npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.7 → 0.7.8 - Mend

@cyanheads/brapi-mcp-server 0.7.7 → 0.7.8

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Files changed (39) hide show

package/CLAUDE.md CHANGED Viewed

@@ -1,7 +1,7 @@
 # Agent Protocol
 **Server:** brapi-mcp-server
-**Version:** 0.7.7
+**Version:** 0.7.8
 **Framework:** [@cyanheads/mcp-ts-core](https://www.npmjs.com/package/@cyanheads/mcp-ts-core) `^0.10.14`
 > **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-0.7.7-blue.svg?style=flat-square)](./CHANGELOG.md) [![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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
+[![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-0.7.8-blue.svg?style=flat-square)](./CHANGELOG.md) [![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-v1.3.14-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
 </div>
@@ -46,7 +46,7 @@
 | `brapi_find_observations` | Pull observation records by study / germplasm / variable / season / unit / timestamp. Dataframe spillover. |
 | `brapi_find_images` | Filter image metadata by unit / study / ontology / MIME type. Bytes via `brapi_get_image`. |
 | `brapi_get_image` | Fetch image bytes for up to 5 imageDbIds inline as `type: image` blocks. Prefers `/imagecontent`, falls back to `imageURL`. |
-| `brapi_find_locations` | Find research stations by country / type / abbreviation, with optional client-side bbox filter. |
+| `brapi_find_locations` | Find research stations by country (ISO alpha-3 code, or English country name resolved client-side) / type / abbreviation, with optional client-side bbox filter. |
 | `brapi_find_variants` | Find variant records by variant set, reference, or genomic region (1-based inclusive / exclusive). |
 | `brapi_find_genotype_calls` | Pull genotype calls via async-search polling. Upstream pull bounded by `BRAPI_GENOTYPE_CALLS_MAX_PULL` (default 100k, max 500k). |
@@ -133,7 +133,7 @@ Within one (tenant, session), dataframes act as a self-cleaning shared notebook:
 - **Dialect adaptation** — `spec` / `brapi-test` / `breedbase` / `cassavabase` / `bms` dialects translate v2.1 plural filter keys to the singular form each server family honors, drop filters known to be broken, normalize sparse-shape encodings, and escalate to POST `/search/{noun}` when GET would silently downcast multi-value filters. Detected from `/serverinfo` (server-name / organization-name); pin per-alias via `BRAPI_<ALIAS>_DIALECT`. Verified-vs-inferred mapping counts surface on the orientation envelope so agents see the confidence floor at a glance.
 - **DuckDB required** — `@duckdb/node-api` is a regular dependency; startup fails closed when the framework canvas is unavailable. Not supported on Cloudflare Workers (no native binary in that runtime).
 - **Async-search transparency** — `brapi_find_genotype_calls` and `brapi_raw_search` handle the `POST /search/{noun}` → `GET /search/{noun}/{id}` 202-retry pattern automatically.
-- **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call); a 1,000-node safety cap bounds the walk and sets `truncated` when reached.
+- **Pedigree DAG walks** — `brapi_walk_pedigree` BFS-traverses ancestry / descendancy with cycle detection (BrAPI only exposes one generation per call); a 1,000-node safety cap bounds the walk and sets `truncated` when reached. Walks larger than `loadLimit` spill their node and edge sets to two JOINable canvas dataframes and return a bounded inline preview.
 - **Image content** — `brapi_get_image` fetches bytes inline as MCP `type: image` blocks, preferring `/images/{id}/imagecontent` with `imageURL` fallback.
 - **Free-text variable ranking** — `OntologyResolver` scores variables against a query (PUI / name / synonym / trait-class) so `find_variables text:"..."` returns ranked candidates even without `/ontologies`.
 - **Auth variants in one schema** — tagged-union covers `none` / `bearer` / `api_key` / `sgn` (session-token exchange) / `oauth2` (client-credentials).

package/changelog/0.7.x/0.7.8.md ADDED Viewed

@@ -0,0 +1,14 @@
+---
+summary: "brapi_germplasm_performance gains an optional studyDbIds bypass for its study-discovery cap; brapi_walk_pedigree spills node and edge sets exceeding loadLimit to two JOINable canvas dataframes; brapi_find_locations resolves free-form country names to ISO 3166-1 alpha-3 codes via a new iso-country service"
+breaking: false
+security: false
+---
+# 0.7.8 — 2026-07-16
+## Added
+- **`brapi_germplasm_performance` `studyDbIds`** — optional input that bypasses automatic study discovery (and its 200-study `STUDY_DISCOVERY_CAP`) entirely. Pass a specific set — e.g. the full germplasm-scoped list retrieved via `brapi_find_studies` with `extraFilters.germplasmDbIds` — to aggregate a slice discovery would otherwise cap. ([#43](https://github.com/cyanheads/brapi-mcp-server/issues/43))
+- **`germplasmDbIds`** — added to the `/studies` filter catalog (`brapi_describe_filters`); the capped-discovery warning on `brapi_germplasm_performance` now names this `brapi_find_studies` retrieval path alongside the `studyDbIds` input above. ([#43](https://github.com/cyanheads/brapi-mcp-server/issues/43))
+- **`brapi_walk_pedigree` dataframe spillover** — new `loadLimit` input; when the node or edge set exceeds it, both spill to two canvas dataframes (`nodesDataframe` / `edgesDataframe`, JOINable on `germplasmDbId`) with a bounded inline preview. Completes [#17](https://github.com/cyanheads/brapi-mcp-server/issues/17) — Part B of the walk's cap handling; the 1,000-node safety cap and truncation warning (Part A) shipped in [0.7.1](https://github.com/cyanheads/brapi-mcp-server/blob/main/changelog/0.7.x/0.7.1.md).
+- **`brapi_find_locations` `countryNames`** — free-form English country names and aliases (e.g. "Uganda", "USA") resolved client-side to ISO 3166-1 alpha-3 codes and merged into `countryCodes`; unresolved names surface as a warning. New `src/services/iso-country/` service backs the resolution — 249 countries, case- and diacritic-insensitive, accepts alpha-2/alpha-3 codes directly. ([#19](https://github.com/cyanheads/brapi-mcp-server/issues/19))

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

@@ -14,6 +14,7 @@ export declare const brapiFindLocations: import("@cyanheads/mcp-ts-core").ToolDe
     locations: z.ZodOptional<z.ZodArray<z.ZodString>>;
     locationNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
     countryCodes: z.ZodOptional<z.ZodArray<z.ZodString>>;
+    countryNames: z.ZodOptional<z.ZodArray<z.ZodString>>;
     locationTypes: z.ZodOptional<z.ZodArray<z.ZodString>>;
     abbreviations: z.ZodOptional<z.ZodArray<z.ZodString>>;
     bbox: z.ZodOptional<z.ZodObject<{

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

	@@ -1 +1 @@
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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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAmY7B,CAAC"}

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

@@ -14,6 +14,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { resolveCountryName } from '../../../services/iso-country/index.js';
 import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, extractCoordinates, hasPointGeometry, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const LocationRowSchema = z
     .object({
@@ -82,7 +83,7 @@ const SERVER_TO_USER = {
     abbreviation: 'abbreviations',
 };
 export const brapiFindLocations = tool('brapi_find_locations', {
-    description: 'Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Optional bbox parameter restricts rows to a latitude/longitude window. When the spec-correct GeoJSON [lon, lat, alt] reading produces zero matches and at least one row carries a Point geometry, the bbox filter retries once with axes swapped (handles non-conformant servers that store [lat, lon, alt]) and surfaces a warning + `coordinateAxisOrder: "swapped"`. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
+    description: 'Find research stations / field sites by country, abbreviation, type, location ID, or free-text. Countries filter by ISO 3166-1 alpha-3 code via countryCodes, or by free-form English country name via countryNames (resolved client-side to alpha-3 — "Uganda" → "UGA"). Optional bbox parameter restricts rows to a latitude/longitude window. When the spec-correct GeoJSON [lon, lat, alt] reading produces zero matches and at least one row carries a Point geometry, the bbox filter retries once with axes swapped (handles non-conformant servers that store [lat, lon, alt]) and surfaces a warning + `coordinateAxisOrder: "swapped"`. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -103,6 +104,10 @@ export const brapiFindLocations = tool('brapi_find_locations', {
         locations: z.array(z.string()).optional().describe('Filter by locationDbIds.'),
         locationNames: z.array(z.string()).optional().describe('Filter by display name.'),
         countryCodes: z.array(z.string()).optional().describe('ISO 3166-1 alpha-3 country codes.'),
+        countryNames: z
+            .array(z.string())
+            .optional()
+            .describe('Free-form English country names or aliases (e.g. "Uganda", "United States", "USA") resolved client-side to ISO 3166-1 alpha-3 codes and merged into countryCodes. Names that do not resolve surface as a warning. Prefer countryCodes when you already have alpha-3 codes.'),
         locationTypes: z
             .array(z.string())
             .optional()
@@ -201,10 +206,14 @@ export const brapiFindLocations = tool('brapi_find_locations', {
         const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const warnings = [];
+        // Resolve free-form country names to ISO 3166-1 alpha-3 codes and union
+        // them into the countryCodes filter slot before mergeFilters runs, so
+        // dialect adaptation, routing, and filter-match checks all see one set.
+        const combinedCountryCodes = resolveCountryCodes(input.countryCodes, input.countryNames, warnings);
         const merged = mergeFilters({
             locationDbIds: input.locations,
             locationNames: input.locationNames,
-            countryCodes: input.countryCodes,
+            countryCodes: combinedCountryCodes,
             locationTypes: input.locationTypes,
             abbreviations: input.abbreviations,
         }, input.extraFilters, warnings);
@@ -290,7 +299,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
         checkFilterMatchRates(warnings, filteredFull.length, [
             {
                 paramName: 'countryCodes',
-                requestedValues: input.countryCodes,
+                requestedValues: combinedCountryCodes,
                 distribution: distributions.countryCode,
                 caseInsensitive: true,
                 requireEveryRowMatch: true,
@@ -310,6 +319,7 @@ export const brapiFindLocations = tool('brapi_find_locations', {
                 'locations',
                 'locationNames',
                 'countryCodes',
+                'countryNames',
                 'locationTypes',
                 'abbreviations',
                 'bbox',
@@ -445,4 +455,36 @@ function insideBbox(row, bbox, axisOrder) {
     const { latitude: lat, longitude: lon } = coords;
     return lat >= bbox.minLat && lat <= bbox.maxLat && lon >= bbox.minLon && lon <= bbox.maxLon;
 }
+/**
+ * Resolve free-form `countryNames` to ISO 3166-1 alpha-3 codes and union them
+ * with any explicit `countryCodes`. Pushes a resolution advisory for names
+ * that mapped and a warning for names that did not. Returns the combined,
+ * de-duplicated code list, or `undefined` when neither input carried a value
+ * (so the upstream call stays unfiltered rather than sending an empty array).
+ */
+function resolveCountryCodes(countryCodes, countryNames, warnings) {
+    const resolved = [];
+    const unresolved = [];
+    for (const name of countryNames ?? []) {
+        const code = resolveCountryName(name);
+        if (code)
+            resolved.push({ input: name, code });
+        else
+            unresolved.push(name);
+    }
+    if (resolved.length > 0) {
+        warnings.push(`Resolved country name(s) to ISO 3166-1 alpha-3: ${resolved
+            .map((p) => `"${p.input}" → ${p.code}`)
+            .join(', ')}.`);
+    }
+    if (unresolved.length > 0) {
+        warnings.push(`Could not resolve country name(s) to an ISO 3166-1 alpha-3 code: ${unresolved
+            .map((n) => `"${n}"`)
+            .join(', ')}. Pass the alpha-3 code directly via countryCodes, or check the spelling.`);
+    }
+    const resolvedCodes = resolved.map((p) => p.code);
+    if (!countryCodes && resolvedCodes.length === 0)
+        return;
+    return [...new Set([...(countryCodes ?? []), ...resolvedCodes])];
+}
 //# sourceMappingURL=brapi-find-locations.tool.js.map

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

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

@@ -25,6 +25,7 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 export declare const brapiGermplasmPerformance: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
     alias: z.ZodOptional<z.ZodString>;
     germplasmDbId: z.ZodString;
+    studyDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
     variables: z.ZodOptional<z.ZodArray<z.ZodString>>;
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-germplasm-performance.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-germplasm-performance.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;AAGH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAwGjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2LpC,CAAC"}

