@cyanheads/brapi-mcp-server 0.6.2 → 0.6.4

package/dist/mcp-server/tools/definitions/brapi-find-variants.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, 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, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariantRowSchema = z
     .object({
     variantDbId: z.string().describe('Server-side identifier for the variant.'),
@@ -64,8 +64,6 @@ const OutputSchema = z.object({
     results: z
         .array(VariantRowSchema)
         .describe('Variant 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({
@@ -80,17 +78,7 @@ const OutputSchema = z.object({
             .describe('Variant set ID → count of variants in that set.'),
     })
         .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.
@@ -135,6 +123,46 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         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();
@@ -197,18 +225,24 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions, {
             availableFilters: ['variantSets', 'variants', 'references', 'referenceName', 'start', 'end'],
         });
+        const appliedFilters = route.kind === 'search' ? route.searchBody : filters;
+        ctx.enrich({
+            totalCount,
+            returnedCount: firstPage.rows.length,
+            appliedFilters,
+            warnings,
+            ...(refinementHint ? { refinementHint } : {}),
+        });
+        if (firstPage.rows.length === 0)
+            ctx.enrich.notice(warnings.length > 0
+                ? 'No rows returned. Check the warnings above for filter issues, or broaden your filters.'
+                : 'No variants matched the applied filters. Try broadening variantSets, references, or referenceName + start/end range.');
         const result = {
             alias: connection.alias,
             results: firstPage.rows,
-            returnedCount: firstPage.rows.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;
@@ -218,8 +252,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         lines.push(renderFindHeader({
             noun: 'variants',
             alias: result.alias,
-            returnedCount: result.returnedCount,
-            totalCount: result.totalCount,
+            returnedCount: result.results.length,
             dataframe: result.dataframe,
         }));
         lines.push('');
@@ -227,12 +260,6 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             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('');
@@ -292,12 +319,6 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             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-variants.tool.js.map

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

@@ -60,5 +60,5 @@ export declare const brapiGetGermplasm: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no germplasm record for the requested DbId";
     readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-get-germplasm.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAuP5B,CAAC"}
+{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA0GjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAuP5B,CAAC"}

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

@@ -58,5 +58,5 @@ export declare const brapiGetImage: import("@cyanheads/mcp-ts-core").ToolDefinit
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "BrAPI server does not advertise /images in /serverinfo";
     readonly recovery: "Run brapi_server_info to inspect the advertised endpoints, or call brapi_connect with a different alias for a server that exposes /images.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-get-image.tool.d.ts.map

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

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

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

@@ -77,5 +77,5 @@ export declare const brapiGetStudy: import("@cyanheads/mcp-ts-core").ToolDefinit
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "Upstream returned no study record for the requested DbId";
     readonly recovery: "Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-get-study.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAqQxB,CAAC"}
+{"version":3,"file":"brapi-get-study.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-study.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6IjE,eAAO,MAAM,aAAa;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAqQxB,CAAC"}

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

@@ -51,5 +51,5 @@ export declare const brapiRawGet: import("@cyanheads/mcp-ts-core").ToolDefinitio
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "path argument was a full URL instead of a relative BrAPI route";
     readonly recovery: "Pass a path like \"/samples\" or \"/methods\" — the connection alias supplies the baseUrl.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-raw-get.tool.d.ts.map

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

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

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

@@ -54,5 +54,5 @@ export declare const brapiRawSearch: import("@cyanheads/mcp-ts-core").ToolDefini
     readonly code: JsonRpcErrorCode.ValidationError;
     readonly when: "The active dialect declares this POST /search/{noun} route as known-dead on this server";
     readonly recovery: "Use the curated find_* tool for this noun — it routes through GET filters instead and avoids the dead search route.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-raw-search.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-raw-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6DjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAmKzB,CAAC"}
+{"version":3,"file":"brapi-raw-search.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-raw-search.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA6DjE,eAAO,MAAM,cAAc;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAmKzB,CAAC"}

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

@@ -74,5 +74,5 @@ export declare const brapiServerInfo: import("@cyanheads/mcp-ts-core").ToolDefin
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "No connection has been registered under the requested alias";
     readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_server_info.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-server-info.tool.d.ts.map

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

@@ -1 +1 @@
-{"version":3,"file":"brapi-server-info.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-server-info.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAUjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA0C1B,CAAC"}
+{"version":3,"file":"brapi-server-info.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-server-info.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAUjE,eAAO,MAAM,eAAe;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cA0C1B,CAAC"}

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

@@ -119,5 +119,5 @@ export declare const brapiSubmitObservations: import("@cyanheads/mcp-ts-core").T
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "User declined the elicitation prompt for the apply write";
     readonly recovery: "Re-run the tool when the user is ready to confirm the write.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-submit-observations.tool.d.ts.map

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

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

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

@@ -60,5 +60,5 @@ export declare const brapiWalkPedigree: import("@cyanheads/mcp-ts-core").ToolDef
     readonly code: JsonRpcErrorCode.NotFound;
     readonly when: "No connection has been registered under the requested alias";
     readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_walk_pedigree.";
-}]>;
+}], undefined>;
 //# sourceMappingURL=brapi-walk-pedigree.tool.d.ts.map

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

@@ -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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkO5B,CAAC"}
+{"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;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;cAkO5B,CAAC"}