@cyanheads/brapi-mcp-server 0.6.3 → 0.6.4

package/CLAUDE.md

@@ -1,7 +1,7 @@
 # Agent Protocol
 
 **Server:** brapi-mcp-server
-**Version:** 0.6.3
+**Version:** 0.6.4
 **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-0.6.3-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-v1.3.11-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-0.6.4-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-v1.3.11-blueviolet.svg?style=flat-square)](https://bun.sh/) [![Status](https://img.shields.io/badge/Status-Beta-yellow.svg?style=flat-square)](./CHANGELOG.md)
 
 </div>
 

package/changelog/0.6.x/0.6.4.md

@@ -0,0 +1,14 @@
+---
+summary: "Enrichment adoption — brapi_find_* tools now surface filter echoes, result totals, and empty-result guidance via ctx.enrich(); @cyanheads/mcp-ts-core ^0.9.13 → ^0.9.16"
+breaking: false
+security: false
+---
+
+# 0.6.4 — 2026-05-30
+
+## Changed
+
+- **`brapi_find_studies`, `brapi_find_germplasm`, `brapi_find_observations`, `brapi_find_variables`, `brapi_find_images`, `brapi_find_locations`, `brapi_find_variants`, `brapi_find_genotype_calls`** — `returnedCount`, `totalCount`, `appliedFilters`, `refinementHint`, and `warnings` moved from the `output` schema into a typed `enrichment` block via `ctx.enrich()`. Both `structuredContent` (JSON) and the `content[]` markdown trailer receive the enrichment; the domain return type no longer carries these fields. An `enrich.notice()` fires when a tool returns zero rows, surfacing filter-broadening guidance.
+- **`renderFindHeader()`** — `totalCount` is now optional; omitted when the server does not report a total (renders `N <noun>` instead of `N of M <noun>`).
+- **`@cyanheads/mcp-ts-core`** ^0.9.13 → ^0.9.16.
+- **`format:unsafe` script** separated from `format` (`biome check --write` vs `biome check --write --unsafe`).

package/changelog/template.md

@@ -43,7 +43,7 @@ security: false
   name the symbol, state what changed, stop. Use a second sentence only when
   it carries weight. If a bullet feels long, it is.
 
-  Cut: mechanism walkthroughs (those belong in JSDoc, AGENTS.md, or the
+  Cut: mechanism walkthroughs (those belong in JSDoc, CLAUDE.md/AGENTS.md, or the
   relevant skill), ceremonial framings ("This release introduces…",
   backwards-compat paragraphs), file-by-file test enumerations, internal
   implementation notes. Prefer code/symbol names over English re-explanations.

package/dist/mcp-server/tools/definitions/brapi-connect.tool.d.ts

@@ -99,5 +99,5 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "Token endpoint responded but did not return an access_token";
     readonly recovery: "Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-connect.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAyFvB,CAAC"}
+{"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAyFvB,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts

@@ -38,5 +38,5 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
     readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-describe.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;GAkCjC,CAAC"}
+{"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts

@@ -15,5 +15,5 @@ export declare const brapiDataframeDrop: import("@cyanheads/mcp-ts-core").ToolDe
 }, z.core.$strip>, z.ZodObject<{
     dataframe: z.ZodString;
     dropped: z.ZodBoolean;
-}, z.core.$strip>, undefined>;
+}, z.core.$strip>, undefined, undefined>;
 //# sourceMappingURL=brapi-dataframe-drop.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-drop.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;6BAqB7B,CAAC"}
+{"version":3,"file":"brapi-dataframe-drop.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-drop.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;GAUG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAmBjD,eAAO,MAAM,kBAAkB;;;;;wCAqB7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts

@@ -65,5 +65,5 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "Both `columns` and `sql` were supplied";
     readonly recovery: "Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-export.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-export.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkH/B,CAAC"}
+{"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkH/B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts

@@ -42,5 +42,5 @@ export declare const brapiDataframeQuery: import("@cyanheads/mcp-ts-core").ToolD
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)";
     readonly recovery: "Submit a single SELECT statement using only registered dataframes. For changes, use `registerAs` in this tool to materialize a result, or brapi_dataframe_drop to remove a dataframe.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-dataframe-query.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;GAmE9B,CAAC"}
+{"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;;;;;cAmE9B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts

@@ -37,5 +37,5 @@ export declare const brapiDescribeFilters: import("@cyanheads/mcp-ts-core").Tool
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "No filter catalog is registered for the requested endpoint";
     readonly recovery: "Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-describe-filters.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-describe-filters.tool.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"brapi-describe-filters.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-describe-filters.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA2E/B,CAAC"}
+{"version":3,"file":"brapi-describe-filters.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-describe-filters.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA2E/B,CAAC"}

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

@@ -41,8 +41,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     callFormatting: z.ZodObject<{
         expandHomozygotes: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
@@ -65,8 +63,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         maxRows: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     truncated: z.ZodBoolean;
-    warnings: z.ZodArray<z.ZodString>;
-    searchBody: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: JsonRpcErrorCode.NotFound;
@@ -82,5 +78,11 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
     readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
-}]>;
+}], {
+    readonly totalCount: z.ZodNumber;
+    readonly returnedCount: z.ZodNumber;
+    readonly appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly warnings: z.ZodArray<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-find-genotype-calls.tool.d.ts.map

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;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8HjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA4NjC,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;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqQjC,CAAC"}

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

@@ -54,12 +54,6 @@ const CallRowSchema = z
 const OutputSchema = z.object({
     alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
     results: z.array(CallRowSchema).describe('Call rows returned in-context (up to loadLimit).'),
-    returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
-    totalCount: z
-        .number()
-        .int()
-        .nonnegative()
-        .describe('Total calls collected across all pages (may be capped by the deployment-wide pull limit; check `truncated`).'),
     hasMore: z
         .boolean()
         .describe('True when the collection was truncated (equivalent to `truncated`).'),
@@ -100,10 +94,6 @@ const OutputSchema = z.object({
     truncated: z
         .boolean()
         .describe('True when the deployment-wide pull limit was reached and more calls exist upstream. Narrow the filters and re-pull, or query the spilled dataframe.'),
-    warnings: z
-        .array(z.string())
-        .describe('Advisory messages (truncation, capability gaps, partial pulls).'),
-    searchBody: z.record(z.string(), z.unknown()).describe('The body sent to /search/calls.'),
 });
 export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
     description: 'Pull genotype calls for a germplasm × variant set. Filter to bound cost — at minimum, set `variantSetDbId` or `germplasmDbIds`. The upstream pull is capped by deployment policy; when the pull is truncated, narrow the filters or query the spilled dataframe. `loadLimit` bounds the rows returned inline; the full collected set is materialized as a dataframe — query it with brapi_dataframe_query (SQL) instead of paging row-by-row.',
@@ -157,6 +147,47 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             .describe('Cap on rows returned inline. Omit for the deployment default. When the collected set exceeds this, the full result lands in a dataframe and only the first `loadLimit` rows return inline — query the dataframe with brapi_dataframe_query (SQL) for the rest. Upstream pageSize is fixed for genotype calls, so this knob only affects the inline preview here (no spillover capacity tradeoff).'),
     }),
     output: OutputSchema,
+    // Agent-facing success-path context: total collected count, in-context count,
+    // the exact body sent to /search/calls, empty-result guidance, and advisory
+    // warnings. Populated via ctx.enrich() so it reaches both structuredContent
+    // and the content[] trailer without living in the domain return.
+    enrichment: {
+        totalCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .describe('Total calls collected across all pages (may be capped by the deployment-wide pull limit; check `truncated`).'),
+        returnedCount: z
+            .number()
+            .int()
+            .nonnegative()
+            .describe('Length of results[] — rows returned in-context (up to loadLimit).'),
+        appliedFilters: z
+            .record(z.string(), z.unknown())
+            .describe('The body sent to POST /search/calls (variant/germplasm/call-set scope plus pageSize).'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance when no calls were returned — how to broaden filters or verify IDs.'),
+        warnings: z
+            .array(z.string())
+            .describe('Advisory messages (truncation, capability gaps, partial pulls).'),
+    },
+    enrichmentTrailer: {
+        appliedFilters: {
+            render: (filters) => {
+                const entries = Object.entries(filters);
+                if (entries.length === 0)
+                    return '**Search body:** none';
+                const lines = entries.map(([k, v]) => `- **${k}:** ${Array.isArray(v) ? v.join(', ') : String(v)}`);
+                return `**Search body:**\n${lines.join('\n')}`;
+            },
+        },
+        warnings: {
+            render: (ws) => (ws.length > 0 ? ws.map((w) => `- ${w}`).join('\n') : '_none_'),
+            label: 'Warnings',
+        },
+    },
     async handler(input, ctx) {
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
@@ -195,9 +226,6 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             variantName: computeDistribution(collected.rows, (r) => asString(r.variantName)),
             variantSetDbId: computeDistribution(collected.rows, (r) => asString(r.variantSetDbId)),
         };
-        if (collected.rows.length === 0) {
-            warnings.push('Upstream returned 0 calls for the requested filters. The variant set or filter combination may not match any data on this server.');
-        }
         const shouldSpill = collected.rows.length > loadLimit;
         let dataframeHandle;
         if (shouldSpill) {
@@ -211,17 +239,21 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
                 maxRows: maxCalls,
             });
         }
+        ctx.enrich({
+            totalCount: collected.rows.length,
+            returnedCount: inContext.length,
+            appliedFilters: searchBody,
+            warnings,
+        });
+        if (collected.rows.length === 0)
+            ctx.enrich.notice('No calls matched the requested filters. The variant set or filter combination may not match any data on this server — broaden the scope (variantSetDbId, germplasmDbIds) or verify the IDs.');
         const result = {
             alias: connection.alias,
             results: inContext,
-            returnedCount: inContext.length,
-            totalCount: collected.rows.length,
             hasMore: collected.truncated,
             callFormatting: collected.callFormatting,
             distributions,
             truncated: collected.truncated,
-            warnings,
-            searchBody,
         };
         if (dataframeHandle)
             result.dataframe = dataframeHandle;
@@ -232,14 +264,11 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
         const headerBase = renderFindHeader({
             noun: 'calls',
             alias: result.alias,
-            returnedCount: result.returnedCount,
-            totalCount: result.totalCount,
+            returnedCount: result.results.length,
             dataframe: result.dataframe,
         });
         lines.push(result.truncated ? `${headerBase} (truncated at deployment pull limit)` : headerBase);
         lines.push('');
-        lines.push(`Search body: \`${JSON.stringify(result.searchBody)}\``);
-        lines.push('');
         lines.push('## Call formatting');
         const f = result.callFormatting;
         lines.push(`- expandHomozygotes: ${f.expandHomozygotes ?? '—'}`);
@@ -290,12 +319,6 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
             lines.push('## Dataframe handle');
             lines.push(...renderDataframeHandle(result.dataframe));
         }
-        if (result.warnings.length > 0) {
-            lines.push('');
-            lines.push('## Warnings');
-            for (const w of result.warnings)
-                lines.push(`- ${w}`);
-        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-find-genotype-calls.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAgB,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAoB,cAAc,EAAE,MAAM,kCAAkC,CAAC;AACpF,OAAO,EAAE,cAAc,EAAE,MAAM,mCAAmC,CAAC;AACnE,OAAO,EAEL,eAAe,GAEhB,MAAM,mCAAmC,CAAC;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAEhF,OAAO,EACL,UAAU,EACV,QAAQ,EACR,mBAAmB,EACnB,uBAAuB,EACvB,mBAAmB,EACnB,qBAAqB,EACrB,qBAAqB,EACrB,mBAAmB,EACnB,gBAAgB,EAChB,2BAA2B,EAC3B,iBAAiB,GAClB,MAAM,2BAA2B,CAAC;AAEnC,MAAM,SAAS,GAAG,MAAM,CAAC;AAEzB,MAAM,aAAa,GAAG,CAAC;KACpB,MAAM,CAAC;IACN,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CAAC,sEAAsE,CAAC;IACnF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IAC3E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IAC7E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IAClF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;IAC3F,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC,CAAC;aACtD,OAAO,EAAE;aACT,QAAQ,CAAC,qEAAqE,CAAC;KACnF,CAAC;SACD,WAAW,EAAE;SACb,OAAO,EAAE;SACT,QAAQ,CACP,mFAAmF,CACpF;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CACP,uFAAuF,CACxF;IACH,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,WAAW,EAAE;KACb,QAAQ,CAAC,wBAAwB,CAAC,CAAC;AAEtC,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;IACrF,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC5F,aAAa,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,GAAG,EAAE,CAAC,WAAW,EAAE,CAAC,QAAQ,CAAC,wBAAwB,CAAC;IAChF,UAAU,EAAE,CAAC;SACV,MAAM,EAAE;SACR,GAAG,EAAE;SACL,WAAW,EAAE;SACb,QAAQ,CACP,8GAA8G,CAC/G;IACH,OAAO,EAAE,CAAC;SACP,OAAO,EAAE;SACT,QAAQ,CAAC,qEAAqE,CAAC;IAClF,cAAc,EAAE,CAAC;SACd,MAAM,CAAC;QACN,iBAAiB,EAAE,CAAC;aACjB,OAAO,EAAE;aACT,OAAO,EAAE;aACT,QAAQ,CAAC,2DAA2D,CAAC;QACxE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,6DAA6D,CAAC;QAC1E,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,yDAAyD,CAAC;QACtE,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,2DAA2D,CAAC;KACzE,CAAC;SACD,QAAQ,CAAC,+CAA+C,CAAC;IAC5D,aAAa,EAAE,CAAC;SACb,MAAM,CAAC;QACN,WAAW,EAAE,CAAC;aACX,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,+CAA+C,CAAC;QAC5D,WAAW,EAAE,CAAC;aACX,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,iDAAiD,CAAC;QAC9D,cAAc,EAAE,CAAC;aACd,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,gDAAgD,CAAC;KAC9D,CAAC;SACD,QAAQ,CAAC,+DAA+D,CAAC;IAC5E,SAAS,EAAE,qBAAqB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAClD,kJAAkJ,CACnJ;IACD,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,CACP,qJAAqJ,CACtJ;IACH,QAAQ,EAAE,CAAC;SACR,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;SACjB,QAAQ,CAAC,iEAAiE,CAAC;IAC9E,UAAU,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,QAAQ,CAAC,iCAAiC,CAAC;CAC1F,CAAC,CAAC;AAIH,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,2BAA2B,EAAE;IACtE,WAAW,EACT,+aAA+a;IACjb,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EACN,6HAA6H;SAChI;QACD;YACE,MAAM,EAAE,YAAY;YACpB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,qEAAqE;YAC3E,QAAQ,EACN,gGAAgG;SACnG;QACD;YACE,MAAM,EAAE,0BAA0B;YAClC,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,6EAA6E;YACnF,QAAQ,EACN,+HAA+H;SAClI;KACO;IACV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,UAAU;QACjB,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,eAAe,EAAE,CAAC;aACf,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,cAAc,EAAE,CAAC;aACd,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,0CAA0C,CAAC;QACvD,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC9F,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QACvF,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,CAAC,CAAC;aAC5C,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,mYAAmY,CACpY;KACJ,CAAC;IACF,MAAM,EAAE,YAAY;IAEpB,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;QAC7C,MAAM,MAAM,GAAG,cAAc,EAAE,CAAC;QAChC,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QAEjC,MAAM,UAAU,GAAG,MAAM,2BAA2B,CAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC;QAEvE,MAAM,gBAAgB,GAA8C,EAAE,CAAC;QACvE,IAAI,UAAU,CAAC,YAAY;YAAE,gBAAgB,CAAC,IAAI,GAAG,UAAU,CAAC,YAAY,CAAC;QAC7E,MAAM,YAAY,CAAC,MAAM,CACvB,UAAU,CAAC,OAAO,EAClB,EAAE,OAAO,EAAE,cAAc,EAAE,MAAM,EAAE,MAAM,EAAE,EAC3C,GAAG,EACH,gBAAgB,CACjB,CAAC;QAEF,MAAM,OAAO,GAAG,MAAM,cAAc,CAAC,UAAU,EAAE,GAAG,EAAE,gBAAgB,CAAC,CAAC;QACxE,IAAI,OAAO,CAAC,uBAAuB,EAAE,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;YAClD,MAAM,GAAG,CAAC,IAAI,CACZ,0BAA0B,EAC1B,YAAY,OAAO,CAAC,EAAE,qIAAqI,EAC3J,EAAE,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,0BAA0B,CAAC,EAAE,CAC1E,CAAC;QACJ,CAAC;QAED,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QACjC,MAAM,QAAQ,GAAG,MAAM,CAAC,oBAAoB,CAAC;QAC7C,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,IAAI,MAAM,CAAC,SAAS,CAAC;QAEtD,MAAM,UAAU,GAAG,eAAe,CAAC,KAAK,CAAC,CAAC;QAC1C,IACE,CAAC,UAAU,CAAC,eAAe;YAC3B,CAAC,UAAU,CAAC,cAAc;YAC1B,CAAC,UAAU,CAAC,YAAY;YACxB,CAAC,UAAU,CAAC,YAAY,EACxB,CAAC;YACD,MAAM,GAAG,CAAC,IAAI,CACZ,YAAY,EACZ,4KAA4K,EAC5K,EAAE,OAAO,EAAE,UAAU,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAC1D,CAAC;QACJ,CAAC;QAED,MAAM,QAAQ,GAAa,EAAE,CAAC;QAC9B,MAAM,SAAS,GAAG,MAAM,YAAY,CAAC;YACnC,MAAM;YACN,UAAU;YACV,GAAG;YACH,IAAI,EAAE,UAAU;YAChB,QAAQ;YACR,QAAQ;SACT,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;QACrD,MAAM,aAAa,GAAG;YACpB,WAAW,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;YAChF,WAAW,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;YAChF,cAAc,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC;SACvF,CAAC;QAEF,IAAI,SAAS,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,QAAQ,CAAC,IAAI,CACX,mIAAmI,CACpI,CAAC;QACJ,CAAC;QAED,MAAM,WAAW,GAAG,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAC;QACtD,IAAI,eAAkE,CAAC;QACvE,IAAI,WAAW,EAAE,CAAC;YAChB,eAAe,GAAG,MAAM,UAAU,CAAC;gBACjC,MAAM;gBACN,GAAG;gBACH,UAAU;gBACV,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,SAAS,CAAC,IAAI;gBACpB,SAAS,EAAE,SAAS,CAAC,SAAS;gBAC9B,OAAO,EAAE,QAAQ;aAClB,CAAC,CAAC;QACL,CAAC;QAED,MAAM,MAAM,GAAW;YACrB,KAAK,EAAE,UAAU,CAAC,KAAK;YACvB,OAAO,EAAE,SAAS;YAClB,aAAa,EAAE,SAAS,CAAC,MAAM;YAC/B,UAAU,EAAE,SAAS,CAAC,IAAI,CAAC,MAAM;YACjC,OAAO,EAAE,SAAS,CAAC,SAAS;YAC5B,cAAc,EAAE,SAAS,CAAC,cAAc;YACxC,aAAa;YACb,SAAS,EAAE,SAAS,CAAC,SAAS;YAC9B,QAAQ;YACR,UAAU;SACX,CAAC;QACF,IAAI,eAAe;YAAE,MAAM,CAAC,SAAS,GAAG,eAAe,CAAC;QACxD,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,MAAM,UAAU,GAAG,gBAAgB,CAAC;YAClC,IAAI,EAAE,OAAO;YACb,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,aAAa,EAAE,MAAM,CAAC,aAAa;YACnC,UAAU,EAAE,MAAM,CAAC,UAAU;YAC7B,SAAS,EAAE,MAAM,CAAC,SAAS;SAC5B,CAAC,CAAC;QACH,KAAK,CAAC,IAAI,CACR,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,UAAU,uCAAuC,CAAC,CAAC,CAAC,UAAU,CACrF,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,kBAAkB,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,UAAU,CAAC,IAAI,CAAC,CAAC;QACpE,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;QACjC,MAAM,CAAC,GAAG,MAAM,CAAC,cAAc,CAAC;QAChC,KAAK,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC,iBAAiB,IAAI,GAAG,EAAE,CAAC,CAAC;QACjE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,aAAa,IAAI,GAAG,EAAE,CAAC,CAAC;QACzD,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,SAAS,IAAI,GAAG,EAAE,CAAC,CAAC;QACjD,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,WAAW,IAAI,GAAG,EAAE,CAAC,CAAC;QACrD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC;QAC/B,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,MAAM,CAAC,aAAa,CAAC,IAAI,2BAA2B,CAAC,CAAC;QACrF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACvB,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC;gBACvB,aAAa;gBACb,aAAa;gBACb,aAAa;gBACb,aAAa;gBACb,gBAAgB;gBAChB,UAAU;gBACV,eAAe;gBACf,UAAU;aACX,CAAC,CAAC;YACH,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBAClC,MAAM,KAAK,GAAa,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,WAAW,IAAI,GAAG,IAAI,CAAC,CAAC;gBACjE,IAAI,IAAI,CAAC,WAAW;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;gBACpE,KAAK,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,WAAW,IAAI,GAAG,EAAE,CAAC,CAAC;gBACrE,IAAI,IAAI,CAAC,WAAW;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;gBACpE,IAAI,IAAI,CAAC,cAAc;oBAAE,KAAK,CAAC,IAAI,CAAC,OAAO,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;gBAClE,IAAI,IAAI,CAAC,QAAQ;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;gBAC3E,IAAI,IAAI,CAAC,aAAa;oBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC;gBAC1E,IAAI,IAAI,CAAC,QAAQ;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;gBAC3D,KAAK,CAAC,IAAI,CAAC,GAAG,uBAAuB,CAAC,IAA+B,EAAE,QAAQ,CAAC,CAAC,CAAC;gBAClF,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YACvC,CAAC;QACH,CAAC;QACD,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;YAClC,KAAK,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC;QACzD,CAAC;QACD,IAAI,MAAM,CAAC,QAAQ,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;YAC/B,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,aAAa,CAAC,CAAC;YAC1B,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,QAAQ;gBAAE,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;QACxD,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC;AAEH,SAAS,eAAe,CACtB,KAA2D;IAE3D,MAAM,IAAI,GAA4B,EAAE,CAAC;IACzC,IAAI,KAAK,CAAC,cAAc;QAAE,IAAI,CAAC,eAAe,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;IACxE,IAAI,KAAK,CAAC,eAAe,EAAE,MAAM,EAAE,CAAC;QAClC,IAAI,CAAC,eAAe,GAAG,KAAK,CAAC,IAAI,CAC/B,IAAI,GAAG,CAAC,CAAC,GAAG,CAAE,IAAI,CAAC,eAA4B,IAAI,EAAE,CAAC,EAAE,GAAG,KAAK,CAAC,eAAe,CAAC,CAAC,CACnF,CAAC;IACJ,CAAC;IACD,IAAI,KAAK,CAAC,cAAc,EAAE,MAAM;QAAE,IAAI,CAAC,cAAc,GAAG,KAAK,CAAC,cAAc,CAAC;IAC7E,IAAI,KAAK,CAAC,YAAY,EAAE,MAAM;QAAE,IAAI,CAAC,YAAY,GAAG,KAAK,CAAC,YAAY,CAAC;IACvE,IAAI,KAAK,CAAC,YAAY,EAAE,MAAM;QAAE,IAAI,CAAC,YAAY,GAAG,KAAK,CAAC,YAAY,CAAC;IACvE,IAAI,KAAK,CAAC,UAAU;QAAE,IAAI,CAAC,UAAU,GAAG,KAAK,CAAC,UAAU,CAAC;IACzD,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAC;IAC1B,OAAO,IAAI,CAAC;AACd,CAAC;AAiBD,KAAK,UAAU,YAAY,CAAC,KAAmB;IAC7C,MAAM,IAAI,GAAoC,EAAE,CAAC;IACjD,IAAI,cAAc,GAA6B,EAAE,CAAC;IAClD,IAAI,SAAS,GAAG,KAAK,CAAC;IAEtB,MAAM,SAAS,GAAG,EAAE,GAAG,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC;IAC7C,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,UAAU,CACzC,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,SAAS,EACT,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;IAEF,IAAI,QAAiD,CAAC;IACtD,IAAI,iBAAqC,CAAC;IAC1C,IAAI,KAAK,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC1B,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAC5B,CAAC;SAAM,CAAC;QACN,iBAAiB,GAAG,KAAK,CAAC,iBAAiB,CAAC;QAC5C,QAAQ,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAC5C,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,KAAK,CAAC,iBAAiB,EACvB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;IACJ,CAAC;IAED,WAAW,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE;QACjC,cAAc,GAAG,EAAE,CAAC;IACtB,CAAC,CAAC,CAAC;IACH,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,EAAE,UAAU,EAAE,UAAU,CAAC;IAE7D,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,CAAC,UAAU,IAAI,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,CAAC;QACpD,IAAI,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;YAClC,SAAS,GAAG,IAAI,CAAC;YACjB,MAAM;QACR,CAAC;QACD,IAAI,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM;QACpC,IAAI,YAAqD,CAAC;QAC1D,IAAI,iBAAiB,EAAE,CAAC;YACtB,YAAY,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAChD,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,iBAAiB,EACjB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,CAAC,CACrE,CAAC;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,UAAU,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,UAAU,CAC9C,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,EAAE,GAAG,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,EACvB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;YACF,IAAI,UAAU,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;gBAC/B,YAAY,GAAG,UAAU,CAAC,QAAQ,CAAC;YACrC,CAAC;iBAAM,CAAC;gBACN,YAAY,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAChD,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,UAAU,CAAC,iBAAiB,EAC5B,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;YACJ,CAAC;QACH,CAAC;QACD,WAAW,CAAC,YAAY,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE;YACrC,cAAc,GAAG,EAAE,CAAC;QACtB,CAAC,CAAC,CAAC;IACL,CAAC;IAED,IAAI,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,QAAQ,EAAE,CAAC;QACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC7B,SAAS,GAAG,IAAI,CAAC;QACjB,KAAK,CAAC,QAAQ,CAAC,IAAI,CACjB,2CAA2C,KAAK,CAAC,QAAQ,mGAAmG,CAC7J,CAAC;IACJ,CAAC;IAED,OAAO,EAAE,IAAI,EAAE,cAAc,EAAE,SAAS,EAAE,CAAC;AAC7C,CAAC;AAED,SAAS,WAAW,CAClB,QAAiD,EACjD,IAAqC,EACrC,iBAAwD;IAExD,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;IAC/B,IAAI,CAAC,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ;QAAE,OAAO;IAClD,MAAM,MAAM,GAAG,MAAiC,CAAC;IACjD,MAAM,EAAE,GAA6B,EAAE,CAAC;IACxC,IAAI,OAAO,MAAM,CAAC,iBAAiB,KAAK,SAAS;QAC/C,EAAE,CAAC,iBAAiB,GAAG,MAAM,CAAC,iBAAiB,CAAC;IAClD,IAAI,OAAO,MAAM,CAAC,aAAa,KAAK,QAAQ;QAAE,EAAE,CAAC,aAAa,GAAG,MAAM,CAAC,aAAa,CAAC;IACtF,IAAI,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ;QAAE,EAAE,CAAC,SAAS,GAAG,MAAM,CAAC,SAAS,CAAC;IAC1E,IAAI,OAAO,MAAM,CAAC,WAAW,KAAK,QAAQ;QAAE,EAAE,CAAC,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;IAChF,iBAAiB,CAAC,EAAE,CAAC,CAAC;IAEtB,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC;IACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;QAAE,OAAO;IACjC,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;YAChD,IAAI,CAAC,IAAI,CAAC,KAAsC,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;AACH,CAAC;AAYD,KAAK,UAAU,UAAU,CAAC,KAAsB;IAC9C,MAAM,aAAa,GAA2B;QAC5C,MAAM,EAAE,qBAAqB;QAC7B,OAAO,EAAE,KAAK,CAAC,UAAU,CAAC,OAAO;QACjC,KAAK,EAAE,KAAK,CAAC,IAAI;QACjB,IAAI,EAAE,KAAK,CAAC,IAAiC;KAC9C,CAAC;IACF,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpB,aAAa,CAAC,SAAS,GAAG,IAAI,CAAC;QAC/B,aAAa,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC;IACxC,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,iBAAiB,CAAC,KAAK,CAAC,GAAG,EAAE,aAAa,CAAC,CAAC;IAC9E,OAAO,iBAAiB,CAAC,MAAM,CAAC,CAAC;AACnC,CAAC"}
+{"version":3,"file":"brapi-find-genotype-calls.tool.js","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAgB,IAAI,EAAE,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,2BAA2B,CAAC;AAC5D,OAAO,EAAoB,cAAc,EAAE,MAAM,kCAAkC,CAAC;AACpF,OAAO,EAAE,cAAc,EAAE,MAAM,mCAAmC,CAAC;AACnE,OAAO,EAEL,eAAe,GAEhB,MAAM,mCAAmC,CAAC;AAC3C,OAAO,EAAE,qBAAqB,EAAE,MAAM,yCAAyC,CAAC;AAEhF,OAAO,EACL,UAAU,EACV,QAAQ,EACR,mBAAmB,EACnB,uBAAuB,EACvB,mBAAmB,EACnB,qBAAqB,EACrB,qBAAqB,EACrB,mBAAmB,EACnB,gBAAgB,EAChB,2BAA2B,EAC3B,iBAAiB,GAClB,MAAM,2BAA2B,CAAC;AAEnC,MAAM,SAAS,GAAG,MAAM,CAAC;AAEzB,MAAM,aAAa,GAAG,CAAC;KACpB,MAAM,CAAC;IACN,WAAW,EAAE,CAAC;SACX,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CAAC,sEAAsE,CAAC;IACnF,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,+BAA+B,CAAC;IAC3E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,iCAAiC,CAAC;IAC7E,WAAW,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,sCAAsC,CAAC;IAClF,cAAc,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,OAAO,EAAE,CAAC,QAAQ,CAAC,4CAA4C,CAAC;IAC3F,QAAQ,EAAE,CAAC;SACR,MAAM,CAAC;QACN,MAAM,EAAE,CAAC;aACN,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,0BAA0B,CAAC,CAAC;aACtD,OAAO,EAAE;aACT,QAAQ,CAAC,qEAAqE,CAAC;KACnF,CAAC;SACD,WAAW,EAAE;SACb,OAAO,EAAE;SACT,QAAQ,CACP,mFAAmF,CACpF;IACH,aAAa,EAAE,CAAC;SACb,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CACP,uFAAuF,CACxF;IACH,QAAQ,EAAE,CAAC;SACR,MAAM,EAAE;SACR,OAAO,EAAE;SACT,QAAQ,CAAC,kEAAkE,CAAC;CAChF,CAAC;KACD,WAAW,EAAE;KACb,QAAQ,CAAC,wBAAwB,CAAC,CAAC;AAEtC,MAAM,YAAY,GAAG,CAAC,CAAC,MAAM,CAAC;IAC5B,KAAK,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC,QAAQ,CAAC,yDAAyD,CAAC;IACrF,OAAO,EAAE,CAAC,CAAC,KAAK,CAAC,aAAa,CAAC,CAAC,QAAQ,CAAC,kDAAkD,CAAC;IAC5F,OAAO,EAAE,CAAC;SACP,OAAO,EAAE;SACT,QAAQ,CAAC,qEAAqE,CAAC;IAClF,cAAc,EAAE,CAAC;SACd,MAAM,CAAC;QACN,iBAAiB,EAAE,CAAC;aACjB,OAAO,EAAE;aACT,OAAO,EAAE;aACT,QAAQ,CAAC,2DAA2D,CAAC;QACxE,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,6DAA6D,CAAC;QAC1E,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,yDAAyD,CAAC;QACtE,WAAW,EAAE,CAAC;aACX,MAAM,EAAE;aACR,OAAO,EAAE;aACT,QAAQ,CAAC,2DAA2D,CAAC;KACzE,CAAC;SACD,QAAQ,CAAC,+CAA+C,CAAC;IAC5D,aAAa,EAAE,CAAC;SACb,MAAM,CAAC;QACN,WAAW,EAAE,CAAC;aACX,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,+CAA+C,CAAC;QAC5D,WAAW,EAAE,CAAC;aACX,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,iDAAiD,CAAC;QAC9D,cAAc,EAAE,CAAC;aACd,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,MAAM,EAAE,CAAC;aAC9B,QAAQ,CAAC,gDAAgD,CAAC;KAC9D,CAAC;SACD,QAAQ,CAAC,+DAA+D,CAAC;IAC5E,SAAS,EAAE,qBAAqB,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAClD,kJAAkJ,CACnJ;IACD,SAAS,EAAE,CAAC;SACT,OAAO,EAAE;SACT,QAAQ,CACP,qJAAqJ,CACtJ;CACJ,CAAC,CAAC;AAIH,MAAM,CAAC,MAAM,sBAAsB,GAAG,IAAI,CAAC,2BAA2B,EAAE;IACtE,WAAW,EACT,+aAA+a;IACjb,WAAW,EAAE,EAAE,YAAY,EAAE,IAAI,EAAE,aAAa,EAAE,IAAI,EAAE;IACxD,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,6DAA6D;YACnE,QAAQ,EACN,6HAA6H;SAChI;QACD;YACE,MAAM,EAAE,YAAY;YACpB,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,qEAAqE;YAC3E,QAAQ,EACN,gGAAgG;SACnG;QACD;YACE,MAAM,EAAE,0BAA0B;YAClC,IAAI,EAAE,gBAAgB,CAAC,eAAe;YACtC,IAAI,EAAE,6EAA6E;YACnF,QAAQ,EACN,+HAA+H;SAClI;KACO;IACV,KAAK,EAAE,CAAC,CAAC,MAAM,CAAC;QACd,KAAK,EAAE,UAAU;QACjB,cAAc,EAAE,CAAC;aACd,MAAM,EAAE;aACR,GAAG,CAAC,CAAC,CAAC;aACN,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,eAAe,EAAE,CAAC;aACf,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,6CAA6C,CAAC;QAC1D,cAAc,EAAE,CAAC;aACd,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,EAAE;aACV,QAAQ,CAAC,0CAA0C,CAAC;QACvD,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,uCAAuC,CAAC;QAC9F,YAAY,EAAE,CAAC,CAAC,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC,CAAC,QAAQ,EAAE,CAAC,QAAQ,CAAC,gCAAgC,CAAC;QACvF,UAAU,EAAE,CAAC;aACV,IAAI,CAAC,CAAC,KAAK,EAAE,UAAU,EAAE,SAAS,EAAE,MAAM,CAAC,CAAC;aAC5C,QAAQ,EAAE;aACV,QAAQ,CAAC,4DAA4D,CAAC;QACzE,SAAS,EAAE,CAAC;aACT,MAAM,EAAE;aACR,GAAG,EAAE;aACL,QAAQ,EAAE;aACV,QAAQ,EAAE;aACV,QAAQ,CACP,mYAAmY,CACpY;KACJ,CAAC;IACF,MAAM,EAAE,YAAY;IAEpB,8EAA8E;IAC9E,4EAA4E;IAC5E,4EAA4E;IAC5E,iEAAiE;IACjE,UAAU,EAAE;QACV,UAAU,EAAE,CAAC;aACV,MAAM,EAAE;aACR,GAAG,EAAE;aACL,WAAW,EAAE;aACb,QAAQ,CACP,8GAA8G,CAC/G;QACH,aAAa,EAAE,CAAC;aACb,MAAM,EAAE;aACR,GAAG,EAAE;aACL,WAAW,EAAE;aACb,QAAQ,CAAC,mEAAmE,CAAC;QAChF,cAAc,EAAE,CAAC;aACd,MAAM,CAAC,CAAC,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC,OAAO,EAAE,CAAC;aAC/B,QAAQ,CACP,uFAAuF,CACxF;QACH,MAAM,EAAE,CAAC;aACN,MAAM,EAAE;aACR,QAAQ,EAAE;aACV,QAAQ,CAAC,8EAA8E,CAAC;QAC3F,QAAQ,EAAE,CAAC;aACR,KAAK,CAAC,CAAC,CAAC,MAAM,EAAE,CAAC;aACjB,QAAQ,CAAC,iEAAiE,CAAC;KAC/E;IAED,iBAAiB,EAAE;QACjB,cAAc,EAAE;YACd,MAAM,EAAE,CAAC,OAAO,EAAE,EAAE;gBAClB,MAAM,OAAO,GAAG,MAAM,CAAC,OAAO,CAAC,OAAO,CAAC,CAAC;gBACxC,IAAI,OAAO,CAAC,MAAM,KAAK,CAAC;oBAAE,OAAO,uBAAuB,CAAC;gBACzD,MAAM,KAAK,GAAG,OAAO,CAAC,GAAG,CACvB,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,OAAO,CAAC,OAAO,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CACzE,CAAC;gBACF,OAAO,qBAAqB,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC;YACjD,CAAC;SACF;QACD,QAAQ,EAAE;YACR,MAAM,EAAE,CAAC,EAAE,EAAE,EAAE,CAAC,CAAC,EAAE,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,CAAC,EAAE,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC,QAAQ,CAAC;YAC/E,KAAK,EAAE,UAAU;SAClB;KACF;IAED,KAAK,CAAC,OAAO,CAAC,KAAK,EAAE,GAAG;QACtB,MAAM,YAAY,GAAG,qBAAqB,EAAE,CAAC;QAC7C,MAAM,MAAM,GAAG,cAAc,EAAE,CAAC;QAChC,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QAEjC,MAAM,UAAU,GAAG,MAAM,2BAA2B,CAAC,GAAG,EAAE,KAAK,CAAC,KAAK,CAAC,CAAC;QAEvE,MAAM,gBAAgB,GAA8C,EAAE,CAAC;QACvE,IAAI,UAAU,CAAC,YAAY;YAAE,gBAAgB,CAAC,IAAI,GAAG,UAAU,CAAC,YAAY,CAAC;QAC7E,MAAM,YAAY,CAAC,MAAM,CACvB,UAAU,CAAC,OAAO,EAClB,EAAE,OAAO,EAAE,cAAc,EAAE,MAAM,EAAE,MAAM,EAAE,EAC3C,GAAG,EACH,gBAAgB,CACjB,CAAC;QAEF,MAAM,OAAO,GAAG,MAAM,cAAc,CAAC,UAAU,EAAE,GAAG,EAAE,gBAAgB,CAAC,CAAC;QACxE,IAAI,OAAO,CAAC,uBAAuB,EAAE,GAAG,CAAC,OAAO,CAAC,EAAE,CAAC;YAClD,MAAM,GAAG,CAAC,IAAI,CACZ,0BAA0B,EAC1B,YAAY,OAAO,CAAC,EAAE,qIAAqI,EAC3J,EAAE,SAAS,EAAE,OAAO,CAAC,EAAE,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,0BAA0B,CAAC,EAAE,CAC1E,CAAC;QACJ,CAAC;QAED,MAAM,MAAM,GAAG,eAAe,EAAE,CAAC;QACjC,MAAM,QAAQ,GAAG,MAAM,CAAC,oBAAoB,CAAC;QAC7C,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,IAAI,MAAM,CAAC,SAAS,CAAC;QAEtD,MAAM,UAAU,GAAG,eAAe,CAAC,KAAK,CAAC,CAAC;QAC1C,IACE,CAAC,UAAU,CAAC,eAAe;YAC3B,CAAC,UAAU,CAAC,cAAc;YAC1B,CAAC,UAAU,CAAC,YAAY;YACxB,CAAC,UAAU,CAAC,YAAY,EACxB,CAAC;YACD,MAAM,GAAG,CAAC,IAAI,CACZ,YAAY,EACZ,4KAA4K,EAC5K,EAAE,OAAO,EAAE,UAAU,EAAE,GAAG,GAAG,CAAC,WAAW,CAAC,YAAY,CAAC,EAAE,CAC1D,CAAC;QACJ,CAAC;QAED,MAAM,QAAQ,GAAa,EAAE,CAAC;QAC9B,MAAM,SAAS,GAAG,MAAM,YAAY,CAAC;YACnC,MAAM;YACN,UAAU;YACV,GAAG;YACH,IAAI,EAAE,UAAU;YAChB,QAAQ;YACR,QAAQ;SACT,CAAC,CAAC;QAEH,MAAM,SAAS,GAAG,SAAS,CAAC,IAAI,CAAC,KAAK,CAAC,CAAC,EAAE,SAAS,CAAC,CAAC;QACrD,MAAM,aAAa,GAAG;YACpB,WAAW,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;YAChF,WAAW,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,WAAW,CAAC,CAAC;YAChF,cAAc,EAAE,mBAAmB,CAAC,SAAS,CAAC,IAAI,EAAE,CAAC,CAAC,EAAE,EAAE,CAAC,QAAQ,CAAC,CAAC,CAAC,cAAc,CAAC,CAAC;SACvF,CAAC;QAEF,MAAM,WAAW,GAAG,SAAS,CAAC,IAAI,CAAC,MAAM,GAAG,SAAS,CAAC;QACtD,IAAI,eAAkE,CAAC;QACvE,IAAI,WAAW,EAAE,CAAC;YAChB,eAAe,GAAG,MAAM,UAAU,CAAC;gBACjC,MAAM;gBACN,GAAG;gBACH,UAAU;gBACV,IAAI,EAAE,UAAU;gBAChB,IAAI,EAAE,SAAS,CAAC,IAAI;gBACpB,SAAS,EAAE,SAAS,CAAC,SAAS;gBAC9B,OAAO,EAAE,QAAQ;aAClB,CAAC,CAAC;QACL,CAAC;QAED,GAAG,CAAC,MAAM,CAAC;YACT,UAAU,EAAE,SAAS,CAAC,IAAI,CAAC,MAAM;YACjC,aAAa,EAAE,SAAS,CAAC,MAAM;YAC/B,cAAc,EAAE,UAAU;YAC1B,QAAQ;SACT,CAAC,CAAC;QACH,IAAI,SAAS,CAAC,IAAI,CAAC,MAAM,KAAK,CAAC;YAC7B,GAAG,CAAC,MAAM,CAAC,MAAM,CACf,6LAA6L,CAC9L,CAAC;QAEJ,MAAM,MAAM,GAAW;YACrB,KAAK,EAAE,UAAU,CAAC,KAAK;YACvB,OAAO,EAAE,SAAS;YAClB,OAAO,EAAE,SAAS,CAAC,SAAS;YAC5B,cAAc,EAAE,SAAS,CAAC,cAAc;YACxC,aAAa;YACb,SAAS,EAAE,SAAS,CAAC,SAAS;SAC/B,CAAC;QACF,IAAI,eAAe;YAAE,MAAM,CAAC,SAAS,GAAG,eAAe,CAAC;QACxD,OAAO,MAAM,CAAC;IAChB,CAAC;IAED,MAAM,EAAE,CAAC,MAAM,EAAE,EAAE;QACjB,MAAM,KAAK,GAAa,EAAE,CAAC;QAC3B,MAAM,UAAU,GAAG,gBAAgB,CAAC;YAClC,IAAI,EAAE,OAAO;YACb,KAAK,EAAE,MAAM,CAAC,KAAK;YACnB,aAAa,EAAE,MAAM,CAAC,OAAO,CAAC,MAAM;YACpC,SAAS,EAAE,MAAM,CAAC,SAAS;SAC5B,CAAC,CAAC;QACH,KAAK,CAAC,IAAI,CACR,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC,GAAG,UAAU,uCAAuC,CAAC,CAAC,CAAC,UAAU,CACrF,CAAC;QACF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC;QACjC,MAAM,CAAC,GAAG,MAAM,CAAC,cAAc,CAAC;QAChC,KAAK,CAAC,IAAI,CAAC,wBAAwB,CAAC,CAAC,iBAAiB,IAAI,GAAG,EAAE,CAAC,CAAC;QACjE,KAAK,CAAC,IAAI,CAAC,oBAAoB,CAAC,CAAC,aAAa,IAAI,GAAG,EAAE,CAAC,CAAC;QACzD,KAAK,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,SAAS,IAAI,GAAG,EAAE,CAAC,CAAC;QACjD,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC,WAAW,IAAI,GAAG,EAAE,CAAC,CAAC;QACrD,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,kBAAkB,CAAC,CAAC;QAC/B,KAAK,CAAC,IAAI,CAAC,mBAAmB,CAAC,MAAM,CAAC,aAAa,CAAC,IAAI,2BAA2B,CAAC,CAAC;QACrF,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QACf,KAAK,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC;QACvB,IAAI,MAAM,CAAC,OAAO,CAAC,MAAM,KAAK,CAAC,EAAE,CAAC;YAChC,KAAK,CAAC,IAAI,CAAC,sBAAsB,CAAC,CAAC;QACrC,CAAC;aAAM,CAAC;YACN,MAAM,QAAQ,GAAG,IAAI,GAAG,CAAC;gBACvB,aAAa;gBACb,aAAa;gBACb,aAAa;gBACb,aAAa;gBACb,gBAAgB;gBAChB,UAAU;gBACV,eAAe;gBACf,UAAU;aACX,CAAC,CAAC;YACH,KAAK,MAAM,IAAI,IAAI,MAAM,CAAC,OAAO,EAAE,CAAC;gBAClC,MAAM,KAAK,GAAa,EAAE,CAAC;gBAC3B,KAAK,CAAC,IAAI,CAAC,KAAK,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,WAAW,IAAI,GAAG,IAAI,CAAC,CAAC;gBACjE,IAAI,IAAI,CAAC,WAAW;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;gBACpE,KAAK,CAAC,IAAI,CAAC,WAAW,IAAI,CAAC,WAAW,IAAI,IAAI,CAAC,WAAW,IAAI,GAAG,EAAE,CAAC,CAAC;gBACrE,IAAI,IAAI,CAAC,WAAW;oBAAE,KAAK,CAAC,IAAI,CAAC,eAAe,IAAI,CAAC,WAAW,EAAE,CAAC,CAAC;gBACpE,IAAI,IAAI,CAAC,cAAc;oBAAE,KAAK,CAAC,IAAI,CAAC,OAAO,IAAI,CAAC,cAAc,EAAE,CAAC,CAAC;gBAClE,IAAI,IAAI,CAAC,QAAQ;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,CAAC,SAAS,CAAC,IAAI,CAAC,QAAQ,CAAC,EAAE,CAAC,CAAC;gBAC3E,IAAI,IAAI,CAAC,aAAa;oBAAE,KAAK,CAAC,IAAI,CAAC,iBAAiB,IAAI,CAAC,aAAa,EAAE,CAAC,CAAC;gBAC1E,IAAI,IAAI,CAAC,QAAQ;oBAAE,KAAK,CAAC,IAAI,CAAC,YAAY,IAAI,CAAC,QAAQ,EAAE,CAAC,CAAC;gBAC3D,KAAK,CAAC,IAAI,CAAC,GAAG,uBAAuB,CAAC,IAA+B,EAAE,QAAQ,CAAC,CAAC,CAAC;gBAClF,KAAK,CAAC,IAAI,CAAC,KAAK,KAAK,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC,CAAC;YACvC,CAAC;QACH,CAAC;QACD,IAAI,MAAM,CAAC,SAAS,EAAE,CAAC;YACrB,KAAK,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;YACf,KAAK,CAAC,IAAI,CAAC,qBAAqB,CAAC,CAAC;YAClC,KAAK,CAAC,IAAI,CAAC,GAAG,qBAAqB,CAAC,MAAM,CAAC,SAAS,CAAC,CAAC,CAAC;QACzD,CAAC;QACD,OAAO,CAAC,EAAE,IAAI,EAAE,MAAM,EAAE,IAAI,EAAE,KAAK,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IACpD,CAAC;CACF,CAAC,CAAC;AAEH,SAAS,eAAe,CACtB,KAA2D;IAE3D,MAAM,IAAI,GAA4B,EAAE,CAAC;IACzC,IAAI,KAAK,CAAC,cAAc;QAAE,IAAI,CAAC,eAAe,GAAG,CAAC,KAAK,CAAC,cAAc,CAAC,CAAC;IACxE,IAAI,KAAK,CAAC,eAAe,EAAE,MAAM,EAAE,CAAC;QAClC,IAAI,CAAC,eAAe,GAAG,KAAK,CAAC,IAAI,CAC/B,IAAI,GAAG,CAAC,CAAC,GAAG,CAAE,IAAI,CAAC,eAA4B,IAAI,EAAE,CAAC,EAAE,GAAG,KAAK,CAAC,eAAe,CAAC,CAAC,CACnF,CAAC;IACJ,CAAC;IACD,IAAI,KAAK,CAAC,cAAc,EAAE,MAAM;QAAE,IAAI,CAAC,cAAc,GAAG,KAAK,CAAC,cAAc,CAAC;IAC7E,IAAI,KAAK,CAAC,YAAY,EAAE,MAAM;QAAE,IAAI,CAAC,YAAY,GAAG,KAAK,CAAC,YAAY,CAAC;IACvE,IAAI,KAAK,CAAC,YAAY,EAAE,MAAM;QAAE,IAAI,CAAC,YAAY,GAAG,KAAK,CAAC,YAAY,CAAC;IACvE,IAAI,KAAK,CAAC,UAAU;QAAE,IAAI,CAAC,UAAU,GAAG,KAAK,CAAC,UAAU,CAAC;IACzD,IAAI,CAAC,QAAQ,GAAG,SAAS,CAAC;IAC1B,OAAO,IAAI,CAAC;AACd,CAAC;AAiBD,KAAK,UAAU,YAAY,CAAC,KAAmB;IAC7C,MAAM,IAAI,GAAoC,EAAE,CAAC;IACjD,IAAI,cAAc,GAA6B,EAAE,CAAC;IAClD,IAAI,SAAS,GAAG,KAAK,CAAC;IAEtB,MAAM,SAAS,GAAG,EAAE,GAAG,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,CAAC,EAAE,CAAC;IAC7C,MAAM,KAAK,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,UAAU,CACzC,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,SAAS,EACT,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;IAEF,IAAI,QAAiD,CAAC;IACtD,IAAI,iBAAqC,CAAC;IAC1C,IAAI,KAAK,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC1B,QAAQ,GAAG,KAAK,CAAC,QAAQ,CAAC;IAC5B,CAAC;SAAM,CAAC;QACN,iBAAiB,GAAG,KAAK,CAAC,iBAAiB,CAAC;QAC5C,QAAQ,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAC5C,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,KAAK,CAAC,iBAAiB,EACvB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;IACJ,CAAC;IAED,WAAW,CAAC,QAAQ,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE;QACjC,cAAc,GAAG,EAAE,CAAC;IACtB,CAAC,CAAC,CAAC;IACH,MAAM,UAAU,GAAG,QAAQ,CAAC,QAAQ,EAAE,UAAU,EAAE,UAAU,CAAC;IAE7D,KAAK,IAAI,IAAI,GAAG,CAAC,EAAE,IAAI,GAAG,CAAC,UAAU,IAAI,CAAC,CAAC,EAAE,IAAI,EAAE,EAAE,CAAC;QACpD,IAAI,IAAI,CAAC,MAAM,IAAI,KAAK,CAAC,QAAQ,EAAE,CAAC;YAClC,SAAS,GAAG,IAAI,CAAC;YACjB,MAAM;QACR,CAAC;QACD,IAAI,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,OAAO;YAAE,MAAM;QACpC,IAAI,YAAqD,CAAC;QAC1D,IAAI,iBAAiB,EAAE,CAAC;YACtB,YAAY,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAChD,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,iBAAiB,EACjB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,EAAE,EAAE,IAAI,EAAE,QAAQ,EAAE,SAAS,EAAE,CAAC,CACrE,CAAC;QACJ,CAAC;aAAM,CAAC;YACN,MAAM,UAAU,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,UAAU,CAC9C,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,EAAE,GAAG,KAAK,CAAC,IAAI,EAAE,IAAI,EAAE,EACvB,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;YACF,IAAI,UAAU,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;gBAC/B,YAAY,GAAG,UAAU,CAAC,QAAQ,CAAC;YACrC,CAAC;iBAAM,CAAC;gBACN,YAAY,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,gBAAgB,CAChD,KAAK,CAAC,UAAU,CAAC,OAAO,EACxB,OAAO,EACP,UAAU,CAAC,iBAAiB,EAC5B,KAAK,CAAC,GAAG,EACT,mBAAmB,CAAC,KAAK,CAAC,UAAU,CAAC,CACtC,CAAC;YACJ,CAAC;QACH,CAAC;QACD,WAAW,CAAC,YAAY,EAAE,IAAI,EAAE,CAAC,EAAE,EAAE,EAAE;YACrC,cAAc,GAAG,EAAE,CAAC;QACtB,CAAC,CAAC,CAAC;IACL,CAAC;IAED,IAAI,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,QAAQ,EAAE,CAAC;QACjC,IAAI,CAAC,MAAM,GAAG,KAAK,CAAC,QAAQ,CAAC;QAC7B,SAAS,GAAG,IAAI,CAAC;QACjB,KAAK,CAAC,QAAQ,CAAC,IAAI,CACjB,2CAA2C,KAAK,CAAC,QAAQ,mGAAmG,CAC7J,CAAC;IACJ,CAAC;IAED,OAAO,EAAE,IAAI,EAAE,cAAc,EAAE,SAAS,EAAE,CAAC;AAC7C,CAAC;AAED,SAAS,WAAW,CAClB,QAAiD,EACjD,IAAqC,EACrC,iBAAwD;IAExD,MAAM,MAAM,GAAG,QAAQ,CAAC,MAAM,CAAC;IAC/B,IAAI,CAAC,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ;QAAE,OAAO;IAClD,MAAM,MAAM,GAAG,MAAiC,CAAC;IACjD,MAAM,EAAE,GAA6B,EAAE,CAAC;IACxC,IAAI,OAAO,MAAM,CAAC,iBAAiB,KAAK,SAAS;QAC/C,EAAE,CAAC,iBAAiB,GAAG,MAAM,CAAC,iBAAiB,CAAC;IAClD,IAAI,OAAO,MAAM,CAAC,aAAa,KAAK,QAAQ;QAAE,EAAE,CAAC,aAAa,GAAG,MAAM,CAAC,aAAa,CAAC;IACtF,IAAI,OAAO,MAAM,CAAC,SAAS,KAAK,QAAQ;QAAE,EAAE,CAAC,SAAS,GAAG,MAAM,CAAC,SAAS,CAAC;IAC1E,IAAI,OAAO,MAAM,CAAC,WAAW,KAAK,QAAQ;QAAE,EAAE,CAAC,WAAW,GAAG,MAAM,CAAC,WAAW,CAAC;IAChF,iBAAiB,CAAC,EAAE,CAAC,CAAC;IAEtB,MAAM,IAAI,GAAG,MAAM,CAAC,IAAI,CAAC;IACzB,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC;QAAE,OAAO;IACjC,KAAK,MAAM,KAAK,IAAI,IAAI,EAAE,CAAC;QACzB,IAAI,OAAO,KAAK,KAAK,QAAQ,IAAI,KAAK,KAAK,IAAI,EAAE,CAAC;YAChD,IAAI,CAAC,IAAI,CAAC,KAAsC,CAAC,CAAC;QACpD,CAAC;IACH,CAAC;AACH,CAAC;AAYD,KAAK,UAAU,UAAU,CAAC,KAAsB;IAC9C,MAAM,aAAa,GAA2B;QAC5C,MAAM,EAAE,qBAAqB;QAC7B,OAAO,EAAE,KAAK,CAAC,UAAU,CAAC,OAAO;QACjC,KAAK,EAAE,KAAK,CAAC,IAAI;QACjB,IAAI,EAAE,KAAK,CAAC,IAAiC;KAC9C,CAAC;IACF,IAAI,KAAK,CAAC,SAAS,EAAE,CAAC;QACpB,aAAa,CAAC,SAAS,GAAG,IAAI,CAAC;QAC/B,aAAa,CAAC,OAAO,GAAG,KAAK,CAAC,OAAO,CAAC;IACxC,CAAC;IACD,MAAM,MAAM,GAAG,MAAM,KAAK,CAAC,MAAM,CAAC,iBAAiB,CAAC,KAAK,CAAC,GAAG,EAAE,aAAa,CAAC,CAAC;IAC9E,OAAO,iBAAiB,CAAC,MAAM,CAAC,CAAC;AACnC,CAAC"}

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

@@ -46,8 +46,6 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
             type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         }, z.core.$loose>>>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     distributions: z.ZodObject<{
         commonCropName: z.ZodRecord<z.ZodString, z.ZodNumber>;
@@ -56,7 +54,6 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
         collection: z.ZodRecord<z.ZodString, z.ZodNumber>;
         countryOfOriginCode: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
-    refinementHint: z.ZodOptional<z.ZodString>;
     dataframe: z.ZodOptional<z.ZodObject<{
         tableName: z.ZodString;
         rowCount: z.ZodNumber;
@@ -66,8 +63,6 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
-    warnings: z.ZodArray<z.ZodString>;
-    appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: JsonRpcErrorCode.NotFound;
@@ -78,5 +73,12 @@ export declare const brapiFindGermplasm: import("@cyanheads/mcp-ts-core").ToolDe
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect dropped every filter the agent supplied — the upstream server does not honor any of the requested scope filters on this endpoint, so the call would silently widen to the unfiltered baseline.";
     readonly recovery: "Drop the unsupported filters and rescope by names, germplasmDbIds, germplasmPUIs, accessionNumbers, crops, synonyms, genus, or species — these filter paths are honored on the active dialect.";
-}]>;
+}], {
+    readonly totalCount: z.ZodNumber;
+    readonly returnedCount: z.ZodNumber;
+    readonly appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    readonly refinementHint: z.ZodOptional<z.ZodString>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly warnings: z.ZodArray<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-find-germplasm.tool.d.ts.map

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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgJjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiU7B,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;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW7B,CAAC"}

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

@@ -13,7 +13,7 @@ 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 { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dedupSynonymsByIdentity, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const GermplasmRowSchema = z
     .object({
     germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
@@ -62,8 +62,6 @@ const OutputSchema = z.object({
     results: z
         .array(GermplasmRowSchema)
         .describe('Germplasm rows returned in-context (up to loadLimit).'),
-    returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
-    totalCount: z.number().int().nonnegative().describe('Total rows reported by the server.'),
     hasMore: z.boolean().describe('True when more rows exist beyond the returned set.'),
     distributions: z
         .object({
@@ -82,17 +80,7 @@ const OutputSchema = z.object({
             .describe('ISO country code → count of rows from that country.'),
     })
         .describe('Value frequency per field across the full result set.'),
-    refinementHint: z
-        .string()
-        .optional()
-        .describe('Suggested next-step query refinement when the result set is large.'),
     dataframe: DataframeHandleSchema.optional().describe('Dataframe handle when the full result set was materialized as a dataframe. Query it with brapi_dataframe_query (SQL).'),
-    warnings: z
-        .array(z.string())
-        .describe('Advisory messages (filter overrides, partial data, capability gaps, etc.).'),
-    appliedFilters: z
-        .record(z.string(), z.unknown())
-        .describe('The final filter map sent to the server (named + extraFilters).'),
 });
 const SERVER_TO_USER = {
     // Plurals — BrAPI v2.1 spec, used by the `spec` dialect.
@@ -154,6 +142,46 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         extraFilters: ExtraFiltersInput,
     }),
     output: OutputSchema,
+    // Agent-facing success-path context: pagination totals, the exact filter map
+    // sent to the server, guidance when the result set is large, and empty-result
+    // notices. Populated via ctx.enrich() so it reaches both structuredContent
+    // and the content[] trailer without living in the domain return.
+    enrichment: {
+        totalCount: z.number().int().nonnegative().describe('Total rows reported by the server.'),
+        returnedCount: z.number().int().nonnegative().describe('Length of results[].'),
+        appliedFilters: z
+            .record(z.string(), z.unknown())
+            .describe('The final filter map sent to the server (named + extraFilters).'),
+        refinementHint: z
+            .string()
+            .optional()
+            .describe('Suggested next-step query refinement when the result set is large.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance when no rows were returned — how to broaden filters or retry.'),
+        warnings: z
+            .array(z.string())
+            .describe('Advisory messages (filter overrides, partial data, capability gaps).'),
+    },
+    enrichmentTrailer: {
+        appliedFilters: {
+            render: (filters) => {
+                const entries = Object.entries(filters);
+                if (entries.length === 0)
+                    return '**Applied Filters:** none';
+                const lines = entries.map(([k, v]) => {
+                    const display = SERVER_TO_USER[k] ?? k;
+                    return `- **${display}:** ${Array.isArray(v) ? v.join(', ') : String(v)}`;
+                });
+                return `**Applied Filters:**\n${lines.join('\n')}`;
+            },
+        },
+        warnings: {
+            render: (ws) => (ws.length > 0 ? ws.map((w) => `- ${w}`).join('\n') : '_none_'),
+            label: 'Warnings',
+        },
+    },
     async handler(input, ctx) {
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
@@ -291,18 +319,24 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             }
         }
         const inContextRows = fullRows.slice(0, loadLimit);
+        const appliedFilters = route.kind === 'search' ? route.searchBody : filters;
+        ctx.enrich({
+            totalCount,
+            returnedCount: inContextRows.length,
+            appliedFilters,
+            warnings,
+            ...(refinementHint ? { refinementHint } : {}),
+        });
+        if (inContextRows.length === 0)
+            ctx.enrich.notice(warnings.length > 0
+                ? 'No rows returned. Check the warnings above for filter issues, or broaden your filters.'
+                : 'No germplasm matched the applied filters. Try broadening names, crops, genus, species, or collections.');
         const result = {
             alias: connection.alias,
             results: inContextRows,
-            returnedCount: inContextRows.length,
-            totalCount,
             hasMore: firstPage.hasMore,
             distributions,
-            warnings,
-            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
-        if (refinementHint)
-            result.refinementHint = refinementHint;
         if (dataframe)
             result.dataframe = dataframe;
         return result;
@@ -312,8 +346,7 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
         lines.push(renderFindHeader({
             noun: 'germplasm',
             alias: result.alias,
-            returnedCount: result.returnedCount,
-            totalCount: result.totalCount,
+            returnedCount: result.results.length,
             dataframe: result.dataframe,
         }));
         lines.push('');
@@ -321,12 +354,6 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push(`⚠ More rows exist beyond the returned set. ${result.dataframe ? `Full set materialized as dataframe \`${result.dataframe.tableName}\` — query with brapi_dataframe_query.` : 'Narrow filters or raise loadLimit.'}`);
             lines.push('');
         }
-        if (result.refinementHint) {
-            lines.push(`**Refinement hint:** ${result.refinementHint}`);
-            lines.push('');
-        }
-        lines.push(renderAppliedFilters(result.appliedFilters, SERVER_TO_USER));
-        lines.push('');
         lines.push('## Distributions');
         lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
         lines.push('');
@@ -402,12 +429,6 @@ export const brapiFindGermplasm = tool('brapi_find_germplasm', {
             lines.push('## Dataframe handle');
             lines.push(...renderDataframeHandle(result.dataframe));
         }
-        if (result.warnings.length > 0) {
-            lines.push('');
-            lines.push('## Warnings');
-            for (const w of result.warnings)
-                lines.push(`- ${w}`);
-        }
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });