npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.3.6 → 0.3.8 - Mend

@cyanheads/brapi-mcp-server 0.3.6 → 0.3.8

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Files changed (68) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.3.6
+**Version:** 0.3.8
 **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.

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-0.3.6-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/)
+[![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-0.3.8-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)
@@ -54,7 +54,7 @@ Nineteen tools grouped by shape — connection tools bootstrap a session, `find_
 | Tool Name | Description |
 |:----------|:------------|
-| `brapi_submit_observations` | Submit new (POST) or updated (PUT) observation rows for a study. Default `mode: preview` validates only; `mode: apply` elicits confirmation, fans POST + PUT in parallel, and reports the post-write count. Additive — no observation is destroyed. |
+| `brapi_submit_observations` | Submit new (POST) or updated (PUT) observation rows for a study. Default `mode: preview` validates only; `mode: apply` elicits confirmation, fans POST + PUT in parallel, and reports the post-write count. Additive — no observation is destroyed. **Opt-in via `BRAPI_ENABLE_WRITES=true`** — omitted from `tools/list` otherwise. |
 ### Escape hatches
@@ -253,6 +253,8 @@ Last-resort passthrough to any BrAPI `POST /search/{noun}`. Handles the 202 / as
 Two-phase write for observation rows. Default `mode: preview` validates rows against the study's variables and returns a routing breakdown; `mode: apply` elicits user confirmation when the client supports it, then POSTs new rows and PUTs rows carrying `observationDbId` in parallel.
+> **Off by default.** Registered only when the operator sets `BRAPI_ENABLE_WRITES=true`; omitted from the surface otherwise. Operator-level deploy-time consent for the only mutation tool — the in-tool preview default, `ctx.elicit` confirmation, `force: true` bypass, and `brapi:write:observations` auth scope all continue to apply when registration is on.
 - POST/PUT routing keyed on per-row `observationDbId` presence — mixed batches in one call
 - Pre-flight pulls `/studies/{id}/observationvariables` to flag rows whose variable isn't exposed by the study (warning, not rejection — the upstream is the source of truth)
 - Apply mode requires `ctx.elicit` confirmation OR an explicit `force: true` flag (rejected with `Forbidden` otherwise)
@@ -443,6 +445,7 @@ Every variable is optional — agents can configure connections entirely at runt
 | `BRAPI_DATASET_STORE_DIR` | Filesystem path for `DatasetStore` payloads when filesystem storage is active. | — |
 | `BRAPI_REFERENCE_CACHE_TTL_SECONDS` | TTL for reference-data cache entries (programs, trials, locations, crops). | `3600` |
 | `BRAPI_ALLOW_PRIVATE_IPS` | Allow connecting to RFC 1918 / loopback targets. Dev-only. | `false` |
+| `BRAPI_ENABLE_WRITES` | Opt-in flag for the write surface (`brapi_submit_observations`). Off by default — the tool is omitted from `tools/list` unless the operator opts in for this deployment. | `false` |
 | `MCP_TRANSPORT_TYPE` | Transport: `stdio` or `http`. | `stdio` |
 | `MCP_HTTP_PORT` | Port for HTTP server. | `3010` |
 | `MCP_AUTH_MODE` | Auth mode: `none`, `jwt`, or `oauth`. | `none` |

package/changelog/0.3.x/0.3.7.md ADDED Viewed

@@ -0,0 +1,18 @@
+---
+summary: "Add `BRAPI_ENABLE_WRITES` env-var gate for the write surface — `brapi_submit_observations` is omitted from `tools/list` unless the operator opts in for the deployment. Mirrors obsidian-mcp-server's `OBSIDIAN_ENABLE_COMMANDS` pattern."
+breaking: false
+---
+# 0.3.7 — 2026-04-29
+A consent-layer release with no behavior change for opted-in deployments. The only mutation tool (`brapi_submit_observations`) is now gated behind an explicit deploy-time env flag, so a hosted instance never exposes writes unless the operator deliberately turns them on. The in-tool preview default, `ctx.elicit` confirmation, `force: true` bypass, and `brapi:write:observations` auth scope all continue to apply when the gate is open. Closes [#2](https://github.com/cyanheads/brapi-mcp-server/issues/2).
+## Added
+- **`BRAPI_ENABLE_WRITES` env var (default `false`)** — opt-in flag for the write surface. When unset or `false`, `brapi_submit_observations` is **not registered** on `createApp()` — it doesn't appear in `tools/list`, agents never see the description, the apply path is structurally unreachable. When `true`, it registers normally and existing in-tool gating layers stay in place. Surfaces as a configured env var on both `stdio` and `streamable-http` packages in `server.json` so the registry shows the flag to operators.
+- **`src/mcp-server/tools/definitions/index.ts`** — new barrel exporting `readOnlyToolDefinitions` (18 tools) and `writeToolDefinitions` (`[brapiSubmitObservations]`). Pure exports — no eager `getServerConfig()` call, so reflective tooling (lint script, future tests) can import the arrays without env-parsing side effects.
+- **`tests/registration-gate.test.ts`** — verifies `readOnlyToolDefinitions` excludes `brapi_submit_observations`, `writeToolDefinitions` contains exactly that tool, the env var parses to the right `enableWrites` value across stub variants, and the entry-point composition produces the expected tool list at both flag positions.
+## Changed
+- **`src/index.ts` registers tools via conditional spread** — `serverConfig.enableWrites ? [...readOnlyToolDefinitions, ...writeToolDefinitions] : readOnlyToolDefinitions`. All other call sites untouched. The 18 individual `import` lines for tools are gone — they live in the new barrel now.

package/changelog/0.3.x/0.3.8.md ADDED Viewed

@@ -0,0 +1,31 @@
+---
+summary: "Field-test fixes from real CassavaBase data — GeoJSON coordinates, `pageSize=0`→`pageSize=1` for v2.1-strict servers, variable text-match by dbId when PUI is sparse, pedigree leaf-count correctness — plus shared `find_*` rendering."
+breaking: false
+---
+# 0.3.8 — 2026-04-29
+A correctness pass shaken out by running the read surface against live BrAPI deployments (CassavaBase, BTI Cassava). Most fixes target single-server quirks that the v2.1 spec allows but our v0.3.x mocks didn't cover: GeoJSON-only coordinate carriers, sparse `observationVariablePUI`, and strict `pageSize` validation. The `find_*` tools also got a shared rendering layer — same data, more legible output, and a new warning when the upstream silently ignores a filter.
+## Added
+- **`renderFindHeader` helper (`src/mcp-server/tools/shared/find-helpers.ts`)** — standardized header for every `find_*` tool. When a dataset spillover is present, shows `{returned} returned · {dataset} in dataset · {total} total {noun}` so the middle number is no longer hidden when filters miss server-side and the dataset row count diverges from both. Falls back to `{returned} of {total}` when no spillover.
+- **`renderAppliedFilters` helper** — translates server-side filter keys (e.g. `commonCropNames`, `studyTypes`) to the user-facing tool param names (`crop`, `trialTypes`) when rendering the `Applied filters` block, so the agent can correlate what they typed with what got sent upstream. Server keys without a user alias (i.e. anything from `extraFilters`) render as-is.
+- **`checkFilterMatchRates` helper** — runs after distributions are computed and emits a warning when none of the requested filter values appear in the returned distribution. Detects upstreams that silently ignore an unsupported filter and return the unfiltered set instead of the requested subset. Wired into `find_studies`, `find_germplasm`, `find_locations`, `find_images`, `find_observations`, `find_variables`.
+- **`extractCoordinates` helper** — pulls WGS84 from a Location record, preferring the BrAPI v2 GeoJSON Feature shape (`coordinates.geometry.coordinates = [lon, lat, alt?]`) and falling back to legacy top-level `latitude`/`longitude`/`altitude`. Used by `find_locations` (rendering + bbox filter) and `get_study` (rendering).
+- **`buildRefinementHint` `availableFilters` option** — when no distribution has enough cardinality to surface a specific narrower (e.g. all distributions are empty or single-valued), falls back to listing the tool's available filter parameter names so the agent gets concrete next-step guidance. Wired across all spillover-capable `find_*` tools.
+- **`OntologyCandidate.observationVariableDbId`** — the resolver now carries the source row's server-side variable DbId on every candidate when present, so callers can map candidates back to their rows even when `observationVariablePUI` is missing.
+- **`Location.coordinates` on `reference-data-cache/types.ts`** — explicit type for the BrAPI v2 GeoJSON Feature carrier, alongside legacy `latitude`/`longitude`. Existing legacy fields gained a comment noting they're the legacy form.
+- **Tests** — `tests/tools/brapi-find-locations.tool.test.ts` covers GeoJSON-only coordinate extraction (CassavaBase real shape) and bbox honoring GeoJSON. `tests/tools/brapi-find-variables.tool.test.ts` covers free-text promotion by dbId when PUI is missing. `tests/tools/brapi-walk-pedigree.tool.test.ts` adds a case asserting unparented ancestors count as leaves and the root does not.
+## Changed
+- **All eight `find_*` tools wired through the shared helpers** — `find_studies`, `find_germplasm`, `find_locations`, `find_images`, `find_observations`, `find_variables`, `find_variants`, `find_genotype_calls` now use `renderFindHeader`, `renderAppliedFilters` (where applicable), and `buildRefinementHint`'s `availableFilters` option. Six of them also surface `checkFilterMatchRates` warnings.
+- **`brapi_get_image` format** — error and warning blocks now lead with a newline so they don't collapse into the previous block. Pure rendering tweak; structuredContent unchanged.
+## Fixed
+- **`pageSize=0` rejected by v2.1-strict servers** — BrAPI v2.1 mandates `pageSize >= 1`, and CassavaBase rejects `pageSize=0` with HTTP 400. The orientation envelope's opportunistic-count probes (`fetchOpportunisticCounts` in `src/mcp-server/tools/shared/orientation-envelope.ts`) now request `pageSize=1` and ignore the row — only `metadata.pagination.totalCount` matters. Docstrings on `brapi_get_study` and `brapi_submit_observations` updated to match.
+- **GeoJSON-only locations rendered as `lat=undefined`** — modern BrAPI v2 servers (CassavaBase, BTI Cassava) return location coordinates as a GeoJSON Feature in `coordinates.geometry.coordinates`, not as top-level `latitude`/`longitude`. `find_locations` (both formatting and the optional `bbox` filter) and `get_study` now extract from either shape via `extractCoordinates`. Also dual-rendered in `get_study` when the legacy fields are absent but the GeoJSON Feature is present.
+- **`find_variables` free-text promotion silently no-op'd against CassavaBase** — promotion was keyed off `observationVariablePUI`, which CassavaBase doesn't populate. The matcher now keys off `observationVariableDbId` (always present) with PUI as a fallback for any candidate that lacked the dbId. Free-text matches now actually surface to the top of the in-context set against real upstreams.
+- **`brapi_walk_pedigree` `leafCount` was off in both directions** — the previous implementation counted nodes with no outgoing edges in the walked direction, which mis-classified seed germplasm as leaves and missed unparented ancestors. `computeLeafCount` now takes the walk direction explicitly, walks `to`-end of the recorded edges (ancestor leaves are nodes nothing points to as a child; descendant leaves are mirror image), and excludes roots. Caller in `brapiWalkPedigree.handler` updated to pass `input.direction`.

package/dist/config/server-config.d.ts CHANGED Viewed

@@ -30,6 +30,10 @@ declare const ServerConfigSchema: z.ZodObject<{
         true: "true";
         false: "false";
     }>>, z.ZodTransform<boolean, "true" | "false">>;
+    enableWrites: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
+        true: "true";
+        false: "false";
+    }>>, z.ZodTransform<boolean, "true" | "false">>;
 }, z.core.$strip>;
 export type ServerConfig = z.infer<typeof ServerConfigSchema>;
 export declare function getServerConfig(): ServerConfig;

package/dist/config/server-config.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/config/server-config.js CHANGED Viewed

@@ -96,6 +96,11 @@ const ServerConfigSchema = z.object({
         .default('false')
         .transform((v) => v === 'true')
         .describe('Allow connecting to RFC 1918 / loopback targets. Dev-only.'),
+    enableWrites: z
+        .enum(['true', 'false'])
+        .default('false')
+        .transform((v) => v === 'true')
+        .describe('Opt-in flag for the write surface (`brapi_submit_observations`). Off by default — the tool is omitted from `tools/list` unless the operator opts in for this deployment.'),
 });
 let _config;
 export function getServerConfig() {
@@ -118,6 +123,7 @@ export function getServerConfig() {
         searchPollTimeoutMs: 'BRAPI_SEARCH_POLL_TIMEOUT_MS',
         searchPollIntervalMs: 'BRAPI_SEARCH_POLL_INTERVAL_MS',
         allowPrivateIps: 'BRAPI_ALLOW_PRIVATE_IPS',
+        enableWrites: 'BRAPI_ENABLE_WRITES',
     });
     return _config;
 }

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package/dist/index.js CHANGED Viewed

@@ -22,47 +22,13 @@ import { brapiFiltersResource } from './mcp-server/resources/definitions/brapi-f
 import { brapiGermplasmResource } from './mcp-server/resources/definitions/brapi-germplasm.resource.js';
 import { brapiServerInfoResource } from './mcp-server/resources/definitions/brapi-server-info.resource.js';
 import { brapiStudyResource } from './mcp-server/resources/definitions/brapi-study.resource.js';
-import { brapiConnect } from './mcp-server/tools/definitions/brapi-connect.tool.js';
-import { brapiDescribeFilters } from './mcp-server/tools/definitions/brapi-describe-filters.tool.js';
-import { brapiFindGenotypeCalls } from './mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js';
-import { brapiFindGermplasm } from './mcp-server/tools/definitions/brapi-find-germplasm.tool.js';
-import { brapiFindImages } from './mcp-server/tools/definitions/brapi-find-images.tool.js';
-import { brapiFindLocations } from './mcp-server/tools/definitions/brapi-find-locations.tool.js';
-import { brapiFindObservations } from './mcp-server/tools/definitions/brapi-find-observations.tool.js';
-import { brapiFindStudies } from './mcp-server/tools/definitions/brapi-find-studies.tool.js';
-import { brapiFindVariables } from './mcp-server/tools/definitions/brapi-find-variables.tool.js';
-import { brapiFindVariants } from './mcp-server/tools/definitions/brapi-find-variants.tool.js';
-import { brapiGetGermplasm } from './mcp-server/tools/definitions/brapi-get-germplasm.tool.js';
-import { brapiGetImage } from './mcp-server/tools/definitions/brapi-get-image.tool.js';
-import { brapiGetStudy } from './mcp-server/tools/definitions/brapi-get-study.tool.js';
-import { brapiManageDataset } from './mcp-server/tools/definitions/brapi-manage-dataset.tool.js';
-import { brapiRawGet } from './mcp-server/tools/definitions/brapi-raw-get.tool.js';
-import { brapiRawSearch } from './mcp-server/tools/definitions/brapi-raw-search.tool.js';
-import { brapiServerInfo } from './mcp-server/tools/definitions/brapi-server-info.tool.js';
-import { brapiSubmitObservations } from './mcp-server/tools/definitions/brapi-submit-observations.tool.js';
-import { brapiWalkPedigree } from './mcp-server/tools/definitions/brapi-walk-pedigree.tool.js';
+import { readOnlyToolDefinitions, writeToolDefinitions, } from './mcp-server/tools/definitions/index.js';
+const serverConfig = getServerConfig();
+const tools = serverConfig.enableWrites
+    ? [...readOnlyToolDefinitions, ...writeToolDefinitions]
+    : readOnlyToolDefinitions;
 await createApp({
-    tools: [
-        brapiConnect,
-        brapiServerInfo,
-        brapiDescribeFilters,
-        brapiFindStudies,
-        brapiGetStudy,
-        brapiFindGermplasm,
-        brapiGetGermplasm,
-        brapiWalkPedigree,
-        brapiFindVariables,
-        brapiFindObservations,
-        brapiFindImages,
-        brapiGetImage,
-        brapiFindLocations,
-        brapiFindVariants,
-        brapiFindGenotypeCalls,
-        brapiManageDataset,
-        brapiSubmitObservations,
-        brapiRawGet,
-        brapiRawSearch,
-    ],
+    tools,
     resources: [
         brapiServerInfoResource,
         brapiCallsResource,
@@ -73,7 +39,6 @@ await createApp({
     ],
     prompts: [brapiEdaStudy, brapiMetaAnalysis],
     setup() {
-        const serverConfig = getServerConfig();
         initBrapiClient(serverConfig);
         initCapabilityRegistry(serverConfig);
         initReferenceDataCache(serverConfig);

package/dist/index.js.map CHANGED Viewed

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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;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAyHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA+LjC,CAAC"}

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

@@ -13,7 +13,7 @@ import { getBrapiClient } from '../../../services/brapi-client/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, toDatasetHandle, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRequestOptions, 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;
@@ -217,7 +217,14 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
     },
     format: (result) => {
         const lines = [];
-        lines.push(`# ${result.returnedCount} of ${result.totalCount} calls — \`${result.alias}\`${result.truncated ? ' (truncated at maxCalls)' : ''}`);
+        const headerBase = renderFindHeader({
+            noun: 'calls',
+            alias: result.alias,
+            returnedCount: result.returnedCount,
+            totalCount: result.totalCount,
+            dataset: result.dataset,
+        });
+        lines.push(result.truncated ? `${headerBase} (truncated at maxCalls)` : headerBase);
         lines.push('');
         lines.push(`Search body: \`${JSON.stringify(result.searchBody)}\``);
         lines.push('');

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

	@@ -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;AA+~~GjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BA4L7B~~,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;AA+HjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA4O7B,CAAC"}

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

@@ -12,7 +12,7 @@ import { getBrapiClient } from '../../../services/brapi-client/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, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -93,6 +93,18 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+const SERVER_TO_USER = {
+    germplasmNames: 'names',
+    germplasmDbIds: 'germplasmDbIds',
+    germplasmPUIs: 'germplasmPUIs',
+    accessionNumbers: 'accessionNumbers',
+    commonCropNames: 'crops',
+    synonyms: 'synonyms',
+    collections: 'collections',
+    genus: 'genus',
+    species: 'species',
+    searchText: 'text',
+};
 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 },
@@ -159,8 +171,47 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             collection: computeDistribution(fullRows, (r) => asString(r.collection)),
             countryOfOriginCode: computeDistribution(fullRows, (r) => asString(r.countryOfOriginCode)),
         };
+        checkFilterMatchRates(warnings, fullRows.length, [
+            {
+                paramName: 'crops',
+                requestedValues: input.crops,
+                distribution: distributions.commonCropName,
+                caseInsensitive: true,
+            },
+            {
+                paramName: 'genus',
+                requestedValues: input.genus !== undefined ? [input.genus] : undefined,
+                distribution: distributions.genus,
+                caseInsensitive: true,
+            },
+            {
+                paramName: 'species',
+                requestedValues: input.species !== undefined ? [input.species] : undefined,
+                distribution: distributions.species,
+                caseInsensitive: true,
+            },
+            {
+                paramName: 'collections',
+                requestedValues: input.collections,
+                distribution: distributions.collection,
+                caseInsensitive: true,
+            },
+        ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
-        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
+        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
+            availableFilters: [
+                'names',
+                'germplasmDbIds',
+                'germplasmPUIs',
+                'accessionNumbers',
+                'crops',
+                'synonyms',
+                'collections',
+                'genus',
+                'species',
+                'text',
+            ],
+        });
         // Heuristic: if the user asked for a text filter and the upstream returned
         // every row that matches all the *other* filters (i.e. the text didn't
         // narrow anything), the server probably doesn't honor the filter.
@@ -189,7 +240,13 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
     },
     format: (result) => {
         const lines = [];
-        lines.push(`# ${result.returnedCount} of ${result.totalCount} germplasm — \`${result.alias}\``);
+        lines.push(renderFindHeader({
+            noun: 'germplasm',
+            alias: result.alias,
+            returnedCount: result.returnedCount,
+            totalCount: result.totalCount,
+            dataset: result.dataset,
+        }));
         lines.push('');
         if (result.hasMore) {
             lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
@@ -199,7 +256,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push(`**Refinement hint:** ${result.refinementHint}`);
             lines.push('');
         }
-        lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
+        lines.push(renderAppliedFilters(result.appliedFilters, SERVER_TO_USER));
         lines.push('');
         lines.push('## Distributions');
         lines.push(renderDistributions(result.distributions) || '_No values to summarize._');

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;~~AAiGjD~~,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAuK1B~~,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;AA8GjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAuM1B,CAAC"}

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

@@ -12,7 +12,7 @@ import { getBrapiClient } from '../../../services/brapi-client/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, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
+import { AliasInput, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const ImageRowSchema = z
     .object({
     imageDbId: z.string().describe('Server-side identifier for the image.'),
@@ -83,6 +83,15 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+const SERVER_TO_USER = {
+    imageDbIds: 'images',
+    observationUnitDbIds: 'observationUnits',
+    observationDbIds: 'observations',
+    studyDbIds: 'studies',
+    imageFileNames: 'imageFileNames',
+    mimeTypes: 'mimeTypes',
+    descriptiveOntologyTerms: 'descriptiveOntologyTerms',
+};
 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 },
@@ -150,8 +159,31 @@ export const brapiFindImages = tool('brapi_find_images', {
                 return terms.filter((t) => typeof t === 'string' && t.length > 0);
             }),
         };
+        checkFilterMatchRates(warnings, fullRows.length, [
+            {
+                paramName: 'mimeTypes',
+                requestedValues: input.mimeTypes,
+                distribution: distributions.mimeType,
+                caseInsensitive: true,
+            },
+            {
+                paramName: 'descriptiveOntologyTerms',
+                requestedValues: input.descriptiveOntologyTerms,
+                distribution: distributions.descriptiveOntologyTerms,
+            },
+        ]);
         const totalCount = firstPage.totalCount ?? firstPage.rows.length;
-        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
+        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
+            availableFilters: [
+                'images',
+                'observationUnits',
+                'observations',
+                'studies',
+                'imageFileNames',
+                'mimeTypes',
+                'descriptiveOntologyTerms',
+            ],
+        });
         const result = {
             alias: connection.alias,
             results: firstPage.rows,
@@ -170,7 +202,13 @@ export const brapiFindImages = tool('brapi_find_images', {
     },
     format: (result) => {
         const lines = [];
-        lines.push(`# ${result.returnedCount} of ${result.totalCount} images — \`${result.alias}\``);
+        lines.push(renderFindHeader({
+            noun: 'images',
+            alias: result.alias,
+            returnedCount: result.returnedCount,
+            totalCount: result.totalCount,
+            dataset: result.dataset,
+        }));
         lines.push('');
         if (result.hasMore) {
             lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
@@ -180,7 +218,7 @@ export const brapiFindImages = tool('brapi_find_images', {
             lines.push(`**Refinement hint:** ${result.refinementHint}`);
             lines.push('');
         }
-        lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
+        lines.push(renderAppliedFilters(result.appliedFilters, SERVER_TO_USER));
         lines.push('');
         lines.push('## Distributions');
         lines.push(renderDistributions(result.distributions) || '_No values to summarize._');