@cyanheads/brapi-mcp-server 0.5.4 → 0.6.0

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-0.6.0-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)
 
@@ -120,6 +120,7 @@ Within one (tenant, session), dataframes act as a self-cleaning shared notebook:
 - **Multi-server session** — `ServerRegistry` maps aliases to live BrAPI connections; one session can span Breedbase, T3, and Sweetpotatobase in parallel.
 - **Built-in known-server registry** — `bti-cassava`, `bti-sweetpotato`, `bti-breedbase-demo`, `t3-wheat`, `t3-oat`, `t3-barley` resolve out-of-the-box without env vars; orientation envelope carries CC-BY attribution.
 - **Capability-aware calls** — `CapabilityRegistry` caches `/serverinfo` per connection and guards every tool call against unsupported endpoints. Falls back to `/calls` when `/serverinfo` is sparse.
+- **Dialect adaptation** — `spec` / `brapi-test` / `breedbase` / `cassavabase` / `bms` dialects translate v2.1 plural filter keys to the singular form each server family honors, drop filters known to be broken, normalize sparse-shape encodings, and escalate to POST `/search/{noun}` when GET would silently downcast multi-value filters. Detected from `/serverinfo` (server-name / organization-name); pin per-alias via `BRAPI_<ALIAS>_DIALECT`. Verified-vs-inferred mapping counts surface on the orientation envelope so agents see the confidence floor at a glance.
 - **DuckDB required** — `@duckdb/node-api` is a regular dependency; startup fails closed when the framework canvas is unavailable. Not supported on Cloudflare Workers (no native binary in that runtime).
 - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern automatically.
 - **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call).

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/0.6.x/0.6.0.md

@@ -0,0 +1,34 @@
+---
+summary: "BMS dialect for the CGIAR crop community, route escalation to POST /search when GET would downcast multi-value filters, walk_pedigree `direction` field, plus fixes for bbox spillover ordering, schemeless `imageURL` resolution, singleton-fetch 5xx retry storms, and large inline JSON in `find_*` text rows."
+breaking: false
+security: false
+---
+
+# 0.6.0 — 2026-05-22
+
+## Added
+
+- **`bms` dialect** ([`src/services/brapi-dialect/bms-dialect.ts`](./src/services/brapi-dialect/bms-dialect.ts)) — covers Breeding Management System servers (CIMMYT, IRRI, ICRISAT, IITA, CIP). v2.1 plural → v2.0 singular translation table per endpoint plus auto-detection from server-name (`BMS`, `BMSAPI`, `Breeding Management System`) and organization-name (CGIAR centers). Mappings ship marked `verified: false` pending live narrowing against pinned test endpoints — agents see an inferred-mapping warning on downcast so they validate result counts via distributions before trusting them. ([#7](https://github.com/cyanheads/brapi-mcp-server/issues/7))
+- **`direction` field on `brapi_walk_pedigree` nodes** — every node now carries `direction: 'root' | 'ancestor' | 'descendant' | 'both'`, so bidirectional walks can distinguish the side of the root each germplasm was reached from. Convergence rule: ancestor + descendant in the same traversal upgrades to `'both'` (backcross / selfing chain). ([#16](https://github.com/cyanheads/brapi-mcp-server/issues/16))
+- **Dialect filter-mapping confidence on the orientation envelope** — `verifiedMappingCount` / `inferredMappingCount` surface on `dialect` in `brapi_connect` and `brapi_server_info` so agents see the dialect's confidence floor at a glance. Drives a softer warning on downcast for inferred mappings. New `DialectFilterMapping` shape (`{ target, verified }`) on the dialect interface; mixed-shape input (string shorthand or explicit object) keeps authoring ergonomic.
+- **SGN-family row normalizer** — `cassavabase` and `breedbase` dialects now strip `null` from upstream rows pre-schema (recursively, one level into nested objects + arrays of objects). Lets row schemas express the natural "field is absent" via `optional()` without every schema absorbing a `.nullish()` per field. New optional `normalizeRow(endpoint, row)` method on `BrapiDialect`; default `spec` dialect omits it (passthrough).
+- **`requireRegisteredConnection` helper** ([`src/mcp-server/tools/shared/find-helpers.ts`](./src/mcp-server/tools/shared/find-helpers.ts)) — replaces inline `registry.get(ctx, alias ?? DEFAULT_ALIAS)` across tools and resources. Throws via `ctx.fail('unknown_alias', …)` so the wire-level error carries `data.recovery.hint` from the calling definition's `errors[]` contract. Adopted by every tool/resource that resolves a connection. ([#29](https://github.com/cyanheads/brapi-mcp-server/issues/29))
+- **`singleton: true` on `BrapiRequestOptions`** ([`src/services/brapi-client/types.ts`](./src/services/brapi-client/types.ts)) — marks a request as a `/{noun}/{id}` fetch. The client reclassifies 5xx responses on these calls as `NotFound`, so `brapi_get_study`, `brapi_get_germplasm`, and `brapi_walk_pedigree`'s per-root probes fast-fail on missing DbIds without burning the retry budget. ([#30](https://github.com/cyanheads/brapi-mcp-server/issues/30))
+
+## Changed
+
+- **Route escalation to POST `/search/{noun}`** ([`src/mcp-server/tools/shared/find-helpers.ts`](./src/mcp-server/tools/shared/find-helpers.ts), [`src/services/brapi-dialect/singularizing-dialect.ts`](./src/services/brapi-dialect/singularizing-dialect.ts)) — when the active dialect would have downcast a multi-value array filter to its first scalar on the GET wire (SGN-family + BMS only honor singular filter keys) and POST `/search/{noun}` is advertised and not disabled, `resolveFindRoute` now picks search. The search body preserves the original multi-value semantics that the GET wire shape would have silently lost. New `requiresEscalation` field on `DialectAdaptation`. ([#15](https://github.com/cyanheads/brapi-mcp-server/issues/15))
+- **`brapi_find_locations` bbox filter runs before spillover** ([`src/mcp-server/tools/definitions/brapi-find-locations.tool.ts`](./src/mcp-server/tools/definitions/brapi-find-locations.tool.ts)) — axis-order pick (`spec` vs `swapped` for non-conformant servers) is now made over the first-page rows, then handed to `maybeSpill` as a `rowFilter`. The dataframe materialized on spillover holds post-bbox rows, so SQL on the `df_*` handle sees the same set the inline result preview did. ([#28](https://github.com/cyanheads/brapi-mcp-server/issues/28))
+- **Orientation envelope headline `Connected` → `Registered` when no services advertised** ([`src/mcp-server/tools/shared/orientation-envelope.ts`](./src/mcp-server/tools/shared/orientation-envelope.ts)) — registering a connection against an unreachable server (or one returning a zero-capability `/serverinfo`) shouldn't read as "Connected" to a skimming agent. The `Registered` headline signals "alias is bound, server is not responding usefully." ([#32](https://github.com/cyanheads/brapi-mcp-server/issues/32))
+- **Canvas dataframe naming `df_<uuid>` → `df_XXXXX_XXXXX`** ([`src/services/canvas-bridge/canvas-bridge.ts`](./src/services/canvas-bridge/canvas-bridge.ts)) — 10 random chars from `A–Z 0–9` split into two 5-char groups by `_`, generated via the framework's `idGenerator`. Keyspace ~3.7×10^15 (36^10), unguessable for the (tenant, session)-bucketed capability-token model and short enough to render cleanly in inline tool output. ([#34](https://github.com/cyanheads/brapi-mcp-server/issues/34))
+- **`AliasInput` description clarified** — omitting `alias` reads the connection registered under alias `default` (i.e. a prior `brapi_connect` call that did not specify an alias). Calls that used a non-default alias must pass that same alias back; previous wording suggested an implicit "most recent connect" which never existed. ([#32](https://github.com/cyanheads/brapi-mcp-server/issues/32))
+- **`brapi_dataframe_describe` shared-HTTP error language** — `list_all_disabled_on_shared_http` no longer mentions `MCP_AUTH_MODE=none` by name (operators may configure shared-trust HTTP differently). Headline and recovery now describe the deployment shape rather than its env-var implementation. ([#32](https://github.com/cyanheads/brapi-mcp-server/issues/32))
+
+## Fixed
+
+- **`brapi_get_image` resolves schemeless `imageURL` values correctly** ([`src/mcp-server/tools/definitions/brapi-get-image.tool.ts`](./src/mcp-server/tools/definitions/brapi-get-image.tool.ts)) — protocol-relative (`//host/path`) gets an `https:` prefix; domain-shaped values (`breedbase.org/data/images/.../medium.jpg`) get an `https://` prefix; root-relative and bare paths still concatenate with the BrAPI `baseUrl` (the legitimate "image lives on the same BrAPI host" case). Previously, the domain-shaped form was silently treated as a relative path and produced an unresolvable URL. ([#31](https://github.com/cyanheads/brapi-mcp-server/issues/31))
+- **Large nested objects no longer dump multi-KB inline in `find_*` text rows** ([`src/mcp-server/tools/shared/find-helpers.ts`](./src/mcp-server/tools/shared/find-helpers.ts)) — passthrough rendering for both `collectPassthroughParts` (bullet rows) and `appendPassthroughLines` (detail-view lines) applies a 240-char inline cap; values over the cap collapse to `<N keys, Xkb — see structuredContent>` (or `<N entries, …>` for arrays). The full payload remains in `structuredContent` so structured clients (Codex Desktop) see the same data. Affects `find_studies` (`additionalInfo`), `find_variables` (`trait`, `scale`), and any other surface that carries large nested objects through the passthrough path. ([#33](https://github.com/cyanheads/brapi-mcp-server/issues/33))
+
+## Dependencies
+
+- **`@duckdb/node-api` `^1.5.2-r.1 → ^1.5.3-r.1`**, **`@types/node` `^25.8.0 → ^25.9.1`**, **`vitest` `^4.1.6 → ^4.1.7`** — 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' });

package/dist/index.js.map

@@ -1 +1 @@
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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/resources/definitions/brapi-calls.resource.d.ts

@@ -5,7 +5,13 @@
  *
  * @module mcp-server/resources/definitions/brapi-calls.resource
  */
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiCallsResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<Readonly<{
     [k: string]: import("zod/v4/core").$ZodType<unknown, unknown, import("zod/v4/core").$ZodTypeInternals<unknown, unknown>>;
-}>, import("zod/v4/core").$strip>, undefined, undefined>;
+}>, import("zod/v4/core").$strip>, undefined, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No default BrAPI connection has been registered";
+    readonly recovery: "Call brapi_connect (without an alias, or with alias `default`) before reading this resource.";
+}]>;
 //# sourceMappingURL=brapi-calls.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-calls.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAuBH,eAAO,MAAM,kBAAkB;;wDAkB7B,CAAC"}
+{"version":3,"file":"brapi-calls.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,kBAAkB;;;;;;;GA2B7B,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js

@@ -6,12 +6,12 @@
  * @module mcp-server/resources/definitions/brapi-calls.resource
  */
 import { resource } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { requireRegisteredConnection } from '../../../mcp-server/tools/shared/find-helpers.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
 async function loadCallsProfile(ctx) {
-    const registry = getServerRegistry();
     const capabilities = getCapabilityRegistry();
-    const connection = await registry.get(ctx, DEFAULT_ALIAS);
+    const connection = await requireRegisteredConnection(ctx, undefined);
     const lookup = {};
     if (connection.resolvedAuth)
         lookup.auth = connection.resolvedAuth;
@@ -30,6 +30,14 @@ export const brapiCallsResource = resource('brapi://calls', {
     title: 'BrAPI capability profile',
     description: 'Capability profile for the default BrAPI connection — supported services, their HTTP methods, declared versions, and crops list. Mirrors what /serverinfo + /calls returned at the last load.',
     mimeType: 'application/json',
+    errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No default BrAPI connection has been registered',
+            recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+        },
+    ],
     handler(_params, ctx) {
         return loadCallsProfile(ctx);
     },

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-calls.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAgB,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAChE,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAChF,OAAO,EAAE,aAAa,EAAE,iBAAiB,EAAE,MAAM,qCAAqC,CAAC;AAEvF,KAAK,UAAU,gBAAgB,CAAC,GAAY;IAC1C,MAAM,QAAQ,GAAG,iBAAiB,EAAE,CAAC;IACrC,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;IAC7C,MAAM,UAAU,GAAG,MAAM,QAAQ,CAAC,GAAG,CAAC,GAAG,EAAE,aAAa,CAAC,CAAC;IAC1D,MAAM,MAAM,GAA8C,EAAE,CAAC;IAC7D,IAAI,UAAU,CAAC,YAAY;QAAE,MAAM,CAAC,IAAI,GAAG,UAAU,CAAC,YAAY,CAAC;IACnE,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;IAC5E,OAAO;QACL,KAAK,EAAE,UAAU,CAAC,KAAK;QACvB,OAAO,EAAE,UAAU,CAAC,OAAO;QAC3B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,SAAS,EAAE,OAAO,CAAC,SAAS;QAC5B,SAAS,EAAE,OAAO,CAAC,SAAS;KAC7B,CAAC;AACJ,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,eAAe,EAAE;IAC1D,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,0BAA0B;IACjC,WAAW,EACT,+LAA+L;IACjM,QAAQ,EAAE,kBAAkB;IAC5B,OAAO,CAAC,OAAO,EAAE,GAAG;QAClB,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC;IAC/B,CAAC;IACD,IAAI,EAAE,GAAG,EAAE,CAAC,CAAC;QACX,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,eAAe;gBACpB,IAAI,EAAE,0BAA0B;gBAChC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"brapi-calls.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAuB,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AACvE,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,2BAA2B,EAAE,MAAM,2CAA2C,CAAC;AACxF,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAEhF,KAAK,UAAU,gBAAgB,CAAC,GAAoC;IAClE,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;IAC7C,MAAM,UAAU,GAAG,MAAM,2BAA2B,CAAC,GAAG,EAAE,SAAS,CAAC,CAAC;IACrE,MAAM,MAAM,GAA8C,EAAE,CAAC;IAC7D,IAAI,UAAU,CAAC,YAAY;QAAE,MAAM,CAAC,IAAI,GAAG,UAAU,CAAC,YAAY,CAAC;IACnE,MAAM,OAAO,GAAG,MAAM,YAAY,CAAC,OAAO,CAAC,UAAU,CAAC,OAAO,EAAE,GAAG,EAAE,MAAM,CAAC,CAAC;IAC5E,OAAO;QACL,KAAK,EAAE,UAAU,CAAC,KAAK;QACvB,OAAO,EAAE,UAAU,CAAC,OAAO;QAC3B,MAAM,EAAE,OAAO,CAAC,MAAM;QACtB,KAAK,EAAE,OAAO,CAAC,KAAK;QACpB,SAAS,EAAE,OAAO,CAAC,SAAS;QAC5B,SAAS,EAAE,OAAO,CAAC,SAAS;KAC7B,CAAC;AACJ,CAAC;AAED,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,eAAe,EAAE;IAC1D,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,0BAA0B;IACjC,WAAW,EACT,+LAA+L;IACjM,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;SACjG;KACO;IACV,OAAO,CAAC,OAAO,EAAE,GAAG;QAClB,OAAO,gBAAgB,CAAC,GAAG,CAAC,CAAC;IAC/B,CAAC;IACD,IAAI,EAAE,GAAG,EAAE,CAAC,CAAC;QACX,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,eAAe;gBACpB,IAAI,EAAE,0BAA0B;gBAChC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts

@@ -10,6 +10,11 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiGermplasmResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
     germplasmDbId: z.ZodString;
 }, z.core.$strip>, undefined, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No default BrAPI connection has been registered";
+    readonly recovery: "Call brapi_connect (without an alias, or with alias `default`) before reading this resource.";
+}, {
     readonly reason: "germplasm_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no germplasm record for the requested DbId";

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-germplasm.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,sBAAsB;;;;;;;GA2BjC,CAAC"}
+{"version":3,"file":"brapi-germplasm.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;GAkCjC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js

@@ -14,6 +14,12 @@ export const brapiGermplasmResource = resource('brapi://germplasm/{germplasmDbId
     description: 'Single-germplasm resource on the default BrAPI connection — same payload as the brapi_get_germplasm tool, addressable by URI.',
     mimeType: 'application/json',
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No default BrAPI connection has been registered',
+            recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+        },
         {
             reason: 'germplasm_not_found',
             code: JsonRpcErrorCode.NotFound,

package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-germplasm.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAE/F,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,mCAAmC,EAAE;IAClF,IAAI,EAAE,iBAAiB;IACvB,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,qBAAqB;YAC7B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8DAA8D;YACpE,QAAQ,EACN,mGAAmG;SACtG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC7F,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,iBAAiB,CAAC,OAAO,CACpC,iBAAiB,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,aAAa,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC,EACtE,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"brapi-germplasm.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-germplasm.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,iBAAiB,EAAE,MAAM,4DAA4D,CAAC;AAE/F,MAAM,CAAC,MAAM,sBAAsB,GAAG,QAAQ,CAAC,mCAAmC,EAAE;IAClF,IAAI,EAAE,iBAAiB;IACvB,KAAK,EAAE,wBAAwB;IAC/B,WAAW,EACT,+HAA+H;IACjI,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;SACjG;QACD;YACE,MAAM,EAAE,qBAAqB;YAC7B,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,8DAA8D;YACpE,QAAQ,EACN,mGAAmG;SACtG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,iDAAiD,CAAC;KAC7F,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,iBAAiB,CAAC,OAAO,CACpC,iBAAiB,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,aAAa,EAAE,MAAM,CAAC,aAAa,EAAE,CAAC,EACtE,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts

@@ -5,7 +5,13 @@
  *
  * @module mcp-server/resources/definitions/brapi-server-info.resource
  */
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiServerInfoResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<Readonly<{
     [k: string]: import("zod/v4/core").$ZodType<unknown, unknown, import("zod/v4/core").$ZodTypeInternals<unknown, unknown>>;
-}>, import("zod/v4/core").$strip>, undefined, undefined>;
+}>, import("zod/v4/core").$strip>, undefined, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No default BrAPI connection has been registered";
+    readonly recovery: "Call brapi_connect (without an alias, or with alias `default`) before reading this resource.";
+}]>;
 //# sourceMappingURL=brapi-server-info.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-server-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAKH,eAAO,MAAM,uBAAuB;;wDAkBlC,CAAC"}
+{"version":3,"file":"brapi-server-info.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,uBAAuB;;;;;;;GA2BlC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js

@@ -6,12 +6,21 @@
  * @module mcp-server/resources/definitions/brapi-server-info.resource
  */
 import { resource } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { brapiServerInfo } from '../../../mcp-server/tools/definitions/brapi-server-info.tool.js';
 export const brapiServerInfoResource = resource('brapi://server/info', {
     name: 'brapi-server-info',
     title: 'BrAPI server orientation envelope',
     description: 'Orientation envelope for the default BrAPI connection — identity, capabilities, content counts, notes. Same payload as the brapi_server_info tool.',
     mimeType: 'application/json',
+    errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No default BrAPI connection has been registered',
+            recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+        },
+    ],
     async handler(_params, ctx) {
         return await brapiServerInfo.handler(brapiServerInfo.input.parse({}), ctx);
     },

package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-server-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,eAAe,EAAE,MAAM,0DAA0D,CAAC;AAE3F,MAAM,CAAC,MAAM,uBAAuB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACrE,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,oJAAoJ;IACtJ,QAAQ,EAAE,kBAAkB;IAC5B,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,OAAO,MAAM,eAAe,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IAC7E,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,qBAAqB;gBAC1B,IAAI,EAAE,mCAAmC;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"brapi-server-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,0DAA0D,CAAC;AAE3F,MAAM,CAAC,MAAM,uBAAuB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACrE,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,oJAAoJ;IACtJ,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;SACjG;KACO;IACV,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,OAAO,MAAM,eAAe,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IAC7E,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,qBAAqB;gBAC1B,IAAI,EAAE,mCAAmC;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts

@@ -10,6 +10,11 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiStudyResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
     studyDbId: z.ZodString;
 }, z.core.$strip>, undefined, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No default BrAPI connection has been registered";
+    readonly recovery: "Call brapi_connect (without an alias, or with alias `default`) before reading this resource.";
+}, {
     readonly reason: "study_not_found";
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no study record for the requested DbId";

package/dist/mcp-server/resources/definitions/brapi-study.resource.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-study.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,kBAAkB;;;;;;;GA2B7B,CAAC"}
+{"version":3,"file":"brapi-study.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;GAkC7B,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-study.resource.js

@@ -14,6 +14,12 @@ export const brapiStudyResource = resource('brapi://study/{studyDbId}', {
     description: 'Single-study resource on the default BrAPI connection — same payload as the brapi_get_study tool, addressable by URI.',
     mimeType: 'application/json',
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No default BrAPI connection has been registered',
+            recovery: 'Call brapi_connect (without an alias, or with alias `default`) before reading this resource.',
+        },
         {
             reason: 'study_not_found',
             code: JsonRpcErrorCode.NotFound,

package/dist/mcp-server/resources/definitions/brapi-study.resource.js.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-study.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,wDAAwD,CAAC;AAEvF,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IACtE,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EACT,uHAAuH;IACzH,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,6FAA6F;SAChG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KACrF,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,aAAa,CAAC,OAAO,CAChC,aAAa,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC,EAC1D,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}
+{"version":3,"file":"brapi-study.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-study.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,aAAa,EAAE,MAAM,wDAAwD,CAAC;AAEvF,MAAM,CAAC,MAAM,kBAAkB,GAAG,QAAQ,CAAC,2BAA2B,EAAE;IACtE,IAAI,EAAE,aAAa;IACnB,KAAK,EAAE,oBAAoB;IAC3B,WAAW,EACT,uHAAuH;IACzH,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;SACjG;QACD;YACE,MAAM,EAAE,iBAAiB;YACzB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,0DAA0D;YAChE,QAAQ,EACN,6FAA6F;SAChG;KACO;IACV,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC;QACf,SAAS,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC,6CAA6C,CAAC;KACrF,CAAC;IACF,KAAK,CAAC,OAAO,CAAC,MAAM,EAAE,GAAG;QACvB,OAAO,MAAM,aAAa,CAAC,OAAO,CAChC,aAAa,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,SAAS,EAAE,MAAM,CAAC,SAAS,EAAE,CAAC,EAC1D,GAAG,CACJ,CAAC;IACJ,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE,EAAE;KACd,CAAC;CACH,CAAC,CAAC"}

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

@@ -71,6 +71,8 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
         envVar: z.ZodString;
         disabledSearchEndpoints: z.ZodArray<z.ZodString>;
         notes: z.ZodArray<z.ZodString>;
+        verifiedMappingCount: z.ZodOptional<z.ZodNumber>;
+        inferredMappingCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>;
     content: z.ZodObject<{
         crops: z.ZodArray<z.ZodString>;

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-dataframe-describe.tool.d.ts

@@ -36,7 +36,7 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
 }, z.core.$strip>, readonly [{
     readonly reason: "list_all_disabled_on_shared_http";
     readonly code: JsonRpcErrorCode.Forbidden;
-    readonly when: "Running under MCP_AUTH_MODE=none on HTTP transport — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
-    readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available.";
+    readonly when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
+    readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.";
 }]>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

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

@@ -51,14 +51,14 @@ const InputSchema = z.object({
         .describe('When set, return only the named dataframe. Omit to list all dataframes.'),
 });
 export const brapiDataframeDescribe = tool('brapi_dataframe_describe', {
-    description: 'Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writing the first brapi_dataframe_query. Listing without a name is gated under shared-tenant HTTP (`MCP_AUTH_MODE=none`); pass a known name instead.',
+    description: 'Start here after a spillover. Lists dataframes (or describes one) with columns, row counts, and originating-source provenance. The dataframe name appears inline on every find_* response that spilled (`result.dataframe.tableName`) — pass it as `dataframe` to inspect schema and provenance before writing the first brapi_dataframe_query. Listing without a name is unavailable when this server runs as a shared HTTP endpoint without per-caller auth; pass a known name instead.',
     annotations: { readOnlyHint: true, idempotentHint: true, openWorldHint: false },
     errors: [
         {
             reason: 'list_all_disabled_on_shared_http',
             code: JsonRpcErrorCode.Forbidden,
-            when: "Running under MCP_AUTH_MODE=none on HTTP transport — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.",
-            recovery: 'Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available.',
+            when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.",
+            recovery: 'Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.',
         },
     ],
     input: InputSchema,

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

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

@@ -68,6 +68,11 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     warnings: z.ZodArray<z.ZodString>;
     searchBody: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_genotype_calls.";
+}, {
     readonly reason: "no_filters";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "No variant set, germplasm, call set, or variant filter was provided";

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8HjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsNjC,CAAC"}
+{"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8HjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4NjC,CAAC"}

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

@@ -18,8 +18,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCanvasBridge, } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, asString, buildRequestOptions, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, toDataframeHandle, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRequestOptions, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
 const PAGE_SIZE = 10_000;
 const CallRowSchema = z
     .object({
@@ -110,6 +109,12 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
     description: 'Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` bounds the rows returned inline; the full collected set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_find_genotype_calls.',
+        },
         {
             reason: 'no_filters',
             code: JsonRpcErrorCode.ValidationError,
@@ -153,11 +158,10 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
         const bridge = getCanvasBridge();
-        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const connection = await requireRegisteredConnection(ctx, input.alias);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;