npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.5.5 → 0.6.0 - Mend

@cyanheads/brapi-mcp-server 0.5.5 → 0.6.0

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Files changed (134) hide show

package/README.md CHANGED Viewed

@@ -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-0.5.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
+[![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/0.6.x/0.6.0.md ADDED Viewed

@@ -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/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-calls.resource.js CHANGED Viewed

@@ -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);
     },

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-germplasm.resource.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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"}

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

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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"}

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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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,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 CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyFvB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts CHANGED Viewed

@@ -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 CHANGED Viewed

@@ -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 CHANGED Viewed

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

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
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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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4NjC,CAAC"}

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

@@ -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;

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

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

@@ -69,6 +69,11 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: 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_germplasm.";
+}, {
     readonly reason: "all_filters_dropped";
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA+IjE~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsT7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgJjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiU7B,CAAC"}

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

@@ -13,8 +13,7 @@ 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, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -120,6 +119,12 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
     description: 'Find germplasm by name, synonym, accession number, PUI, crop, or free-text query. Matches across registered synonyms. When the upstream total exceeds loadLimit, the full result 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_germplasm.',
+        },
         {
             reason: 'all_filters_dropped',
             code: JsonRpcErrorCode.ValidationError,
@@ -150,12 +155,11 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
     }),
     output: OutputSchema,
     async handler(input, ctx) {
-        const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
         const bridge = getCanvasBridge();
         const config = getServerConfig();
-        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;
@@ -173,7 +177,8 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             genus: input.genus,
             species: input.species,
         }, input.extraFilters, warnings);
-        const filters = applyDialectFiltersOrFail(ctx, dialect, 'germplasm', merged, warnings);
+        const adapted = applyDialectFiltersOrFail(ctx, dialect, 'germplasm', merged, warnings);
+        const filters = adapted.filters;
         const route = resolveFindRoute({
             profile,
             dialect,
@@ -181,9 +186,11 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             filters,
             searchBody: merged,
             warnings,
+            ...(adapted.requiresEscalation ? { requiresEscalation: true } : {}),
         });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
+        const normalizeRow = dialectRowMapper(dialect, 'germplasm');
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx, normalizeRow ? { normalizeRow } : {});
         // Free-text matching is client-side. No BrAPI server reliably honors a
         // free-text query parameter on /germplasm — earlier versions of this tool
         // sent `searchText`, which CassavaBase and the Test Server both silently
@@ -215,6 +222,8 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             // the cleaned shape consistently.
             rowMapper: dedupSynonymsByIdentity,
         };
+        if (normalizeRow)
+            spillInput.normalizeRow = normalizeRow;
         if (text)
             spillInput.rowFilter = (row) => rowMatchesText(row, text);
         const { fullRows, dataframe } = await maybeSpill(spillInput);