npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.6.1 → 0.6.3 - Mend

@cyanheads/brapi-mcp-server 0.6.1 → 0.6.3

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (29) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.6.1
+**Version:** 0.6.3
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **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.
@@ -34,6 +34,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
 - **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
 - **Secrets in env vars only** — never hardcoded.
+- **Close the loop on issues.** When implementing work tracked by a GitHub issue, comment on the issue with what landed and close it. Do both — a comment without a close leaves stale issues open; a close without a comment leaves no record of what shipped. The comment is for future readers — state the concrete changes, not the conversation that produced them.
 ---
@@ -306,13 +307,14 @@ Available skills:
 | `add-service` | Scaffold a new service integration |
 | `add-test` | Scaffold test file for a tool, resource, or service |
 | `field-test` | Exercise tools/resources/prompts with real inputs, verify behavior, report issues |
-| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface (12 categories) |
+| `tool-defs-analysis` | Read-only audit of MCP definition language across the surface — voice, leaks, defaults, recovery hints, output descriptions |
 | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
+| `code-simplifier` | Post-session cleanup against `git diff` — modernize syntax, consolidate duplication, align with the codebase |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
+| `git-wrapup` | Land working-tree changes as a versioned commit + annotated tag — version bump, changelog, verify, tag. Local only. |
+| `release-and-publish` | Push + npm + MCP Registry + GH Release + Docker. Picks up from `git-wrapup` |
 | `maintenance` | Investigate changelogs, adopt upstream changes, sync skills to agent dirs |
-| `release-and-publish` | Post-wrapup ship workflow: verification gate, push, publish to npm / MCP Registry / GHCR |
-| `migrate-mcp-ts-template` | Migrate legacy `mcp-ts-template` fork to package dependency |
 | `report-issue-framework` | File a bug or feature request against `@cyanheads/mcp-ts-core` via `gh` CLI |
 | `report-issue-local` | File a bug or feature request against this server's own repo via `gh` CLI |
 | `api-auth` | Auth modes, scopes, JWT/OAuth |
@@ -341,9 +343,13 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `bun run rebuild` | Clean + build |
 | `bun run clean` | Remove build artifacts |
 | `bun run devcheck` | Lint + format + typecheck + security + changelog sync |
+| `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. |
+| `bun run list-skills` | Print the skill index for this project (name, version, description) |
 | `bun run tree` | Generate `docs/tree.md` |
 | `bun run format` | Auto-fix formatting via Biome |
 | `bun run lint:mcp` | Validate MCP tool / resource / prompt definitions against the spec |
+| `bun run lint:packaging` | Verify env var alignment between `manifest.json` and `server.json` |
+| `bun run bundle` | Build and pack as `.mcpb` for one-click Claude Desktop install |
 | `bun run test` | Vitest suite |
 | `bun run start` | Production mode — defers transport selection to `MCP_TRANSPORT_TYPE` (stdio default) |
 | `bun run start:stdio` | Production mode (stdio) — requires prior `bun run build` |
@@ -353,6 +359,14 @@ When you complete a skill's checklist, check the boxes and add a completion time
 ---
+## Bundling
+`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. 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.
+**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.
+---
 ## Changelog
 Directory-based, grouped by minor series using the `.x` semver-wildcard convention. Source of truth is `changelog/<major.minor>.x/<version>.md` (e.g. `changelog/0.1.x/0.1.0.md`) — one file per released version, shipped in the npm package. At release time, author the per-version file with a concrete version and date, then run `npm run changelog:build` to regenerate the rollup. `changelog/template.md` is a **pristine format reference** — never edited, never renamed, never moved. Read it to remember the frontmatter + section layout when scaffolding a new per-version file. `CHANGELOG.md` is a **navigation index** (header + link + one-line summary per version), regenerated by `npm run changelog:build`. Devcheck hard-fails on drift. Never hand-edit `CHANGELOG.md`.
@@ -372,8 +386,12 @@ security: false                          # optional — true flags security fixe
 `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`.
+`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.
 **Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
+**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.
 ---
 ## Imports
@@ -405,4 +423,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] Tests include at least one sparse upstream payload (fields omitted) alongside the happy path
 - [ ] Registered in the `tools` array of `createApp()` in `src/index.ts`
 - [ ] Tests use `createMockContext()` from `@cyanheads/mcp-ts-core/testing`
+- [ ] `.codex-plugin/plugin.json` populated — `name`, `version`, `description`, `repository`, `license` from `package.json`; `interface.displayName` = package name; `interface.shortDescription` from `package.json` description
+- [ ] `.codex-plugin/mcp.json` updated — server name key matches `package.json` name; env vars added for any required API keys
+- [ ] `.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
 - [ ] `bun run devcheck` passes

package/README.md CHANGED Viewed

@@ -7,9 +7,15 @@
 <div align="center">
-[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.6.1-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.6.3-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
-[![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
+</div>
+<div align="center">
+[![Install in Claude Desktop](https://img.shields.io/badge/Install_in-Claude_Desktop-D97757?style=for-the-badge&logo=anthropic&logoColor=white)](https://github.com/cyanheads/brapi-mcp-server/releases/latest/download/brapi-mcp-server.mcpb) [![Install in Cursor](https://cursor.com/deeplink/mcp-install-dark.svg)](https://cursor.com/en/install-mcp?name=brapi-mcp-server&config=eyJjb21tYW5kIjoibnB4IiwiYXJncyI6WyIteSIsIkBjeWFuaGVhZHMvYnJhcGktbWNwLXNlcnZlciJdfQ==) [![Install in VS Code](https://img.shields.io/badge/VS_Code-Install_Server-0098FF?style=for-the-badge&logo=visualstudiocode&logoColor=white)](https://vscode.dev/redirect?url=vscode:mcp/install?%7B%22name%22%3A%22brapi-mcp-server%22%2C%22command%22%3A%22npx%22%2C%22args%22%3A%5B%22-y%22%2C%22%40cyanheads/brapi-mcp-server%22%5D%7D)
+[![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-67E8F9?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 </div>

package/changelog/0.6.x/0.6.2.md ADDED Viewed

@@ -0,0 +1,23 @@
+---
+summary: "mcp-ts-core ^0.9.1 → ^0.9.6: RequestContextLike adoption removes the manual asRequestContext shim in canvas-bridge, format-parity fixes in find-observations and submit-observations, manifest.json + .mcpbignore scaffolded for MCPB bundle support, install badges added to README."
+breaking: false
+security: false
+---
+# 0.6.2 — 2026-05-23
+## Added
+- **`manifest.json` + `.mcpbignore`** scaffolded — `bun run bundle` now produces a `.mcpb` extension bundle for one-click Claude Desktop install. MCPB is stdio-only; HTTP deployments are unaffected. `lint:packaging` (run by `devcheck`) verifies env var names are aligned between `manifest.json` and `server.json`.
+- **Install badges added to README** — Claude Desktop and VS Code one-click install badges now appear in the header.
+- **`audit:refresh`, `list-skills`, `lint:packaging`, `bundle` commands** documented in `AGENTS.md` / `CLAUDE.md` command tables; `Bundling` section added to both agent protocol files.
+## Changed
+- **`@cyanheads/mcp-ts-core`** `^0.9.1` → `^0.9.6` — notably introduces `RequestContextLike` so `canvas.acquire()` and related canvas calls now accept the handler `Context` directly without a manual shim.
+- **`canvas-bridge.ts` drops `asRequestContext` shim** — `CanvasBridge.acquireDefault` now passes `ctx` directly to `canvas.acquire()`. The local `RequestContext` import and the 15-line conversion function are removed.
+- **`brapi-client.ts` comment updated** — JSDoc on the remaining `asRequestContext` cast (for `fetchWithTimeout` / `withRetry`) updated to reflect `RequestContextLike` context.
+- **`brapi-find-observations.tool.ts` `season` schema simplified** — structured season object collapsed to `z.object({}).passthrough()` with a single aggregated `.describe()`. The prior per-field schema (seasonDbId, year, season, seasonName) conflicted with real-world sparsity; `format()` normalizes both flat-string and object variants regardless of which fields are present.
+- **`brapi-submit-observations.tool.ts` `format()` surfaces `result.warnings`** — top-level `warnings[]` from the apply-mode response now renders under a `## Warnings` section. Previously the field was included in the output schema but silently dropped by `format()`.
+- **`devcheck.ts`** changelog-sync check integrated (no external behavior change — already covered by `changelog:check`).
+- **Skills synced** — `field-test`, `maintenance`, `polish-docs-meta`, `release-and-publish` updated to framework v0.9.x conventions; `code-simplifier` removed from project skills (promoted to global install).

package/changelog/0.6.x/0.6.3.md ADDED Viewed

@@ -0,0 +1,24 @@
+---
+summary: "@cyanheads/mcp-ts-core ^0.9.6 → ^0.9.13: HTTP 413 body cap, session-init gate, quieter error logs, landing inventory open-catalog override, URL placeholder guard"
+breaking: false
+security: false
+---
+# 0.6.3 — 2026-05-28
+## Changed
+- **`@cyanheads/mcp-ts-core`** ^0.9.6 → ^0.9.13 — picks up HTTP transport hardening, session-init gate, and quieter client-error logs (see below).
+- **`landing.requireAuth: false`** set in `createApp()` (`src/index.ts`) — restores the open-catalog UX for the hosted public endpoint; framework 0.9.13 gates landing inventory behind auth by default when `MCP_AUTH_MODE` is `jwt`/`oauth`.
+- **`BRAPI_DEFAULT_BASE_URL` Zod preprocessor** (`src/config/server-config.ts`) — strips `${...}` placeholder strings (injected by MCPB when no value is supplied) to `undefined` before the URL validator runs, preventing startup failures on optional URL fields.
+- **`@duckdb/node-api`** ^1.5.3-r.1 → ^1.5.3-r.2.
+- **`@biomejs/biome`** ^2.4.15 → ^2.4.16.
+## Framework changes (0.9.7–0.9.13)
+User-facing items from the adopted range:
+- **`MCP_HTTP_MAX_BODY_BYTES`** (0.9.13) — configurable inbound request-body cap; oversized requests rejected with `413` before SDK parse. Default 1 MiB; `0` disables.
+- **HTTP session-init gate** (0.9.10) — stateful HTTP mode rejects non-`initialize` requests without `Mcp-Session-Id` with `400`, preventing uninitialized sessions from being minted on first contact.
+- **Quieter 401/403/400/404 logging** (0.9.10) — expected client errors now log at `warning` instead of full error pipeline with stack traces, reducing noise.
+- **`GET /mcp` surfaces `package.json` keywords** (0.9.12) — `server.keywords` included in the HTTP status response alongside `name`, `version`, and `description`.

package/changelog/template.md CHANGED Viewed

@@ -19,6 +19,14 @@ breaking: false
 # `## Security` section below. Flagged as `Security` in the rollup so
 # users can triage upgrade urgency at a glance.
 security: false
+# Optional free-form notes for maintenance agents processing this release.
+# Not rendered in CHANGELOG — consumed by agents running `maintenance` on
+# downstream servers. Use for adoption instructions that don't fit the
+# human-facing sections: new files to create, fields to populate, one-time
+# migration steps. Omit the field entirely when there's nothing to say.
+# agent-notes: |
+#   <instructions for downstream maintenance agents>
 ---
 # <version> — YYYY-MM-DD
@@ -66,6 +74,32 @@ security: false
   Never speculate on a future number — `#42` for an upcoming PR silently
   resolves to whatever real item already owns 42, and timeline previews pull
   in that unrelated item's metadata.
+  TAG ANNOTATIONS — the annotated tag body renders as the GitHub Release body
+  via `gh release create --notes-from-tag`. The tag is a derivative of this
+  changelog entry — a condensed, scannable version, not a copy. Format:
+    <theme — omit version number, GitHub prepends it>
+                                                          ← blank line
+    <1-2 sentence context: what this release does>
+                                                          ← blank line
+    Dependency bumps:                                     ← section header
+                                                          ← blank line
+    - `@cyanheads/mcp-ts-core` ^0.9.1 → ^0.9.6          ← bullet
+                                                          ← blank line
+    Changed:                                              ← only sections with entries
+                                                          ← blank line
+    - `format()` output includes `query` in text mode
+                                                          ← blank line
+    Added:
+                                                          ← blank line
+    - `manifest.json` scaffolded for MCPB bundle support
+    - Install badges (Claude Desktop, Cursor, VS Code)
+                                                          ← blank line
+    <N> tests pass; `bun run devcheck` clean.             ← footer
+  Never a flat comma-separated string. Always structured markdown with
+  sections. The tag must scan well as a rendered GitHub Release page.
 -->
 ## Added

