npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.4 → 0.4.6 - Mend

@cyanheads/brapi-mcp-server 0.4.4 → 0.4.6

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Files changed (91) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.4.4
+**Version:** 0.4.6
 **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.
@@ -12,7 +12,7 @@
 When the user asks what to do next, what's left, or needs direction, suggest relevant options based on the current project state:
-1. **Re-run the `setup` skill** — ensures CLAUDE.md, skills, structure, and metadata are populated and up to date with the current codebase
+1. **Re-run the `setup` skill** — ensures AGENTS.md, skills, structure, and metadata are populated and up to date with the current codebase
 2. **Run the `design-mcp-server` skill** — if the tool/resource surface hasn't been mapped yet, work through domain design
 3. **Add tools/resources/prompts** — scaffold new definitions using the `add-tool`, `add-app-tool`, `add-resource`, `add-prompt` skills
 4. **Add services** — scaffold domain service integrations using the `add-service` skill
@@ -284,7 +284,7 @@ src/
 Skills are modular instructions in `skills/` at the project root. Read them directly when a task matches — e.g., `skills/add-tool/SKILL.md` when adding a tool.
-**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
+**Agent skill directory:** Copy skills into the directory your agent discovers (Claude Code: `.claude/skills/`, Codex: `.codex/skills/`, shared: `.agents/skills/`, others: equivalent). This makes skills available as context without needing to reference `skills/` paths manually. After framework updates, run the `maintenance` skill — it re-syncs the agent directory automatically (Phase B).
 Available skills:
@@ -380,7 +380,7 @@ 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 (Claude Code → `structuredContent`, Claude Desktop → `content[]`); both must carry the same data
+- [ ] `format()` renders all data the LLM needs — different clients forward different surfaces (Codex → `structuredContent`, Codex 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/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-0.4.4-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-0.4.6-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)
@@ -70,7 +70,7 @@ Nineteen tools grouped by shape — connection tools bootstrap a session, `find_
 Session bootstrap. Authenticates to a BrAPI v2 server, registers the connection under a named alias, loads the capability profile via `CapabilityRegistry`, and inlines the full orientation envelope in the response. One call fully orients the agent.
 - `baseUrl` and `auth` are optional — when omitted they fall back to `BRAPI_<ALIAS>_*`, then `BRAPI_DEFAULT_*` env vars. Agents can call `brapi_connect({ alias: 'cassava' })` with nothing else and credentials never enter the LLM context (see [Per-alias credentials](#per-alias-credentials))
-- Tagged-union auth input: `none`, `sgn` (session-token exchange), `oauth2` (accepted at schema level, rejected at runtime pending client-credentials flow), `bearer`, `api_key`
+- Tagged-union auth input: `none`, `sgn` (session-token exchange), `oauth2` (client-credentials exchange), `bearer`, `api_key`
 - Multiple concurrent connections per session via distinct aliases
 - Forces a fresh capability load on every connect — the agent expects current state
 - Returns the same envelope as `brapi_server_info` — server identity, auth status, capability profile (supported/missing calls), content summary, server-specific notes
@@ -310,13 +310,16 @@ BrAPI-specific:
 - **Multi-server session** — `ServerRegistry` maps aliases to live BrAPI connections, so one agent session can span Breedbase, T3, and Sweetpotatobase in parallel
 - **Capability-aware calls** — `CapabilityRegistry` caches the `/serverinfo` profile per connection and guards every tool call against unsupported endpoints before they hit the wire
+- **Tolerant capability discovery** — if `/serverinfo` is unavailable or sparse, discovery falls back to `/calls` and returns a partial orientation envelope with explicit notes
+- **Find-route planning** — curated `find_*` tools prefer GET list endpoints, then fall back to POST `/search/{noun}` when only search is advertised
 - **Dataset spillover** — `find_*` tools cap in-context rows at `loadLimit` and transparently persist larger unions (up to 50k rows / 50 pages) as handles in `DatasetStore`; `brapi_manage_dataset` pages / projects / deletes them
 - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern without the agent needing to know
 - **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry or descendancy with cycle detection, depth limits, and traversal stats — BrAPI only exposes one generation per call
 - **Image content** — `brapi_get_image` fetches image bytes inline as MCP `type: image` blocks, preferring `/images/{id}/imagecontent` and falling back to the metadata `imageURL` field
 - **Free-text variable ranking** — `OntologyResolver` scores variable records against a query (PUI / name / synonym / trait-class) so `find_variables text:"..."` returns ranked candidates even when the server has no `/ontologies` endpoint
 - **Dynamic filter discovery** — static v2.1 filter catalog plus an `extraFilters` passthrough lets agents drive any server-specific filter without schema churn
-- **Auth variants in one schema** — tagged-union connection auth covers none / bearer / api-key / SGN session-token exchange in a single input shape
+- **Auth variants in one schema** — tagged-union connection auth covers none / bearer / api-key / SGN session-token exchange / OAuth2 client-credentials exchange in a single input shape
+- **Compatibility matrix** — live server probes are tracked in [docs/compatibility.md](./docs/compatibility.md)
 - **Typed error contracts** — every declared failure mode carries a stable `data.reason`, an HTTP-style `code`, and a `recovery.hint` mirrored onto the wire, so agent clients can route errors deterministically (e.g. `unknown_alias` → re-run `brapi_connect`, `dataset_not_found` → drop the stale handle)
 - **Last-resort escape hatches** — `brapi_raw_get` and `brapi_raw_search` pass through to any endpoint with routing nudges pointing at the curated tool when one exists
@@ -487,6 +490,12 @@ BRAPI_CASSAVA_PASSWORD=...
 BRAPI_PROD_BASE_URL=https://my-brapi.example.com/brapi/v2
 BRAPI_PROD_API_KEY=...
 BRAPI_PROD_API_KEY_HEADER=X-API-Key
+# Register an OAuth2 client-credentials server as alias 'secure'
+BRAPI_SECURE_BASE_URL=https://my-oauth-brapi.example.com/brapi/v2
+BRAPI_SECURE_OAUTH_CLIENT_ID=...
+BRAPI_SECURE_OAUTH_CLIENT_SECRET=...
+BRAPI_SECURE_OAUTH_TOKEN_URL=https://auth.example.com/oauth/token
 ```
 Then the agent calls `brapi_connect({ alias: 'cassava' })` — no `baseUrl`, no `auth`, no secrets in the prompt.

package/changelog/0.4.x/0.4.5.md ADDED Viewed

@@ -0,0 +1,25 @@
+---
+summary: "Compatibility upgrade: OAuth2 client credentials, tolerant capability fallback, route-planned find tools, and live server matrix."
+breaking: false
+---
+# 0.4.5 — 2026-05-01
+This release widens real-server compatibility without changing tool names or required inputs. The focus is making connection setup, capability discovery, and curated find tools adapt to what each BrAPI server actually advertises.
+## Added
+- **OAuth2 client-credentials auth** — `brapi_connect` now exchanges `mode: "oauth2"` credentials for an access token at connect time. Env-derived aliases support `BRAPI_<ALIAS>_OAUTH_CLIENT_ID`, `BRAPI_<ALIAS>_OAUTH_CLIENT_SECRET`, and optional `BRAPI_<ALIAS>_OAUTH_TOKEN_URL`.
+- **Find-route planner** — curated `find_*` tools now prefer advertised GET list endpoints and fall back to POST `/search/{noun}` when the server only advertises search.
+- **Dialect coverage** — added `breedbase` and `brapi-test` dialect ids. CassavaBase keeps the historical `cassavabase` id; sister SGN/Breedbase deployments now resolve to `breedbase`.
+- **Compatibility matrix** — `docs/compatibility.md` records live `/serverinfo` probes for BrAPI Test Server, CassavaBase, SweetpotatoBase, T3/Wheat, and FAIDARE/GnpIS.
+## Changed
+- **Capability discovery** now tolerates missing or malformed `/serverinfo` by falling back to `/calls`, returning a partial orientation envelope with explicit notes instead of failing the connection outright.
+- **Orientation envelopes** now surface dialect-level compatibility notes alongside disabled search routes.
+## Fixed
+- `oauth2` is no longer a schema-only auth variant that fails at runtime.
+- Curated find tools no longer fail solely because a server advertises only POST `/search/{noun}` for a supported resource.

package/changelog/0.4.x/0.4.6.md ADDED Viewed

@@ -0,0 +1,26 @@
+---
+summary: "BrAPI Test Server v2.0 dialect, shared singularizing engine, and typed all_filters_dropped guard across find_* tools."
+breaking: false
+---
+# 0.4.6 — 2026-05-01
+Real-server dialect work. The BrAPI Community Test Server advertises v2.1 but its GET list endpoints honor only the older v2.0 singular filter names — `studyDbIds` is silently ignored, `studyDbId` filters correctly. Two Issues surfaced from live probing: `find_observations` returned the unfiltered set when scoped by study, and `get_germplasm`'s studyCount probe returned the global studies total instead of the per-germplasm count. Both root in the same v2.0/v2.1 mismatch. This release adds a real `brapi-test` dialect, factors the SGN/Breedbase translation engine into a shared module, and wires a typed `all_filters_dropped` failure across the `find_*` surface so an upstream that drops every supplied scope filter no longer silently widens to the unfiltered baseline.
+## Added
+- **`brapi-test` dialect** — was a stub that passed filters through verbatim; now translates v2.1 plurals to v2.0 singulars on `/studies`, `/germplasm`, `/observations`, `/locations`, `/variables`, `/images`, `/variants`, `/trials`, `/programs`. Drops `searchText` on `/germplasm` and `observationLevel(s)` + `studyDbId(s)` on `/observations` (broken upstream in both forms — verified empirically). POST `/search/{noun}` routes are NOT marked disabled — the test server serves them correctly with v2.1 plurals, so multi-value queries can still escalate to `/search`.
+- **`createSingularizingDialect` factory** — `src/services/brapi-dialect/singularizing-dialect.ts`. Generic engine for dialects that translate plural BrAPI v2.1 filter names to v2.0 singulars, drop blacklisted keys, and downcast multi-value arrays to the first element with a loud warning. Used by both the SGN/Breedbase family and the BrAPI Community Test Server — the engine is shared, only the per-server data (mapping, drop list, disabled-search list, notes) lives in each dialect module.
+- **Typed `all_filters_dropped` error contract** — declared on every `find_*` tool (`brapi_find_germplasm`, `brapi_find_images`, `brapi_find_locations`, `brapi_find_observations`, `brapi_find_studies`, `brapi_find_variables`, `brapi_find_variants`). When the active dialect drops every agent-supplied scope filter, the tool now throws a `ValidationError` with `data.reason = 'all_filters_dropped'`, the dropped filter list, and a per-tool recovery hint listing the supported filter paths — instead of silently widening the query to the unfiltered baseline. Bare-baseline calls (no filters supplied) are exempt.
+## Changed
+- **CassavaBase dialect refactor** — the per-endpoint translation engine moved out of `cassavabase-dialect.ts` into the shared `singularizing-dialect.ts` factory. CassavaBase now supplies only its SGN-specific data (mapping, drop list, disabled-search list, notes) and delegates the engine. No behavior change for SGN-family servers; the same plural→singular translation, search-route gating, and warning text apply.
+- **`DialectAdaptation`** now carries a structured `dropped: readonly string[]` alongside `filters` and `warnings`. Lets callers detect "agent intended to scope, dialect couldn't honor any of it" without parsing warning strings.
+- **`get_germplasm` studyCount probe** routes through the dialect adapter so per-server key translation takes effect. Previously sent `germplasmDbIds` (plural) verbatim, which the BrAPI Test Server silently ignored — the probe returned the global studies total instead of the per-germplasm count. Now sends the dialect-translated key (`germplasmDbId` on the test server, the relevant v2.0 form on SGN-family servers) and skips the probe entirely with a warning when the dialect drops the filter.
+- **`applyDialectFiltersOrFail` helper** in `src/mcp-server/tools/shared/find-helpers.ts` consolidates the dialect-apply + all-dropped-throw block that was previously duplicated 13 lines per tool across all seven `find_*` tools. ~85 lines net removed.
+## Fixed
+- **`find_observations` on the BrAPI Test Server** — `studies: ['studyN']` no longer returns the unfiltered observation set. The dialect now drops `studyDbId(s)` entirely (broken in both GET singular and POST `/search` plural forms upstream — neither shape narrows the result set), surfaces a warning, and the typed `all_filters_dropped` guard prevents the query from running unfiltered when `studies` was the only filter supplied. Agents should scope by `germplasm`, `observationUnits`, or `variables` instead — all of which DO filter correctly on the test server.
+- **`get_germplasm` studyCount on the BrAPI Test Server** — was returning the global studies total because `/studies?germplasmDbIds=X` is silently ignored upstream; now sends `germplasmDbId=X` (singular) via the dialect adapter and the cross-check confirms the filtered count differs from the unfiltered baseline.

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

@@ -69,6 +69,7 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
         }>;
         envVar: z.ZodString;
         disabledSearchEndpoints: z.ZodArray<z.ZodString>;
+        notes: z.ZodArray<z.ZodString>;
     }, 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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0FvB,CAAC"}

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

@@ -7,6 +7,7 @@
  * @module mcp-server/tools/definitions/brapi-find-germplasm.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     alias: z.ZodOptional<z.ZodString>;
     names: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -68,5 +69,10 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, readonly [{
+    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.";
+    readonly recovery: "Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.";
+}]>;
 //# sourceMappingURL=brapi-find-germplasm.tool.d.ts.map

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;~~AA4IjD~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAqS7B~~,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;AA6IjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiT7B,CAAC"}

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

@@ -7,13 +7,14 @@
  * @module mcp-server/tools/definitions/brapi-find-germplasm.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -118,6 +119,14 @@ const SERVER_TO_USER = {
 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. Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'all_filters_dropped',
+            code: JsonRpcErrorCode.ValidationError,
+            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.',
+            recovery: 'Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.',
+        },
+    ],
     input: z.object({
         alias: AliasInput,
         names: z.array(z.string()).optional().describe('Filter by germplasm display names.'),
@@ -150,7 +159,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'germplasm', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -164,9 +173,17 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             genus: input.genus,
             species: input.species,
         }, input.extraFilters, warnings);
-        const filters = applyDialectFilters(dialect, 'germplasm', merged, warnings);
+        const filters = applyDialectFiltersOrFail(ctx, dialect, 'germplasm', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'germplasm',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/germplasm', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         // 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
@@ -188,6 +205,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             connection,
             path: '/germplasm',
             filters,
+            route,
             source: 'find_germplasm',
             loadLimit,
             ctx,
@@ -267,7 +285,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;

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

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

@@ -7,6 +7,7 @@
  * @module mcp-server/tools/definitions/brapi-find-images.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     alias: z.ZodOptional<z.ZodString>;
     images: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -61,5 +62,10 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, readonly [{
+    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.";
+    readonly recovery: "Drop the unsupported filters and rescope by images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — these filter paths are honored on the active dialect.";
+}]>;
 //# sourceMappingURL=brapi-find-images.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA2HjD~~,eAAO,MAAM,eAAe~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiO1B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA4HjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6O1B,CAAC"}

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

@@ -7,13 +7,14 @@
  * @module mcp-server/tools/definitions/brapi-find-images.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const ImageRowSchema = z
     .object({
     imageDbId: z.string().describe('Server-side identifier for the image.'),
@@ -105,6 +106,14 @@ const SERVER_TO_USER = {
 export const brapiFindImages = tool('brapi_find_images', {
     description: 'Filter images by observation unit, observation, study, descriptive ontology term, file name, or MIME type. Returns metadata only — use brapi_get_image to fetch bytes inline. Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'all_filters_dropped',
+            code: JsonRpcErrorCode.ValidationError,
+            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.',
+            recovery: 'Drop the unsupported filters and rescope by images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — these filter paths are honored on the active dialect.',
+        },
+    ],
     input: z.object({
         alias: AliasInput,
         images: z.array(z.string()).optional().describe('Filter by imageDbIds.'),
@@ -134,7 +143,7 @@ export const brapiFindImages = tool('brapi_find_images', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'images', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -146,15 +155,24 @@ export const brapiFindImages = tool('brapi_find_images', {
             mimeTypes: input.mimeTypes,
             descriptiveOntologyTerms: input.descriptiveOntologyTerms,
         }, input.extraFilters, warnings);
-        const filters = applyDialectFilters(dialect, 'images', merged, warnings);
+        const filters = applyDialectFiltersOrFail(ctx, dialect, 'images', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'images',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/images', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         const { fullRows, dataset: datasetMeta } = await maybeSpill({
             firstPage,
             client,
             connection,
             path: '/images',
             filters,
+            route,
             source: 'find_images',
             loadLimit,
             ctx,
@@ -206,7 +224,7 @@ export const brapiFindImages = tool('brapi_find_images', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
         if (refinementHint)
             result.refinementHint = refinementHint;

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

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

@@ -8,6 +8,7 @@
  * @module mcp-server/tools/definitions/brapi-find-locations.tool
  */
 import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     alias: z.ZodOptional<z.ZodString>;
     locations: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -64,5 +65,10 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
         spec: "spec";
         swapped: "swapped";
     }>;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, readonly [{
+    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.";
+    readonly recovery: "Drop the unsupported filters and rescope by locations, locationNames, countryCodes, locationTypes, abbreviations, or bbox — these filter paths are honored on the active dialect.";
+}]>;
 //# sourceMappingURL=brapi-find-locations.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AAqIjD~~,eAAO,MAAM,kBAAkB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiR7B~~,CAAC"}
1	+ {"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6R7B,CAAC"}

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

@@ -8,13 +8,14 @@
  * @module mcp-server/tools/definitions/brapi-find-locations.tool
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const LocationRowSchema = z
     .object({
     locationDbId: z.string().describe('Server-side identifier for the location.'),
@@ -104,6 +105,14 @@ const SERVER_TO_USER = {
 export const brapiFindLocations = tool('brapi_find_locations', {
     description: 'Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Optional bbox parameter restricts rows to a latitude/longitude window. When the spec-correct GeoJSON [lon, lat, alt] reading produces zero matches and at least one row carries a Point geometry, the bbox filter retries once with axes swapped (handles non-conformant servers that store [lat, lon, alt]) and surfaces a warning + `coordinateAxisOrder: "swapped"`. Returns a dataset handle when the upstream total exceeds loadLimit.',
     annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'all_filters_dropped',
+            code: JsonRpcErrorCode.ValidationError,
+            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.',
+            recovery: 'Drop the unsupported filters and rescope by locations, locationNames, countryCodes, locationTypes, abbreviations, or bbox — these filter paths are honored on the active dialect.',
+        },
+    ],
     input: z.object({
         alias: AliasInput,
         locations: z.array(z.string()).optional().describe('Filter by locationDbIds.'),
@@ -157,7 +166,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
-        await capabilities.ensure(connection.baseUrl, { service: 'locations', method: 'GET' }, ctx, capabilityLookup);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
         const merged = mergeFilters({
@@ -167,15 +176,24 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             locationTypes: input.locationTypes,
             abbreviations: input.abbreviations,
         }, input.extraFilters, warnings);
-        const filters = applyDialectFilters(dialect, 'locations', merged, warnings);
+        const filters = applyDialectFiltersOrFail(ctx, dialect, 'locations', merged, warnings);
+        const route = resolveFindRoute({
+            profile,
+            dialect,
+            endpoint: 'locations',
+            filters,
+            searchBody: merged,
+            warnings,
+        });
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/locations', filters, loadLimit, ctx);
+        const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
         const { fullRows, dataset: datasetMeta } = await maybeSpill({
             firstPage,
             client,
             connection,
             path: '/locations',
             filters,
+            route,
             source: 'find_locations',
             loadLimit,
             ctx,
@@ -249,7 +267,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             hasMore: firstPage.hasMore,
             distributions,
             warnings,
-            appliedFilters: filters,
+            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
             coordinateAxisOrder,
         };
         if (refinementHint)