@cyanheads/brapi-mcp-server 0.7.11 → 0.7.12

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Files changed (33) hide show
  1. package/CLAUDE.md +18 -16
  2. package/README.md +3 -3
  3. package/changelog/0.7.x/0.7.12.md +35 -0
  4. package/changelog/template.md +7 -24
  5. package/dist/config/alias-credentials.d.ts +1 -1
  6. package/dist/config/alias-credentials.d.ts.map +1 -1
  7. package/dist/config/alias-credentials.js +24 -8
  8. package/dist/config/alias-credentials.js.map +1 -1
  9. package/dist/config/server-config.d.ts +1 -1
  10. package/dist/config/server-config.d.ts.map +1 -1
  11. package/dist/config/server-config.js +3 -1
  12. package/dist/config/server-config.js.map +1 -1
  13. package/dist/mcp-server/resources/definitions/brapi-calls.resource.js +1 -1
  14. package/dist/mcp-server/resources/definitions/brapi-filters.resource.js +1 -1
  15. package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js +1 -1
  16. package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js +1 -1
  17. package/dist/mcp-server/resources/definitions/brapi-study.resource.js +1 -1
  18. package/dist/mcp-server/resources/definitions/brapi-variable.resource.js +1 -1
  19. package/dist/services/brapi-client/brapi-client.d.ts.map +1 -1
  20. package/dist/services/brapi-client/brapi-client.js +5 -5
  21. package/dist/services/brapi-client/brapi-client.js.map +1 -1
  22. package/dist/services/brapi-client/types.d.ts +1 -1
  23. package/dist/services/brapi-dialect/detect.d.ts +1 -1
  24. package/dist/services/brapi-dialect/index.d.ts +2 -2
  25. package/dist/services/brapi-dialect/index.js +1 -1
  26. package/dist/services/capability-registry/capability-registry.d.ts +1 -1
  27. package/dist/services/capability-registry/capability-registry.js +1 -1
  28. package/dist/services/reference-data-cache/reference-data-cache.d.ts +2 -2
  29. package/dist/services/reference-data-cache/reference-data-cache.js +1 -1
  30. package/dist/services/server-registry/types.d.ts +1 -1
  31. package/manifest.json +8 -6
  32. package/package.json +10 -9
  33. package/server.json +3 -3
package/CLAUDE.md CHANGED
@@ -1,9 +1,9 @@
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  # Agent Protocol
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  **Server:** brapi-mcp-server
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- **Version:** 0.7.11
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- **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
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- **Engines:** Bun ≥1.3.0, Node ≥24.0.0
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+ **Version:** 0.7.12
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+ **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.13.0`
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+ **Engines:** Bun ≥1.4.0, Node ≥24.0.0
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  **MCP SDK:** `@modelcontextprotocol/server` ^2.0.0 (protocol revisions 2026-07-28 and 2025-*)
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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.
@@ -180,7 +180,7 @@ Handlers receive a unified `ctx` object. Currently used surface:
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  Handlers throw — the framework catches, classifies, and formats.
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- **Default for new tools: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated); to surface it on the wire, spread `...ctx.recoveryFor('reason')` into `data` or pass an explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`) bubble freely and don't need declaring. Live across the BrAPI surface today: `brapi_build_phenotype_matrix`, `brapi_dataframe_describe`, `brapi_dataframe_export`, `brapi_dataframe_query`, `brapi_describe_filters`, `brapi_export_genotype_matrix`, `brapi_find_genotype_calls`, `brapi_germplasm_performance`, `brapi_get_germplasm`, `brapi_get_image`, `brapi_get_study`, `brapi_raw_get`, `brapi_raw_search`, `brapi_submit_observations`, plus the `brapi://variable/{observationVariableDbId}` resource.
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+ **Default for new tools: typed error contract.** Declare `errors: [{ reason, code, when, recovery, retryable? }]` on `tool()` to receive a typed `ctx.fail(reason, …)` keyed by the declared reason union. TypeScript catches `ctx.fail('typo')` at compile time, `data.reason` is auto-populated for observability, and the linter enforces conformance against the handler body. The `recovery` field is required descriptive metadata (≥ 5 words, lint-validated); to surface it on the wire, spread `...ctx.recoveryFor('reason')` into `data` or pass an explicit `{ recovery: { hint: '...' } }` when runtime context matters. Baseline codes (`InternalError`, `ServiceUnavailable`, `Timeout`, `ValidationError`, `SerializationError`, `RequestCancelled`) bubble freely and don't need declaring. Live across the BrAPI surface today: `brapi_build_phenotype_matrix`, `brapi_dataframe_describe`, `brapi_dataframe_export`, `brapi_dataframe_query`, `brapi_describe_filters`, `brapi_export_genotype_matrix`, `brapi_find_genotype_calls`, `brapi_germplasm_performance`, `brapi_get_germplasm`, `brapi_get_image`, `brapi_get_study`, `brapi_raw_get`, `brapi_raw_search`, `brapi_submit_observations`, plus the `brapi://variable/{observationVariableDbId}` resource.
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  ```ts
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  errors: [
@@ -301,9 +301,9 @@ src/
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  ## Skills
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- Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
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+ Skills are modular instructions in `framework-skills/` at the project root. Read them directly when a task matches — e.g., `framework-skills/add-tool/SKILL.md` when adding a tool. Keep development skills out of root `skills/`: plugin hosts load that directory for installing agents.
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- **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, Codex: `.codex/skills/`, shared: `.agents/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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+ **Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, Codex: `.codex/skills/`, shared: `.agents/skills/`, others: equivalent). This makes skills available as context without needing to reference `framework-skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
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  Available skills:
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@@ -324,8 +324,9 @@ Available skills:
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  | `techniques` | Catalog of response/data-shaping techniques — overflow handling, payload shaping, retrieval patterns |
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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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- | `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
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- | `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
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+ | `git-wrapup` | Land working-tree changes as a versioned commit stack; opens a release PR when the project declares release PR mode. |
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+ | `release-pr-review` | Review an open release PR, land fixups, and keep its body current. Release PR mode only. |
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+ | `release-and-publish` | Tag + push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup`. |
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  | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
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  | `orchestrations` | Chain task skills into a gated multi-phase pipeline — build-out, QA-fix, update-ship — when you can spawn sub-agents |
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  | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
@@ -343,7 +344,7 @@ Available skills:
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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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- **Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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+ **Chaining skills into pipelines.** When the user wants a multi-phase effort — build this server out, QA-and-fix the surface, update-and-ship — *and you can spawn sub-agents*, `framework-skills/orchestrations/SKILL.md` sequences the task skills above into a gated pipeline with verification at each step. Read it to drive the run. Optional: skip it if you can't orchestrate sub-agents, and ignore it entirely if you were *spawned* as one — you've already been scoped to a single phase.
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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`).
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@@ -359,7 +360,8 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  | `bun run rebuild` | Clean + build |
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  | `bun run clean` | Remove build artifacts |
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  | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
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- | `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit. Use when `devcheck` flags a transitive advisory — Bun's `update` is sticky on transitive resolutions, so the advisory may be a stale-lockfile false positive. If it survives the refresh, it's real. |
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+ | `bun run audit:fix` | Upgrade vulnerable packages within existing ranges with `bun audit fix`; try before `bun update <name>` and `bun dedupe`. |
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+ | `bun run audit:refresh` | Delete `bun.lock`, reinstall, re-audit. Last resort after in-place fixes; re-resolves ranged dependencies, including the framework. |
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  | `bun run list-skills` | Print the skill index for this project (name, version, description) |
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  | `bun run tree` | Generate `docs/tree.md` |
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  | `bun run format` | Auto-fix formatting via Biome |
@@ -377,7 +379,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
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  ## Bundling
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- `bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. The bundle therefore ships portable without the DuckDB native — `@duckdb/node-api` is loaded lazily, so canvas tools report an actionable install hint and every other tool works normally. MCPB is stdio-only — HTTP deployments are unaffected. To opt out, delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly when `manifest.json` is absent.