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

@@ -9,7 +9,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 export declare const ServerConfigSchema: z.ZodObject<{
-    defaultBaseUrl: z.ZodOptional<z.ZodString>;
+    defaultBaseUrl: z.ZodPreprocess<z.ZodOptional<z.ZodString>>;
     defaultUsername: z.ZodOptional<z.ZodString>;
     defaultPassword: z.ZodOptional<z.ZodString>;
     defaultOauthClientId: z.ZodOptional<z.ZodString>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAqJ7B,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CA6B9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

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

@@ -11,9 +11,7 @@ import { z } from '@cyanheads/mcp-ts-core';
 import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
 export const ServerConfigSchema = z.object({
     defaultBaseUrl: z
-        .string()
-        .url()
-        .optional()
+        .preprocess((v) => (typeof v === 'string' && /^\$\{/.test(v) ? undefined : v), z.string().url().optional())
         .describe('Default BrAPI v2 base URL if no connection is opened via brapi_connect.'),
     defaultUsername: z
         .string()

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

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

@@ -103,6 +103,10 @@ await createApp({
         brapiFiltersResource,
     ],
     prompts: [brapiEdaStudy, brapiMetaAnalysis],
+    // Public-catalog deployment: keep landing inventory visible to unauthenticated
+    // visitors even when MCP_AUTH_MODE is jwt/oauth. Framework default (0.9.13+)
+    // gates the inventory behind auth; this override restores the open-catalog UX.
+    landing: { requireAuth: false },
     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.',
     setup(core) {
         if (!core.canvas) {

package/dist/index.js.map CHANGED Viewed

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

@@ -37,12 +37,7 @@ export declare const brapiFindObservations: import("@cyanheads/mcp-ts-core").Too
         germplasmDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         germplasmName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         observationLevel: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-        season: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
-            seasonDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-            year: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodNumber, z.ZodNull]>>;
-            season: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-            seasonName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-        }, z.core.$loose>, z.ZodNull]>>;
+        season: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{}, z.core.$loose>, z.ZodNull]>>;
         value: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         observationTimeStamp: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         collector: z.ZodOptional<z.ZodNullable<z.ZodString>>;

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

	@@ -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~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GAuUhC,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;AA4KjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuUhC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js CHANGED Viewed

@@ -43,28 +43,13 @@ const ObservationRowSchema = z
         .union([
         z.string().describe('Season identifier as a flat string (older BrAPI servers).'),
         z
-            .object({
-            seasonDbId: z.string().nullish().describe('Server-side season identifier.'),
-            year: z
-                .union([
-                z.string().describe('Calendar year as a string (e.g. "2024").'),
-                z.number().describe('Calendar year as an integer (e.g. 2024).'),
-                z.null().describe('Field present but null on the upstream.'),
-            ])
-                .optional()
-                .describe('Calendar year — accepts string or numeric form depending on server.'),
-            season: z.string().nullish().describe('Season label (e.g. "wet", "dry", "Q1").'),
-            seasonName: z
-                .string()
-                .nullish()
-                .describe('Season display name (BrAPI v2.1 alternate field).'),
-        })
+            .object({})
             .passthrough()
-            .describe('Structured season block per BrAPI v2.1.'),
+            .describe('Structured season block per BrAPI v2.1 — may carry seasonDbId, year, season, or seasonName. Fields vary by server; all pass through and are collapsed into a single label by format().'),
         z.null().describe('Field present but null on the upstream.'),
     ])
         .optional()
-        .describe('Season — either a flat string or a structured `{seasonDbId, year, season}` object depending on the server.'),
+        .describe('Season — either a flat string or a structured object depending on the server. format() normalizes both into a single label.'),
     value: z
         .string()
         .nullish()

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map CHANGED Viewed

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA2C,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACpF,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkPjE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GA4SlC~~,CAAC"}
1	+ {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA2C,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACpF,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkPjE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmTlC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js CHANGED Viewed

@@ -449,6 +449,13 @@ export const brapiSubmitObservations = tool('brapi_submit_observations', {
                     lines.push(`- row ${w.rowIndex}:${id}${unit} — ${w.warning}`);
                 }
             }
+            if (r.warnings && r.warnings.length > 0) {
+                lines.push('');
+                lines.push('## Warnings');
+                for (const w of r.warnings) {
+                    lines.push(`- ${w}`);
+                }
+            }
         }
         return [{ type: 'text', text: lines.join('\n') }];
     },

package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js.map CHANGED Viewed

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

@@ -658,12 +658,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         germplasmDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
         germplasmName: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
         observationLevel: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
-        season: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodObject<{
-            seasonDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
-            year: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber, import("zod").ZodNull]>>;
-            season: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
-            seasonName: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
-        }, import("zod/v4/core").$loose>, import("zod").ZodNull]>>;
+        season: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodObject<{}, import("zod/v4/core").$loose>, import("zod").ZodNull]>>;
         value: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
         observationTimeStamp: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
         collector: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;

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

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package/dist/services/brapi-client/brapi-client.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/services/brapi-client/brapi-client.js CHANGED Viewed

@@ -12,11 +12,10 @@ import { forbidden, internalError, JsonRpcErrorCode, McpError, notFound, rateLim
 import { fetchWithTimeout, withRetry } from '@cyanheads/mcp-ts-core/utils';
 import { DIALECT_ALL_DROPPED_REASON } from './types.js';
 /**
- * The framework's `Context` and `RequestContext` are structurally compatible
- * at runtime — framework docs confirm passing `Context` to `fetchWithTimeout`
- * and `withRetry` is safe. The types diverge only under
- * `exactOptionalPropertyTypes` (Context marks some fields as `| undefined`).
- * One cast, one place.
+ * `fetchWithTimeout` and `withRetry` accept `RequestContext`, not the broader
+ * `RequestContextLike` that canvas uses. `Context` is structurally compatible
+ * at runtime but diverges under `exactOptionalPropertyTypes` — one cast here
+ * covers all call sites.
  */
 const asRequestContext = (ctx) => ctx;
 const defaultFetcher = (url, timeoutMs, context, options) => fetchWithTimeout(url, timeoutMs, asRequestContext(context), options);

package/dist/services/brapi-client/brapi-client.js.map CHANGED Viewed

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

@@ -17,25 +17,6 @@
 import { unlink } from 'node:fs/promises';
 import { JsonRpcErrorCode, McpError, validationError } from '@cyanheads/mcp-ts-core/errors';
 import { idGenerator } from '@cyanheads/mcp-ts-core/utils';
-/**
- * Construct a `RequestContext` slice from the handler `Context`. The
- * framework's `RequestContext` carries an `[key: string]: unknown` index
- * signature which the strict `Context` interface lacks, so direct
- * assignment fails despite the 0.8.12 optional-field widening.
- */
-function asRequestContext(ctx) {
-    const rc = {
-        requestId: ctx.requestId,
-        timestamp: ctx.timestamp,
-    };
-    if (ctx.tenantId !== undefined)
-        rc.tenantId = ctx.tenantId;
-    if (ctx.traceId !== undefined)
-        rc.traceId = ctx.traceId;
-    if (ctx.spanId !== undefined)
-        rc.spanId = ctx.spanId;
-    return rc;
-}
 /**
  * State keys holding the default canvasId (opaque 10-char token).
  *
@@ -94,7 +75,7 @@ export class CanvasBridge {
         const key = this.defaultCanvasKey(ctx);
         const cached = await ctx.state.get(key);
         try {
-            const instance = await this.canvas.acquire(cached ?? undefined, asRequestContext(ctx));
+            const instance = await this.canvas.acquire(cached ?? undefined, ctx);
             if (!cached || instance.isNew) {
                 await ctx.state.set(key, instance.canvasId);
             }
@@ -103,7 +84,7 @@ export class CanvasBridge {
         catch (err) {
             if (cached && isCanvasNotFound(err)) {
                 await ctx.state.delete(key);
-                const fresh = await this.canvas.acquire(undefined, asRequestContext(ctx));
+                const fresh = await this.canvas.acquire(undefined, ctx);
                 await ctx.state.set(key, fresh.canvasId);
                 return fresh;
             }

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

	@@ -1 +1 @@
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package/manifest.json ADDED Viewed

@@ -0,0 +1,61 @@
+{
+  "manifest_version": "0.3",
+  "name": "brapi-mcp-server",
+  "version": "0.6.3",
+  "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
+  "author": {
+    "name": "cyanheads"
+  },
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/cyanheads/brapi-mcp-server"
+  },
+  "homepage": "https://github.com/cyanheads/brapi-mcp-server#readme",
+  "license": "Apache-2.0",
+  "server": {
+    "type": "node",
+    "entry_point": "dist/index.js",
+    "mcp_config": {
+      "command": "node",
+      "args": ["${__dirname}/dist/index.js"],
+      "env": {
+        "MCP_TRANSPORT_TYPE": "stdio",
+        "MCP_AUTH_MODE": "none",
+        "NODE_ENV": "production",
+        "BRAPI_DEFAULT_BASE_URL": "${BRAPI_DEFAULT_BASE_URL}",
+        "BRAPI_ENABLE_WRITES": "${BRAPI_ENABLE_WRITES}",
+        "MCP_LOG_LEVEL": "${MCP_LOG_LEVEL}"
+      }
+    }
+  },
+  "compatibility": {
+    "runtimes": {
+      "node": ">=24.0.0"
+    }
+  },
+  "tools_generated": true,
+  "prompts_generated": true,
+  "user_config": {
+    "BRAPI_DEFAULT_BASE_URL": {
+      "title": "Default BrAPI Base URL",
+      "description": "Default BrAPI v2 base URL. Optional — connections can be opened at runtime via brapi_connect instead.",
+      "type": "string",
+      "required": false,
+      "default": ""
+    },
+    "BRAPI_ENABLE_WRITES": {
+      "title": "Enable Write Surface",
+      "description": "Opt-in flag for brapi_submit_observations. Off by default.",
+      "type": "string",
+      "required": false,
+      "default": "false"
+    },
+    "MCP_LOG_LEVEL": {
+      "title": "Log Level",
+      "description": "Minimum log level for output (debug, info, warn, error).",
+      "type": "string",
+      "required": false,
+      "default": "info"
+    }
+  }
+}

package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.6.1",
+  "version": "0.6.3",
   "description": "A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, & more - across Breedbase, T3, Sweetpotatobase, & any BrAPI v2-compliant server.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -17,6 +17,7 @@
     "LICENSE",
     "CLAUDE.md",
     "Dockerfile",
+    "manifest.json",
     "server.json"
   ],
   "scripts": {
@@ -27,6 +28,10 @@
     "tree": "bun run scripts/tree.ts",
     "format": "biome check --write --unsafe .",
     "lint:mcp": "bun run scripts/lint-mcp.ts",
+    "lint:packaging": "bun run scripts/lint-packaging.ts",
+    "list-skills": "bun run scripts/list-skills.ts",
+    "bundle": "bun run build && bunx -y @anthropic-ai/mcpb pack . dist/brapi-mcp-server.mcpb",
+    "audit:refresh": "rm -f bun.lock && bun install && bun audit",
     "changelog:build": "bun run scripts/build-changelog.ts",
     "changelog:check": "bun run scripts/build-changelog.ts --check",
     "test": "bunx --bun vitest run",
@@ -40,6 +45,9 @@
     "mcp-server",
     "model-context-protocol",
     "claude",
+    "bun",
+    "stdio",
+    "streamable-http",
     "brapi",
     "breedbase",
     "plant-breeding",
@@ -71,12 +79,13 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.1",
-    "@duckdb/node-api": "^1.5.3-r.1",
-    "pino-pretty": "^13.1.3"
+    "@cyanheads/mcp-ts-core": "^0.9.13",
+    "@duckdb/node-api": "^1.5.3-r.2",
+    "pino-pretty": "^13.1.3",
+    "zod": "^4.4.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.15",
+    "@biomejs/biome": "^2.4.16",
     "@types/node": "^25.9.1",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",

package/server.json CHANGED Viewed

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.6.1",
+  "version": "0.6.3",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.6.1",
+      "version": "0.6.3",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.6.1",
+      "version": "0.6.3",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }