npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.6.3 → 0.7.0 - Mend

@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (106) hide show

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

@@ -15,7 +15,7 @@ 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 { getOntologyResolver, } from '../../../services/ontology-resolver/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 VariableRowSchema = z
     .object({
     observationVariableDbId: z
@@ -96,8 +96,6 @@ const OutputSchema = z.object({
     results: z
         .array(VariableRowSchema)
         .describe('Observation variable rows returned in-context (up to loadLimit). Rows matching `text` are promoted to the top when the free-text query produces candidates.'),
-    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({
@@ -115,17 +113,7 @@ const OutputSchema = z.object({
     ontologyCandidates: z
         .array(CandidateSchema)
         .describe('Top ranked candidates from the free-text query (if any). Empty when `text` was not supplied.'),
-    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.
@@ -187,6 +175,46 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         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();
@@ -330,19 +358,25 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         // Applied to in-context rows only; the dataframe keeps the raw
         // upstream shape for research traceability.
         const inContextRows = rankedResults.map(pruneEmptyNestedObjects);
+        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 variables matched the applied filters. Try broadening variableNames, traitClasses, ontologies, or using the text parameter.');
         const result = {
             alias: connection.alias,
             results: inContextRows,
-            returnedCount: inContextRows.length,
-            totalCount,
             hasMore: firstPage.hasMore,
             distributions,
             ontologyCandidates: candidates,
-            warnings,
-            appliedFilters: route.kind === 'search' ? route.searchBody : filters,
         };
-        if (refinementHint)
-            result.refinementHint = refinementHint;
         if (dataframe)
             result.dataframe = dataframe;
         return result;
@@ -352,8 +386,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         lines.push(renderFindHeader({
             noun: 'variables',
             alias: result.alias,
-            returnedCount: result.returnedCount,
-            totalCount: result.totalCount,
+            returnedCount: result.results.length,
             dataframe: result.dataframe,
         }));
         lines.push('');
@@ -361,12 +394,6 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             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('');
         if (result.ontologyCandidates.length > 0) {
             lines.push('## Ontology candidates (ranked)');
             for (const c of result.ontologyCandidates) {
@@ -433,12 +460,6 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             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-variables.tool.js.map CHANGED Viewed

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

@@ -35,15 +35,12 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
         filtersApplied: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
         filtersFailed: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     distributions: z.ZodObject<{
         variantType: z.ZodRecord<z.ZodString, z.ZodNumber>;
         referenceName: z.ZodRecord<z.ZodString, z.ZodNumber>;
         variantSetDbId: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
-    refinementHint: z.ZodOptional<z.ZodString>;
     dataframe: z.ZodOptional<z.ZodObject<{
         tableName: z.ZodString;
         rowCount: z.ZodNumber;
@@ -53,8 +50,6 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
         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;
@@ -65,5 +60,12 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
     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 variants, variantSets, references, or referenceName + start/end — 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-variants.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwP5B,CAAC"}

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

@@ -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 CHANGED Viewed

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

@@ -0,0 +1,60 @@
+/**
+ * @fileoverview `brapi_germplasm_performance` — aggregate a single germplasm's
+ * observations across the studies it appears in, returning per-variable summary
+ * statistics (n, mean, median, sd, min, max) plus the contributing studies and
+ * seasons. Answers the breeder's primary question — "how does line X perform
+ * across the pool's history?" — in one call.
+ *
+ * Study-anchored by design: a naked `/observations?germplasmDbId=…` pull stalls
+ * on SGN/Breedbase deployments (the count-probe bailout). Instead the tool
+ * discovers the germplasm's studies via `/studies?germplasmDbIds=…` (with a
+ * dialect-honor cross-check, since some servers silently drop that filter and
+ * return the global list), then pulls observations per study through the shared
+ * `pullStudyObservations` machinery — the same `/observations` →
+ * `/observationunits` fallback chain `brapi_build_phenotype_matrix` uses.
+ *
+ * Returned rows are filtered to the iterated study and the target germplasm, so
+ * the aggregate stays correct even on servers that ignore the studyDbId filter
+ * on `/observations` (the BrAPI Community Test Server does) or over-return from
+ * the germplasm-anchored fallback.
+ *
+ * @module mcp-server/tools/definitions/brapi-germplasm-performance.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+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;
+    variables: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    germplasmDbId: z.ZodString;
+    germplasmName: z.ZodOptional<z.ZodString>;
+    studyCount: z.ZodNumber;
+    studyDbIds: z.ZodArray<z.ZodString>;
+    perVariable: z.ZodArray<z.ZodObject<{
+        observationVariableDbId: z.ZodString;
+        observationVariableName: z.ZodOptional<z.ZodString>;
+        n: z.ZodNumber;
+        mean: z.ZodOptional<z.ZodNumber>;
+        median: z.ZodOptional<z.ZodNumber>;
+        sd: z.ZodOptional<z.ZodNumber>;
+        min: z.ZodOptional<z.ZodString>;
+        max: z.ZodOptional<z.ZodString>;
+        studyCount: z.ZodNumber;
+        studyDbIds: z.ZodArray<z.ZodString>;
+        seasons: z.ZodArray<z.ZodString>;
+    }, z.core.$strip>>;
+    warnings: z.ZodArray<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    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_germplasm_performance.";
+}, {
+    readonly reason: "germplasm_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
+    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+}], undefined>;
+//# sourceMappingURL=brapi-germplasm-performance.tool.d.ts.map

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

	@@ -0,0 +1 @@
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