MAAM,GAAG,cAAc,EAAE,CAAC;QAEhC,MAAM,QAAQ,GAAG,mBAAmB,CAAC,KAAK,CAAC,KAAK,EAAE;YAChD,OAAO,EAAE,KAAK,CAAC,OAAO;YACtB,IAAI,EAAE,KAAK,CAAC,IAAI;SACjB,CAAC,CAAC;QAEH,MAAM,UAAU,GAAG,MAAM,QAAQ,CAAC,QAAQ,CAAC,GAAG,EAAE;YAC9C,KAAK,EAAE,KAAK,CAAC,KAAK;YAClB,OAAO,EAAE,QAAQ,CAAC,OAAO;YACzB,IAAI,EAAE,QAAQ,CAAC,IAAI;SACpB,CAAC,CAAC;QAEH,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,6BAA6B,EAAE;YAC1C,KAAK,EAAE,UAAU,CAAC,KAAK;YACvB,OAAO,EAAE,UAAU,CAAC,OAAO;YAC3B,QAAQ,EAAE,UAAU,CAAC,QAAQ;YAC7B,UAAU,EAAE,KAAK,CAAC,IAAI,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC,KAAK;SACzC,CAAC,CAAC;QAEH,IAAI,2BAA2B,EAAE,IAAI,UAAU,CAAC,QAAQ,KAAK,MAAM,EAAE,CAAC;YACpE,GAAG,CAAC,GAAG,CAAC,MAAM,CACZ,wHAAwH,EACxH;gBACE,KAAK,EAAE,UAAU,CAAC,KAAK;gBACvB,OAAO,EAAE,UAAU,CAAC,OAAO;gBAC3B,QAAQ,EAAE,UAAU,CAAC,QAAQ;gBAC7B,YAAY,EAAE,OAAO,CAAC,GAAG,CAAC,kBAAkB;gBAC5C,WAAW,EAAE,OAAO,CAAC,GAAG,CAAC,aAAa,IAAI,MAAM;aACjD,CACF,CAAC;QACJ,CAAC;QAED,8EAA8E;QAC9E,MAAM,YAAY,CAAC,UAAU,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,CAAC,CAAC;QACvD,OAAO,wBAAwB,CAAC,GAAG,EAAE,UAAU,EAAE;YAC/C,QAAQ,EAAE,YAAY;YACtB,MAAM;SACP,CAAC,CAAC;IACL,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,yBAAyB,CAAC,MAAM,CAAC,EAAE,CAAC;CAChF,CAAC,CAAC;AAEH;;;;GAIG;AACH,SAAS,2BAA2B;IAClC,MAAM,SAAS,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,OAAO,CAAC,CAAC,WAAW,EAAE,CAAC;IAC5E,IAAI,SAAS,KAAK,MAAM;QAAE,OAAO,KAAK,CAAC;IACvC,MAAM,QAAQ,GAAG,CAAC,OAAO,CAAC,GAAG,CAAC,aAAa,IAAI,MAAM,CAAC,CAAC,WAAW,EAAE,CAAC;IACrE,OAAO,QAAQ,KAAK,KAAK,IAAI,QAAQ,KAAK,OAAO,CAAC;AACpD,CAAC"}
package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts CHANGED
@@ -37,12 +37,12 @@ export declare const brapiFindObservations: import("@cyanheads/mcp-ts-core").Too
37
37
  germplasmDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
38
38
  germplasmName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
39
39
  observationLevel: z.ZodOptional<z.ZodNullable<z.ZodString>>;
40
- season: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
40
+ season: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
41
41
  seasonDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
42
- year: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>>;
42
+ year: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodNull]>>;
43
43
  season: z.ZodOptional<z.ZodNullable<z.ZodString>>;
44
44
  seasonName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
45
- }, z.core.$loose>]>>>;
45
+ }, z.core.$loose>, z.ZodNull]>>;
46
46
  value: z.ZodOptional<z.ZodNullable<z.ZodString>>;
47
47
  observationTimeStamp: z.ZodOptional<z.ZodNullable<z.ZodString>>;
48
48
  collector: z.ZodOptional<z.ZodNullable<z.ZodString>>;
package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyLjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsThC,CAAC"}
1
+ {"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA2LjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsThC,CAAC"}
package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js CHANGED
@@ -50,8 +50,9 @@ const ObservationRowSchema = z
50
50
  .union([
51
51
  z.string().describe('Calendar year as a string (e.g. "2024").'),
52
52
  z.number().describe('Calendar year as an integer (e.g. 2024).'),
53
+ z.null().describe('Field present but null on the upstream.'),
53
54
  ])
54
- .nullish()
55
+ .optional()
55
56
  .describe('Calendar year — accepts string or numeric form depending on server.'),
56
57
  season: z.string().nullish().describe('Season label (e.g. "wet", "dry", "Q1").'),
57
58
  seasonName: z
@@ -61,8 +62,9 @@ const ObservationRowSchema = z
61
62
  })
62
63
  .passthrough()
63
64
  .describe('Structured season block per BrAPI v2.1.'),
65
+ z.null().describe('Field present but null on the upstream.'),
64
66
  ])
65
- .nullish()
67
+ .optional()
66
68
  .describe('Season — either a flat string or a structured `{seasonDbId, year, season}` object depending on the server.'),
67
69
  value: z
68
70
  .string()
package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts CHANGED
@@ -23,7 +23,7 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
23
23
  results: z.ZodArray<z.ZodObject<{
24
24
  variantDbId: z.ZodString;
25
25
  variantNames: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
26
- variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>>;
26
+ variantSetDbId: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>, z.ZodNull]>>;
27
27
  variantSetDbIds: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
28
28
  variantType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
29
29
  referenceBases: z.ZodOptional<z.ZodNullable<z.ZodString>>;
package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiIjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsM5B,CAAC"}
1
+ {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkIjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsM5B,CAAC"}
package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js CHANGED
@@ -28,8 +28,9 @@ const VariantRowSchema = z
28
28
  z
29
29
  .array(z.string().describe('One variant-set FK.'))
30
30
  .describe('Variant-set FK array — a variant may belong to multiple sets.'),
31
+ z.null().describe('Field present but null on the upstream.'),
31
32
  ])
32
- .nullish()
33
+ .optional()
33
34
  .describe('FK to the variant set(s) this variant belongs to. May be a string or string[] depending on server.'),
34
35
  variantSetDbIds: z
35
36
  .array(z.string().describe('Variant-set FK.'))
package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map CHANGED
@@ -1 +1 @@
1
- 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package/dist/mcp-server/tools/definitions/index.d.ts CHANGED
@@ -619,12 +619,12 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
619
619
  germplasmDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
620
620
  germplasmName: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
621
621
  observationLevel: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
622
- season: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodObject<{
622
+ season: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodObject<{
623
623
  seasonDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
624
- year: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>>;
624
+ year: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber, import("zod").ZodNull]>>;
625
625
  season: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
626
626
  seasonName: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
627
- }, import("zod/v4/core").$loose>]>>>;
627
+ }, import("zod/v4/core").$loose>, import("zod").ZodNull]>>;
628
628
  value: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
629
629
  observationTimeStamp: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
630
630
  collector: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
@@ -811,7 +811,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
811
811
  results: import("zod").ZodArray<import("zod").ZodObject<{
812
812
  variantDbId: import("zod").ZodString;
813
813
  variantNames: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodArray<import("zod").ZodString>>>;
814
- variantSetDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodArray<import("zod").ZodString>]>>>;
814
+ variantSetDbId: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodArray<import("zod").ZodString>, import("zod").ZodNull]>>;
815
815
  variantSetDbIds: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodArray<import("zod").ZodString>>>;
816
816
  variantType: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
817
817
  referenceBases: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"connect-auth-schema.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;2BA0D3B,CAAC;AAEJ,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC"}
1
+ {"version":3,"file":"connect-auth-schema.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;2BA2D3B,CAAC;AAEJ,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC"}
package/dist/mcp-server/tools/shared/connect-auth-schema.js CHANGED
@@ -54,9 +54,8 @@ export const ConnectAuthSchema = z
54
54
  clientSecret: z.string().min(1).describe('OAuth2 client secret paired with the clientId.'),
55
55
  tokenUrl: z
56
56
  .string()
57
- .url()
58
57
  .optional()
59
- .describe('OAuth2 token endpoint URL. Defaults derived from the base URL when omitted.'),
58
+ .describe('OAuth2 token endpoint (absolute URL). Defaults derived from the base URL when omitted.'),
60
59
  })
61
60
  .describe('OAuth2 client-credentials variant.'),
62
61
  ])
package/dist/mcp-server/tools/shared/connect-auth-schema.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"connect-auth-schema.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,kBAAkB,CAAC,MAAM,EAAE;IAC1B,CAAC;SACE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC,EAAE,CAAC;SAClE,QAAQ,CAAC,2CAA2C,CAAC;IACxD,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QAChE,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,mEAAmE,CAAC;KACjF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC;IACzE,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACzE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;SACD,QAAQ,CAAC,6DAA6D,CAAC;IAC1E,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC7D,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,yDAAyD,CAAC;KACvE,CAAC;SACD,QAAQ,CAAC,2EAA2E,CAAC;IACxF,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,QAAQ,CAAC;aACjB,QAAQ,CACP,gFAAgF,CACjF;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC;QACzE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC1F,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC;CAClD,CAAC;KACD,QAAQ,CACP,2GAA2G,CAC5G,CAAC"}
1
+ {"version":3,"file":"connect-auth-schema.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,kBAAkB,CAAC,MAAM,EAAE;IAC1B,CAAC;SACE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC,EAAE,CAAC;SAClE,QAAQ,CAAC,2CAA2C,CAAC;IACxD,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QAChE,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,mEAAmE,CAAC;KACjF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC;IACzE,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACzE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;SACD,QAAQ,CAAC,6DAA6D,CAAC;IAC1E,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC7D,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,yDAAyD,CAAC;KACvE,CAAC;SACD,QAAQ,CAAC,2EAA2E,CAAC;IACxF,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,QAAQ,CAAC;aACjB,QAAQ,CACP,gFAAgF,CACjF;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC;QACzE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC1F,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wFAAwF,CACzF;KACJ,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC;CAClD,CAAC;KACD,QAAQ,CACP,2GAA2G,CAC5G,CAAC"}
package/dist/services/canvas-bridge/canvas-bridge.d.ts CHANGED
@@ -65,7 +65,7 @@ export declare class CanvasBridge {
65
65
  * folds the session ID in, so concurrent HTTP sessions in the same tenant
66
66
  * end up on distinct canvases. When isolation is disabled or no session ID
67
67
  * is available (stdio, stateless HTTP without opt-in), falls back to the
68
- * legacy per-tenant shared canvas.
68
+ * tenant-shared canvas.
69
69
  */
70
70
  getInstance(ctx: Context): Promise<CanvasInstance>;
71
71
  /**
package/dist/services/canvas-bridge/canvas-bridge.js CHANGED
@@ -38,9 +38,9 @@ function asRequestContext(ctx) {
38
38
  /**
39
39
  * State keys holding the default canvasId (opaque 10-char token).
40
40
  *
41
- * `DEFAULT_CANVAS_KEY` keys the per-tenant default canvas — the legacy
42
- * shared workspace; used for stdio, stateless HTTP without opt-in, and any
43
- * deployment where `BRAPI_SESSION_ISOLATION=false`.
41
+ * `DEFAULT_CANVAS_KEY` keys the per-tenant default canvas — the
42
+ * tenant-shared workspace; used for stdio, stateless HTTP without opt-in,
43
+ * and any deployment where `BRAPI_SESSION_ISOLATION=false`.
44
44
  *
45
45
  * `SESSION_CANVAS_PREFIX` keys per-session canvases when isolation is on
46
46
  * and `ctx.sessionId` is present. Each session gets its own canvas and
@@ -87,7 +87,7 @@ export class CanvasBridge {
87
87
  * folds the session ID in, so concurrent HTTP sessions in the same tenant
88
88
  * end up on distinct canvases. When isolation is disabled or no session ID
89
89
  * is available (stdio, stateless HTTP without opt-in), falls back to the
90
- * legacy per-tenant shared canvas.
90
+ * tenant-shared canvas.
91
91
  */
92
92
  async getInstance(ctx) {
93
93
  const key = this.defaultCanvasKey(ctx);
package/package.json CHANGED
@@ -1,7 +1,7 @@
1
1
  {
2
2
  "name": "@cyanheads/brapi-mcp-server",
3
3
  "mcpName": "io.github.cyanheads/brapi-mcp-server",
4
- "version": "0.5.3",
4
+ "version": "0.5.5",
5
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.",
6
6
  "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
7
7
  "type": "module",
@@ -63,25 +63,25 @@
63
63
  },
64
64
  "license": "Apache-2.0",
65
65
  "engines": {
66
- "node": ">=22.0.0",
67
- "bun": ">=1.2.0"
66
+ "node": ">=24.0.0",
67
+ "bun": ">=1.3.0"
68
68
  },
69
69
  "packageManager": "bun@1.3.11",
70
70
  "publishConfig": {
71
71
  "access": "public"
72
72
  },
73
73
  "dependencies": {
74
- "@cyanheads/mcp-ts-core": "^0.8.17",
74
+ "@cyanheads/mcp-ts-core": "^0.9.1",
75
75
  "@duckdb/node-api": "^1.5.2-r.1",
76
76
  "pino-pretty": "^13.1.3"
77
77
  },
78
78
  "devDependencies": {
79
- "@biomejs/biome": "^2.4.14",
80
- "@types/node": "^25.6.0",
79
+ "@biomejs/biome": "^2.4.15",
80
+ "@types/node": "^25.8.0",
81
81
  "depcheck": "^1.4.7",
82
82
  "ignore": "^7.0.5",
83
83
  "tsc-alias": "^1.8.17",
84
84
  "typescript": "^6.0.3",
85
- "vitest": "^4.1.5"
85
+ "vitest": "^4.1.6"
86
86
  }
87
87
  }
package/server.json CHANGED
@@ -6,14 +6,14 @@
6
6
  "url": "https://github.com/cyanheads/brapi-mcp-server",
7
7
  "source": "github"
8
8
  },
9
- "version": "0.5.3",
9
+ "version": "0.5.5",
10
10
  "packages": [
11
11
  {
12
12
  "registryType": "npm",
13
13
  "registryBaseUrl": "https://registry.npmjs.org",
14
14
  "identifier": "@cyanheads/brapi-mcp-server",
15
15
  "runtimeHint": "bun",
16
- "version": "0.5.3",
16
+ "version": "0.5.5",
17
17
  "packageArguments": [
18
18
  { "type": "positional", "value": "run" },
19
19
  { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
49
49
  "registryBaseUrl": "https://registry.npmjs.org",
50
50
  "identifier": "@cyanheads/brapi-mcp-server",
51
51
  "runtimeHint": "bun",
52
- "version": "0.5.3",
52
+ "version": "0.5.5",
53
53
  "packageArguments": [
54
54
  { "type": "positional", "value": "run" },
55
55
  { "type": "positional", "value": "start:http" }