@cyanheads/brapi-mcp-server 0.5.4 → 0.5.5

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.5.4
+**Version:** 0.5.5
 **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.
@@ -306,13 +306,17 @@ 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) |
 | `security-pass` | Audit server for MCP-flavored security gaps: output injection, scope blast radius, input sinks, tenant isolation |
 | `devcheck` | Lint, format, typecheck, audit |
 | `polish-docs-meta` | Finalize docs, README, metadata, and agent protocol for shipping |
 | `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 |
+| `api-linter` | Definition lint rule reference (`format-parity`, `schema-*`, `name-*`, `server-json-*`, …) |
 | `api-canvas` | DataCanvas: register tabular data, run SQL, export, plus the `spillover()` helper for big result sets — Tier 3 opt-in |
 | `api-config` | AppConfig, parseConfig, env vars |
 | `api-context` | Context interface, logger, state, progress |
@@ -357,15 +361,18 @@ Each per-version file opens with YAML frontmatter:
 
 ```markdown
 ---
-summary: One-line headline, ≤250 chars  # required — powers the rollup index
+summary: One-line headline, ≤350 chars  # required — powers the rollup index
 breaking: false                          # optional — true flags breaking changes
+security: false                          # optional — true flags security fixes
 ---
 
 # 0.1.0 — YYYY-MM-DD
 ...
 ```
 
-`breaking: true` renders a `· ⚠️ Breaking` badge in the rollup — use it when consumers must update code on upgrade (signature changes, removed APIs, config renames).
+`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`.
+
+**Section order** (Keep a Changelog): Added, Changed, Deprecated, Removed, Fixed, Security. Include only sections with entries — don't ship empty headers.
 
 ---
 

package/README.md

@@ -7,7 +7,7 @@
 
 <div align="center">
 
-[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.5.4-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.5.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
 
 [![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)
 

package/changelog/0.5.x/0.5.5.md

@@ -0,0 +1,25 @@
+---
+summary: "Adopt framework 0.9.1 — wire `instructions` field for server-level orientation, port two raw schemas off `z.url()` and three off `.nullish()` unions to clear the new cross-vendor portability lint family (`schema-format-portability`, `schema-anyof-needs-type`)."
+breaking: false
+security: false
+---
+
+# 0.5.5 — 2026-05-16
+
+## Added
+
+- **Server-level `instructions` on `createApp()`** — agents now receive a one-paragraph orientation on `initialize` describing the connect-first handshake, the `find_*` / `get_*` / `raw_*` tool families, the spillover-to-canvas flow, and which tools to prefer. Spec-compliant clients forward it as session-level system context, so the same guidance reaches the model without bloating individual tool descriptions. ([@cyanheads/mcp-ts-core#91](https://github.com/cyanheads/mcp-ts-core/issues/91))
+
+## Changed
+
+- **`brapi_connect` and OAuth2 auth schemas dropped `z.url()`** ([`src/mcp-server/tools/definitions/brapi-connect.tool.ts`](./src/mcp-server/tools/definitions/brapi-connect.tool.ts), [`src/mcp-server/tools/shared/connect-auth-schema.ts`](./src/mcp-server/tools/shared/connect-auth-schema.ts)) — `z.url()` emits `format: "uri"` which OpenAI's tool validator hard-rejects, so `gpt-5-codex` was silently dropping the tools. Replaced with `z.string()` and moved the "absolute URL" constraint into `.describe()` text where the model actually reads it; clears the new default-on `schema-format-portability` lint rule. ([@cyanheads/mcp-ts-core#132](https://github.com/cyanheads/mcp-ts-core/issues/132), field report: [cyanheads/git-mcp-server#47](https://github.com/cyanheads/git-mcp-server/issues/47))
+- **`find_observations` season + season.year and `find_variants` variantSetDbId unions ported off `.nullish()`** ([`src/mcp-server/tools/definitions/brapi-find-observations.tool.ts`](./src/mcp-server/tools/definitions/brapi-find-observations.tool.ts), [`src/mcp-server/tools/definitions/brapi-find-variants.tool.ts`](./src/mcp-server/tools/definitions/brapi-find-variants.tool.ts)) — `.nullish()` on a `z.union([...])` emits a typeless `anyOf` branch that Gemini rejects with `400: reference to undefined schema`. Switched to `.optional()` + explicit `z.null()` in the union so every branch carries a top-level `type`; clears the new default-on `schema-anyof-needs-type` lint rule.
+- **`scripts/devcheck.ts` `bun outdated` parser fixed** — `bun outdated` emits markdown-style rows (`| pkg | … |`) with an empty leading cell, so `split('|')[0]` was always empty and the allowlist never matched. Now reads index `[1]` and strips the trailing `(dev|peer|prod|optional)` workspace marker so bare package names match. Synced from framework 0.9.1.
+- **Changelog summary cap raised 250 → 350 chars** — `SUMMARY_MAX_LENGTH` in `scripts/build-changelog.ts`, `changelog/template.md`, and the AGENTS.md / CLAUDE.md changelog section. Synced from framework 0.9.0 — 250 was forcing operator-relevant context out of recent summaries. ([@cyanheads/mcp-ts-core#129](https://github.com/cyanheads/mcp-ts-core/issues/129))
+- **AGENTS.md / CLAUDE.md skill table** — added rows for `tool-defs-analysis`, `release-and-publish`, `migrate-mcp-ts-template`, and `api-linter`; refreshed the changelog frontmatter section with the `security: boolean` flag and Keep-a-Changelog section-order guidance.
+- **Skills resynced from `@cyanheads/mcp-ts-core@0.9.1`** — `api-auth` 1.0 → 1.1 (`mcp_tool_scopes` union claim, Authentik/Keycloak/Zitadel operator setup, `MCP_AUTH_DISABLE_SCOPE_CHECKS` bypass), `api-linter` 1.2 → 1.3 (new portability rule family), `api-workers` 1.3 → 1.4 (`instructions` resolver form documented), `polish-docs-meta` 1.7 → 1.8 (350-char summary cap), `add-tool`, `api-config`, `api-errors`, `design-mcp-server`, `field-test`, `security-pass`, `tool-defs-analysis`. Phase B mirrored into `.claude/skills/` and `.agents/skills/`.
+
+## Dependencies
+
+- **`@cyanheads/mcp-ts-core` `^0.8.19 → ^0.9.1`** — Workers boot under `nodejs_compat` ([#124](https://github.com/cyanheads/mcp-ts-core/issues/124); not used by this server but unblocks anyone bridging to Workers), `instructions` field on `createApp` ([#91](https://github.com/cyanheads/mcp-ts-core/issues/91)), cross-vendor JSON Schema portability lint family ([#132](https://github.com/cyanheads/mcp-ts-core/issues/132)), build-time-only definition linting (no longer gates `createApp()` startup), RFC 8414 §3 path-suffixed well-known mount, SSRF DNS validation now enforced in Workers, IPv6-mapped/unique-local/link-local SSRF blocklist, FileSystemProvider tenant-id boundary check, rate-limit metric cardinality bound. ⚠️ Breaking: `schema-format-portability` is default-on `error` — the two `z.url()` migrations above are this server's response. ([changelog](https://github.com/cyanheads/mcp-ts-core/blob/main/changelog/0.9.x/0.9.0.md))
+- **`@biomejs/biome` `^2.4.14 → ^2.4.15`**, **`@types/node` `^25.6.2 → ^25.8.0`**, **`vitest` `^4.1.5 → ^4.1.6`** — patch refreshes.

package/changelog/template.md

@@ -4,7 +4,7 @@
 # to author a new release. Set that file's H1 to `# <version> — YYYY-MM-DD`
 # with a concrete date.
 
-# Required. One-line GitHub Release-style headline. ~250 character soft cap.
+# Required. One-line GitHub Release-style headline. 350 character cap.
 # Default short and scannable. Don't pad, don't stitch unrelated changes with
 # semicolons — pick the headline. Quotes required: unquoted YAML treats `: `
 # inside the value as a key separator and fails GitHub's strict parser.

package/dist/index.js

@@ -103,6 +103,7 @@ await createApp({
         brapiFiltersResource,
     ],
     prompts: [brapiEdaStudy, brapiMetaAnalysis],
+    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) {
             throw configurationError('brapi-mcp-server requires the framework canvas service (DuckDB) for dataframe spillover. Set CANVAS_PROVIDER_TYPE=duckdb (the default) and ensure @duckdb/node-api is installed.', { canvasProviderType: process.env.CANVAS_PROVIDER_TYPE ?? 'duckdb' });

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+{"version":3,"file":"index.js","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;;GAMG;AAEH,0EAA0E;AAC1E,yEAAyE;AACzE,qEAAqE;AACrE,uEAAuE;AACvE,0BAA0B;AAC1B,EAAE;AACF,2EAA2E;AAC3E,uEAAuE;AACvE,0EAA0E;AAC1E,gEAAgE;AAChE,wDAAwD;AACxD,OAAO,CAAC,GAAG,CAAC,oBAAoB,KAAK,QAAQ,CAAC;AAE9C,6EAA6E;AAC7E,wEAAwE;AACxE,4EAA4E;AAC5E,yEAAyE;AACzE,wEAAwE;AACxE,yEAAyE;AACzE,kBAAkB;AAClB,IAAI,OAAO,CAAC,GAAG,CAAC,gBAAgB,EAAE,CAAC;IACjC,OAAO,CAAC,GAAG,CAAC,kBAAkB,KAAK,OAAO,CAAC,GAAG,CAAC,gBAAgB,CAAC;AAClE,CAAC;AAED,OAAO,EAAE,SAAS,EAAE,MAAM,wBAAwB,CAAC;AACnD,OAAO,EAAE,kBAAkB,EAAE,MAAM,+BAA+B,CAAC;AACnE,OAAO,EAAE,YAAY,EAAE,MAAM,8BAA8B,CAAC;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AACnE,OAAO,EAAE,wBAAwB,EAAE,MAAM,mCAAmC,CAAC;AAC7E,OAAO,EAAE,gBAAgB,EAAE,MAAM,mCAAmC,CAAC;AACrE,OAAO,EAAE,sBAAsB,EAAE,MAAM,yCAAyC,CAAC;AACjF,OAAO,EAAE,oBAAoB,EAAE,MAAM,uCAAuC,CAAC;AAC7E,OAAO,EAAE,sBAAsB,EAAE,MAAM,0CAA0C,CAAC;AAClF,OAAO,EAAE,kBAAkB,EAAE,MAAM,qCAAqC,CAAC;AACzE,OAAO,EAAE,aAAa,EAAE,MAAM,4DAA4D,CAAC;AAC3F,OAAO,EAAE,iBAAiB,EAAE,MAAM,gEAAgE,CAAC;AACnG,OAAO,EAAE,kBAAkB,EAAE,MAAM,4DAA4D,CAAC;AAChG,OAAO,EAAE,oBAAoB,EAAE,MAAM,8DAA8D,CAAC;AACpG,OAAO,EAAE,sBAAsB,EAAE,MAAM,gEAAgE,CAAC;AACxG,OAAO,EAAE,uBAAuB,EAAE,MAAM,kEAAkE,CAAC;AAC3G,OAAO,EAAE,kBAAkB,EAAE,MAAM,4DAA4D,CAAC;AAChG,OAAO,EACL,mBAAmB,EACnB,qBAAqB,EACrB,uBAAuB,EACvB,oBAAoB,GACrB,MAAM,yCAAyC,CAAC;AAEjD,MAAM,YAAY,GAAG,eAAe,EAAE,CAAC;AAEvC;;;;GAIG;AACH,MAAM,YAAY,GAAG;IACnB,MAAM,EAAE,gEAAgE;IACxE,IAAI,EAAE,iHAAiH;CACxH,CAAC;AAEF,MAAM,cAAc,GAAG;IACrB,MAAM,EAAE,kDAAkD;IAC1D,IAAI,EAAE,gEAAgE;CACvE,CAAC;AAEF;;;;;;;;GAQG;AACH,SAAS,iBAAiB;IACxB,MAAM,aAAa,GAAG,OAAO,CAAC,GAAG,CAAC,kBAAkB,IAAI,OAAO,CAAC;IAChE,IAAI,aAAa,KAAK,OAAO,EAAE,CAAC;QAC9B,OAAO;YACL,MAAM,EAAE,4CAA4C;YACpD,IAAI,EAAE,mHAAmH;SAC1H,CAAC;IACJ,CAAC;IACD,IAAI,CAAC,YAAY,CAAC,SAAS,EAAE,CAAC;QAC5B,OAAO;YACL,MAAM,EAAE,4DAA4D;YACpE,IAAI,EAAE,wFAAwF;SAC/F,CAAC;IACJ,CAAC;IACD,OAAO,IAAI,CAAC;AACd,CAAC;AAED,MAAM,cAAc,GAAG,iBAAiB,EAAE,CAAC;AAE3C,MAAM,KAAK,GAAG;IACZ,GAAG,uBAAuB;IAC1B,GAAG,mBAAmB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAC/B,YAAY,CAAC,iBAAiB,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,YAAY,CAAC,CACnE;IACD,GAAG,qBAAqB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,cAAc,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,cAAc,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC;IAC3F,GAAG,oBAAoB,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAChC,YAAY,CAAC,YAAY,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,YAAY,CAAC,CAAC,EAAE,cAAc,CAAC,CAChE;CACF,CAAC;AAEF,MAAM,SAAS,CAAC;IACd,KAAK;IACL,SAAS,EAAE;QACT,uBAAuB;QACvB,kBAAkB;QAClB,kBAAkB;QAClB,sBAAsB;QACtB,oBAAoB;KACrB;IACD,OAAO,EAAE,CAAC,aAAa,EAAE,iBAAiB,CAAC;IAC3C,YAAY,EACV,onBAAonB;IACtnB,KAAK,CAAC,IAAI;QACR,IAAI,CAAC,IAAI,CAAC,MAAM,EAAE,CAAC;YACjB,MAAM,kBAAkB,CACtB,kLAAkL,EAClL,EAAE,kBAAkB,EAAE,OAAO,CAAC,GAAG,CAAC,oBAAoB,IAAI,QAAQ,EAAE,CACrE,CAAC;QACJ,CAAC;QACD,gBAAgB,CAAC,IAAI,CAAC,MAAM,EAAE,YAAY,CAAC,CAAC;QAC5C,eAAe,CAAC,YAAY,CAAC,CAAC;QAC9B,sBAAsB,CAAC,YAAY,CAAC,CAAC;QACrC,wBAAwB,EAAE,CAAC;QAC3B,sBAAsB,CAAC,YAAY,CAAC,CAAC;QACrC,kBAAkB,CAAC,YAAY,CAAC,CAAC;QACjC,oBAAoB,EAAE,CAAC;IACzB,CAAC;CACF,CAAC,CAAC"}

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0FvB,CAAC"}
+{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyFvB,CAAC"}

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

@@ -43,9 +43,8 @@ export const brapiConnect = tool('brapi_connect', {
     input: z.object({
         baseUrl: z
             .string()
-            .url()
             .optional()
-            .describe('BrAPI v2 base URL including any path prefix — e.g. https://test-server.brapi.org/brapi/v2. Omit to use the configured default for this alias.'),
+            .describe('BrAPI v2 base URL (absolute URL) including any path prefix — e.g. https://test-server.brapi.org/brapi/v2. Omit to use the configured default for this alias.'),
         auth: ConnectAuthSchema.optional().describe('Auth payload. Omit to use credentials configured server-side for this alias (or no auth when none are configured).'),
         alias: z
             .string()

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

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

@@ -37,12 +37,12 @@ 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.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
+        season: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodObject<{
             seasonDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
-            year: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodNumber]>>>;
+            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.$loose>]>>>;
+        }, z.core.$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

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyLjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsThC,CAAC"}
+{"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA2LjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsThC,CAAC"}

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

@@ -50,8 +50,9 @@ const ObservationRowSchema = 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.'),
             ])
-                .nullish()
+                .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
@@ -61,8 +62,9 @@ const ObservationRowSchema = z
         })
             .passthrough()
             .describe('Structured season block per BrAPI v2.1.'),
+        z.null().describe('Field present but null on the upstream.'),
     ])
-        .nullish()
+        .optional()
         .describe('Season — either a flat string or a structured `{seasonDbId, year, season}` object depending on the server.'),
     value: z
         .string()

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

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

@@ -23,7 +23,7 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
     results: z.ZodArray<z.ZodObject<{
         variantDbId: z.ZodString;
         variantNames: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
-        variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>]>>>;
+        variantSetDbId: z.ZodOptional<z.ZodUnion<readonly [z.ZodString, z.ZodArray<z.ZodString>, z.ZodNull]>>;
         variantSetDbIds: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
         variantType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         referenceBases: z.ZodOptional<z.ZodNullable<z.ZodString>>;

package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiIjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsM5B,CAAC"}
+{"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkIjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsM5B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js

@@ -28,8 +28,9 @@ const VariantRowSchema = z
         z
             .array(z.string().describe('One variant-set FK.'))
             .describe('Variant-set FK array — a variant may belong to multiple sets.'),
+        z.null().describe('Field present but null on the upstream.'),
     ])
-        .nullish()
+        .optional()
         .describe('FK to the variant set(s) this variant belongs to. May be a string or string[] depending on server.'),
     variantSetDbIds: z
         .array(z.string().describe('Variant-set FK.'))

package/dist/mcp-server/tools/definitions/brapi-find-variants.tool.js.map

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

@@ -619,12 +619,12 @@ 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").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodObject<{
+        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").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodNumber]>>>;
+            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").$loose>]>>>;
+        }, import("zod/v4/core").$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>>;
@@ -811,7 +811,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     results: import("zod").ZodArray<import("zod").ZodObject<{
         variantDbId: import("zod").ZodString;
         variantNames: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodArray<import("zod").ZodString>>>;
-        variantSetDbId: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodArray<import("zod").ZodString>]>>>;
+        variantSetDbId: import("zod").ZodOptional<import("zod").ZodUnion<readonly [import("zod").ZodString, import("zod").ZodArray<import("zod").ZodString>, import("zod").ZodNull]>>;
         variantSetDbIds: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodArray<import("zod").ZodString>>>;
         variantType: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;
         referenceBases: import("zod").ZodOptional<import("zod").ZodNullable<import("zod").ZodString>>;

package/dist/mcp-server/tools/shared/connect-auth-schema.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"connect-auth-schema.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;2BA0D3B,CAAC;AAEJ,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC"}
+{"version":3,"file":"connect-auth-schema.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;2BA2D3B,CAAC;AAEJ,MAAM,MAAM,gBAAgB,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,iBAAiB,CAAC,CAAC"}

package/dist/mcp-server/tools/shared/connect-auth-schema.js

@@ -54,9 +54,8 @@ export const ConnectAuthSchema = z
         clientSecret: z.string().min(1).describe('OAuth2 client secret paired with the clientId.'),
         tokenUrl: z
             .string()
-            .url()
             .optional()
-            .describe('OAuth2 token endpoint URL. Defaults derived from the base URL when omitted.'),
+            .describe('OAuth2 token endpoint (absolute URL). Defaults derived from the base URL when omitted.'),
     })
         .describe('OAuth2 client-credentials variant.'),
 ])

package/dist/mcp-server/tools/shared/connect-auth-schema.js.map

@@ -1 +1 @@
-{"version":3,"file":"connect-auth-schema.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,kBAAkB,CAAC,MAAM,EAAE;IAC1B,CAAC;SACE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC,EAAE,CAAC;SAClE,QAAQ,CAAC,2CAA2C,CAAC;IACxD,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QAChE,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,mEAAmE,CAAC;KACjF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC;IACzE,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACzE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;SACD,QAAQ,CAAC,6DAA6D,CAAC;IAC1E,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC7D,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,yDAAyD,CAAC;KACvE,CAAC;SACD,QAAQ,CAAC,2EAA2E,CAAC;IACxF,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,QAAQ,CAAC;aACjB,QAAQ,CACP,gFAAgF,CACjF;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC;QACzE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC1F,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,CAAC,6EAA6E,CAAC;KAC3F,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC;CAClD,CAAC;KACD,QAAQ,CACP,2GAA2G,CAC5G,CAAC"}
+{"version":3,"file":"connect-auth-schema.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/connect-auth-schema.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE3C,MAAM,CAAC,MAAM,iBAAiB,GAAG,CAAC;KAC/B,kBAAkB,CAAC,MAAM,EAAE;IAC1B,CAAC;SACE,MAAM,CAAC,EAAE,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,MAAM,CAAC,CAAC,QAAQ,CAAC,oBAAoB,CAAC,EAAE,CAAC;SAClE,QAAQ,CAAC,2CAA2C,CAAC;IACxD,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,QAAQ,CAAC,CAAC,QAAQ,CAAC,4BAA4B,CAAC;QAChE,KAAK,EAAE,CAAC;aACL,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,mEAAmE,CAAC;KACjF,CAAC;SACD,QAAQ,CAAC,4DAA4D,CAAC;IACzE,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC,CAAC,OAAO,CAAC,SAAS,CAAC,CAAC,QAAQ,CAAC,oCAAoC,CAAC;QACzE,MAAM,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,qCAAqC,CAAC;QACzE,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,kEAAkE,CAAC;KAChF,CAAC;SACD,QAAQ,CAAC,6DAA6D,CAAC;IAC1E,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,KAAK,CAAC;aACd,QAAQ,CAAC,0EAA0E,CAAC;QACvF,QAAQ,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,uBAAuB,CAAC;QAC7D,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,yDAAyD,CAAC;KACvE,CAAC;SACD,QAAQ,CAAC,2EAA2E,CAAC;IACxF,CAAC;SACE,MAAM,CAAC;QACN,IAAI,EAAE,CAAC;aACJ,OAAO,CAAC,QAAQ,CAAC;aACjB,QAAQ,CACP,gFAAgF,CACjF;QACH,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,CAAC,4DAA4D,CAAC;QACzE,YAAY,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,gDAAgD,CAAC;QAC1F,QAAQ,EAAE,CAAC;aACR,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CACP,wFAAwF,CACzF;KACJ,CAAC;SACD,QAAQ,CAAC,oCAAoC,CAAC;CAClD,CAAC;KACD,QAAQ,CACP,2GAA2G,CAC5G,CAAC"}

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.5.4",
+  "version": "0.5.5",
   "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.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -71,17 +71,17 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.8.19",
+    "@cyanheads/mcp-ts-core": "^0.9.1",
     "@duckdb/node-api": "^1.5.2-r.1",
     "pino-pretty": "^13.1.3"
   },
   "devDependencies": {
-    "@biomejs/biome": "^2.4.14",
-    "@types/node": "^25.6.2",
+    "@biomejs/biome": "^2.4.15",
+    "@types/node": "^25.8.0",
     "depcheck": "^1.4.7",
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.5"
+    "vitest": "^4.1.6"
   }
 }

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.5.4",
+  "version": "0.5.5",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.5.4",
+      "version": "0.5.5",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.5.4",
+      "version": "0.5.5",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }