npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.3 → 0.4.5 - Mend

@cyanheads/brapi-mcp-server 0.4.3 → 0.4.5

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Files changed (88) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.4.3
+**Version:** 0.4.5
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core)
 > **Read the framework docs first:** `node_modules/@cyanheads/mcp-ts-core/CLAUDE.md` contains the full API reference — builders, Context, error codes, exports, patterns. This file covers server-specific conventions only.
@@ -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-0.4.3-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-0.4.5-blue.svg?style=flat-square)](./CHANGELOG.md) [![Framework](https://img.shields.io/badge/Built%20on-@cyanheads/mcp--ts--core-259?style=flat-square)](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) [![MCP SDK](https://img.shields.io/badge/MCP%20SDK-^1.29.0-green.svg?style=flat-square)](https://modelcontextprotocol.io/)
 [![License](https://img.shields.io/badge/License-Apache%202.0-orange.svg?style=flat-square)](./LICENSE) [![TypeScript](https://img.shields.io/badge/TypeScript-^6.0.3-3178C6.svg?style=flat-square)](https://www.typescriptlang.org/) [![Bun](https://img.shields.io/badge/Bun-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
@@ -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/0.4.4.md ADDED Viewed

@@ -0,0 +1,22 @@
+---
+summary: "format() / structuredContent parity — every find_* and get_* tool now emits passthrough fields so text-only clients see the full upstream payload."
+breaking: false
+---
+# 0.4.4 — 2026-04-30
+Cross-client parity fix for the `format()` rendering path. Different MCP clients consume different surfaces — Claude Code reads `structuredContent`, Claude Desktop reads `content[]` text blocks — and the agent-protocol checklist requires both to carry the same data. Until now, every `find_*` and `get_*` tool curated a hand-picked bullet list in `format()`, so any field the schema declared but the bullet list omitted (and any field the upstream returned beyond the schema) was visible to Claude Code but invisible to Claude Desktop. This release closes that gap with two new shared helpers and updates all eleven affected tools to use them.
+## Added
+- **`collectPassthroughParts(row, renderedKeys)` and `appendPassthroughLines(lines, record, renderedKeys)`** in `src/mcp-server/tools/shared/find-helpers.ts`. The former returns `key=value` strings for the bullet-list `find_*` layout; the latter appends `- **key:** value` lines for the line-per-field `get_*` layout. Each helper iterates the record's top-level keys, skips keys already rendered by the curated formatter, and stringifies object values via `JSON.stringify`. Reusable across any future tool that exposes a schema-typed envelope to text-only clients.
+## Fixed
+- **`brapi_find_studies`, `brapi_find_germplasm`, `brapi_find_observations`, `brapi_find_images`, `brapi_find_locations`, `brapi_find_variables`, `brapi_find_variants`, `brapi_find_genotype_calls`** — every list-shaped `find_*` `format()` now ends each row with `collectPassthroughParts`, so any field the upstream returns beyond the curated bullet set is preserved in the `content[]` text block instead of being silently dropped on text-only clients.
+- **`brapi_get_study`, `brapi_get_germplasm`, `brapi_get_image`** — the detail-view `get_*` formatters now call `appendPassthroughLines` after the curated header lines, surfacing every top-level field the upstream returned. `brapi_get_study.renderKeyValues` also stringifies non-array object values instead of skipping them.
+- **Nested-object renderings collapsed to inline JSON** where the curated key-by-key extraction was lossy: `germplasmOrigin` (was `${.length} record(s)`), `find_variables.trait` / `scale` / `method` (was a fan-out of seven optional sub-fields), and `find_genotype_calls.genotype` (was `values.join('|')`). Inline JSON keeps the full object visible without per-tool key fanout.
+## Changed
+- **`find_locations` `coordinates` is intentionally excluded from the rendered set** so the passthrough helper renders the full GeoJSON object alongside the extracted lat/lon. Other rendered sets enumerate exactly the keys the curated formatter handles, so the passthrough helper's set difference produces the right surface.

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/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-genotype-calls.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AA0HjE~~,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GA+MjC~~,CAAC"}
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;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA2HjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0NjC,CAAC"}

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

@@ -14,7 +14,7 @@ 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, asString, buildRequestOptions, computeDistribution, DatasetHandleSchema, renderDatasetHandle, renderDistributions, renderFindHeader, toDatasetHandle, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRequestOptions, collectPassthroughParts, computeDistribution, DatasetHandleSchema, renderDatasetHandle, renderDistributions, renderFindHeader, toDatasetHandle, } from '../shared/find-helpers.js';
 const DEFAULT_MAX_CALLS = 100_000;
 const HARD_MAX_CALLS = 500_000;
 const PAGE_SIZE = 10_000;
@@ -254,6 +254,16 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             lines.push('_No calls returned._');
         }
         else {
+            const RENDERED = new Set([
+                'callSetName',
+                'callSetDbId',
+                'variantName',
+                'variantDbId',
+                'variantSetDbId',
+                'genotype',
+                'genotypeValue',
+                'phaseSet',
+            ]);
             for (const call of result.results) {
                 const parts = [];
                 parts.push(`**${call.callSetName ?? call.callSetDbId ?? '?'}**`);
@@ -264,12 +274,13 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
                     parts.push(`variantDbId=${call.variantDbId}`);
                 if (call.variantSetDbId)
                     parts.push(`set=${call.variantSetDbId}`);
-                if (call.genotype?.values?.length)
-                    parts.push(`genotype=${call.genotype.values.join('|')}`);
+                if (call.genotype)
+                    parts.push(`genotype=${JSON.stringify(call.genotype)}`);
                 if (call.genotypeValue)
                     parts.push(`genotypeValue=${call.genotypeValue}`);
                 if (call.phaseSet)
                     parts.push(`phaseSet=${call.phaseSet}`);
+                parts.push(...collectPassthroughParts(call, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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.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;~~AA2IjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAiR7B~~,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;AA6IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAwS7B,CAAC"}

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

@@ -13,7 +13,7 @@ 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, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, 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.'),
@@ -150,7 +150,7 @@ 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({
@@ -165,8 +165,16 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             species: input.species,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(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 +196,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             connection,
             path: '/germplasm',
             filters,
+            route,
             source: 'find_germplasm',
             loadLimit,
             ctx,
@@ -267,7 +276,7 @@ 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;
@@ -303,6 +312,25 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'germplasmName',
+                'defaultDisplayName',
+                'germplasmDbId',
+                'germplasmPUI',
+                'accessionNumber',
+                'commonCropName',
+                'genus',
+                'species',
+                'subtaxa',
+                'countryOfOriginCode',
+                'collection',
+                'instituteCode',
+                'instituteName',
+                'germplasmOrigin',
+                'biologicalStatusOfAccessionDescription',
+                'pedigree',
+                'synonyms',
+            ]);
             for (const g of result.results) {
                 const parts = [
                     `**${g.germplasmName ?? g.defaultDisplayName ?? g.germplasmDbId}**`,
@@ -329,7 +357,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                 if (g.instituteName)
                     parts.push(`instituteName=${g.instituteName}`);
                 if (g.germplasmOrigin?.length)
-                    parts.push(`germplasmOrigin=${g.germplasmOrigin.length} record(s)`);
+                    parts.push(`germplasmOrigin=${JSON.stringify(g.germplasmOrigin)}`);
                 if (g.biologicalStatusOfAccessionDescription)
                     parts.push(`status=${g.biologicalStatusOfAccessionDescription}`);
                 if (g.pedigree)
@@ -342,6 +370,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                         .join(',');
                     parts.push(`synonyms=${synStr}`);
                 }
+                parts.push(...collectPassthroughParts(g, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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.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;~~AA0HjD~~,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BA6M1B~~,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;AA4HjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAoO1B,CAAC"}

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

@@ -13,7 +13,7 @@ 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, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, 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.'),
@@ -134,7 +134,7 @@ 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({
@@ -147,14 +147,23 @@ export const brapiFindImages = tool('brapi_find_images', {
             descriptiveOntologyTerms: input.descriptiveOntologyTerms,
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(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 +215,7 @@ 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;
@@ -242,6 +251,25 @@ export const brapiFindImages = tool('brapi_find_images', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'imageName',
+                'imageFileName',
+                'imageDbId',
+                'mimeType',
+                'imageWidth',
+                'imageHeight',
+                'imageFileSize',
+                'observationUnitName',
+                'observationUnitDbId',
+                'observationDbIds',
+                'studyName',
+                'studyDbId',
+                'descriptiveOntologyTerms',
+                'imageTimeStamp',
+                'imageURL',
+                'copyright',
+                'description',
+            ]);
             for (const img of result.results) {
                 const parts = [`**${img.imageName ?? img.imageFileName ?? img.imageDbId}**`];
                 parts.push(`id=\`${img.imageDbId}\``);
@@ -275,6 +303,7 @@ export const brapiFindImages = tool('brapi_find_images', {
                     parts.push(`©${img.copyright}`);
                 if (img.description)
                     parts.push(`desc=${img.description}`);
+                parts.push(...collectPassthroughParts(img, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

	@@ -1 +1 @@
1	- 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