@cyanheads/brapi-mcp-server 0.4.7 → 0.4.8

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.4.7
+**Version:** 0.4.8
 **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

@@ -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-0.4.7-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-0.4.8-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)
 

package/changelog/0.4.x/0.4.8.md

@@ -0,0 +1,30 @@
+---
+summary: "Generalize the /observations preflight from germplasm-only to any unanchored query, and make the probe fail-soft via companion call options so a stalled count surfaces as a warning instead of a hard error."
+breaking: false
+---
+
+# 0.4.8 — 2026-05-01
+
+The v0.4.6 / v0.4.7 fixes routed the right *singular* filters to CassavaBase. v0.4.8 closes the remaining hole on the matching tool: even with the right filter names on the wire, an unanchored `/observations` query still triggers a full join and stalls past the timeout. v0.4.7's preflight only covered the germplasm-only shape; field-testing surfaced the same blow-up on variable-only and bare-query shapes (verified with `curl --max-time 60` against `cassavabase.org/brapi/v2`: `?observationVariableDbId=…` and bare `/observations` both never respond). On top of that, the preflight itself ran on the global retry budget — when the count probe stalled, the agent waited the full 4 × 30 s before getting any signal back.
+
+This release generalizes the preflight to **every unanchored shape** (no `studies` / `trials` / `observationUnits` / `observations` scope), routes the probe through `companionRequestOptions` (8 s timeout, 0 retries), and treats probe failure as a soft skip — the agent gets a single "narrow your query" warning instead of a 2-minute hang or a propagated error.
+
+## Added
+
+- **`probeObservationCount(...)`** in `brapi-find-observations.tool.ts` — pulls a 1-row sample on `/observations` with companion-call shape (short timeout, zero retries) so a stalled upstream count operation surfaces as `null` instead of throwing. The handler converts that to a "preflight count probe stalled" warning and skips the bulk pull entirely.
+- **Three new specs** on `brapi_find_observations`:
+  - variable-only queries trigger the preflight and bail above the threshold (locks in the symmetry with germplasm-only).
+  - bare `/observations` queries (no filters at all) trigger the preflight.
+  - probe-failure path emits a "stalled" warning, returns an empty result, and skips the bulk pull instead of throwing.
+
+## Changed
+
+- **`brapi_find_observations` preflight trigger** generalized from `!hasScope && germplasm.length > 0` to `!hasAnchor` — i.e. *any* unanchored shape (germplasm-only, variable-only, season-only, programs-only, bare). The four anchors (`studies`, `trials`, `observationUnits`, `observations`) still skip the preflight as before; the common, well-anchored case pays no extra HTTP.
+- **Preflight probe** no longer reuses `loadInitialFindPage` (which threads the global retry budget). It now calls `BrapiClient.get` directly with `companionRequestOptions(...)` so the wall-clock budget is bounded by `BRAPI_COMPANION_TIMEOUT_MS` (8 s default) and a stalled count operation can't pin the response.
+- **Three pre-existing specs** that exercised data-handling paths via bare `{}` input now anchor with `studies: ['s-1']` so the test still reads as one logical fetch (it was previously coincidentally one HTTP call; with the broader preflight that test would now consume the same `Response` body twice and fail with `ERR_BODY_ALREADY_USED`). The behavior under test is unchanged.
+
+## Fixed
+
+- **CassavaBase variable-only `/observations` queries** no longer hang. Before: `?observationVariableDbId=X` (alone) issued, upstream stalled past 60 s, retry budget escalated to ≥ 120 s, agent eventually got a hard timeout. After: preflight fails fast under 8 s, agent gets a "narrow your query — add a `studies` / `trials` / `observationUnits` anchor" warning and an empty result.
+- **CassavaBase bare `/observations` queries** (no filters) no longer hang. Same shape as above — verified `curl` against the live server times out at 30 s+ on the bare endpoint.
+- **`brapi_find_observations` total wall time** on stalled unanchored shapes drops from ≥ 60 s (or longer if retries kicked in) to ≤ 8 s + a single warning.

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"brapi-find-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqLjE,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuShC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js

@@ -10,12 +10,12 @@
 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 { getBrapiClient, isDialectAllDropped, } 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, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { DEFAULT_ALIAS, getServerRegistry, } from '../../../services/server-registry/index.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, companionRequestOptions, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractRows, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const ObservationRowSchema = z
     .object({
     observationDbId: z.string().nullish().describe('Server-side identifier for the observation.'),
@@ -116,8 +116,8 @@ const OutputSchema = z.object({
 /**
  * Upstream observation totals above this threshold trigger the preflight
  * bail-out: the bulk pull is skipped and the user is told to narrow the
- * query. Empirically, CassavaBase germplasm-only queries above ~5k rows
- * stall past the default request timeout.
+ * query. Empirically, CassavaBase unanchored observation queries above
+ * ~5k rows stall past the default request timeout.
  */
 const PREFLIGHT_BULK_THRESHOLD = 5_000;
 const SERVER_TO_USER = {
@@ -214,30 +214,52 @@ export const brapiFindObservations = tool('brapi_find_observations', {
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const loadObservations = (pageSize) => loadInitialFindPage(client, connection, route, pageSize, ctx);
         /**
-         * Danger pattern: querying /observations by germplasm with no anchoring
-         * scope (study, trial, observation, observation-unit). On large servers
-         * (CassavaBase, T3) `germplasmDbIds=X` alone joins across every study the
-         * germplasm appeared in — the upstream count query takes tens of seconds
-         * and a `pageSize=loadLimit` pull stalls past the request timeout. Probe
-         * with `pageSize=1` first; if the upstream advertises more rows than we'd
-         * safely pull, skip the bulk fetch and surface a warning recommending a
-         * study scope. Other unscoped patterns (variable-only, bare query) are
-         * left alone — they don't carry the same join blow-up risk and adding a
-         * preflight to every call would double HTTP for the common case.
+         * Danger pattern: querying `/observations` without one of the four
+         * anchors (study, trial, observation-unit, observation). On large
+         * servers (CassavaBase, T3) any unanchored variant —
+         * `?germplasmDbId=X`, `?observationVariableDbId=X`, `?seasonDbId=X`,
+         * or a bare `/observations` — joins across the full observations
+         * table and stalls past the request timeout. Probe with `pageSize=1`
+         * using companion-call options (short timeout, zero retries) so a
+         * stalled count operation surfaces as a single warning instead of
+         * pinning the response. Outcomes:
+         *   1. probe stalls/fails → warn and skip the bulk pull entirely
+         *   2. probe returns a count above the threshold → warn, return the
+         *      1-row preflight as the only in-context observation
+         *   3. probe returns a count under the threshold → fall through to
+         *      the normal bulk pull
+         *
+         * Empirically verified on cassavabase.org/brapi/v2:
+         *   - `?germplasmDbId=X`              alone: timeout (>60 s)
+         *   - `?observationVariableDbId=X`    alone: timeout (>60 s)
+         *   - bare `/observations`                  : timeout (>30 s)
+         *   - `?studyDbId=X` (anchored)             : ~15 s OK
          */
-        const hasScope = (input.studies?.length ?? 0) > 0 ||
+        const hasAnchor = (input.studies?.length ?? 0) > 0 ||
             (input.trials?.length ?? 0) > 0 ||
             (input.observationUnits?.length ?? 0) > 0 ||
             (input.observations?.length ?? 0) > 0;
-        const shouldPreflight = !hasScope && (input.germplasm?.length ?? 0) > 0;
         let firstPage;
         let bulkPullSkipped = false;
-        if (shouldPreflight) {
-            const preflight = await loadObservations(1);
-            const upstreamTotal = preflight.totalCount;
-            if (typeof upstreamTotal === 'number' && upstreamTotal > PREFLIGHT_BULK_THRESHOLD) {
-                warnings.push(`Preflight detected ${upstreamTotal} observations matching this query (germplasm/variable/season scope, no study or trial anchor). Bulk pull skipped to avoid an upstream timeout — narrow with \`studies: ['…']\` or \`trials: ['…']\`, or accept a partial view by re-calling with a tighter scope. Returning the 1-row preflight as the only in-context observation.`);
-                firstPage = preflight;
+        if (!hasAnchor && route.kind === 'get') {
+            const probe = await probeObservationCount({
+                client,
+                connection,
+                route,
+                dialect,
+                config,
+                warnings,
+                ctx,
+            });
+            if (probe === null) {
+                warnings.push("Observations preflight count probe stalled — the upstream count operation appears unbounded for this query shape, indicating a likely full-table scan. Bulk pull skipped to avoid a long hang. Narrow with `studies: ['…']`, `trials: ['…']`, or scope to specific `observationUnits` / `observations`.");
+                firstPage = { rows: [], hasMore: false, pagesFetched: 0, totalCount: 0 };
+                bulkPullSkipped = true;
+            }
+            else if (typeof probe.totalCount === 'number' &&
+                probe.totalCount > PREFLIGHT_BULK_THRESHOLD) {
+                warnings.push(`Preflight detected ${probe.totalCount} observations matching this query (no study / trial / observationUnit / observation anchor). Bulk pull skipped to avoid an upstream timeout — narrow with \`studies: ['…']\`, \`trials: ['…']\`, or scope to specific \`observationUnits\` / \`observations\`. Returning the 1-row preflight as the only in-context observation.`);
+                firstPage = probe;
                 bulkPullSkipped = true;
             }
         }
@@ -420,4 +442,38 @@ function normalizeSeason(value) {
         return year ? `${label} ${year}` : label;
     return year;
 }
+/**
+ * Probe the upstream observation count without burning the global retry
+ * budget. Uses companion-call options (short timeout, zero retries) so a
+ * stalled count operation surfaces as a single warning instead of pinning
+ * the response. Returns:
+ *   - `LoadedRows` on success (1-row sample + totalCount when reported)
+ *   - `null` when the probe fails (timeout, 5xx) — caller treats as
+ *     "scope too large" and bails with a warning.
+ *
+ * Re-throws `dialect_all_filters_dropped` so the typed error contract
+ * still surfaces; that's a programming/dialect mismatch, not a probe
+ * failure.
+ */
+async function probeObservationCount(args) {
+    const { client, connection, route, dialect, config, warnings, ctx } = args;
+    try {
+        const envelope = await client.get(connection.baseUrl, route.path, ctx, companionRequestOptions(connection, dialect, config, warnings, {
+            ...route.filters,
+            pageSize: 1,
+        }));
+        const rows = extractRows(envelope.result);
+        const totalCount = envelope.metadata?.pagination?.totalCount;
+        const hasMore = typeof totalCount === 'number' && totalCount > rows.length && totalCount > 0;
+        const result = { rows, hasMore, pagesFetched: 1 };
+        if (totalCount !== undefined)
+            result.totalCount = totalCount;
+        return result;
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
 //# sourceMappingURL=brapi-find-observations.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js.map

@@ -1 +1 @@
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package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.4.7",
+  "version": "0.4.8",
   "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.4.7",
+  "version": "0.4.8",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.7",
+      "version": "0.4.8",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.7",
+      "version": "0.4.8",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }