@cyanheads/brapi-mcp-server 0.7.9 → 0.7.11

package/CLAUDE.md

@@ -1,8 +1,10 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.7.9
-**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
+**Version:** 0.7.11
+**Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.12.3`
+**Engines:** Bun ≥1.3.0, Node ≥24.0.0
+**MCP SDK:** `@modelcontextprotocol/server` ^2.0.0 (protocol revisions 2026-07-28 and 2025-*)
 
 > **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.
 
@@ -32,7 +34,7 @@ Tailor suggestions to what's actually missing or stale — don't recite the full
 - **Logic throws, framework catches.** Tool/resource handlers are pure — throw on failure, no `try/catch`. The framework catches, classifies, and formats. Default to typed contracts: declare `errors: [...]` and throw via `ctx.fail(reason, …)` so failures carry stable `data.reason` codes for agent-client routing. Fall back to error factories (`notFound()`, `validationError()`, etc.) only for services or when no contract entry fits.
 - **Use `ctx.log`** for request-scoped logging. No `console` calls.
 - **Use `ctx.state`** for tenant-scoped storage. Never access persistence directly.
-- **Check `ctx.elicit` / `ctx.sample`** for presence before calling.
+- **Need input the caller didn't supply?** `return ctx.requestInput(...)` and read `ctx.inputs` when the handler is re-entered. Never `await` for user input mid-handler.
 - **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.
 
@@ -161,14 +163,16 @@ Handlers receive a unified `ctx` object. Currently used surface:
 
 | Property | Description |
 |:---------|:------------|
-| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. |
+| `ctx.log` | Request-scoped logger — `.debug()`, `.info()`, `.notice()`, `.warning()`, `.error()`. Auto-correlates requestId, traceId, tenantId. Dual-sink: Pino **and** `notifications/message` to the client, so treat it as client-visible. |
 | `ctx.state` | Tenant-scoped KV — used by `ServerRegistry` (connection aliases), `CanvasBridge` (default canvas pointer + per-table provenance), and `CapabilityRegistry` (cached profiles). Spilled `find_*` rows live on the canvas (DuckDB), not in `ctx.state`. |
-| `ctx.sessionId` | Mcp-Session-Id (HTTP stateful/auto); `undefined` for stdio and stateless HTTP unless `exposeStatelessSessionId` is opted in. Composed into `ServerRegistry.connKey` and `CanvasBridge.defaultCanvasKey` when `BRAPI_SESSION_ISOLATION=true` (default), so concurrent HTTP sessions in the same tenant don't share connection state or canvas. Discovery / scoping key on top of tenant-keyed state — not an authorization principal. |
+| `ctx.sessionId` | Mcp-Session-Id (HTTP stateful/auto); `undefined` for stdio, stateless HTTP unless `exposeStatelessSessionId` is opted in, and every request on protocol revision 2026-07-28, which is session-less by design. Composed into `ServerRegistry.connKey` and `CanvasBridge.defaultCanvasKey` when `BRAPI_SESSION_ISOLATION=true` (default), so concurrent HTTP sessions in the same tenant don't share connection state or canvas. Discovery / scoping key on top of tenant-keyed state — not an authorization principal. |
 | `ctx.signal` | `AbortSignal` — threaded into every BrAPI HTTP call so client-side cancellation aborts the upstream request. |
 | `ctx.requestId` | Unique request ID — auto-attached to every `ctx.log` entry. |
 | `ctx.tenantId` | Tenant ID from JWT or `'default'` for stdio / HTTP+`auth=none` — outer scope on all `ctx.state` reads/writes. |
+| `ctx.requestInput` / `ctx.inputs` | Multi-round-trip input. `brapi_submit_observations` gates apply-mode writes on a `confirm` elicitation: it reads `ctx.inputs.view('confirm')`, returns `ctx.requestInput({ inputRequests: … })` when the answer is missing, and treats a declined, cancelled, or unparseable answer as terminal (`user_declined`). `force: true` skips the round. |
+| `ctx.enrich` | Success-path agent context. `brapi_dataframe_query` and `brapi_build_phenotype_matrix` disclose capped results with `ctx.enrich.truncated({ shown, cap, guidance })`. |
 
-`ctx.elicit` is used by `brapi_submit_observations` to gate apply-mode writes behind user confirmation (with explicit `force: true` as the bypass). `ctx.sample` and `ctx.progress` are not used yet — they'll show up when long-running workflows (pedigree traversal, genotype-call pulls) need progress reporting or LLM sampling. `ctx.fail(reason, …)` is the typed thrower keyed off declared `errors[]` contracts — used by 14 tools and 1 resource today. `ctx.recoveryFor(reason)` resolves the matching contract entry's recovery hint into `data.recovery.hint` so it surfaces on the wire.
+`ctx.fail(reason, …)` is the typed thrower keyed off declared `errors[]` contracts — used by 14 tools and 1 resource today. `ctx.recoveryFor(reason)` resolves the matching contract entry's recovery hint into `data.recovery.hint` so it surfaces on the wire. `ctx.content` is unused — no tool emits media blocks outside `brapi_get_image`, which returns image bytes through its own output schema.
 
 ---
 
@@ -257,7 +261,7 @@ src/
         brapi-build-phenotype-matrix.tool.ts  # Germplasm × trait matrix from studies; materialized as canvas dataframe
         brapi-germplasm-performance.tool.ts   # Per-variable aggregates (n, mean, median, sd) for a single germplasm
         brapi-export-genotype-matrix.tool.ts  # Genotype calls → germplasm × variant dataframe + VCF-lite / PLINK serialization
-        brapi-submit-observations.tool.ts # Two-phase observation write — preview / apply (POST + PUT) with elicit gate
+        brapi-submit-observations.tool.ts # Two-phase observation write — preview / apply (POST + PUT) behind a confirmation round trip
         brapi-raw-get.tool.ts             # Last-resort GET passthrough with routing nudge
         brapi-raw-search.tool.ts          # Last-resort POST /search passthrough with async polling
       shared/
@@ -317,6 +321,7 @@ Available skills:
 | `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 |
+| `techniques` | Catalog of response/data-shaping techniques — overflow handling, payload shaping, retrieval patterns |
 | `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. |
@@ -329,7 +334,7 @@ Available skills:
 | `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 |
+| `api-context` | Context interface, RequestContext, logger, state, multi-round-trip input |
 | `api-errors` | McpError, JsonRpcErrorCode, error patterns |
 | `api-mirror` | MirrorService: persistent SQLite-backed local mirror of a bulk upstream dataset with FTS5 — Tier 3 opt-in |
 | `api-services` | LLM, Speech, Graph services |
@@ -360,7 +365,7 @@ When you complete a skill's checklist, check the boxes and add a completion time
 | `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 bundle` | Build, pack, and clean a `.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` |
@@ -372,7 +377,7 @@ 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.
+`bun run bundle` produces a `.mcpb` extension bundle for one-click install in Claude Desktop. The pack step is followed by `scripts/clean-mcpb.ts`, which prunes dev dependencies (`mcpb clean`) and strips two classes of `node_modules/**` content that root-anchored `.mcpbignore` patterns cannot reach: dependency-shipped agent docs (`skills/`, `.claude/`, `.agents/`, `SKILL.md`) and platform-specific native bindings, which would otherwise lock the bundle to the platform it was packed on. The bundle therefore ships portable without the DuckDB native — `@duckdb/node-api` is loaded lazily, so canvas tools report an actionable install hint and every other tool works normally. MCPB is stdio-only — HTTP deployments are unaffected. To opt out, delete `manifest.json` and `.mcpbignore`; `lint:packaging` skips cleanly when `manifest.json` is absent.
 
 **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.
 
@@ -388,14 +393,14 @@ Each per-version file opens with YAML frontmatter:
 ---
 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
+security: false                          # optional — true ONLY for a source-code security fix, never a dependency CVE bump
 ---
 
 # 0.1.0 — YYYY-MM-DD
 ...
 ```
 
-`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`.
+`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 — set it only for a security fix in this server's *own source code*, never for a routine dependency or transitive CVE bump (record those under `## Dependencies`). 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.
 
@@ -425,7 +430,7 @@ import { getMyService } from '@/services/my-domain/my-service.js';
 - [ ] JSDoc `@fileoverview` + `@module` on every file
 - [ ] `ctx.log` for logging, `ctx.state` for storage — no `console`, no direct persistence access
 - [ ] Handlers throw on failure — error factories or plain `Error`, no try/catch
-- [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Codex → `structuredContent`, Codex Desktop → `content[]`); both must carry the same data
+- [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Claude Code → `structuredContent`, Claude Desktop → `content[]`); both must carry the same data
 - [ ] BrAPI tool: resolves connection via `ServerRegistry.get(ctx, alias ?? DEFAULT_ALIAS)` before touching the client
 - [ ] BrAPI tool: gates the call with `CapabilityRegistry.ensure(...)` — never fires against an endpoint the server didn't advertise
 - [ ] BrAPI tool: raw / domain / output schemas reviewed against real upstream sparsity (most `/germplasm` and `/studies` fields are optional in the wild)

package/Dockerfile

@@ -3,8 +3,16 @@
 #
 # This stage installs all dependencies (including dev), builds the TypeScript
 # source code into JavaScript, and prepares the production assets.
+#
+# Pinned to BUILDPLATFORM, not the target platform. `bun run build` emits
+# platform-independent JavaScript and only `dist/` is copied forward, so this
+# stage has no reason to run under emulation — and under QEMU it does not run
+# at all: Bun's JavaScriptCore aborts with a spurious MemoryExhaustion
+# assertion (~21 MB peak), so a cross-arch build of this stage fails outright
+# on an arm64 host. Building natively also removes emulation from the slowest
+# stage of a multi-arch build.
 # ==============================================================================
-FROM oven/bun:1.3.14 AS build
+FROM --platform=$BUILDPLATFORM oven/bun:1.4.0 AS build
 
 WORKDIR /usr/src/app
 
@@ -33,7 +41,7 @@ RUN bun run build
 # application. It uses a slim base image and only includes production
 # dependencies and build artifacts.
 # ==============================================================================
-FROM oven/bun:1.3.14-slim AS production
+FROM oven/bun:1.4.0-slim AS production
 
 WORKDIR /usr/src/app
 
@@ -54,8 +62,14 @@ COPY package.json bun.lock ./
 
 # Install only production dependencies, ignoring any lifecycle scripts (like 'prepare')
 # that are not needed in the final production image.
+# `--omit=peer` drops the framework's optional peer tiers (test runner, service
+# SDKs, parsers) that Bun would otherwise auto-install. Anything this server
+# actually imports belongs in its own `dependencies` — @duckdb/node-api among
+# them — so nothing needed at runtime is lost. The two `bun add` steps below
+# carry the same flag; without it, they re-resolve the graph and pull every
+# optional peer back in.
 RUN --mount=type=cache,target=/root/.bun/install/cache \
-    bun install --production --frozen-lockfile --ignore-scripts
+    bun install --production --omit=peer --frozen-lockfile --ignore-scripts
 
 # Conditionally install OpenTelemetry optional peer dependencies (Tier 3).
 # These are not bundled by default to keep the base image lean. Enable at build time
@@ -63,7 +77,7 @@ RUN --mount=type=cache,target=/root/.bun/install/cache \
 ARG OTEL_ENABLED=true
 RUN --mount=type=cache,target=/root/.bun/install/cache \
     if [ "$OTEL_ENABLED" = "true" ]; then \
-      bun add @hono/otel \
+      bun add --omit=dev --omit=peer --ignore-scripts @hono/otel \
         @opentelemetry/instrumentation-http \
         @opentelemetry/exporter-metrics-otlp-http \
         @opentelemetry/exporter-trace-otlp-http \
@@ -82,7 +96,7 @@ RUN --mount=type=cache,target=/root/.bun/install/cache \
 ARG CANVAS_ENABLED=true
 RUN --mount=type=cache,target=/root/.bun/install/cache \
     if [ "$CANVAS_ENABLED" = "true" ]; then \
-      bun add @duckdb/node-api; \
+      bun add --omit=dev --omit=peer @duckdb/node-api; \
     fi
 
 # Copy the compiled application code from the build stage

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-0.7.9-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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
+[![npm](https://img.shields.io/npm/v/@cyanheads/brapi-mcp-server?style=flat-square&logo=npm&logoColor=white)](https://www.npmjs.com/package/@cyanheads/brapi-mcp-server) [![Version](https://img.shields.io/badge/Version-0.7.11-blue.svg?style=flat-square)](./CHANGELOG.md) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^2.0.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/) [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^7.0.2-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.4.0-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
 
 </div>
 
@@ -66,7 +66,7 @@
 
 | Tool | Description |
 |:-----|:------------|
-| `brapi_submit_observations` | Two-phase observation write — `mode: preview` validates; `mode: apply` elicits confirmation, then fans POST + PUT in parallel. Additive only — no destructive deletion. |
+| `brapi_submit_observations` | Two-phase observation write — `mode: preview` validates; `mode: apply` asks the caller to confirm, then fans POST + PUT in parallel. Additive only — no destructive deletion. |
 
 ### Escape hatches
 
@@ -118,6 +118,8 @@ Within one (tenant, session), dataframes act as a self-cleaning shared notebook:
 
 **Default (isolated) shape.** Under `MCP_AUTH_MODE=none` + HTTP stateful (the default), each MCP session carves its own connection state and its own canvas. Two researchers connected to the same host don't see each other's `brapi_connect` aliases, exchanged SGN/OAuth tokens, or spilled `df_<uuid>` rows. Stdio always behaves as one session (single-process, no concurrency).
 
+**Clients on MCP revision 2026-07-28.** That revision is session-less on every transport — requests carry no `Mcp-Session-Id` — so `ctx.sessionId` is undefined and a client negotiating it falls back to the shared tenant workspace even under `MCP_SESSION_MODE=stateful`. Session isolation applies to 2025-era clients; deployments that need a hard boundary for 2026-era clients should carve tenants with `MCP_AUTH_MODE=jwt`/`oauth`.
+
 **Shared-workspace shape.** Set `BRAPI_SESSION_ISOLATION=false` for cross-session collaboration in one tenant — multiple MCP sessions then share connection state and one default canvas, the way pre-0.5.3 deployments behaved. Useful when planning, analysis, and writeup agents run as separate MCP clients but operate as one researcher on shared upstream credentials.
 
 **On privileged data.** The `df_<uuid>` name is a capability token within a canvas — not row-level access control. Anyone holding the name within the same (tenant, session) bucket can read its rows. Under default isolation, that bucket is one MCP session. Under `BRAPI_SESSION_ISOLATION=false`, the bucket widens to the whole tenant (all callers under `auth=none`, or one user's sessions under `jwt`/`oauth`). Treat dataframe names like authenticated share links — pass within the bucket, not externally. The 24h TTL caps blast radius; the provenance trail (originating tool, baseUrl, query) supports audit. Belt-and-braces: `brapi_dataframe_describe` requires an explicit `dataframe` name on shared-trust HTTP (no list-all enumeration), and `brapi_dataframe_query` rejects system-catalog reads (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*`) — so a caller without a known `df_<uuid>` name can't fish through either surface.
@@ -223,7 +225,7 @@ Every variable is optional.
 | `BRAPI_CANVAS_DROP_ENABLED` | Opt-in for `brapi_dataframe_drop` registration. Off by default; dataframes expire via TTL when left unmanaged. | `false` |
 | `BRAPI_EXPORT_DIR` | Directory for `brapi_dataframe_export` output files. Setting a path is the opt-in (no separate enable flag); unset leaves the tool out of `tools/list`. Stdio-only — the tool stays disabled under HTTP transport regardless of this value. Bridged to the framework's `CANVAS_EXPORT_PATH` automatically. | — |
 | `BRAPI_CANVAS_MAX_ROWS` / `BRAPI_CANVAS_QUERY_TIMEOUT_MS` | Per-query response row cap and wall-clock timeout for `brapi_dataframe_query`. | `10000` / `30000` |
-| `MCP_TRANSPORT_TYPE` / `MCP_HTTP_PORT` / `MCP_SESSION_MODE` | Transport (`stdio` \| `http`), HTTP port, session mode (`stateful` \| `stateless` \| `auto`). | `stdio` / `3010` / `auto` |
+| `MCP_TRANSPORT_TYPE` / `MCP_HTTP_PORT` / `MCP_SESSION_MODE` | Transport (`stdio` \| `http`), HTTP port, session mode (`stateful` \| `stateless` \| `auto`; `auto` resolves to stateful for HTTP). | `stdio` / `3010` / `stateful` |
 | `MCP_AUTH_MODE` / `MCP_LOG_LEVEL` / `STORAGE_PROVIDER_TYPE` / `OTEL_ENABLED` | Auth mode (`none` \| `jwt` \| `oauth`), log level, storage backend, OpenTelemetry. | `none` / `info` / `in-memory` / `false` |
 | `BRAPI_SESSION_ISOLATION` | When `true`, scope ServerRegistry connection state and the CanvasBridge default canvas to `ctx.sessionId` (HTTP stateful/auto). Concurrent callers under `MCP_AUTH_MODE=none` operate in isolated workspaces. Set `false` for the shared-workspace collaboration model. No effect on stdio. | `true` |
 
@@ -326,6 +328,7 @@ Defaults to HTTP transport, stateful session mode (engages the `mcp-session-id`
 - **Multi-user with institutional SSO.** `MCP_AUTH_MODE=jwt` (HS256, `MCP_AUTH_SECRET_KEY`) or `oauth` (JWKS, `OAUTH_ISSUER_URL` + `OAUTH_AUDIENCE`). Each user's `tid` claim carves a tenant — the outer scope. `BRAPI_SESSION_ISOLATION=true` (default) then sub-scopes inside each tenant for users running parallel sessions, and JWT/OAuth identity binding gives real session-hijack protection on top.
 - **One researcher, parallel agents.** If multiple agents (planner, analyst, writeup) connect as separate MCP clients but should share one workspace, set `BRAPI_SESSION_ISOLATION=false` and rely on shared trust. This is the shared-workspace shape.
 - **Stdio.** Always one session; isolation is moot. The flag has no effect.
+- **Clients on MCP revision 2026-07-28.** Session-less by protocol, so they land in the shared tenant workspace whatever `BRAPI_SESSION_ISOLATION` says. Only the per-user-credentials shape isolates them.
 
 **Belt-and-braces under shared trust.** Even with `BRAPI_SESSION_ISOLATION=false`, `brapi_dataframe_describe` requires an explicit `dataframe` name on HTTP (no list-all enumeration), and `brapi_dataframe_query` rejects system-catalog reads (`information_schema`, `pg_catalog`, `sqlite_master`, `duckdb_*`). The dataframe name is the capability token; possession proves it.
 

package/changelog/0.7.x/0.7.10.md

@@ -0,0 +1,12 @@
+---
+summary: "brapi_germplasm_performance and brapi_build_phenotype_matrix now pull per-study observations in bounded-concurrency batches sized by BRAPI_MAX_CONCURRENT_REQUESTS (default 4, previously inert) instead of serially; outcomes reassemble in input order, so matrix column/row order and each tool's failure behavior are unchanged."
+breaking: false
+security: false
+---
+
+# 0.7.10 — 2026-07-16
+
+## Changed
+
+- **`brapi_germplasm_performance` / `brapi_build_phenotype_matrix` per-study observation pull** — now fetches across studies in bounded-concurrency batches sized by `BRAPI_MAX_CONCURRENT_REQUESTS` (default 4) instead of one study at a time, so a multi-study pull no longer serializes each upstream request. Outcomes reassemble in input order, keeping matrix column/row layout deterministic; each tool keeps its failure policy — `brapi_germplasm_performance` warns and continues, `brapi_build_phenotype_matrix` fails fast. ([#48](https://github.com/cyanheads/brapi-mcp-server/issues/48))
+- **`BRAPI_MAX_CONCURRENT_REQUESTS`** — previously parsed but never consumed; now bounds the per-study observation fan-out (its first consumer). ([#48](https://github.com/cyanheads/brapi-mcp-server/issues/48))

package/changelog/0.7.x/0.7.11.md

@@ -0,0 +1,43 @@
+---
+summary: "Adopts @cyanheads/mcp-ts-core ^0.12.3 (MCP SDK v2): every HTTP endpoint serves protocol revision 2026-07-28 alongside the 2025 era, undeclared tool arguments are rejected instead of stripped, and brapi_submit_observations' apply-mode confirmation becomes a multi-round-trip input_required result."
+breaking: false
+security: false
+---
+
+# 0.7.11 — 2026-08-22
+
+The wire-level changes below arrive with the framework and apply across the whole tool surface; this server changes no contract of its own.
+
+## Added
+
+- **`brapi_dataframe_query` and `brapi_build_phenotype_matrix` disclose truncation** — `truncated` / `shown` / `cap` / `notice` in `structuredContent` and the `content[]` trailer. `dataframe_query`'s `cap` is the ceiling that actually bound, and the notice names which lever produced it (`preview` or `rowLimit`).
+
+## Changed
+
+- **Undeclared top-level tool arguments are rejected by name** instead of silently stripped, and every `inputSchema` advertises `additionalProperties: false`. A nested `z.object()` still strips.
+- **Advertised schemas are JSON Schema 2020-12**, and every `outputSchema` declares the error envelope — clients that validate `structuredContent` without checking `isError` stop rejecting error results.
+- **Protocol revision 2026-07-28 is served on every HTTP endpoint**, alongside the 2025 era.
+- **`brapi_submit_observations` `mode: apply` confirmation is a multi-round-trip `input_required` result.** A 2026-07-28 client re-invokes the tool with the answer; a 2025-era client is fulfilled through the SDK's legacy shim on its live session. `force: true` is unchanged.
+- **Per-session isolation does not apply to 2026-07-28 clients** — that revision is session-less, so `ctx.sessionId` is undefined and those callers share the tenant workspace whatever `BRAPI_SESSION_ISOLATION` says. `MCP_SESSION_MODE` stays pinned `stateful`; `.env.example` and the README env row now carry the reason.
+- **`ctx.log` lines also reach the client** as `notifications/message` at their RFC 5424 level — treat log text as client-visible.
+- **Docker** — Bun 1.4.0 in both stages, the build stage pinned to `$BUILDPLATFORM` (Bun's JavaScriptCore aborts under emulated amd64), and the production install omits the framework's optional peer tiers. `bundle` packs via `npx -y @anthropic-ai/mcpb`.
+
+## Removed
+
+- **`elicit_unavailable`** — apply mode no longer probes for client elicitation support, so the reason is gone from `brapi_submit_observations`' error contract. A declined, cancelled, or malformed answer returns `user_declined`.
+
+## Fixed
+
+- **Singleton `GET` 404s log at debug**, not as incidents — every caller catches them and reports an absent record. Upstream status now reads from the canonical `error.data.status`.
+
+## Dependencies
+
+- `@cyanheads/mcp-ts-core` ^0.10.14 → ^0.12.3
+- `@duckdb/node-api` ^1.5.4-r.1 → ^1.5.5-r.4
+- `@biomejs/biome` ^2.5.0 → ^2.5.9
+- `@types/node` ^26.1.1 → ^26.2.0
+- `tsc-alias` ^1.9.1 → ^1.9.2
+- `typescript` ^6.0.3 → ^7.0.2
+- `vitest` ^4.1.10 → ^4.1.11
+- `packageManager` bun@1.3.14 → bun@1.4.0
+- Skills and `scripts/` resynced from the framework.

package/changelog/template.md

@@ -4,10 +4,11 @@
 # 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. 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.
+# Required. One-line GitHub Release-style headline. 350 character cap — a
+# ceiling, not a target. Default short and scannable. Don't pad, don't stitch
+# unrelated changes with commas/semicolons into an inventory — pick the
+# headline, like a tag's theme line. Quotes required: unquoted YAML treats
+# `: ` inside the value as a key separator and fails GitHub's strict parser.
 summary: ""
 
 # Set `true` when consumers must change code to upgrade: API removals,
@@ -24,9 +25,10 @@ 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.
+# downstream servers. ADOPTION STEPS ONLY — new files to create, fields to
+# populate, one-time migration steps. Never a second rendering of the body:
+# if a body bullet already says it, name the bullet's symbol instead of
+# re-explaining. Omit the field entirely when there's nothing to say.
 # agent-notes: |
 #   <instructions for downstream maintenance agents>
 ---
@@ -41,17 +43,54 @@ security: false
   each bullet with the symbol or concept name in **bold** so they can skip
   what's irrelevant and zoom in on what's not.
 
-  Tone: terse, fact-dense, not verbose. Default to one sentence per bullet —
-  name the symbol, state what changed, stop. Use a second sentence only when
-  it carries weight. If a bullet feels long, it is.
-
-  Cut: mechanism walkthroughs (those belong in JSDoc, CLAUDE.md/AGENTS.md, or the
-  relevant skill), ceremonial framings ("This release introduces…",
-  backwards-compat paragraphs), file-by-file test enumerations, internal
-  implementation notes. Prefer code/symbol names over English re-explanations.
+  Tone: terse, fact-dense, not verbose. Bullet shape: **symbol** + what
+  changed + at most one consumer-facing caveat. One sentence by default, two
+  when the second carries weight — a bullet past ~40 words or three sentences
+  is wrong. The depth lives one hop away: the linked issue carries the why,
+  the commit diff carries the how. The changelog names what changed and what
+  a consumer does about it; a reader who wants mechanism opens the link.
+
+  Model length on THIS guide, never on the previous entry — entries modeled
+  on entries compound.
+
+  Cut (each has shipped as a wall of text; these are the cruft):
+  - History/justification narration — how the bug worked, why the old
+    behavior was wrong. One short clause at most; the issue carries the story.
+  - Design-rationale defense — "chosen over Y because…", "guarding the
+    getter is not enough…". That is the author arguing with a reviewer;
+    reviewers read the PR, not the changelog.
+  - Defensive unchanged-clauses — "X is unchanged", "byte-identical to
+    <prev>". Keep one only where its absence would cause a real misread,
+    as a short parenthetical.
+  - Edge-case inventories — marker lists, not-flagged lists, escape tables.
+    Tests and the issue carry those.
+  - Mechanism walkthroughs (JSDoc, CLAUDE.md/AGENTS.md, or the relevant
+    skill own those), ceremonial framings ("This release introduces…"),
+    backwards-compat paragraphs, file-by-file test enumerations. Prefer
+    code/symbol names over English re-explanations.
+
+  Verified ≠ included: the every-claim-verified-from-the-diff rule bounds
+  the TRUTH of what you write, never the AMOUNT.
+
+  Example — same fact, right size:
+
+    TOO LONG: **`fetchWithTimeout`'s `timeoutMs` bounds the whole exchange**
+    (#341). `fetch` resolves once headers arrive and the deadline was
+    cleared as the helper returned, so a peer that answered promptly and
+    then stalled the stream held the request open indefinitely. A 2xx
+    carrying a body now comes back as a passthrough wrapper that disarms
+    the deadline when the body closes, errors, or is cancelled; …
+    [+90 more words of mechanism and edge cases]
+
+    RIGHT: **`fetchWithTimeout`'s `timeoutMs` now bounds the whole
+    exchange, not just the headers** (#341). A stalled body aborts with
+    the same `Timeout` error; the returned `Response` is a wrapper, so
+    identity assertions (`toBe(response)`) no longer hold.
 
   Narrative intro: skip by default. Add one short sentence only when the
-  release theme genuinely needs framing the bullets can't carry.
+  release theme genuinely needs framing the bullets can't carry. When many
+  bullets share one upgrade consequence, state it ONCE — intro line or
+  agent-notes — never per bullet.
 
   Sections: Keep a Changelog order — Added, Changed, Deprecated, Removed,
   Fixed, Security. Include only sections with entries; delete the rest

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package/dist/config/builtin-aliases.js.map

@@ -1 +1 @@
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+{"version":3,"file":"builtin-aliases.js","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,MAAM,kBAAkB,GACtB,+IAA+I,CAAC;AAalJ;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,eAAe,GAAgC,MAAM,CAAC,MAAM,CAAC;IACxE,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,aAAa;QACpB,OAAO,EAAE,kCAAkC;QAC3C,QAAQ,EAAE,0BAA0B;QACpC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,SAAS;QACpB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,iBAAiB;QACxB,OAAO,EAAE,sCAAsC;QAC/C,QAAQ,EAAE,8BAA8B;QACxC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,aAAa;QACxB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,UAAU;QACjB,OAAO,EAAE,6CAA6C;QACtD,QAAQ,EAAE,qCAAqC;QAC/C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,OAAO;QAClB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,QAAQ;QACf,OAAO,EAAE,2CAA2C;QACpD,QAAQ,EAAE,mCAAmC;QAC7C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,KAAK;QAChB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,WAAW;QAClB,OAAO,EAAE,8CAA8C;QACvD,QAAQ,EAAE,sCAAsC;QAChD,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,QAAQ;QACnB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,oBAAoB;QAC3B,OAAO,EAAE,gCAAgC;QACzC,QAAQ,EAAE,wBAAwB;QAClC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,oBAAoB;QAC/B,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;QAC5B,MAAM,EAAE,IAAI;KACb,CAAC;CACH,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAE1D;;;GAGG;AACH,SAAS,eAAe,CAAC,GAAsB;IAC7C,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAC;IAClC,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,GAAG,EAAE,CAAC;IAC3B,MAAM,GAAG,GAAG,IAAI,GAAG,EAAU,CAAC;IAC9B,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QAC1C,IAAI,OAAO;YAAE,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,KAAa,EACb,GAAG,GAAsB,OAAO,CAAC,GAAG;IAEpC,MAAM,GAAG,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;IAChC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,OAAO;IAC9B,OAAO,eAAe,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,KAAK,GAAG,CAAC,CAAC;AAC9D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAChC,GAAG,GAAsB,OAAO,CAAC,GAAG;IAEpC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,IAAI,KAAK,CAAC;QAAE,OAAO,eAAe,CAAC;IAChD,OAAO,eAAe,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;AACvE,CAAC"}

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

@@ -9,9 +9,9 @@ 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, readonly [{
-    readonly reason: "unknown_alias";
+    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 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;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoBjE,eAAO,MAAM,kBAAkB;;;;;;;GA2B7B,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;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;GAepG,CAAC"}

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

@@ -11,9 +11,9 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiFiltersResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
     endpoint: z.ZodString;
 }, z.core.$strip>, undefined, readonly [{
-    readonly reason: "unknown_endpoint";
+    readonly reason: 'unknown_endpoint';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "No filter catalog is registered for the requested endpoint";
-    readonly recovery: `Pick a known endpoint (${string}) \u2014 listing brapi://filters returns one resource per supported endpoint.`;
+    readonly when: 'No filter catalog is registered for the requested endpoint';
+    readonly recovery: `Pick a known endpoint (${string}) — listing brapi://filters returns one resource per supported endpoint.`;
 }]>;
 //# sourceMappingURL=brapi-filters.resource.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-filters.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-filters.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAMjE,eAAO,MAAM,oBAAoB;;;;;;;GAkC/B,CAAC"}
+{"version":3,"file":"brapi-filters.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-filters.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAMjE,eAAO,MAAM,oBAAoB;;;qBAQnB,kBAAkB;;mBAEpB,4DAA4D;;GAwBtE,CAAC"}

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

@@ -10,14 +10,14 @@ 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 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 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 reason: 'germplasm_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no germplasm record for the requested DbId";
-    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+    readonly when: 'Upstream returned no germplasm record for the requested DbId';
+    readonly recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.';
 }]>;
 //# sourceMappingURL=brapi-germplasm.resource.d.ts.map

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;;;;;;;;;;;;GAkCjC,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;;;qBAQrB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;qBAGxF,qBAAqB;;mBAEvB,8DAA8D;uBAElE,mGAAmG;GAezG,CAAC"}

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

@@ -9,9 +9,9 @@ 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, readonly [{
-    readonly reason: "unknown_alias";
+    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 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;AAGH,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAGjE,eAAO,MAAM,uBAAuB;;;;;;;GA2BlC,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;;;qBAQtB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;GAepG,CAAC"}

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

@@ -10,14 +10,14 @@ 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 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 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 reason: 'study_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no study record for the requested DbId";
-    readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
+    readonly when: 'Upstream returned no study record for the requested DbId';
+    readonly recovery: 'Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.';
 }]>;
 //# sourceMappingURL=brapi-study.resource.d.ts.map

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;;;;;;;;;;;;GAkC7B,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;;;qBAQjB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;qBAGxF,iBAAiB;;mBAEnB,0DAA0D;uBAE9D,6FAA6F;GAenG,CAAC"}

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

@@ -17,14 +17,14 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiVariableResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
     observationVariableDbId: z.ZodString;
 }, z.core.$strip>, undefined, readonly [{
-    readonly reason: "unknown_alias";
+    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 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: "variable_not_found";
+    readonly reason: 'variable_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "Upstream returned no observation variable record for the requested DbId";
-    readonly recovery: "Verify the observationVariableDbId on the target server, or run brapi_find_variables to discover valid IDs.";
+    readonly when: 'Upstream returned no observation variable record for the requested DbId';
+    readonly recovery: 'Verify the observationVariableDbId on the target server, or run brapi_find_variables to discover valid IDs.';
 }]>;
 //# sourceMappingURL=brapi-variable.resource.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-variable.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-variable.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAQjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;GA8EhC,CAAC"}
+{"version":3,"file":"brapi-variable.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-variable.resource.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;GAaG;AAEH,OAAO,EAAY,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACrD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAQjE,eAAO,MAAM,qBAAqB;;;qBAQpB,eAAe;;mBAEjB,iDAAiD;uBAErD,8FAA8F;;qBAGxF,oBAAoB;;mBAEtB,yEAAyE;uBAE7E,6GAA6G;GA2DnH,CAAC"}