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

@@ -100,7 +100,7 @@ const OutputSchema = z.object({
 // Tool definition
 // ---------------------------------------------------------------------------
 export const brapiGermplasmPerformance = tool('brapi_germplasm_performance', {
-    description: "Aggregate a single germplasm's observations across every study it appears in, returning per-variable summary statistics (n, mean, median, sd, min, max), the contributing studies, and seasons. Study-anchored: discovers the germplasm's studies first (with a dialect-honor cross-check), then pulls observations per study — avoids the unanchored germplasm-only pull that stalls on SGN/Breedbase. For the underlying observation matrix, use brapi_build_phenotype_matrix.",
+    description: "Aggregate a single germplasm's observations across every study it appears in, returning per-variable summary statistics (n, mean, median, sd, min, max), the contributing studies, and seasons. Study-anchored: discovers the germplasm's studies first (with a dialect-honor cross-check, capped at 200 studies), then pulls observations per study — avoids the unanchored germplasm-only pull that stalls on SGN/Breedbase. Pass an explicit studyDbIds set to skip discovery and its 200-study cap — e.g. process a chunk of the full study list retrieved via brapi_find_studies with extraFilters.germplasmDbIds. For the underlying observation matrix, use brapi_build_phenotype_matrix.",
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -119,6 +119,10 @@ export const brapiGermplasmPerformance = tool('brapi_germplasm_performance', {
     input: z.object({
         alias: AliasInput,
         germplasmDbId: z.string().min(1).describe('The germplasmDbId to summarize performance for.'),
+        studyDbIds: z
+            .array(z.string().min(1))
+            .optional()
+            .describe('Optional explicit set of studyDbIds to aggregate over. When supplied, skips automatic study discovery and its 200-study cap entirely — use it to process a specific slice of studies, e.g. the full germplasm-scoped study set retrieved via brapi_find_studies with extraFilters.germplasmDbIds. Omit to let the tool discover the germplasm’s studies automatically.'),
         variables: z
             .array(z.string())
             .optional()
@@ -140,27 +144,37 @@ export const brapiGermplasmPerformance = tool('brapi_germplasm_performance', {
         const dialect = await resolveDialect(connection, ctx, capabilityLookup);
         const loadLimit = config.loadLimit;
         const warnings = [];
-        // 2. Discover the germplasm's studies (study-anchoring requirement).
-        const discovery = await discoverStudiesForGermplasm({
-            client,
-            connection,
-            dialect,
-            germplasmDbId: input.germplasmDbId,
-            ctx,
-            warnings,
-        });
-        if (discovery.studyDbIds.length === 0) {
-            warnings.push(`No studies discovered for germplasm '${input.germplasmDbId}'. It may not be associated with any study on this server, or /studies does not support a germplasm filter — use brapi_build_phenotype_matrix with explicit studies instead.`);
+        // 2. Determine the study set. An explicit studyDbIds set bypasses automatic
+        //    discovery (and its STUDY_DISCOVERY_CAP) entirely — e.g. a caller
+        //    feeding back a chunk of the full germplasm-scoped study list retrieved
+        //    via brapi_find_studies with extraFilters.germplasmDbIds.
+        let studyDbIds;
+        if (input.studyDbIds && input.studyDbIds.length > 0) {
+            studyDbIds = [...new Set(input.studyDbIds)];
         }
-        else if (discovery.studyDbIds.length >= STUDY_DISCOVERY_CAP) {
-            warnings.push(`Study discovery capped at ${STUDY_DISCOVERY_CAP} studies — aggregates may be incomplete. Narrow with brapi_build_phenotype_matrix on specific studies if needed.`);
+        else {
+            const discovery = await discoverStudiesForGermplasm({
+                client,
+                connection,
+                dialect,
+                germplasmDbId: input.germplasmDbId,
+                ctx,
+                warnings,
+            });
+            studyDbIds = discovery.studyDbIds;
+            if (studyDbIds.length === 0) {
+                warnings.push(`No studies discovered for germplasm '${input.germplasmDbId}'. It may not be associated with any study on this server, or /studies does not support a germplasm filter — use brapi_build_phenotype_matrix with explicit studies instead.`);
+            }
+            else if (studyDbIds.length >= STUDY_DISCOVERY_CAP) {
+                warnings.push(`Study discovery capped at ${STUDY_DISCOVERY_CAP} studies — aggregates may be incomplete. To retrieve the full study set, call brapi_find_studies with extraFilters.germplasmDbIds set to ['${input.germplasmDbId}'] — it pages the complete germplasm-scoped study list (dataframe-backed when large) — then pass those studyDbIds back as the studyDbIds input here to aggregate the omitted slice. Or narrow with brapi_build_phenotype_matrix on specific studies.`);
+            }
         }
         // 3. Pull observations per study, scoped to the germplasm. Filter returned
         //    rows to the iterated study + target germplasm so the aggregate stays
         //    correct on servers that ignore the studyDbId filter or over-return.
         const collected = [];
         const wantVariables = input.variables?.length ? new Set(input.variables) : undefined;
-        for (const studyDbId of discovery.studyDbIds) {
+        for (const studyDbId of studyDbIds) {
             let studyObs;
             try {
                 studyObs = await pullStudyObservations({

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package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.d.ts CHANGED Viewed

@@ -18,6 +18,7 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
         descendants: "descendants";
     }>>;
     maxDepth: z.ZodDefault<z.ZodNumber>;
+    loadLimit: z.ZodOptional<z.ZodNumber>;
     alias: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;
@@ -55,6 +56,28 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
     deadEndCount: z.ZodNumber;
     truncated: z.ZodBoolean;
     warnings: z.ZodArray<z.ZodString>;
+    nodesDataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
+        rowCount: z.ZodNumber;
+        columns: z.ZodArray<z.ZodString>;
+        columnLegend: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodString>>;
+        createdAt: z.ZodString;
+        expiresAt: z.ZodString;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+        maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>>;
+    edgesDataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
+        rowCount: z.ZodNumber;
+        columns: z.ZodArray<z.ZodString>;
+        columnLegend: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodString>>;
+        createdAt: z.ZodString;
+        expiresAt: z.ZodString;
+        truncated: z.ZodOptional<z.ZodBoolean>;
+        maxRows: z.ZodOptional<z.ZodNumber>;
+        totalCount: z.ZodOptional<z.ZodNumber>;
+    }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: JsonRpcErrorCode.NotFound;

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-walk-pedigree.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;~~AAmGjE~~,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmP5B~~,CAAC"}
1	+ {"version":3,"file":"brapi-walk-pedigree.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-walk-pedigree.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAoT5B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js CHANGED Viewed

@@ -10,9 +10,11 @@
  */
 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 { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { AliasInput, buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { AliasInput, buildRequestOptions, DataframeHandleSchema, isUpstreamNotFound, LoadLimitInput, renderDataframeHandle, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
 const DEFAULT_MAX_DEPTH = 3;
 const MAX_NODES = 1_000;
 const NodeSchema = z
@@ -86,6 +88,8 @@ const OutputSchema = z.object({
     warnings: z
         .array(z.string())
         .describe('Advisory messages (capability gaps, per-node expansion failures).'),
+    nodesDataframe: DataframeHandleSchema.optional().describe('Canvas dataframe holding the full node set, present when the walk exceeds loadLimit — nodes[] is then a bounded preview. Query with brapi_dataframe_query (SQL); JOIN to the edges dataframe on germplasmDbId.'),
+    edgesDataframe: DataframeHandleSchema.optional().describe('Canvas dataframe holding the full edge set, present when the walk exceeds loadLimit — edges[] is then a bounded preview. Any edge field that is a reserved SQL word (e.g. `from` → `from_`) is renamed to a SQL-safe identifier; columnLegend maps it back. Query with brapi_dataframe_query (SQL).'),
 });
 export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
     description: 'Walk germplasm ancestry or descendancy as a deduplicated DAG, with multi-generation traversal, cycle detection, and depth limits. Returns nodes + edges plus traversal stats (depthReached, rootCount, leafCount, cycleCount, deadEndCount).',
@@ -115,6 +119,7 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
             .max(10)
             .default(DEFAULT_MAX_DEPTH)
             .describe(`Max generations to walk per direction (default ${DEFAULT_MAX_DEPTH}, cap 10).`),
+        loadLimit: LoadLimitInput,
         alias: AliasInput,
     }),
     output: OutputSchema,
@@ -238,12 +243,53 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         const nodes = Array.from(state.nodes.values()).sort((a, b) => a.depth - b.depth || a.germplasmDbId.localeCompare(b.germplasmDbId));
         const edges = Array.from(state.edges.values());
         const leafCount = computeLeafCount(nodes, edges, input.direction);
+        // Spillover: when the full graph exceeds loadLimit, materialize the node
+        // and edge sets as two canvas dataframes (JOINable on germplasmDbId) and
+        // return a bounded preview inline — mirrors the find_* pattern. The stats
+        // above still describe the full walk; small walks stay inline-only.
+        const loadLimit = input.loadLimit ?? getServerConfig().loadLimit;
+        let previewNodes = nodes;
+        let previewEdges = edges;
+        let nodesDataframe;
+        let edgesDataframe;
+        if (nodes.length > loadLimit || edges.length > loadLimit) {
+            const bridge = getCanvasBridge();
+            const query = {
+                germplasmDbIds: input.germplasmDbIds,
+                direction: input.direction,
+                maxDepth: input.maxDepth,
+            };
+            // Register sequentially, not in parallel: the first call resolves and
+            // caches the default canvas in ctx.state; a concurrent second call would
+            // race that cache and land the two tables on different canvases, breaking
+            // the JOIN. Both tables must share one canvas.
+            if (nodes.length > 0) {
+                const reg = await bridge.registerDataframe(ctx, {
+                    source: 'walk_pedigree_nodes',
+                    baseUrl: connection.baseUrl,
+                    query,
+                    rows: nodes,
+                });
+                nodesDataframe = toDataframeHandle(reg, nodes.length);
+                previewNodes = nodes.slice(0, loadLimit);
+            }
+            if (edges.length > 0) {
+                const reg = await bridge.registerDataframe(ctx, {
+                    source: 'walk_pedigree_edges',
+                    baseUrl: connection.baseUrl,
+                    query,
+                    rows: edges,
+                });
+                edgesDataframe = toDataframeHandle(reg, edges.length);
+                previewEdges = edges.slice(0, loadLimit);
+            }
+        }
         const result = {
             alias: connection.alias,
             direction: input.direction,
             maxDepth: input.maxDepth,
-            nodes,
-            edges,
+            nodes: previewNodes,
+            edges: previewEdges,
             depthReached,
             rootCount: input.germplasmDbIds.length,
             leafCount,
@@ -252,6 +298,10 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
             truncated,
             warnings,
         };
+        if (nodesDataframe)
+            result.nodesDataframe = nodesDataframe;
+        if (edgesDataframe)
+            result.edgesDataframe = edgesDataframe;
         return result;
     },
     format: (result) => {
@@ -268,7 +318,9 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         lines.push(`- truncated: ${result.truncated}`);
         if (result.nodes.length > 0) {
             lines.push('');
-            lines.push('## Nodes');
+            lines.push(result.nodesDataframe
+                ? `## Nodes (preview — ${result.nodes.length} of ${result.nodesDataframe.rowCount}; full set in dataframe \`${result.nodesDataframe.tableName}\`)`
+                : '## Nodes');
             for (const node of result.nodes) {
                 const parts = [`**${node.germplasmName ?? node.germplasmDbId}**`];
                 parts.push(`id=\`${node.germplasmDbId}\``);
@@ -279,13 +331,25 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         }
         if (result.edges.length > 0) {
             lines.push('');
-            lines.push('## Edges');
+            lines.push(result.edgesDataframe
+                ? `## Edges (preview — ${result.edges.length} of ${result.edgesDataframe.rowCount}; full set in dataframe \`${result.edgesDataframe.tableName}\`)`
+                : '## Edges');
             for (const edge of result.edges) {
                 const suffix = edge.parentType ? ` (${edge.parentType})` : '';
                 const arrow = edge.relationship === 'parent' ? '→' : '←';
                 lines.push(`- \`${edge.from}\` ${arrow} \`${edge.to}\` · ${edge.relationship}${suffix}`);
             }
         }
+        if (result.nodesDataframe) {
+            lines.push('');
+            lines.push('## Nodes dataframe');
+            lines.push(...renderDataframeHandle(result.nodesDataframe));
+        }
+        if (result.edgesDataframe) {
+            lines.push('');
+            lines.push('## Edges dataframe');
+            lines.push(...renderDataframeHandle(result.edgesDataframe));
+        }
         if (result.warnings.length > 0) {
             lines.push('');
             lines.push('## Warnings');