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+ `bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`framework-skills/`, `skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. The bundle therefore ships portable without the DuckDB native — `@duckdb/node-api` is loaded lazily, so canvas tools report an actionable install hint and every other tool works normally. MCPB is stdio-only — HTTP deployments are unaffected. To opt out, delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly when `manifest.json` is absent.
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  **Adding an env var requires both files:** `server.json` (registry discovery, `environmentVariables[]`) and `manifest.json` (bundle install UX, `mcp_config.env` + `user_config`). `lint:packaging` (run by `devcheck`) verifies the env var names match.
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  `agent-notes` is an optional free-form field for maintenance agents processing the release downstream. Content here won't appear in the rendered CHANGELOG — it's consumed by agents running the `maintenance` skill. Use it for adoption instructions that don't fit the human-facing sections: new files to create, fields to populate, one-time migration steps. Omit entirely when there's nothing to say.
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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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+ **Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security, then Dependencies. Include only sections with entries — don't ship empty headers.
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- **Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. They must be structured markdown — never a flat comma-separated string. Subject omits the version number (GitHub prepends it). See `changelog/template.md` for the full format reference.
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+ **Tag annotations** render as GitHub Release bodies via `--notes-from-tag`. Subject omits the version number (GitHub prepends it). Follow `framework-skills/release-and-publish/SKILL.md` for the tag format.
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  ---
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@@ -439,7 +441,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
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  - [ ] Tests include at least one sparse upstream payload (fields omitted) alongside the happy path
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  - [ ] Registered in the `tools` array of `createApp()` in `src/index.ts`
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  - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
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- - [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
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- - [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
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- - [ ] `.claude-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; inline `mcpServers` entry with server name key, env vars for any required API keys
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+ - [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = the unscoped repo name; `interface.shortDescription` from `package.json` description
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+ - [ ] `.codex-plugin/mcp.json` updated — server name key is the unscoped repo name; user-supplied variables are listed in `env_vars`, never set to empty strings in `env`
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+ - [ ] `.claude-plugin/plugin.json` populated — metadata from `package.json`; inline `mcpServers` entry keyed by the unscoped repo name; user-supplied variables declared under `userConfig` and referenced as `${user_config.<option>}`
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  - [ ] `bun run devcheck` passes
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-0.7.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-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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+ [![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.7.12-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-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-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-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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  </div>
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@@ -194,7 +194,7 @@ 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 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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+ **Prerequisites:** [Bun v1.4.0+](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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@@ -225,7 +225,7 @@ Every variable is optional.
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  | `BRAPI_CANVAS_DROP_ENABLED` | Opt-in for `brapi_dataframe_drop` registration. Off by default; dataframes expire via TTL when left unmanaged. | `false` |
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  | `BRAPI_EXPORT_DIR` | Directory for `brapi_dataframe_export` output files. Setting a path is the opt-in (no separate enable flag); unset leaves the tool out of `tools/list`. Stdio-only — the tool stays disabled under HTTP transport regardless of this value. Bridged to the framework's `CANVAS_EXPORT_PATH` automatically. | — |
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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`; `auto` resolves to stateful for HTTP). | `stdio` / `3010` / `stateful` |
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+ | `MCP_TRANSPORT_TYPE` / `MCP_HTTP_PORT` / `MCP_SESSION_MODE` | Transport (`stdio` \| `http`), HTTP port, session mode: `stateful` retains 2025 client sessions for observation-write confirmation; `stateless` cannot perform that confirmation round; `auto` (framework default) resolves to stateful for HTTP. Docker and the env example pin `stateful`. | `stdio` / `3010` / `stateful` |
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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 shared-workspace collaboration model. No effect on stdio. | `true` |
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package/changelog/0.7.x/0.7.12.md ADDED
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+ ---
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+ summary: "Adopts @cyanheads/mcp-ts-core ^0.13.0: empty and unsubstituted ${…} env values read as unset across every BRAPI_* path, async-search cancellation and poll deadlines classify as RequestCancelled and Timeout, and the framework skill tree moves out of the plugin-loaded skills/ directory."
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+ security: false
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+ ---
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+
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+ # 0.7.12 — 2026-09-13
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+ A framework-adoption release; this server changes no tool contract of its own.
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+ ## Changed
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+ - **Plugin manifests declare their user config** — `.claude-plugin/plugin.json` gains a `userConfig` block, and it and `manifest.json` reference every option as `${user_config.<key>}`; `.codex-plugin/mcp.json` forwards `BRAPI_DEFAULT_BASE_URL` through `env_vars` rather than setting it to an empty string, which would replace a value the operator exported (mcp-ts-core 0.13.0).
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+ - **Tool argument rejections classify as `InvalidParams` (-32602)** instead of `ValidationError`, carrying the same structured error envelope and message text (mcp-ts-core 0.12.7).
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+ - **HTTP transport** — a trailing slash on `MCP_PUBLIC_URL` no longer doubles in advertised links (mcp-ts-core 0.12.8); the landing page's curl snippet sends a handshake `initialize` accepts, and a cancelled request's SSE stream closes immediately rather than at keep-alive (mcp-ts-core 0.12.9).
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+ - **`MCP_RESPONSE_VERBOSITY` and `OAUTH_PROXY_*` are no longer recognized** by framework config (mcp-ts-core 0.12.8). Neither is set by this server's Docker image or `.env.example`.
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+ - **Records logged from `setup()` survive startup** — buffered and replayed once the logger initializes, or drained to stderr when startup fails, instead of dropped (mcp-ts-core 0.12.5).
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+ - **The framework skill tree moved from `skills/` to `framework-skills/`** — plugin hosts auto-load a root `skills/`, which handed this server's development skills to every installing agent. `.mcpbignore`, the agent protocol, and `docs/tree.md` follow the path; no runtime surface changed (mcp-ts-core 0.13.0).
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+ - **Bun engines floor raised to `>=1.4.0`** (mcp-ts-core 0.12.9), and `audit:fix` runs `bun audit fix` — the previous script ran a read-only audit and changed nothing (mcp-ts-core 0.13.0).
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+ ## Fixed
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+
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+ - **An unsubstituted `${…}` env value no longer registers a phantom alias or fails URL validation** — `BRAPI_<ALIAS>_*` credentials and the `BRAPI_*` server config both read empty strings and whole-value placeholders as unset through `parseEnvConfig`, so a builtin alias is no longer shadowed by its own unfilled placeholder. A URL containing a literal `${…}` segment is still preserved (mcp-ts-core 0.13.0).
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+ - **A cancelled async search throws `RequestCancelled` (-32011) and an exhausted poll deadline throws `Timeout`** — they were `InternalError` and `ServiceUnavailable`. Neither issues a further poll, and both the `structuredContent.error` envelope and the `content[]` trailer carry the same message.
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+ - **An upstream 500 reaches the client's reclassifier again** — no HTTP status maps to `InternalError` now, so a singleton `GET` that an upstream answers 500 for an unknown DbId maps to `NotFound` without retrying, an ordinary 500 retries, and a 501 carries `data.retryable: false` so an unimplemented method is not retried (mcp-ts-core 0.12.4).
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+ ## Dependencies
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+
29
+ - `@cyanheads/mcp-ts-core` ^0.12.3 → ^0.13.0
30
+ - `zod` ^4.4.3 → ^4.6.1
31
+ - `@biomejs/biome` ^2.5.9 → ^2.5.13
32
+ - `@types/node` ^26.2.0 → ^26.5.1
33
+ - `ignore` ^7.0.6 → ^7.0.9
34
+ - `tsc-alias` ^1.9.2 → ^1.9.4
35
+ - `vitest` ^4.1.11 → ^5.0.0
package/changelog/template.md CHANGED
@@ -117,30 +117,13 @@ security: false
117
117
  in that unrelated item's metadata.
118
118
 
119
119
  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
120
- via `gh release create --notes-from-tag`. The tag is a derivative of this
121
- changelog entry — a condensed, scannable version, not a copy. Format:
122
-
123
- <theme — omit version number, GitHub prepends it>
124
- ← blank line
125
- <1-2 sentence context: what this release does>
126
- ← blank line
127
- Dependency bumps: ← section header
128
- ← blank line
129
- - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6 ← bullet
130
- ← blank line
131
- Changed: ← only sections with entries
132
- ← blank line
133
- - `format()` output includes `query` in text mode
134
- ← blank line
135
- Added:
136
- ← blank line
137
- - `manifest.json` scaffolded for MCPB bundle support
138
- - Install badges (Claude Desktop, Cursor, VS Code)
139
- ← blank line
140
- <N> tests pass; `bun run devcheck` clean. ← footer
141
-
142
- Never a flat comma-separated string. Always structured markdown with
143
- sections. The tag must scan well as a rendered GitHub Release page.
120
+ via `gh release create --notes-from-tag`. It is a condensed digest of this
121
+ entry, never a copy, and its format is owned by the `release-and-publish`
122
+ skill (step 4, "Create the annotated tag"): the entry's `summary:` as the
123
+ theme line without the version, flat headline bullets — no Keep-a-Changelog
124
+ section headers, no gates line — at most one deps line, issue backlinks,
125
+ and the changelog link last. In release-PR mode the `git-wrapup` skill
126
+ authors that digest as the PR body's `## Changes` and the tag copies it.
144
127
  -->
145
128
 
146
129
  ## Added
package/dist/config/alias-credentials.d.ts CHANGED
@@ -26,7 +26,7 @@ export interface AliasCredentials {
26
26
  }
27
27
  /** Compute the env-var prefix for an alias. `my-server` → `BRAPI_MY_SERVER_`. */
28
28
  export declare function aliasEnvPrefix(alias: string): string;
29
- /** Read all `BRAPI_<ALIAS>_*` vars for an alias. Empty strings treated as unset. */
29
+ /** Read alias env vars; empty strings and whole-value host placeholders are unset. */
30
30
  export declare function readAliasCredentials(alias: string, env?: NodeJS.ProcessEnv): AliasCredentials;
31
31
  /**
32
32
  * Pick a `ConnectAuth` from the credential bundle. Returns `undefined` when no
package/dist/config/alias-credentials.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"alias-credentials.d.ts","sourceRoot":"","sources":["../../src/config/alias-credentials.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAIH,OAAO,KAAK,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAC;AAEjF;;;GAGG;AACH,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AAiBD,iFAAiF;AACjF,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEpD;AAED,oFAAoF;AACpF,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,gBAAgB,CAQlB;AAED;;;;GAIG;AACH,wBAAgB,yBAAyB,CACvC,KAAK,EAAE,gBAAgB,EACvB,KAAK,EAAE,MAAM,GACZ,WAAW,GAAG,SAAS,CAwCzB;AAED,MAAM,WAAW,oBAAoB;IACnC,IAAI,EAAE,WAAW,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CACjC,KAAK,EAAE,MAAM,EACb,KAAK,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,IAAI,CAAC,EAAE,WAAW,GAAG,SAAS,CAAA;CAAE,EACvE,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,oBAAoB,CAwBtB;AAED;;;;;;GAMG;AACH,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,QAAQ,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,KAAK,GAAG,SAAS,CAAC;CAC3B;AAID;;;;;;;;;GASG;AACH,wBAAgB,yBAAyB,CAAC,GAAG,GAAE,MAAM,CAAC,UAAwB,GAAG,eAAe,EAAE,CA2CjG;AAaD;;;;;;GAMG;AACH,wBAAgB,2BAA2B,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG,MAAM,CAmB9E"}
1
+ {"version":3,"file":"alias-credentials.d.ts","sourceRoot":"","sources":["../../src/config/alias-credentials.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAMH,OAAO,KAAK,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAC;AAEjF;;;GAGG;AACH,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AA6BD,iFAAiF;AACjF,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEpD;AAED,sFAAsF;AACtF,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,gBAAgB,CAalB;AAED;;;;GAIG;AACH,wBAAgB,yBAAyB,CACvC,KAAK,EAAE,gBAAgB,EACvB,KAAK,EAAE,MAAM,GACZ,WAAW,GAAG,SAAS,CAwCzB;AAED,MAAM,WAAW,oBAAoB;IACnC,IAAI,EAAE,WAAW,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED;;;;;;;;;;;;;;;;GAgBG;AACH,wBAAgB,mBAAmB,CACjC,KAAK,EAAE,MAAM,EACb,KAAK,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,IAAI,CAAC,EAAE,WAAW,GAAG,SAAS,CAAA;CAAE,EACvE,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,oBAAoB,CAwBtB;AAED;;;;;;GAMG;AACH,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,QAAQ,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,KAAK,GAAG,SAAS,CAAC;CAC3B;AAID;;;;;;;;;GASG;AACH,wBAAgB,yBAAyB,CAAC,GAAG,GAAE,MAAM,CAAC,UAAwB,GAAG,eAAe,EAAE,CA4CjG;AAaD;;;;;;GAMG;AACH,wBAAgB,2BAA2B,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG,MAAM,CAmB9E"}
package/dist/config/alias-credentials.js CHANGED
@@ -8,8 +8,10 @@
8
8
  *
9
9
  * @module config/alias-credentials
10
10
  */
11
+ import { z } from '@cyanheads/mcp-ts-core';
12
+ import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
11
13
  import { validationError } from '@cyanheads/mcp-ts-core/errors';
12
- import { findBuiltinAlias, listBuiltinAliases } from '../config/builtin-aliases.js';
14
+ import { findBuiltinAlias, listBuiltinAliases } from './builtin-aliases.js';
13
15
  const FIELD_SUFFIXES = [
14
16
  ['baseUrl', 'BASE_URL'],
15
17
  ['username', 'USERNAME'],
@@ -21,19 +23,31 @@ const FIELD_SUFFIXES = [
21
23
  ['oauthClientSecret', 'OAUTH_CLIENT_SECRET'],
22
24
  ['oauthTokenUrl', 'OAUTH_TOKEN_URL'],
23
25
  ];
26
+ const AliasCredentialsSchema = z.object({
27
+ baseUrl: z.string().optional(),
28
+ username: z.string().optional(),
29
+ password: z.string().optional(),
30
+ apiKey: z.string().optional(),
31
+ apiKeyHeader: z.string().optional(),
32
+ bearerToken: z.string().optional(),
33
+ oauthClientId: z.string().optional(),
34
+ oauthClientSecret: z.string().optional(),
35
+ oauthTokenUrl: z.string().optional(),
36
+ });
24
37
  const DEFAULT_ALIAS = 'default';
25
38
  const NONE_AUTH = { mode: 'none' };
26
39
  /** Compute the env-var prefix for an alias. `my-server` → `BRAPI_MY_SERVER_`. */
27
40
  export function aliasEnvPrefix(alias) {
28
41
  return `BRAPI_${alias.replace(/-/g, '_').toUpperCase()}_`;
29
42
  }
30
- /** Read all `BRAPI_<ALIAS>_*` vars for an alias. Empty strings treated as unset. */
43
+ /** Read alias env vars; empty strings and whole-value host placeholders are unset. */
31
44
  export function readAliasCredentials(alias, env = process.env) {
32
45
  const prefix = aliasEnvPrefix(alias);
46
+ const parsed = parseEnvConfig(AliasCredentialsSchema, Object.fromEntries(FIELD_SUFFIXES.map(([field, suffix]) => [field, `${prefix}${suffix}`])), env);
33
47
  const result = {};
34
- for (const [field, suffix] of FIELD_SUFFIXES) {
35
- const value = env[`${prefix}${suffix}`];
36
- if (value !== undefined && value !== '')
48
+ for (const [field] of FIELD_SUFFIXES) {
49
+ const value = parsed[field];
50
+ if (value !== undefined)
37
51
  result[field] = value;
38
52
  }
39
53
  return result;
@@ -136,18 +150,20 @@ export function discoverConfiguredAliases(env = process.env) {
136
150
  // the underscored form. Without this map, an env var that shadows a
137
151
  // hyphenated builtin would be reported as a separate `bti_cassava` alias.
138
152
  const builtinByUnderscoredName = new Map(builtins.map((b) => [b.alias.replace(/-/g, '_'), b]));
139
- for (const [key, value] of Object.entries(env)) {
153
+ for (const key of Object.keys(env)) {
140
154
  const match = key.match(ALIAS_BASE_URL_PATTERN);
141
155
  const captured = match?.[1];
142
- if (!captured || !value)
156
+ if (!captured)
143
157
  continue;
144
158
  const lowerCaptured = captured.toLowerCase();
145
159
  const alias = builtinByUnderscoredName.get(lowerCaptured)?.alias ?? lowerCaptured;
146
160
  const creds = readAliasCredentials(alias, env);
161
+ if (!creds.baseUrl)
162
+ continue;
147
163
  result.push({
148
164
  alias,
149
165
  authMode: deriveModeForDiscovery(creds, alias),
150
- baseUrl: value,
166
+ baseUrl: creds.baseUrl,
151
167
  origin: 'env',
152
168
  });
153
169
  seen.add(alias);
package/dist/config/alias-credentials.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/config/server-config.d.ts CHANGED
@@ -27,7 +27,7 @@ export declare const GENOTYPE_CALLS_MAX_PULL_CEILING = 500000;
27
27
  */
28
28
  export declare const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500000;
29
29
  export declare const ServerConfigSchema: z.ZodObject<{
30
- defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
30
+ defaultBaseUrl: z.ZodOptional<z.ZodString>;
31
31
  defaultUsername: z.ZodOptional<z.ZodString>;
32
32
  defaultPassword: z.ZodOptional<z.ZodString>;
33
33
  defaultOauthClientId: z.ZodOptional<z.ZodString>;
package/dist/config/server-config.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C;;;;;;GAMG;AACH,eAAO,MAAM,+BAA+B,SAAU,CAAC;AAEvD;;;;;;;;GAQG;AACH,eAAO,MAAM,mCAAmC,SAAU,CAAC;AAE3D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAkK7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA+B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}
1
+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C;;;;;;GAMG;AACH,eAAO,MAAM,+BAA+B,SAAU,CAAC;AAEvD;;;;;;;;GAQG;AACH,eAAO,MAAM,mCAAmC,SAAU,CAAC;AAE3D,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAiK7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA+B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}
package/dist/config/server-config.js CHANGED
@@ -29,7 +29,9 @@ export const GENOTYPE_CALLS_MAX_PULL_CEILING = 500_000;
29
29
  export const GENOTYPE_MATRIX_MAX_COLUMNS_CEILING = 500_000;
30
30
  export const ServerConfigSchema = z.object({
31
31
  defaultBaseUrl: z
32
- .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
32
+ .string()
33
+ .url()
34
+ .optional()
33
35
  .describe('Default BrAPI v2 base URL if no connection is opened via brapi_connect.'),
34
36
  defaultUsername: z
35
37
  .string()
package/dist/config/server-config.js.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,+BAA+B,GAAG,OAAO,CAAC;AAEvD;;;;;;;;GAQG;AACH,MAAM,CAAC,MAAM,mCAAmC,GAAG,OAAO,CAAC;AAE3D,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IACzC,cAAc,EAAE,CAAC;SACd,UAAU,CACT,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,OAAO,CAAC,KAAK,QAAQ,IAAI,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,SAAS,CAAC,CAAC,CAAC,CAAC,CAAC,EACjE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,QAAQ,EAAE,CAC5B;SACA,QAAQ,CAAC,yEAAyE,CAAC;IACtF,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,qDAAqD,CAAC;IAClE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,qDAAqD,CAAC;IAClE,oBAAoB,EAAE,CAAC;SACpB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,uDAAuD,CAAC;IACpE,wBAAwB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IACzF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IACxE,mBAAmB,EAAE,CAAC;SACnB,MAAM,EAAE;SACR,OAAO,CAAC,eAAe,CAAC;SACxB,QAAQ,CAAC,0CAA0C,CAAC;IAEvD,iBAAiB,EAAE,CAAC,CAAC,MAAM;SACxB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,mFAAmF,CAAC;IAEhG,SAAS,EAAE,CAAC,CAAC,MAAM;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,gLAAgL,CACjL;IACH,QAAQ,EAAE,CAAC,CAAC,MAAM;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,oQAAoQ,CACrQ;IACH,qBAAqB,EAAE,CAAC,CAAC,MAAM;SAC5B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,+DAA+D,CAAC;IAC5E,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,0CAA0C,CAAC;IACvD,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,GAAG,CAAC;SACZ,QAAQ,CAAC,8CAA8C,CAAC;IAC3D,wBAAwB,EAAE,CAAC,CAAC,MAAM;SAC/B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,0EAA0E,CAAC;IAEvF,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,2BAA2B,CAAC;IACxC,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,4MAA4M,CAC7M;IACH,mBAAmB,EAAE,CAAC,CAAC,MAAM;SAC1B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,0DAA0D,CAAC;IACvE,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,mDAAmD,CAAC;IAChE,eAAe,EAAE,CAAC;SACf,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,4DAA4D,CAAC;IACzE,YAAY,EAAE,CAAC;SACZ,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,0KAA0K,CAC3K;IACH,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,GAAG,CAAC,+BAA+B,CAAC;SACpC,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,CACP,+fAA+f,CAChgB;IACH,wBAAwB,EAAE,CAAC,CAAC,MAAM;SAC/B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,GAAG,CAAC,mCAAmC,CAAC;SACxC,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,ixBAAixB,CAClxB;IAEH,iBAAiB,EAAE,CAAC;SACjB,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,kLAAkL,CACnL;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,6gBAA6gB,CAC9gB;IACH,aAAa,EAAE,CAAC,CAAC,MAAM;SACpB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,4JAA4J,CAC7J;IACH,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,yDAAyD,CAAC;IAEtE,gBAAgB,EAAE,CAAC;SAChB,UAAU,EAAE;SACZ,OAAO,CAAC,IAAI,CAAC;SACb,QAAQ,CACP,2pBAA2pB,CAC5pB;CACJ,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,cAAc,EAAE,wBAAwB;QACxC,eAAe,EAAE,wBAAwB;QACzC,eAAe,EAAE,wBAAwB;QACzC,oBAAoB,EAAE,+BAA+B;QACrD,wBAAwB,EAAE,mCAAmC;QAC7D,aAAa,EAAE,uBAAuB;QACtC,mBAAmB,EAAE,8BAA8B;QACnD,iBAAiB,EAAE,2BAA2B;QAC9C,SAAS,EAAE,kBAAkB;QAC7B,QAAQ,EAAE,iBAAiB;QAC3B,qBAAqB,EAAE,+BAA+B;QACtD,gBAAgB,EAAE,0BAA0B;QAC5C,gBAAgB,EAAE,2BAA2B;QAC7C,wBAAwB,EAAE,mCAAmC;QAC7D,gBAAgB,EAAE,0BAA0B;QAC5C,kBAAkB,EAAE,4BAA4B;QAChD,mBAAmB,EAAE,8BAA8B;QACnD,oBAAoB,EAAE,+BAA+B;QACrD,eAAe,EAAE,yBAAyB;QAC1C,YAAY,EAAE,qBAAqB;QACnC,oBAAoB,EAAE,+BAA+B;QACrD,wBAAwB,EAAE,mCAAmC;QAC7D,iBAAiB,EAAE,2BAA2B;QAC9C,SAAS,EAAE,kBAAkB;QAC7B,aAAa,EAAE,uBAAuB;QACtC,oBAAoB,EAAE,+BAA+B;QACrD,gBAAgB,EAAE,yBAAyB;KAC5C,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,uDAAuD;AACvD,MAAM,UAAU,iBAAiB;IAC/B,OAAO,GAAG,SAAS,CAAC;AACtB,CAAC"}
1
+ {"version":3,"file":"server-config.js","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC3C,OAAO,EAAE,cAAc,EAAE,MAAM,+BAA+B,CAAC;AAE/D;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,+BAA+B,GAAG,OAAO,CAAC;AAEvD;;;;;;;;GAQG;AACH,MAAM,CAAC,MAAM,mCAAmC,GAAG,OAAO,CAAC;AAE3D,MAAM,CAAC,MAAM,kBAAkB,GAAG,CAAC,CAAC,MAAM,CAAC;IACzC,cAAc,EAAE,CAAC;SACd,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,QAAQ,CAAC,yEAAyE,CAAC;IACtF,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,qDAAqD,CAAC;IAClE,eAAe,EAAE,CAAC;SACf,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,qDAAqD,CAAC;IAClE,oBAAoB,EAAE,CAAC;SACpB,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CAAC,uDAAuD,CAAC;IACpE,wBAAwB,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IACzF,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,yBAAyB,CAAC;IACxE,mBAAmB,EAAE,CAAC;SACnB,MAAM,EAAE;SACR,OAAO,CAAC,eAAe,CAAC;SACxB,QAAQ,CAAC,0CAA0C,CAAC;IAEvD,iBAAiB,EAAE,CAAC,CAAC,MAAM;SACxB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,mFAAmF,CAAC;IAEhG,SAAS,EAAE,CAAC,CAAC,MAAM;SAChB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,gLAAgL,CACjL;IACH,QAAQ,EAAE,CAAC,CAAC,MAAM;SACf,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,oQAAoQ,CACrQ;IACH,qBAAqB,EAAE,CAAC,CAAC,MAAM;SAC5B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,+DAA+D,CAAC;IAC5E,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,GAAG,CAAC,CAAC,CAAC;SACN,OAAO,CAAC,CAAC,CAAC;SACV,QAAQ,CAAC,0CAA0C,CAAC;IACvD,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,GAAG,CAAC;SACZ,QAAQ,CAAC,8CAA8C,CAAC;IAC3D,wBAAwB,EAAE,CAAC,CAAC,MAAM;SAC/B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,0EAA0E,CAAC;IAEvF,gBAAgB,EAAE,CAAC,CAAC,MAAM;SACvB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,2BAA2B,CAAC;IACxC,kBAAkB,EAAE,CAAC,CAAC,MAAM;SACzB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,4MAA4M,CAC7M;IACH,mBAAmB,EAAE,CAAC,CAAC,MAAM;SAC1B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,0DAA0D,CAAC;IACvE,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,mDAAmD,CAAC;IAChE,eAAe,EAAE,CAAC;SACf,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CAAC,4DAA4D,CAAC;IACzE,YAAY,EAAE,CAAC;SACZ,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,0KAA0K,CAC3K;IACH,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,GAAG,CAAC,+BAA+B,CAAC;SACpC,OAAO,CAAC,OAAO,CAAC;SAChB,QAAQ,CACP,+fAA+f,CAChgB;IACH,wBAAwB,EAAE,CAAC,CAAC,MAAM;SAC/B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,GAAG,CAAC,mCAAmC,CAAC;SACxC,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,ixBAAixB,CAClxB;IAEH,iBAAiB,EAAE,CAAC;SACjB,UAAU,EAAE;SACZ,OAAO,CAAC,KAAK,CAAC;SACd,QAAQ,CACP,kLAAkL,CACnL;IACH,SAAS,EAAE,CAAC;SACT,MAAM,EAAE;SACR,QAAQ,EAAE;SACV,QAAQ,CACP,6gBAA6gB,CAC9gB;IACH,aAAa,EAAE,CAAC,CAAC,MAAM;SACpB,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CACP,4JAA4J,CAC7J;IACH,oBAAoB,EAAE,CAAC,CAAC,MAAM;SAC3B,MAAM,EAAE;SACR,GAAG,EAAE;SACL,QAAQ,EAAE;SACV,OAAO,CAAC,MAAM,CAAC;SACf,QAAQ,CAAC,yDAAyD,CAAC;IAEtE,gBAAgB,EAAE,CAAC;SAChB,UAAU,EAAE;SACZ,OAAO,CAAC,IAAI,CAAC;SACb,QAAQ,CACP,2pBAA2pB,CAC5pB;CACJ,CAAC,CAAC;AAIH,IAAI,OAAiC,CAAC;AAEtC,MAAM,UAAU,eAAe;IAC7B,OAAO,KAAK,cAAc,CAAC,kBAAkB,EAAE;QAC7C,cAAc,EAAE,wBAAwB;QACxC,eAAe,EAAE,wBAAwB;QACzC,eAAe,EAAE,wBAAwB;QACzC,oBAAoB,EAAE,+BAA+B;QACrD,wBAAwB,EAAE,mCAAmC;QAC7D,aAAa,EAAE,uBAAuB;QACtC,mBAAmB,EAAE,8BAA8B;QACnD,iBAAiB,EAAE,2BAA2B;QAC9C,SAAS,EAAE,kBAAkB;QAC7B,QAAQ,EAAE,iBAAiB;QAC3B,qBAAqB,EAAE,+BAA+B;QACtD,gBAAgB,EAAE,0BAA0B;QAC5C,gBAAgB,EAAE,2BAA2B;QAC7C,wBAAwB,EAAE,mCAAmC;QAC7D,gBAAgB,EAAE,0BAA0B;QAC5C,kBAAkB,EAAE,4BAA4B;QAChD,mBAAmB,EAAE,8BAA8B;QACnD,oBAAoB,EAAE,+BAA+B;QACrD,eAAe,EAAE,yBAAyB;QAC1C,YAAY,EAAE,qBAAqB;QACnC,oBAAoB,EAAE,+BAA+B;QACrD,wBAAwB,EAAE,mCAAmC;QAC7D,iBAAiB,EAAE,2BAA2B;QAC9C,SAAS,EAAE,kBAAkB;QAC7B,aAAa,EAAE,uBAAuB;QACtC,oBAAoB,EAAE,+BAA+B;QACrD,gBAAgB,EAAE,yBAAyB;KAC5C,CAAC,CAAC;IACH,OAAO,OAAO,CAAC;AACjB,CAAC;AAED,uDAAuD;AACvD,MAAM,UAAU,iBAAiB;IAC/B,OAAO,GAAG,SAAS,CAAC;AACtB,CAAC"}
package/dist/mcp-server/resources/definitions/brapi-calls.resource.js CHANGED
@@ -7,7 +7,7 @@
7
7
  */
8
8
  import { resource } from '@cyanheads/mcp-ts-core';
9
9
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
- import { requireRegisteredConnection } from '../../../mcp-server/tools/shared/find-helpers.js';
10
+ import { requireRegisteredConnection } from '../../tools/shared/find-helpers.js';
11
11
  import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
12
12
  async function loadCallsProfile(ctx) {
13
13
  const capabilities = getCapabilityRegistry();
package/dist/mcp-server/resources/definitions/brapi-filters.resource.js CHANGED
@@ -8,7 +8,7 @@
8
8
  */
9
9
  import { resource, z } from '@cyanheads/mcp-ts-core';
10
10
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
11
- import { brapiDescribeFilters } from '../../../mcp-server/tools/definitions/brapi-describe-filters.tool.js';
11
+ import { brapiDescribeFilters } from '../../tools/definitions/brapi-describe-filters.tool.js';
12
12
  import { listFilterEndpoints } from '../../../services/brapi-filters/index.js';
13
13
  const ENDPOINTS = listFilterEndpoints();
14
14
  export const brapiFiltersResource = resource('brapi://filters/{endpoint}', {
package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js CHANGED
@@ -7,7 +7,7 @@
7
7
  */
8
8
  import { resource, z } from '@cyanheads/mcp-ts-core';
9
9
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
- import { brapiGetGermplasm } from '../../../mcp-server/tools/definitions/brapi-get-germplasm.tool.js';
10
+ import { brapiGetGermplasm } from '../../tools/definitions/brapi-get-germplasm.tool.js';
11
11
  export const brapiGermplasmResource = resource('brapi://germplasm/{germplasmDbId}', {
12
12
  name: 'brapi-germplasm',
13
13
  title: 'BrAPI germplasm record',
package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js CHANGED
@@ -7,7 +7,7 @@
7
7
  */
8
8
  import { resource } from '@cyanheads/mcp-ts-core';
9
9
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
- import { brapiServerInfo } from '../../../mcp-server/tools/definitions/brapi-server-info.tool.js';
10
+ import { brapiServerInfo } from '../../tools/definitions/brapi-server-info.tool.js';
11
11
  export const brapiServerInfoResource = resource('brapi://server/info', {
12
12
  name: 'brapi-server-info',
13
13
  title: 'BrAPI server orientation envelope',
package/dist/mcp-server/resources/definitions/brapi-study.resource.js CHANGED
@@ -7,7 +7,7 @@
7
7
  */
8
8
  import { resource, z } from '@cyanheads/mcp-ts-core';
9
9
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
10
- import { brapiGetStudy } from '../../../mcp-server/tools/definitions/brapi-get-study.tool.js';
10
+ import { brapiGetStudy } from '../../tools/definitions/brapi-get-study.tool.js';
11
11
  export const brapiStudyResource = resource('brapi://study/{studyDbId}', {
12
12
  name: 'brapi-study',
13
13
  title: 'BrAPI study record',
package/dist/mcp-server/resources/definitions/brapi-variable.resource.js CHANGED
@@ -14,7 +14,7 @@
14
14
  */
15
15
  import { resource, z } from '@cyanheads/mcp-ts-core';
16
16
  import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
17
- import { buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../../../mcp-server/tools/shared/find-helpers.js';
17
+ import { buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../../tools/shared/find-helpers.js';
18
18
  import { getBrapiClient } from '../../../services/brapi-client/index.js';
19
19
  export const brapiVariableResource = resource('brapi://variable/{observationVariableDbId}', {
20
20
  name: 'brapi-variable',
package/dist/services/brapi-client/brapi-client.d.ts.map CHANGED
@@ -1 +1 @@
1
- {"version":3,"file":"brapi-client.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-client/brapi-client.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,EAIL,QAAQ,EAMT,MAAM,+BAA+B,CAAC;AACvC,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,8BAA8B,CAAC;AAE5E,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAC9D,OAAO,KAAK,EACV,cAAc,EACd,aAAa,EACb,mBAAmB,EAEnB,cAAc,EACf,MAAM,YAAY,CAAC;AAGpB;;;GAGG;AACH,MAAM,MAAM,OAAO,GAAG,CACpB,GAAG,EAAE,MAAM,GAAG,GAAG,EACjB,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,OAAO,EAChB,OAAO,CAAC,EAAE,uBAAuB,KAC9B,OAAO,CAAC,QAAQ,CAAC,CAAC;AAKvB,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,YAAY;IAC7B,OAAO,CAAC,QAAQ,CAAC,OAAO;IAF1B,YACmB,YAAY,EAAE,YAAY,EAC1B,OAAO,GAAE,OAAwB,EAChD;IAEJ;;;;;;;;OAQG;IACG,GAAG,CAAC,CAAC,EACT,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAqB3B;IAED;;;;OAIG;IACH,SAAS,CACP,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAmB,GAAG;QAAE,MAAM,CAAC,EAAE,MAAM,CAAA;KAAO,GACtD,OAAO,CAAC,cAAc,CAAC,CAuBzB;IAED;;;;;;OAMG;IACG,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,SAAY,GAAG,OAAO,CAAC,cAAc,CAAC,CAU3F;IAED;;;;OAIG;IACH,UAAU,CAAC,CAAC,EACV,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CA+B5B;IAED;;;;OAIG;IACH,IAAI,CAAC,CAAC,EACJ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,EACb,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAE3B;IAED;;;OAGG;IACH,GAAG,CAAC,CAAC,EACH,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,EACb,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAE3B;IAED,OAAO,CAAC,QAAQ;IAmChB;;;;OAIG;IACG,gBAAgB,CAAC,CAAC,EACtB,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,iBAAiB,EAAE,MAAM,EACzB,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAqC3B;YAEa,OAAO;IAuBrB,OAAO,CAAC,QAAQ;IAiBhB,OAAO,CAAC,YAAY;YAQN,aAAa;CAyB5B;AAoGD;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,OAAO,GAAG,GAAG,IAAI,QAAQ,CAQjE;AAoCD,wBAAgB,eAAe,CAAC,YAAY,EAAE,YAAY,EAAE,OAAO,CAAC,EAAE,OAAO,GAAG,IAAI,CAEnF;AAED,wBAAgB,cAAc,IAAI,WAAW,CAK5C;AAED,yEAAyE;AACzE,wBAAgB,gBAAgB,IAAI,IAAI,CAEvC"}
1
+ {"version":3,"file":"brapi-client.d.ts","sourceRoot":"","sources":["../../../src/services/brapi-client/brapi-client.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,OAAO,EAAE,MAAM,wBAAwB,CAAC;AACtD,OAAO,EAGL,QAAQ,EAQT,MAAM,+BAA+B,CAAC;AACvC,OAAO,KAAK,EAAE,uBAAuB,EAAE,MAAM,8BAA8B,CAAC;AAE5E,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,2BAA2B,CAAC;AAC9D,OAAO,KAAK,EACV,cAAc,EACd,aAAa,EACb,mBAAmB,EAEnB,cAAc,EACf,MAAM,YAAY,CAAC;AAGpB;;;GAGG;AACH,MAAM,MAAM,OAAO,GAAG,CACpB,GAAG,EAAE,MAAM,GAAG,GAAG,EACjB,SAAS,EAAE,MAAM,EACjB,OAAO,EAAE,OAAO,EAChB,OAAO,CAAC,EAAE,uBAAuB,KAC9B,OAAO,CAAC,QAAQ,CAAC,CAAC;AAKvB,qBAAa,WAAW;IAEpB,OAAO,CAAC,QAAQ,CAAC,YAAY;IAC7B,OAAO,CAAC,QAAQ,CAAC,OAAO;IAF1B,YACmB,YAAY,EAAE,YAAY,EAC1B,OAAO,GAAE,OAAwB,EAChD;IAEJ;;;;;;;;OAQG;IACG,GAAG,CAAC,CAAC,EACT,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAqB3B;IAED;;;;OAIG;IACH,SAAS,CACP,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAmB,GAAG;QAAE,MAAM,CAAC,EAAE,MAAM,CAAA;KAAO,GACtD,OAAO,CAAC,cAAc,CAAC,CAuBzB;IAED;;;;;;OAMG;IACG,cAAc,CAAC,GAAG,EAAE,MAAM,EAAE,GAAG,EAAE,OAAO,EAAE,MAAM,SAAY,GAAG,OAAO,CAAC,cAAc,CAAC,CAU3F;IAED;;;;OAIG;IACH,UAAU,CAAC,CAAC,EACV,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC7B,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,cAAc,CAAC,CAAC,CAAC,CAAC,CA+B5B;IAED;;;;OAIG;IACH,IAAI,CAAC,CAAC,EACJ,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,EACb,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAE3B;IAED;;;OAGG;IACH,GAAG,CAAC,CAAC,EACH,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,IAAI,EAAE,OAAO,EACb,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAE3B;IAED,OAAO,CAAC,QAAQ;IAmChB;;;;OAIG;IACG,gBAAgB,CAAC,CAAC,EACtB,OAAO,EAAE,MAAM,EACf,IAAI,EAAE,MAAM,EACZ,iBAAiB,EAAE,MAAM,EACzB,GAAG,EAAE,OAAO,EACZ,OAAO,GAAE,mBAAwB,GAChC,OAAO,CAAC,aAAa,CAAC,CAAC,CAAC,CAAC,CAqC3B;YAEa,OAAO;IAuBrB,OAAO,CAAC,QAAQ;IAiBhB,OAAO,CAAC,YAAY;YAQN,aAAa;CAyB5B;AAoGD;;;;GAIG;AACH,wBAAgB,mBAAmB,CAAC,GAAG,EAAE,OAAO,GAAG,GAAG,IAAI,QAAQ,CAQjE;AAoCD,wBAAgB,eAAe,CAAC,YAAY,EAAE,YAAY,EAAE,OAAO,CAAC,EAAE,OAAO,GAAG,IAAI,CAEnF;AAED,wBAAgB,cAAc,IAAI,WAAW,CAK5C;AAED,yEAAyE;AACzE,wBAAgB,gBAAgB,IAAI,IAAI,CAEvC"}
package/dist/services/brapi-client/brapi-client.js CHANGED
@@ -8,7 +8,7 @@
8
8
  *
9
9
  * @module services/brapi-client/brapi-client
10
10
  */
11
- import { forbidden, internalError, JsonRpcErrorCode, McpError, notFound, rateLimited, serviceUnavailable, unauthorized, validationError, } from '@cyanheads/mcp-ts-core/errors';
11
+ import { forbidden, JsonRpcErrorCode, McpError, notFound, rateLimited, requestCancelled, serviceUnavailable, timeout, unauthorized, validationError, } from '@cyanheads/mcp-ts-core/errors';
12
12
  import { fetchWithTimeout, withRetry } from '@cyanheads/mcp-ts-core/utils';
13
13
  import { DIALECT_ALL_DROPPED_REASON } from './types.js';
14
14
  const defaultFetcher = (url, timeoutMs, context, options) => fetchWithTimeout(url, timeoutMs, context, options);
@@ -150,13 +150,13 @@ export class BrapiClient {
150
150
  const startedAt = Date.now();
151
151
  for (;;) {
152
152
  if (ctx.signal.aborted) {
153
- throw internalError('Async search polling aborted by caller', {
153
+ throw requestCancelled('Async search polling aborted by caller', {
154
154
  noun,
155
155
  searchResultsDbId,
156
156
  });
157
157
  }
158
158
  if (Date.now() - startedAt > pollTimeoutMs) {
159
- throw serviceUnavailable(`Async search ${noun}/${searchResultsDbId} timed out after ${pollTimeoutMs}ms`, { noun, searchResultsDbId, pollTimeoutMs });
159
+ throw timeout(`Async search ${noun}/${searchResultsDbId} timed out after ${pollTimeoutMs}ms`, { noun, searchResultsDbId, pollTimeoutMs });
160
160
  }
161
161
  const response = await this.doFetch(url, ctx, { method: 'GET', headers: this.buildHeaders(options.auth) }, options.timeoutMs);
162
162
  if (response.status === 202) {
@@ -357,7 +357,7 @@ function extractAsyncId(envelope) {
357
357
  function sleep(ms, ctx) {
358
358
  return new Promise((resolve, reject) => {
359
359
  if (ctx.signal.aborted) {
360
- reject(internalError('Sleep aborted by caller'));
360
+ reject(requestCancelled('Sleep aborted by caller'));
361
361
  return;
362
362
  }
363
363
  const timer = setTimeout(() => {
@@ -366,7 +366,7 @@ function sleep(ms, ctx) {
366
366
  }, ms);
367
367
  const onAbort = () => {
368
368
  clearTimeout(timer);
369
- reject(internalError('Sleep aborted by caller'));
369
+ reject(requestCancelled('Sleep aborted by caller'));
370
370
  };
371
371
  ctx.signal.addEventListener('abort', onAbort, { once: true });
372
372
  });
package/dist/services/brapi-client/brapi-client.js.map CHANGED
@@ -1 +1 @@
1
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package/dist/services/brapi-client/types.d.ts CHANGED
@@ -4,7 +4,7 @@
4
4
  *
5
5
  * @module services/brapi-client/types
6
6
  */
7
- import type { BrapiDialect } from '../../services/brapi-dialect/types.js';
7
+ import type { BrapiDialect } from '../brapi-dialect/types.js';
8
8
  /** BrAPI v2 standard response envelope. */
9
9
  export interface BrapiEnvelope<T> {
10
10
  metadata: BrapiMetadata;
package/dist/services/brapi-dialect/detect.d.ts CHANGED
@@ -10,7 +10,7 @@
10
10
  *
11
11
  * @module services/brapi-dialect/detect
12
12
  */
13
- import type { CapabilityProfile } from '../../services/capability-registry/types.js';
13
+ import type { CapabilityProfile } from '../capability-registry/types.js';
14
14
  /**
15
15
  * Where the resolved dialect id came from. Surfaced in the orientation
16
16
  * envelope so agents (and operators reading logs) can tell whether the
package/dist/services/brapi-dialect/index.d.ts CHANGED
@@ -9,8 +9,8 @@
9
9
  * @module services/brapi-dialect
10
10
  */
11
11
  import type { Context } from '@cyanheads/mcp-ts-core';
12
- import type { ResolvedAuth } from '../../services/brapi-client/index.js';
13
- import type { RegisteredServer } from '../../services/server-registry/index.js';
12
+ import type { ResolvedAuth } from '../brapi-client/index.js';
13
+ import type { RegisteredServer } from '../server-registry/index.js';
14
14
  import type { BrapiDialect } from './types.js';
15
15
  export { bmsDialect } from './bms-dialect.js';
16
16
  export { brapiTestDialect } from './brapi-test-dialect.js';
package/dist/services/brapi-dialect/index.js CHANGED
@@ -8,7 +8,7 @@
8
8
  *
9
9
  * @module services/brapi-dialect
10
10
  */
11
- import { getCapabilityRegistry } from '../../services/capability-registry/index.js';
11
+ import { getCapabilityRegistry } from '../capability-registry/index.js';
12
12
  import { detectDialectId } from './detect.js';
13
13
  import { getDialectById } from './registry.js';
14
14
  export { bmsDialect } from './bms-dialect.js';
package/dist/services/capability-registry/capability-registry.d.ts CHANGED
@@ -10,7 +10,7 @@
10
10
  */
11
11
  import type { Context } from '@cyanheads/mcp-ts-core';
12
12
  import type { ServerConfig } from '../../config/server-config.js';
13
- import { type BrapiClient, type BrapiRequestOptions } from '../../services/brapi-client/index.js';
13
+ import { type BrapiClient, type BrapiRequestOptions } from '../brapi-client/index.js';
14
14
  import type { CallDescriptor, CapabilityProfile, EndpointProbe } from './types.js';
15
15
  export interface CapabilityLookupOptions extends Pick<BrapiRequestOptions, 'auth'> {
16
16
  /** Force a fresh fetch, bypassing the cached profile. */
package/dist/services/capability-registry/capability-registry.js CHANGED
@@ -9,7 +9,7 @@
9
9
  * @module services/capability-registry/capability-registry
10
10
  */
11
11
  import { validationError } from '@cyanheads/mcp-ts-core/errors';
12
- import { getBrapiClient, } from '../../services/brapi-client/index.js';
12
+ import { getBrapiClient, } from '../brapi-client/index.js';
13
13
  const STATE_KEY_PREFIX = 'brapi/capability/';
14
14
  export class CapabilityRegistry {
15
15
  serverConfig;
package/dist/services/reference-data-cache/reference-data-cache.d.ts CHANGED
@@ -9,8 +9,8 @@
9
9
  */
10
10
  import type { Context } from '@cyanheads/mcp-ts-core';
11
11
  import type { ServerConfig } from '../../config/server-config.js';
12
- import { type BrapiClient, type BrapiRequestOptions } from '../../services/brapi-client/index.js';
13
- import type { BrapiDialect } from '../../services/brapi-dialect/index.js';
12
+ import { type BrapiClient, type BrapiRequestOptions } from '../brapi-client/index.js';
13
+ import type { BrapiDialect } from '../brapi-dialect/index.js';
14
14
  import type { Location, Program, Trial } from './types.js';
15
15
  export interface ReferenceLookupOptions {
16
16
  auth?: BrapiRequestOptions['auth'];
package/dist/services/reference-data-cache/reference-data-cache.js CHANGED
@@ -7,7 +7,7 @@
7
7
  *
8
8
  * @module services/reference-data-cache/reference-data-cache
9
9
  */
10
- import { getBrapiClient, isDialectAllDropped, } from '../../services/brapi-client/index.js';
10
+ import { getBrapiClient, isDialectAllDropped, } from '../brapi-client/index.js';
11
11
  const PROGRAM_CFG = {
12
12
  endpoint: '/programs',
13
13
  idFilter: 'programDbIds',
package/dist/services/server-registry/types.d.ts CHANGED
@@ -6,7 +6,7 @@
6
6
  *
7
7
  * @module services/server-registry/types
8
8
  */
9
- import type { ResolvedAuth } from '../../services/brapi-client/index.js';
9
+ import type { ResolvedAuth } from '../brapi-client/index.js';
10
10
  export type AuthMode = 'none' | 'sgn' | 'oauth2' | 'api_key' | 'bearer';
11
11
  export interface RegisteredServer {
12
12
  alias: string;
package/manifest.json CHANGED
@@ -1,10 +1,12 @@
1
1
  {
2
2
  "manifest_version": "0.3",
3
3
  "name": "brapi-mcp-server",
4
- "version": "0.7.11",
4
+ "version": "0.7.12",
5
5
  "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
6
6
  "author": {
7
- "name": "cyanheads"
7
+ "name": "cyanheads",
8
+ "email": "casey@caseyjhand.com",
9
+ "url": "https://caseyjhand.com"
8
10
  },
9
11
  "repository": {
10
12
  "type": "git",
@@ -22,10 +24,10 @@
22
24
  "MCP_TRANSPORT_TYPE": "stdio",
23
25
  "MCP_AUTH_MODE": "none",
24
26
  "NODE_ENV": "production",
25
- "BRAPI_DEFAULT_BASE_URL": "${BRAPI_DEFAULT_BASE_URL}",
26
- "BRAPI_ENABLE_WRITES": "${BRAPI_ENABLE_WRITES}",
27
- "BRAPI_PAGE_SIZE": "${BRAPI_PAGE_SIZE}",
28
- "MCP_LOG_LEVEL": "${MCP_LOG_LEVEL}"
27
+ "BRAPI_DEFAULT_BASE_URL": "${user_config.BRAPI_DEFAULT_BASE_URL}",
28
+ "BRAPI_ENABLE_WRITES": "${user_config.BRAPI_ENABLE_WRITES}",
29
+ "BRAPI_PAGE_SIZE": "${user_config.BRAPI_PAGE_SIZE}",
30
+ "MCP_LOG_LEVEL": "${user_config.MCP_LOG_LEVEL}"
29
31
  }
30
32
  }
31
33
  },
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": "0.7.11",
4
+ "version": "0.7.12",
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 <casey@caseyjhand.com> (https://caseyjhand.com)",
7
7
  "type": "module",
@@ -32,6 +32,7 @@
32
32
  "lint:packaging": "bun run scripts/lint-packaging.ts",
33
33
  "list-skills": "bun run scripts/list-skills.ts",
34
34
  "bundle": "bun run build && npx -y @anthropic-ai/mcpb pack . dist/brapi-mcp-server.mcpb && bun run scripts/clean-mcpb.ts dist/brapi-mcp-server.mcpb",
35
+ "audit:fix": "bun audit fix",
35
36
  "audit:refresh": "rm -f bun.lock && bun install && bun audit",
36
37
  "changelog:build": "bun run scripts/build-changelog.ts",
37
38
  "changelog:check": "bun run scripts/build-changelog.ts --check",
@@ -74,26 +75,26 @@
74
75
  "license": "Apache-2.0",
75
76
  "engines": {
76
77
  "node": ">=24.0.0",
77
- "bun": ">=1.3.0"
78
+ "bun": ">=1.4.0"
78
79
  },
79
80
  "packageManager": "bun@1.4.0",
80
81
  "publishConfig": {
81
82
  "access": "public"
82
83
  },
83
84
  "dependencies": {
84
- "@cyanheads/mcp-ts-core": "^0.12.3",
85
+ "@cyanheads/mcp-ts-core": "^0.13.0",
85
86
  "@duckdb/node-api": "^1.5.5-r.4",
86
87
  "pino-pretty": "^13.1.3",
87
- "zod": "^4.4.3"
88
+ "zod": "^4.6.1"
88
89
  },
89
90
  "devDependencies": {
90
- "@biomejs/biome": "^2.5.9",
91
+ "@biomejs/biome": "^2.5.13",
91
92
  "@socketsecurity/bun-security-scanner": "^1.1.2",
92
- "@types/node": "^26.2.0",
93
+ "@types/node": "^26.5.1",
93
94
  "depcheck": "^1.4.7",
94
- "ignore": "^7.0.6",
95
- "tsc-alias": "^1.9.2",
95
+ "ignore": "^7.0.9",
96
+ "tsc-alias": "^1.9.4",
96
97
  "typescript": "^7.0.2",
97
- "vitest": "^4.1.11"
98
+ "vitest": "^5.0.0"
98
99
  }
99
100
  }
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": "0.7.11",
9
+ "version": "0.7.12",
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": "0.7.11",
16
+ "version": "0.7.12",
17
17
  "packageArguments": [
18
18
  { "type": "positional", "value": "run" },
19
19
  { "type": "positional", "value": "start:stdio" }
@@ -56,7 +56,7 @@
56
56
  "registryBaseUrl": "https://registry.npmjs.org",
57
57
  "identifier": "@cyanheads/brapi-mcp-server",
58
58
  "runtimeHint": "bun",
59
- "version": "0.7.11",
59
+ "version": "0.7.12",
60
60
  "packageArguments": [
61
61
  { "type": "positional", "value": "run" },
62
62
  { "type": "positional", "value": "start:http" }