npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.2 → 0.4.3 - Mend

@cyanheads/brapi-mcp-server 0.4.2 → 0.4.3

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Files changed (18) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.4.2
+**Version:** 0.4.3
 **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-0.4.2-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-0.4.3-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/)
 [![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/0.4.3.md ADDED Viewed

@@ -0,0 +1,27 @@
+---
+summary: "Field-test follow-up: studyCount cross-check, find_germplasm text spillover guard, find_observations preflight on unscoped germplasm queries, honest zero-match distributions, prominent dataset expiry."
+breaking: false
+---
+# 0.4.3 — 2026-04-30
+Five field-test-driven correctness and DX gaps closed after live testing the 0.4.2 release against `https://cassavabase.org/brapi/v2`. Each fix is server-agnostic — no new dialect-specific code paths — and uses the dialect adapter as the front-line check with a generic safety net for unknown servers.
+## Fixed
+- **`brapi_get_germplasm` `studyCount` returned the global `/studies` total** when the upstream silently dropped the `germplasmDbIds` filter (observed: TMS30572 reported `studyCount: 8340`, the entire CassavaBase studies count). The probe now routes through the dialect adapter and runs a parallel unfiltered baseline; if the filtered total equals the unfiltered baseline, `studyCount` is omitted with a warning explaining why a per-germplasm count cannot be trusted. Catches silent filter drops on any server, not just the SGN family.
+- **`brapi_find_germplasm` text spillover trap** — querying `text: "TMS30572"` against an 842k-row catalog returned a 50k-row dataset of unrelated germplasm under a tiny "matched 0 of 10" warning. Two fixes: (1) when text matches 0 first-page rows, the spillover is skipped entirely with a strong warning recommending exact filters (`names`, `accessionNumbers`, `germplasmDbIds`); (2) when text has matches and spillover happens, the persisted dataset only contains text-matched rows via a new `rowFilter` predicate on `maybeSpill` / `spillToDataset`. The 50k-row dataset of unrelated rows is gone.
+- **`brapi_find_observations` preflight for unscoped germplasm queries** — `germplasmDbIds=X` with no `studies` / `trials` / `observationUnits` / `observations` anchor was issuing `?pageSize=loadLimit` directly, stalling past the request timeout on large servers (CassavaBase observations join across every study a germplasm appeared in). Now probes with `pageSize=1` first; when the upstream advertises more than `PREFLIGHT_BULK_THRESHOLD` (5,000) rows, the bulk pull is skipped and the agent receives a warning recommending a study or trial scope. Other unscoped patterns (variable-only, bare query) keep their single-call path — only the documented danger pattern gets the extra preflight.
+- **Distribution block on zero-match queries was misleading** — `find_germplasm` computed distributions from the full upstream rows and rendered them alongside an empty result set. Distributions are now computed from the post-filter `fullRows`, so a zero-match query produces an empty (honest) block instead of a confusing "Cassava (500)" line that looks like signal.
+- **Dataset handle expiry was buried in a bullet** at the bottom of the format output. New `formatExpiresIn` helper renders `expiresAt: <iso> (expires in 24h)` on every dataset handle and the find_* header line shows `N in dataset (expires in 24h) · M total`. Applies automatically to all 8 find_* tools without per-tool wiring.
+## Added
+- **`rowFilter?: (row: T) => boolean` on `maybeSpill` / `spillToDataset`** in `find-helpers` — generic client-side predicate applied to every row (first-page + spilled) before persistence. The persisted dataset only contains rows that pass; `fullRows` returns the post-filter set so distributions reflect the matched rows. Re-usable for any future find_* tool that needs predicate-based narrowing.
+- **`formatExpiresIn(expiresAt, now?)` in `find-helpers`** — coarsens an absolute ISO timestamp to a compact relative label (`<1m`, `30m`, `24h`, `7d`) with `expires in` / `expired ... ago` framing.
+- **Tests** — 5 new cases. `tests/tools/brapi-get-germplasm.tool.test.ts` covers the silent-filter cross-check (filtered total == unfiltered baseline → drop). `tests/tools/brapi-find-germplasm.tool.test.ts` covers the spillover skip on text-miss and the dataset row count after text filtering. `tests/tools/brapi-find-observations.tool.test.ts` covers preflight skip above threshold, preflight skip when scoped, and the proceeds-with-bulk-pull case below threshold.
+## Changed
+- **`renderFindHeader` accepts `dataset.expiresAt`** — optional field on the dataset summary; when present, the relative expiry label appears in the dataset segment of the headline.
+- **`brapi_find_observations` preflight pull** uses a local `loadObservations(pageSize)` closure that consolidates three near-identical `loadInitialPage` call sites into one — saves ~14 lines and makes the preflight intent obvious at the call site.

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;~~AA0IjD~~,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BA6P7B~~,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;AA2IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiR7B,CAAC"}

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

@@ -167,8 +167,23 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         const filters = applyDialectFilters(dialect, 'germplasm', merged, warnings);
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const firstPage = await loadInitialPage(client, connection, '/germplasm', filters, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
-            firstPage,
+        // 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
+        // ignore. Decide upfront whether to spill: when text is set and matches
+        // 0 rows on the first page, pulling more pages is unlikely to surface
+        // hits and we'd just bury the agent in 50k unrelated rows.
+        const text = input.text;
+        const wouldSpill = firstPage.hasMore && firstPage.totalCount !== undefined && firstPage.totalCount > loadLimit;
+        const firstPageMatched = text
+            ? firstPage.rows.filter((row) => rowMatchesText(row, text))
+            : firstPage.rows;
+        const skipSpillForTextMiss = Boolean(text && wouldSpill && firstPage.rows.length > 0 && firstPageMatched.length === 0);
+        const spillInput = {
+            firstPage: skipSpillForTextMiss
+                ? // Treat the first page as the whole result — no further pages pulled.
+                    { rows: firstPage.rows, hasMore: false, pagesFetched: 1 }
+                : firstPage,
             client,
             connection,
             path: '/germplasm',
@@ -177,7 +192,10 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             loadLimit,
             ctx,
             store: datasetStore,
-        });
+        };
+        if (text)
+            spillInput.rowFilter = (row) => rowMatchesText(row, text);
+        const { fullRows, dataset: datasetMeta } = await maybeSpill(spillInput);
         const distributions = {
             commonCropName: computeDistribution(fullRows, (r) => asString(r.commonCropName)),
             genus: computeDistribution(fullRows, (r) => asString(r.genus)),
@@ -226,26 +244,21 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                 'text',
             ],
         });
-        // 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
-        // ignore. Filter the in-context rows here so the agent gets a useful
-        // narrowing; the dataset (if any) still carries the full upstream set so
-        // a follow-up `brapi_manage_dataset` call can re-query without losing
-        // rows. Distributions come from the un-filtered fullRows so the agent can
-        // still see the real spread of crops / genus / etc.
-        let inContextRows = firstPage.rows;
-        const text = input.text;
         if (text) {
-            const matched = firstPage.rows.filter((row) => rowMatchesText(row, text));
-            if (firstPage.rows.length > 0 && matched.length === 0) {
-                warnings.push(`Free-text '${text}' matched 0 of ${firstPage.rows.length} returned rows. Combine with \`crops\` / \`genus\` / \`accessionNumbers\` to narrow the upstream pull first, or check spelling.`);
+            if (skipSpillForTextMiss) {
+                warnings.push(`Free-text '${text}' matched 0 of ${firstPage.rows.length} first-page rows out of ${totalCount} upstream. Spillover skipped — pulling more pages is unlikely to surface hits. Use exact filters: \`names: ['${text}']\`, \`accessionNumbers: ['${text}']\`, or \`germplasmDbIds: ['${text}']\` for direct lookup.`);
+            }
+            else if (fullRows.length === 0 && firstPage.rows.length > 0) {
+                warnings.push(`Free-text '${text}' matched 0 of ${firstPage.rows.length} returned rows. Use exact filters (\`names\`, \`accessionNumbers\`, \`germplasmDbIds\`) for direct lookup, or check spelling.`);
+            }
+            else if (datasetMeta) {
+                warnings.push(`Free-text '${text}' filtered the dataset to ${datasetMeta.rowCount} matched row(s) across the upstream union.`);
             }
-            else if (matched.length < firstPage.rows.length) {
-                warnings.push(`Free-text '${text}' narrowed in-context view to ${matched.length} of ${firstPage.rows.length} returned rows. ${datasetMeta ? 'Full set retained in the dataset for follow-up.' : 'No dataset spillover — un-matched rows are not retained.'}`);
+            else if (fullRows.length < firstPage.rows.length) {
+                warnings.push(`Free-text '${text}' narrowed in-context view to ${fullRows.length} of ${firstPage.rows.length} returned rows.`);
             }
-            inContextRows = matched;
         }
+        const inContextRows = fullRows.slice(0, loadLimit);
         const result = {
             alias: connection.alias,
             results: inContextRows,

package/dist/mcp-server/tools/definitions/brapi-find-germplasm.tool.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 @@
1	- {"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,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;~~AA8JjD~~,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~6BAiNhC~~,CAAC"}
1	+ {"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,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAsKjD,eAAO,MAAM,qBAAqB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAsPhC,CAAC"}

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

@@ -112,6 +112,13 @@ const OutputSchema = z.object({
         .record(z.string(), z.unknown())
         .describe('The final filter map sent to the server (named + extraFilters).'),
 });
+/**
+ * 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.
+ */
+const PREFLIGHT_BULK_THRESHOLD = 5_000;
 const SERVER_TO_USER = {
     // Plurals — BrAPI v2.1 spec, used by the `spec` dialect.
     studyDbIds: 'studies',
@@ -188,18 +195,49 @@ export const brapiFindObservations = tool('brapi_find_observations', {
         }, input.extraFilters, warnings);
         const filters = applyDialectFilters(dialect, 'observations', merged, warnings);
         const loadLimit = input.loadLimit ?? config.loadLimit;
-        const firstPage = await loadInitialPage(client, connection, '/observations', filters, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
-            firstPage,
-            client,
-            connection,
-            path: '/observations',
-            filters,
-            source: 'find_observations',
-            loadLimit,
-            ctx,
-            store: datasetStore,
-        });
+        const loadObservations = (pageSize) => loadInitialPage(client, connection, '/observations', filters, 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.
+         */
+        const hasScope = (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;
+                bulkPullSkipped = true;
+            }
+        }
+        firstPage ??= await loadObservations(loadLimit);
+        const { fullRows, dataset: datasetMeta } = bulkPullSkipped
+            ? { fullRows: firstPage.rows, dataset: undefined }
+            : await maybeSpill({
+                firstPage,
+                client,
+                connection,
+                path: '/observations',
+                filters,
+                source: 'find_observations',
+                loadLimit,
+                ctx,
+                store: datasetStore,
+            });
         const distributions = {
             observationVariableName: computeDistribution(fullRows, (r) => asString(r.observationVariableName)),
             studyName: computeDistribution(fullRows, (r) => asString(r.studyName)),

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAkGjE~~,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GA8M5B~~,CAAC"}
1	+ {"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAgN5B,CAAC"}

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

@@ -9,6 +9,7 @@
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 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, isUpstreamNotFound } from '../shared/find-helpers.js';
@@ -146,6 +147,9 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
         const supportsAttributes = Boolean(profile.supported['germplasm/{germplasmDbId}/attributes']);
         const supportsProgeny = Boolean(profile.supported['germplasm/{germplasmDbId}/progeny']);
         const supportsStudies = profile.supported.studies?.methods?.includes('GET') ?? false;
+        const dialect = supportsStudies
+            ? await resolveDialect(connection, ctx, capabilityLookup)
+            : undefined;
         const [pedigree, attributes, studyCount, progenyCount] = await Promise.all([
             supportsPedigree
                 ? fetchPedigree(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'pedigree lookup failed', err))
@@ -153,11 +157,15 @@ export const brapiGetGermplasm = tool('brapi_get_germplasm', {
             supportsAttributes
                 ? fetchAttributes(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'attributes lookup failed', err))
                 : Promise.resolve(undefined),
-            supportsStudies
-                ? fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, {
-                    germplasmDbIds: [input.germplasmDbId],
-                    pageSize: 1,
-                })).catch((err) => recordWarning(warnings, 'study count probe failed', err))
+            supportsStudies && dialect
+                ? fetchValidatedStudyCount({
+                    client,
+                    connection,
+                    germplasmDbId: input.germplasmDbId,
+                    dialect,
+                    ctx,
+                    warnings,
+                }).catch((err) => recordWarning(warnings, 'study count probe failed', err))
                 : Promise.resolve(undefined),
             supportsProgeny
                 ? fetchTotalCount(client, connection.baseUrl, `/germplasm/${id}/progeny`, ctx, buildRequestOptions(connection, { pageSize: 1 })).catch((err) => recordWarning(warnings, 'progeny count probe failed', err))
@@ -303,4 +311,44 @@ async function fetchTotalCount(client, baseUrl, path, ctx, options) {
     const total = env.metadata?.pagination?.totalCount;
     return typeof total === 'number' ? total : undefined;
 }
+/**
+ * Probe `/studies?germplasmDbIds=X` and a parallel unfiltered baseline.
+ * Some servers (notably the SGN family) silently drop the germplasm filter on
+ * `/studies` and return the global studies total — which would be wildly
+ * misleading as a per-germplasm `studyCount`. The cross-check catches that:
+ * if the filtered total matches the unfiltered baseline, the filter was
+ * ignored and we drop the count rather than report a misleading global.
+ *
+ * Routes the filtered probe through the dialect adapter so any per-server
+ * key translation (or filter drop) takes effect, and surfaces the dialect's
+ * own warnings so the agent sees why a count is missing.
+ */
+async function fetchValidatedStudyCount(input) {
+    const { client, connection, ctx, dialect, germplasmDbId, warnings } = input;
+    const adapted = dialect.adaptGetFilters('studies', {
+        germplasmDbIds: [germplasmDbId],
+    });
+    warnings.push(...adapted.warnings);
+    // If the dialect dropped the filter entirely, the count would be the
+    // global studies total — useless. Skip and let the caller render `—`.
+    if (Object.keys(adapted.filters).length === 0) {
+        warnings.push('studyCount probe skipped: the active dialect dropped the germplasm filter for /studies (server does not honor it).');
+        return;
+    }
+    const filteredParams = {
+        ...adapted.filters,
+        pageSize: 1,
+    };
+    const [filtered, baseline] = await Promise.all([
+        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, filteredParams)),
+        fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, { pageSize: 1 })).catch(() => undefined),
+    ]);
+    if (typeof filtered !== 'number')
+        return;
+    if (typeof baseline === 'number' && baseline > 0 && filtered === baseline) {
+        warnings.push(`studyCount omitted: /studies returned the same total (${baseline}) for both the germplasm-filtered probe and an unfiltered baseline — the upstream silently ignored the germplasm filter, so a per-germplasm count cannot be trusted.`);
+        return;
+    }
+    return filtered;
+}
 //# sourceMappingURL=brapi-get-germplasm.tool.js.map

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/shared/find-helpers.d.ts CHANGED Viewed

@@ -56,6 +56,7 @@ export declare function renderFindHeader(opts: {
     totalCount: number;
     dataset?: {
         rowCount: number;
+        expiresAt?: string;
     } | undefined;
 }): string;
 /**
@@ -91,6 +92,14 @@ export interface SpillInput<T> {
     firstPage: T[];
     loadLimit: number;
     path: string;
+    /**
+     * Optional client-side predicate applied to every row (first-page + spilled)
+     * before persistence. When present, only rows that pass are persisted to
+     * DatasetStore and returned in `fullRows`. The unfiltered upstream total is
+     * preserved separately on the LoadedRows envelope so distributions and
+     * headers can still report the true upstream size.
+     */
+    rowFilter?: (row: T) => boolean;
     source: string;
     store: DatasetStore;
     /** Total reported by the server on the first page. */
@@ -98,7 +107,7 @@ export interface SpillInput<T> {
 }
 export interface SpillResult<T> {
     dataset: DatasetMetadata;
-    /** All rows that were persisted — used for distributions. */
+    /** Rows that were persisted (post-filter when `rowFilter` was supplied). */
     fullRows: T[];
     pagesFetched: number;
 }
@@ -121,8 +130,16 @@ export type DatasetHandle = z.infer<typeof DatasetHandleSchema>;
 /**
  * Render a DatasetHandle as bullet lines, matching the existing find_* tool
  * format. Centralized so the truncated/maxRows fields surface consistently.
+ * `expiresAt` is paired with a human-readable `expires in Xh / Xd` so the
+ * agent doesn't have to subtract dates to know when the handle goes stale.
  */
 export declare function renderDatasetHandle(handle: DatasetHandle): string[];
+/**
+ * Render an absolute `expiresAt` timestamp as a relative human label
+ * (`expires in 24h`, `expires in 30m`, `expired 5m ago`). Coarsens to the
+ * most useful unit so the value reads at a glance.
+ */
+export declare function formatExpiresIn(expiresAt: string, now?: Date): string;
 /** Project a `DatasetMetadata` to the in-context handle shape. */
 export declare function toDatasetHandle(metadata: DatasetMetadata): DatasetHandle;
 export interface MaybeSpillInput<T> {
@@ -133,12 +150,18 @@ export interface MaybeSpillInput<T> {
     firstPage: LoadedRows<T>;
     loadLimit: number;
     path: string;
+    /**
+     * Optional client-side predicate applied to every row before persistence.
+     * Forwarded to `spillToDataset`. When present and no spillover happens, the
+     * first-page rows are also filtered before being returned.
+     */
+    rowFilter?: (row: T) => boolean;
     source: string;
     store: DatasetStore;
 }
 export interface MaybeSpillResult<T> {
     dataset?: DatasetHandle;
-    /** Full row set if a spillover happened, otherwise the first-page rows. */
+    /** Row set after `rowFilter` (when supplied), spilled or first-page only. */
     fullRows: T[];
 }
 /**

package/dist/mcp-server/tools/shared/find-helpers.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- 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1	+ 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package/dist/mcp-server/tools/shared/find-helpers.js CHANGED Viewed

@@ -122,7 +122,8 @@ export function computeDistribution(rows, accessor) {
  */
 export function renderFindHeader(opts) {
     if (opts.dataset) {
-        return `# ${opts.returnedCount} returned · ${opts.dataset.rowCount} in dataset · ${opts.totalCount} total ${opts.noun} — \`${opts.alias}\``;
+        const expiry = opts.dataset.expiresAt ? ` (${formatExpiresIn(opts.dataset.expiresAt)})` : '';
+        return `# ${opts.returnedCount} returned · ${opts.dataset.rowCount} in dataset${expiry} · ${opts.totalCount} total ${opts.noun} — \`${opts.alias}\``;
     }
     return `# ${opts.returnedCount} of ${opts.totalCount} ${opts.noun} — \`${opts.alias}\``;
 }
@@ -208,6 +209,8 @@ export const DatasetHandleSchema = z.object({
 /**
  * Render a DatasetHandle as bullet lines, matching the existing find_* tool
  * format. Centralized so the truncated/maxRows fields surface consistently.
+ * `expiresAt` is paired with a human-readable `expires in Xh / Xd` so the
+ * agent doesn't have to subtract dates to know when the handle goes stale.
  */
 export function renderDatasetHandle(handle) {
     const lines = [
@@ -216,7 +219,7 @@ export function renderDatasetHandle(handle) {
         `- sizeBytes: ${handle.sizeBytes}`,
         `- columns: ${handle.columns.join(', ')}`,
         `- createdAt: ${handle.createdAt}`,
-        `- expiresAt: ${handle.expiresAt}`,
+        `- expiresAt: ${handle.expiresAt} (${formatExpiresIn(handle.expiresAt)})`,
     ];
     if (handle.truncated)
         lines.push(`- truncated: true`);
@@ -224,6 +227,31 @@ export function renderDatasetHandle(handle) {
         lines.push(`- maxRows: ${handle.maxRows}`);
     return lines;
 }
+/**
+ * Render an absolute `expiresAt` timestamp as a relative human label
+ * (`expires in 24h`, `expires in 30m`, `expired 5m ago`). Coarsens to the
+ * most useful unit so the value reads at a glance.
+ */
+export function formatExpiresIn(expiresAt, now = new Date()) {
+    const expiry = Date.parse(expiresAt);
+    if (Number.isNaN(expiry))
+        return 'expiry unknown';
+    const deltaMs = expiry - now.getTime();
+    const absMs = Math.abs(deltaMs);
+    const minutes = Math.round(absMs / 60_000);
+    const hours = Math.round(absMs / 3_600_000);
+    const days = Math.round(absMs / 86_400_000);
+    let label;
+    if (absMs < 60_000)
+        label = '<1m';
+    else if (minutes < 60)
+        label = `${minutes}m`;
+    else if (hours < 48)
+        label = `${hours}h`;
+    else
+        label = `${days}d`;
+    return deltaMs >= 0 ? `expires in ${label}` : `expired ${label} ago`;
+}
 /** Project a `DatasetMetadata` to the in-context handle shape. */
 export function toDatasetHandle(metadata) {
     const handle = {
@@ -247,13 +275,14 @@ export function toDatasetHandle(metadata) {
  * union to DatasetStore and returns both the full set and the handle.
  */
 export async function maybeSpill(input) {
-    const { firstPage } = input;
+    const { firstPage, rowFilter } = input;
     if (!firstPage.hasMore ||
         firstPage.totalCount === undefined ||
         firstPage.totalCount <= input.loadLimit) {
-        return { fullRows: firstPage.rows };
+        const rows = rowFilter ? firstPage.rows.filter(rowFilter) : firstPage.rows;
+        return { fullRows: rows };
     }
-    const spill = await spillToDataset({
+    const spillInput = {
         store: input.store,
         client: input.client,
         connection: input.connection,
@@ -264,7 +293,10 @@ export async function maybeSpill(input) {
         ctx: input.ctx,
         firstPage: firstPage.rows,
         totalCount: firstPage.totalCount,
-    });
+    };
+    if (rowFilter)
+        spillInput.rowFilter = rowFilter;
+    const spill = await spillToDataset(spillInput);
     return {
         fullRows: spill.fullRows,
         dataset: toDatasetHandle(spill.dataset),
@@ -302,18 +334,19 @@ export async function spillToDataset(input) {
     const reachedRowCap = rows.length >= remainingTarget && input.totalCount > rows.length;
     const reachedPageCap = pagesFetched >= MAX_SPILLOVER_PAGES && input.totalCount > rows.length;
     const truncated = reachedRowCap || reachedPageCap;
+    const persistedRows = input.rowFilter ? rows.filter(input.rowFilter) : rows;
     const createInput = {
         source: input.source,
         baseUrl: input.connection.baseUrl,
         query: input.filters,
-        rows,
+        rows: persistedRows,
     };
     if (truncated) {
         createInput.truncated = true;
         createInput.maxRows = MAX_SPILLOVER_ROWS;
     }
     const dataset = await input.store.create(input.ctx, createInput);
-    return { dataset, fullRows: rows, pagesFetched };
+    return { dataset, fullRows: persistedRows, pagesFetched };
 }
 export function extractRows(result) {
     if (Array.isArray(result))

package/dist/mcp-server/tools/shared/find-helpers.js.map CHANGED Viewed

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package/package.json CHANGED Viewed

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.4.2",
+  "version": "0.4.3",
   "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 CHANGED Viewed

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.4.2",
+  "version": "0.4.3",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.4.2",
+      "version": "0.4.3",
       "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": "0.4.2",
+      "version": "0.4.3",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }