npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.6 → 0.4.8 - Mend

@cyanheads/brapi-mcp-server 0.4.6 → 0.4.8

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Files changed (48) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.4.6
+**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 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-0.4.6-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-0.4.8-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/0.4.7.md ADDED Viewed

@@ -0,0 +1,35 @@
+---
+summary: "Foundational dialect-bypass fix — every BrAPI client GET routes through the dialect adapter, with tight companion-call budgets so slow upstreams no longer 4× the response time."
+breaking: false
+---
+# 0.4.7 — 2026-05-01
+The v0.4.6 release wired the dialect adapter into the `find_*` surface and one `get_germplasm` probe. Every other call site that built GET filter params — `ReferenceDataCache` (programs / trials / locations), `get_study`'s observation / observation-unit / variable count probes, and `submit_observations`'s preflight — bypassed the dialect entirely and shipped the v2.1 plurals to the wire. On SGN-family servers (CassavaBase, Breedbase) those plurals are silently ignored: `/trials?trialDbIds=7526` returns the unfiltered set's row zero (`5CP_Kenya / trialDbId 1911`), and `/observations?studyDbIds=X` triggers a full table scan that exceeds the 30 s timeout. With the global retry budget that meant 4 × 30 s ≈ 2 minutes of waiting per failing companion, every time.
+This release pushes the dialect adapter to the `BrapiClient` edge so every GET — current and future — translates plurals to per-server singulars without each call site having to remember. Companion enrichments now run with their own tight budget (8 s timeout, 0 retries) so a slow upstream surfaces as a single warning instead of stretching the response.
+## Added
+- **`BrapiRequestOptions.dialect`** — when supplied, `BrapiClient.get` extracts the endpoint segment from the path and routes `params` through `dialect.adaptGetFilters` before serializing. Single source of truth for plural/singular translation across every call site. `raw_get` continues to opt out by omitting the field.
+- **`BrapiRequestOptions.warnings`** — sink for dialect translation warnings (downcast, dropped). Threaded through to the same `warnings[]` array the calling tool surfaces in its envelope.
+- **`BrapiRequestOptions.retryMaxAttempts`** — per-call override of the global retry budget. Companion calls set it to `0` so a slow upstream surfaces as one warning rather than 4× the per-attempt timeout.
+- **`DIALECT_ALL_DROPPED_REASON`** + `isDialectAllDropped(err)` — stable error-code constant and type guard. Companion call sites catch and convert to "skip with warning" instead of propagating; find-style call sites continue to throw via their `all_filters_dropped` typed contract.
+- **`companionRequestOptions(connection, dialect, config, warnings, params?)`** in `find-helpers` — bundles the companion-call shape (tight timeout + zero retries + dialect + warnings) so future companion sites stay consistent.
+- **`BRAPI_COMPANION_TIMEOUT_MS`** env var (default 8 s) — per-call timeout for non-critical enrichments. Falls under the existing `BRAPI_REQUEST_TIMEOUT_MS` (30 s) which still governs the main path.
+- **`observationunits` mapping** added to the `cassavabase` and `brapi-test` dialects — `studyDbIds → studyDbId` plus the rest of the cross-FK plurals so observation-unit count probes reach the wire as singulars.
+## Changed
+- **`ReferenceDataCache.fetchBatch`** threads `dialect` through to the client. On `dialect_all_filters_dropped` returns an empty Map and pushes a warning into the supplied sink — caller treats the FK as unavailable instead of receiving a page-zero row keyed off the wrong ID. Retry budget set to 0; timeout to `companionTimeoutMs`. **CassavaBase trial/program/location FK lookups now actually filter** instead of returning row zero.
+- **`brapi_get_study`** companion probes (`/observations`, `/observationunits`, `/variables`) now use `companionRequestOptions(...)` and route through the dialect. The screenshot-class failure mode is fixed: where v0.4.6 burned ~2 minutes retrying `?studyDbIds=12642` on cassavabase (silently ignored, full table scan), v0.4.7 sends `?studyDbId=12642` (15 s on cassavabase, no retry). Total wall time on the same study drops from ≥120 s to <20 s on the worst path. The companion failure mode also reverts cleanly — when the upstream is genuinely slow the call surfaces a "probe failed" warning instead of pinning the response.
+- **`brapi_submit_observations`** post-write count probe routes through the dialect with the same companion budget. `ApplyBranchSchema` gains an optional `warnings: string[]` field for connection-level diagnostics from the dialect translation.
+- **`BrapiClient.get`** is now `async` so synchronous throws from the dialect adapter (the all-dropped throw) become rejected promises rather than escaping the call stack.
+## Fixed
+- **CassavaBase trial / program / location FK lookups** no longer return wrong rows. Before: `GET /trials?trialDbIds=7526` upstream-ignored, returned `5CP_Kenya / trialDbId 1911`, ReferenceDataCache cached under the wrong key, `getTrials([7526])` returned undefined. After: dialect translates to `?trialDbId=7526`, returns the correct row, FK enrichment lands.
+- **CassavaBase observation count probe** no longer triggers a full table scan that times out. Before: `GET /observations?studyDbIds=X` ≥ 180 s (timeout × 4 retries). After: `GET /observations?studyDbId=X` ~15 s, no retry.
+- **CassavaBase observation-unit count probe** same shape, same fix — singular `studyDbId` honored, plural ignored.
+- **`get_study` response time** on cassavabase drops from ~2 min worst-case (the screenshot) to <20 s when companion endpoints are responsive, or <10 s with a single "probe failed" warning when they aren't. Companion failures no longer pin the main response.
+- **Tests** — `BrapiClient` gains 5 new specs covering dialect translation, warnings sink, all-dropped throw, raw_get passthrough, and retry override. `ReferenceDataCache` gains 3 new specs covering dialect threading, all-dropped graceful degradation, and non-dialect error propagation. `get_study` gains a cassavabase-shape end-to-end spec verifying every companion call reaches the wire as a singular key.

package/changelog/0.4.x/0.4.8.md ADDED Viewed

@@ -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/config/server-config.d.ts CHANGED Viewed

@@ -24,6 +24,7 @@ declare const ServerConfigSchema: z.ZodObject<{
     retryBaseDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     referenceCacheTtlSeconds: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     requestTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    companionTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     searchPollTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     searchPollIntervalMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
     allowPrivateIps: z.ZodPipe<z.ZodDefault<z.ZodEnum<{

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"server-config.d.ts","sourceRoot":"","sources":["../../src/config/server-config.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAG3C,QAAA,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;iBAyGtB,CAAC;AAEH,MAAM,MAAM,YAAY,GAAG,CAAC,CAAC,KAAK,CAAC,OAAO,kBAAkB,CAAC,CAAC;AAI9D,wBAAgB,eAAe,IAAI,YAAY,CAwB9C;AAED,uDAAuD;AACvD,wBAAgB,iBAAiB,IAAI,IAAI,CAExC"}

package/dist/config/server-config.js CHANGED Viewed

@@ -79,6 +79,12 @@ const ServerConfigSchema = z.object({
         .positive()
         .default(30_000)
         .describe('Per-request HTTP timeout.'),
+    companionTimeoutMs: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(8_000)
+        .describe('Tighter timeout for non-critical companion enrichments (FK lookups, count probes). Companions also bypass the retry budget so a slow upstream surfaces a warning instead of stretching the response by 4×.'),
     searchPollTimeoutMs: z.coerce
         .number()
         .int()
@@ -120,6 +126,7 @@ export function getServerConfig() {
         retryBaseDelayMs: 'BRAPI_RETRY_BASE_DELAY_MS',
         referenceCacheTtlSeconds: 'BRAPI_REFERENCE_CACHE_TTL_SECONDS',
         requestTimeoutMs: 'BRAPI_REQUEST_TIMEOUT_MS',
+        companionTimeoutMs: 'BRAPI_COMPANION_TIMEOUT_MS',
         searchPollTimeoutMs: 'BRAPI_SEARCH_POLL_TIMEOUT_MS',
         searchPollIntervalMs: 'BRAPI_SEARCH_POLL_INTERVAL_MS',
         allowPrivateIps: 'BRAPI_ALLOW_PRIVATE_IPS',

package/dist/config/server-config.js.map CHANGED Viewed

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-observations.tool.js CHANGED Viewed

@@ -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 CHANGED Viewed

	@@ -1 +1 @@
1	- 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	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqIjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8PxB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js CHANGED Viewed

@@ -8,11 +8,13 @@
  */
 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 { getReferenceDataCache } from '../../../services/reference-data-cache/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, appendPassthroughLines, buildRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, appendPassthroughLines, buildRequestOptions, companionRequestOptions, extractCoordinates, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const StudySchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -134,13 +136,15 @@ export const brapiGetStudy = tool('brapi_get_study', {
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
         const referenceData = getReferenceDataCache();
+        const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
         await capabilities.ensure(connection.baseUrl, { service: 'studies', method: 'GET' }, ctx, capabilityLookup);
+        const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
-        const referenceLookup = {};
+        const referenceLookup = { dialect, warnings };
         if (connection.resolvedAuth)
             referenceLookup.auth = connection.resolvedAuth;
         let studyEnv;
@@ -189,19 +193,23 @@ export const brapiGetStudy = tool('brapi_get_study', {
                     .catch((err) => recordWarning(warnings, 'location FK lookup failed', err))
                 : Promise.resolve(undefined),
             supportsObservations
-                ? fetchTotalCount(client, connection.baseUrl, '/observations', ctx, buildRequestOptions(connection, {
+                ? fetchTotalCount(client, connection.baseUrl, '/observations', ctx, companionRequestOptions(connection, dialect, config, warnings, {
                     studyDbIds: [input.studyDbId],
                     pageSize: 1,
                 })).catch((err) => recordWarning(warnings, 'observation count probe failed', err))
                 : Promise.resolve(undefined),
             supportsObservationUnits
-                ? fetchTotalCount(client, connection.baseUrl, '/observationunits', ctx, buildRequestOptions(connection, {
+                ? fetchTotalCount(client, connection.baseUrl, '/observationunits', ctx, companionRequestOptions(connection, dialect, config, warnings, {
                     studyDbIds: [input.studyDbId],
                     pageSize: 1,
                 })).catch((err) => recordWarning(warnings, 'observation-unit count probe failed', err))
                 : Promise.resolve(undefined),
             supportsVariables
-                ? fetchTotalCount(client, connection.baseUrl, '/variables', ctx, buildRequestOptions(connection, {
+                ? fetchTotalCount(client, connection.baseUrl, '/variables', ctx, companionRequestOptions(connection, dialect, config, warnings, {
+                    // /variables historically responded to singular `studyDbId` on
+                    // SGN deployments — keep the singular here so the dialect (which
+                    // doesn't carry a `variables.studyDbIds → studyDbId` entry) is a
+                    // pass-through, not a silent translation that breaks the probe.
                     studyDbId: input.studyDbId,
                     pageSize: 1,
                 })).catch((err) => recordWarning(warnings, 'variable count probe failed', err))

package/dist/mcp-server/tools/definitions/brapi-get-study.tool.js.map CHANGED Viewed

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

@@ -82,6 +82,7 @@ export declare const brapiSubmitObservations: import("@cyanheads/mcp-ts-core").T
             observationUnitDbId: z.ZodOptional<z.ZodString>;
             warning: z.ZodString;
         }, z.core.$strip>>;
+        warnings: z.ZodOptional<z.ZodArray<z.ZodString>>;
     }, z.core.$strip>], "mode">;
 }, z.core.$strip>, readonly [{
     readonly reason: "observations_unsupported";

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA2C,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACpF,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAkOjE~~,eAAO,MAAM,uBAAuB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAsSlC~~,CAAC"}
1	+ {"version":3,"file":"brapi-submit-observations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-submit-observations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAA2C,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACpF,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA2OjE,eAAO,MAAM,uBAAuB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA6SlC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-submit-observations.tool.js CHANGED Viewed

@@ -11,10 +11,12 @@
  */
 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 { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, buildRequestOptions, extractRows, isUpstreamNotFound, } from '../shared/find-helpers.js';
+import { AliasInput, buildRequestOptions, companionRequestOptions, extractRows, isUpstreamNotFound, } from '../shared/find-helpers.js';
 const ObservationRowSchema = z
     .object({
     observationDbId: z
@@ -150,6 +152,10 @@ const ApplyBranchSchema = z
     perRowWarnings: z
         .array(PerRowWarningSchema)
         .describe('Per-row notes — unknown variables, empty values, missing IDs.'),
+    warnings: z
+        .array(z.string().describe('Connection-level diagnostic note (e.g. dialect translation).'))
+        .optional()
+        .describe('Connection-level notes from companion enrichment — dialect drops, downcasts, FK probe gaps. Empty / absent on the happy path.'),
 })
     .describe('Apply output — writes succeeded, post-state attached.');
 const OutputSchema = z.object({
@@ -228,11 +234,14 @@ export const brapiSubmitObservations = tool('brapi_submit_observations', {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
+        const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
         if (connection.resolvedAuth)
             capabilityLookup.auth = connection.resolvedAuth;
         const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const dialect = await resolveDialect(connection, ctx, capabilityLookup);
+        const companionWarnings = [];
         const obsDescriptor = profile.supported.observations;
         const supportsPost = obsDescriptor?.methods?.includes('POST') ?? false;
         const supportsPut = obsDescriptor?.methods?.includes('PUT') ?? false;
@@ -348,7 +357,7 @@ export const brapiSubmitObservations = tool('brapi_submit_observations', {
         const updated = updatedEnv
             ? extractObservationRows(updatedEnv.result).filter((r) => typeof r.observationDbId === 'string')
             : [];
-        const studyObservationCount = await fetchStudyObservationCount(input.studyDbId, connection, client, ctx);
+        const studyObservationCount = await fetchStudyObservationCount(input.studyDbId, connection, dialect, config, companionWarnings, client, ctx);
         const latestTimestamp = pickLatestTimestamp(input.observations);
         const branch = {
             mode: 'apply',
@@ -363,6 +372,8 @@ export const brapiSubmitObservations = tool('brapi_submit_observations', {
             branch.studyObservationCount = studyObservationCount;
         if (latestTimestamp)
             branch.latestObservationTimestamp = latestTimestamp;
+        if (companionWarnings.length > 0)
+            branch.warnings = companionWarnings;
         return { alias: connection.alias, result: branch };
     },
     format: (output) => {
@@ -511,9 +522,12 @@ async function fetchStudyExistence(studyDbId, connection, client, ctx) {
         throw err;
     }
 }
-async function fetchStudyObservationCount(studyDbId, connection, client, ctx) {
+async function fetchStudyObservationCount(studyDbId, connection, dialect, config, warnings, client, ctx) {
     try {
-        const env = await client.get(connection.baseUrl, '/observations', ctx, buildRequestOptions(connection, { studyDbIds: [studyDbId], pageSize: 1 }));
+        const env = await client.get(connection.baseUrl, '/observations', ctx, companionRequestOptions(connection, dialect, config, warnings, {
+            studyDbIds: [studyDbId],
+            pageSize: 1,
+        }));
         const total = env.metadata?.pagination?.totalCount;
         return typeof total === 'number' ? total : undefined;
     }