@cyanheads/brapi-mcp-server 0.4.2 → 0.4.4

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.4.2
+**Version:** 0.4.4
 **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-0.4.2-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-0.4.4-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

@@ -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/changelog/0.4.x/0.4.4.md

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

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

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

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

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

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

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

@@ -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"}
+{"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;AA4IjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAqS7B,CAAC"}

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

@@ -13,7 +13,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, 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.'),
@@ -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 ${firstPage.rows.length} returned rows.`);
             }
-            inContextRows = matched;
         }
+        const inContextRows = fullRows.slice(0, loadLimit);
         const result = {
             alias: connection.alias,
             results: inContextRows,
@@ -290,6 +303,25 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'germplasmName',
+                'defaultDisplayName',
+                'germplasmDbId',
+                'germplasmPUI',
+                'accessionNumber',
+                'commonCropName',
+                'genus',
+                'species',
+                'subtaxa',
+                'countryOfOriginCode',
+                'collection',
+                'instituteCode',
+                'instituteName',
+                'germplasmOrigin',
+                'biologicalStatusOfAccessionDescription',
+                'pedigree',
+                'synonyms',
+            ]);
             for (const g of result.results) {
                 const parts = [
                     `**${g.germplasmName ?? g.defaultDisplayName ?? g.germplasmDbId}**`,
@@ -316,7 +348,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                 if (g.instituteName)
                     parts.push(`instituteName=${g.instituteName}`);
                 if (g.germplasmOrigin?.length)
-                    parts.push(`germplasmOrigin=${g.germplasmOrigin.length} record(s)`);
+                    parts.push(`germplasmOrigin=${JSON.stringify(g.germplasmOrigin)}`);
                 if (g.biologicalStatusOfAccessionDescription)
                     parts.push(`status=${g.biologicalStatusOfAccessionDescription}`);
                 if (g.pedigree)
@@ -329,6 +361,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
                         .join(',');
                     parts.push(`synonyms=${synStr}`);
                 }
+                parts.push(...collectPassthroughParts(g, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-images.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-images.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-images.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AA0HjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BA6M1B,CAAC"}
+{"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;AA2HjD,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiO1B,CAAC"}

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

@@ -13,7 +13,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, 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.'),
@@ -242,6 +242,25 @@ export const brapiFindImages = tool('brapi_find_images', {
             lines.push('_No rows returned._');
         }
         else {
+            const RENDERED = new Set([
+                'imageName',
+                'imageFileName',
+                'imageDbId',
+                'mimeType',
+                'imageWidth',
+                'imageHeight',
+                'imageFileSize',
+                'observationUnitName',
+                'observationUnitDbId',
+                'observationDbIds',
+                'studyName',
+                'studyDbId',
+                'descriptiveOntologyTerms',
+                'imageTimeStamp',
+                'imageURL',
+                'copyright',
+                'description',
+            ]);
             for (const img of result.results) {
                 const parts = [`**${img.imageName ?? img.imageFileName ?? img.imageDbId}**`];
                 parts.push(`id=\`${img.imageDbId}\``);
@@ -275,6 +294,7 @@ export const brapiFindImages = tool('brapi_find_images', {
                     parts.push(`©${img.copyright}`);
                 if (img.description)
                     parts.push(`desc=${img.description}`);
+                parts.push(...collectPassthroughParts(img, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-locations.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAoIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAgQ7B,CAAC"}
+{"version":3,"file":"brapi-find-locations.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-locations.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAqIjD,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;6BAiR7B,CAAC"}

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

@@ -14,7 +14,7 @@ import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFilters, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, } from '../shared/find-helpers.js';
 const LocationRowSchema = z
     .object({
     locationDbId: z.string().describe('Server-side identifier for the location.'),
@@ -287,6 +287,22 @@ export const brapiFindLocations = tool('brapi_find_locations', {
             lines.push('_No rows returned._');
         }
         else {
+            // `coordinates` intentionally excluded: passthrough helper renders the full
+            // GeoJSON object so text-only clients see it alongside the extracted lat/lon.
+            const RENDERED = new Set([
+                'locationName',
+                'locationDbId',
+                'abbreviation',
+                'locationType',
+                'countryCode',
+                'countryName',
+                'latitude',
+                'longitude',
+                'altitude',
+                'instituteName',
+                'instituteAddress',
+                'documentationURL',
+            ]);
             for (const loc of result.results) {
                 const parts = [`**${loc.locationName ?? loc.locationDbId}**`];
                 parts.push(`id=\`${loc.locationDbId}\``);
@@ -314,6 +330,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
                     parts.push(`addr=${loc.instituteAddress}`);
                 if (loc.documentationURL)
                     parts.push(`docs=${loc.documentationURL}`);
+                parts.push(...collectPassthroughParts(loc, RENDERED));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }