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-genotype-calls.tool.js CHANGED Viewed

@@ -18,8 +18,8 @@ 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, asString, buildRequestOptions, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
-const PAGE_SIZE = 10_000;
+import { AliasInput, asString, collectPassthroughParts, computeDistribution, DataframeHandleSchema, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
+import { buildCallsSearchBody, collectCalls } from '../shared/genotype-calls.js';
 const CallRowSchema = z
     .object({
     callSetDbId: z
@@ -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();
@@ -182,7 +213,7 @@ export const brapiFindGenotypeCalls = tool('brapi_find_genotype_calls', {
         }
         const warnings = [];
         const collected = await collectCalls({
-            client,
+            client: client,
             connection,
             ctx,
             body: searchBody,
@@ -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 ?? '—'}`);
@@ -290,106 +319,24 @@ 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') }];
     },
 });
 function buildSearchBody(input) {
-    const body = {};
-    if (input.variantSetDbId)
-        body.variantSetDbIds = [input.variantSetDbId];
-    if (input.variantSetDbIds?.length) {
-        body.variantSetDbIds = Array.from(new Set([...(body.variantSetDbIds ?? []), ...input.variantSetDbIds]));
-    }
-    if (input.germplasmDbIds?.length)
-        body.germplasmDbIds = input.germplasmDbIds;
-    if (input.callSetDbIds?.length)
-        body.callSetDbIds = input.callSetDbIds;
-    if (input.variantDbIds?.length)
-        body.variantDbIds = input.variantDbIds;
-    if (input.callFormat)
-        body.callFormat = input.callFormat;
-    body.pageSize = PAGE_SIZE;
-    return body;
-}
-async function collectCalls(input) {
-    const rows = [];
-    let callFormatting = {};
-    let truncated = false;
-    const firstBody = { ...input.body, page: 0 };
-    const first = await input.client.postSearch(input.connection.baseUrl, 'calls', firstBody, input.ctx, buildRequestOptions(input.connection));
-    let envelope;
-    let searchResultsDbId;
-    if (first.kind === 'sync') {
-        envelope = first.envelope;
-    }
-    else {
-        searchResultsDbId = first.searchResultsDbId;
-        envelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', first.searchResultsDbId, input.ctx, buildRequestOptions(input.connection));
-    }
-    consumePage(envelope, rows, (cf) => {
-        callFormatting = cf;
-    });
-    const totalPages = envelope.metadata?.pagination?.totalPages;
-    for (let page = 1; page < (totalPages ?? 1); page++) {
-        if (rows.length >= input.maxCalls) {
-            truncated = true;
-            break;
-        }
-        if (input.ctx.signal.aborted)
-            break;
-        let pageEnvelope;
-        if (searchResultsDbId) {
-            pageEnvelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', searchResultsDbId, input.ctx, buildRequestOptions(input.connection, { page, pageSize: PAGE_SIZE }));
-        }
-        else {
-            const nextSearch = await input.client.postSearch(input.connection.baseUrl, 'calls', { ...input.body, page }, input.ctx, buildRequestOptions(input.connection));
-            if (nextSearch.kind === 'sync') {
-                pageEnvelope = nextSearch.envelope;
-            }
-            else {
-                pageEnvelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', nextSearch.searchResultsDbId, input.ctx, buildRequestOptions(input.connection));
-            }
-        }
-        consumePage(pageEnvelope, rows, (cf) => {
-            callFormatting = cf;
-        });
-    }
-    if (rows.length > input.maxCalls) {
-        rows.length = input.maxCalls;
-        truncated = true;
-        input.warnings.push(`Truncated at the deployment pull limit (${input.maxCalls} rows). Narrow the filters and re-pull; the captured slice is preserved in the spilled dataframe.`);
-    }
-    return { rows, callFormatting, truncated };
-}
-function consumePage(envelope, rows, setCallFormatting) {
-    const result = envelope.result;
-    if (!result || typeof result !== 'object')
-        return;
-    const record = result;
-    const cf = {};
-    if (typeof record.expandHomozygotes === 'boolean')
-        cf.expandHomozygotes = record.expandHomozygotes;
-    if (typeof record.unknownString === 'string')
-        cf.unknownString = record.unknownString;
-    if (typeof record.sepPhased === 'string')
-        cf.sepPhased = record.sepPhased;
-    if (typeof record.sepUnphased === 'string')
-        cf.sepUnphased = record.sepUnphased;
-    setCallFormatting(cf);
-    const data = record.data;
-    if (!Array.isArray(data))
-        return;
-    for (const entry of data) {
-        if (typeof entry === 'object' && entry !== null) {
-            rows.push(entry);
-        }
-    }
+    const opts = {};
+    if (input.variantSetDbId !== undefined)
+        opts.variantSetDbId = input.variantSetDbId;
+    if (input.variantSetDbIds !== undefined)
+        opts.variantSetDbIds = input.variantSetDbIds;
+    if (input.germplasmDbIds !== undefined)
+        opts.germplasmDbIds = input.germplasmDbIds;
+    if (input.callSetDbIds !== undefined)
+        opts.callSetDbIds = input.callSetDbIds;
+    if (input.variantDbIds !== undefined)
+        opts.variantDbIds = input.variantDbIds;
+    if (input.callFormat !== undefined)
+        opts.callFormat = input.callFormat;
+    return buildCallsSearchBody(opts);
 }
 async function spillCalls(input) {
     const registerInput = {

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

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

@@ -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 CHANGED Viewed

	@@ -1 +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"}
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;AAmIjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAwW7B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-find-germplasm.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, 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') }];
     },
 });

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

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

@@ -40,8 +40,6 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         copyright: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         description: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     distributions: z.ZodObject<{
         mimeType: z.ZodRecord<z.ZodString, z.ZodNumber>;
@@ -49,7 +47,6 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         observationUnitName: z.ZodRecord<z.ZodString, z.ZodNumber>;
         descriptiveOntologyTerms: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
-    refinementHint: z.ZodOptional<z.ZodString>;
     dataframe: z.ZodOptional<z.ZodObject<{
         tableName: z.ZodString;
         rowCount: z.ZodNumber;
@@ -59,8 +56,6 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
         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;
@@ -71,5 +66,12 @@ export declare const brapiFindImages: import("@cyanheads/mcp-ts-core").ToolDefin
     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 images, observationUnits, observations, studies, descriptiveOntologyTerms, imageFileNames, or mimeTypes — 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-images.tool.d.ts.map

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

	@@ -1 +1 @@
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