npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.4.13 → 0.5.0 - Mend

@cyanheads/brapi-mcp-server 0.4.13 → 0.5.0

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 (120) hide show

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

@@ -1,8 +1,8 @@
 /**
  * @fileoverview `brapi_find_studies` — locate studies matching crop / trial
  * type / season / location / program filters. Pulls an initial page and, if
- * the server reports more rows than loadLimit, spills the union into
- * DatasetStore and returns a handle. Companion response: per-field
+ * the server reports more rows than loadLimit, materializes the union as a
+ * dataframe and returns a handle. Companion response: per-field
  * distributions computed from the full row set plus a refinement hint.
  *
  * @module mcp-server/tools/definitions/brapi-find-studies.tool
@@ -12,10 +12,10 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 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 { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, asStringArray, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, asStringArray, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, ExtraFiltersInput, fkMatchCheck, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const StudyRowSchema = z
     .object({
     studyDbId: z.string().describe('Server-side identifier for the study.'),
@@ -73,7 +73,7 @@ const OutputSchema = z.object({
         .string()
         .optional()
         .describe('Suggested next-step query refinement when the result set is large.'),
-    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
+    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, etc.).'),
@@ -107,7 +107,7 @@ const SERVER_TO_USER = {
     active: 'active',
 };
 export const brapiFindStudies = tool('brapi_find_studies', {
-    description: 'Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. Returns a dataset handle when the upstream total exceeds loadLimit.',
+    description: 'Locate studies matching crop, trial type, season, location, or program. Enriches results with program/trial/location context in one call. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -138,7 +138,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const datasetStore = getDatasetStore();
+        const bridge = getCanvasBridge();
         const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
@@ -168,7 +168,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
         });
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
+        const { fullRows, dataframe } = await maybeSpill({
             firstPage,
             client,
             connection,
@@ -178,7 +178,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             source: 'find_studies',
             loadLimit,
             ctx,
-            store: datasetStore,
+            bridge,
         });
         const distributions = {
             programName: computeDistribution(fullRows, (r) => asString(r.programName)),
@@ -222,7 +222,7 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             baseUrl: connection.baseUrl,
             totalCount,
             returnedCount: firstPage.rows.length,
-            spilled: datasetMeta !== undefined,
+            spilled: dataframe !== undefined,
         });
         const result = {
             alias: connection.alias,
@@ -236,8 +236,8 @@ export const brapiFindStudies = tool('brapi_find_studies', {
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
-        if (datasetMeta)
-            result.dataset = datasetMeta;
+        if (dataframe)
+            result.dataframe = dataframe;
         return result;
     },
     format: (result) => {
@@ -247,11 +247,11 @@ export const brapiFindStudies = tool('brapi_find_studies', {
             alias: result.alias,
             returnedCount: result.returnedCount,
             totalCount: result.totalCount,
-            dataset: result.dataset,
+            dataframe: result.dataframe,
         }));
         lines.push('');
         if (result.hasMore) {
-            lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
+            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) {
@@ -326,10 +326,10 @@ export const brapiFindStudies = tool('brapi_find_studies', {
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
-        if (result.dataset) {
+        if (result.dataframe) {
             lines.push('');
-            lines.push('## Dataset handle');
-            lines.push(...renderDatasetHandle(result.dataset));
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
         }
         if (result.warnings.length > 0) {
             lines.push('');

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

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

@@ -72,16 +72,14 @@ export declare const brapiFindVariables: import("@cyanheads/mcp-ts-core").ToolDe
         }>;
     }, z.core.$strip>>;
     refinementHint: z.ZodOptional<z.ZodString>;
-    dataset: z.ZodOptional<z.ZodObject<{
-        datasetId: z.ZodString;
+    dataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
         rowCount: z.ZodNumber;
-        sizeBytes: z.ZodNumber;
         columns: z.ZodArray<z.ZodString>;
         createdAt: z.ZodString;
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
-        dataframe: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-find-variables.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variables.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAiLjE,eAAO,MAAM,kBAAkB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAiT7B,CAAC"}

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

@@ -12,11 +12,11 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 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 { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { getOntologyResolver, } from '../../../services/ontology-resolver/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariableRowSchema = z
     .object({
     observationVariableDbId: z
@@ -120,7 +120,7 @@ const OutputSchema = z.object({
         .string()
         .optional()
         .describe('Suggested next-step query refinement when the result set is large.'),
-    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
+    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.).'),
@@ -150,7 +150,7 @@ const SERVER_TO_USER = {
     commonCropName: 'crop',
 };
 export const brapiFindVariables = tool('brapi_find_variables', {
-    description: 'Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against the returned set and may resolve to ontology URIs when the server advertises them. Returns a dataset handle when the upstream total exceeds loadLimit.',
+    description: 'Find observation variables (traits) by name, trait class, ontology term, or free-text query. Free-text queries are ranked against the returned set and may resolve to ontology URIs when the server advertises them. When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -177,7 +177,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         text: z
             .string()
             .optional()
-            .describe('Free-text query. **Re-ranks (does not subset)** the returned rows client-side — matched rows are promoted to the top, unmatched rows still appear below. Use exact filters (`variables`, `variableNames`, `variablePUIs`, `traitClasses`, `ontologies`) to actually narrow the result set. Differs from `brapi_find_germplasm.text`, which subsets client-side.'),
+            .describe('Free-text query. Ranks the **full upstream union** (the spilled dataframe when one is produced, otherwise the first page) via the ontology resolver, then fills the in-context window up to loadLimit with matches first and unmatched rows for context. Use exact filters (`variables`, `variableNames`, `variablePUIs`, `traitClasses`, `ontologies`) to actually narrow the upstream pull. Differs from `brapi_find_germplasm.text`, which drops unmatched rows.'),
         loadLimit: LoadLimitInput,
         extraFilters: ExtraFiltersInput,
     }),
@@ -186,7 +186,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const datasetStore = getDatasetStore();
+        const bridge = getCanvasBridge();
         const resolver = getOntologyResolver();
         const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
@@ -225,7 +225,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         }
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
+        const { fullRows, dataframe } = await maybeSpill({
             firstPage,
             client,
             connection,
@@ -235,7 +235,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             source: 'find_variables',
             loadLimit,
             ctx,
-            store: datasetStore,
+            bridge,
         });
         let rankedResults = firstPage.rows;
         let candidates = [];
@@ -247,9 +247,16 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 // and fall back to PUI for any candidate that lacked the dbId.
                 const matchedDbIds = new Set(candidates.map((c) => c.observationVariableDbId).filter((v) => Boolean(v)));
                 const matchedPuis = new Set(candidates.map((c) => c.termId).filter((v) => Boolean(v)));
+                // Iterate the full spilled union, not just firstPage.rows. The
+                // ontology resolver matches against fullRows, so matched dbIds
+                // routinely sit past the in-context window (e.g. "dry matter
+                // content" hits CO_334:0002058, which is row ~700 of 750 in
+                // alphabetical order). Walking firstPage.rows alone produced an
+                // empty `matched` set and a no-op rerank. After the merge, slice
+                // back to loadLimit so the response stays bounded.
                 const matched = [];
                 const rest = [];
-                for (const row of firstPage.rows) {
+                for (const row of fullRows) {
                     const dbId = row.observationVariableDbId;
                     const pui = row.observationVariablePUI;
                     const isMatch = (typeof dbId === 'string' && matchedDbIds.has(dbId)) ||
@@ -259,7 +266,7 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                     else
                         rest.push(row);
                 }
-                rankedResults = [...matched, ...rest];
+                rankedResults = [...matched, ...rest].slice(0, loadLimit);
             }
         }
         const distributions = {
@@ -305,10 +312,19 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 'text',
             ],
         });
+        // Strip top-level keys whose value is a non-array object with no
+        // meaningful fields (every leaf null/undefined/empty). CassavaBase
+        // emits `method: {}` and similar empty containers on every variable,
+        // and the bloat is pure noise in the in-context view. Objects that
+        // carry any non-empty field are kept untouched — including their null
+        // siblings — so no information is dropped, only empty containers.
+        // Applied to in-context rows only; the dataframe keeps the raw
+        // upstream shape for research traceability.
+        const inContextRows = rankedResults.map(pruneEmptyNestedObjects);
         const result = {
             alias: connection.alias,
-            results: rankedResults,
-            returnedCount: rankedResults.length,
+            results: inContextRows,
+            returnedCount: inContextRows.length,
             totalCount,
             hasMore: firstPage.hasMore,
             distributions,
@@ -318,8 +334,8 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
-        if (datasetMeta)
-            result.dataset = datasetMeta;
+        if (dataframe)
+            result.dataframe = dataframe;
         return result;
     },
     format: (result) => {
@@ -329,11 +345,11 @@ export const brapiFindVariables = tool('brapi_find_variables', {
             alias: result.alias,
             returnedCount: result.returnedCount,
             totalCount: result.totalCount,
-            dataset: result.dataset,
+            dataframe: result.dataframe,
         }));
         lines.push('');
         if (result.hasMore) {
-            lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
+            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) {
@@ -403,10 +419,10 @@ export const brapiFindVariables = tool('brapi_find_variables', {
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
-        if (result.dataset) {
+        if (result.dataframe) {
             lines.push('');
-            lines.push('## Dataset handle');
-            lines.push(...renderDatasetHandle(result.dataset));
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
         }
         if (result.warnings.length > 0) {
             lines.push('');
@@ -417,4 +433,29 @@ export const brapiFindVariables = tool('brapi_find_variables', {
         return [{ type: 'text', text: lines.join('\n') }];
     },
 });
+/**
+ * Drop top-level keys whose value is a non-array object with no meaningful
+ * content. Used to suppress bloat-only containers like `method: {}` that
+ * some Breedbase deployments attach to every variable record. An object is
+ * considered meaningful iff at least one of its values is non-null,
+ * non-undefined, and non-empty-string. Arrays (including empty arrays) are
+ * always preserved — `[]` carries the semantic "no entries" rather than
+ * "container exists but empty".
+ */
+function pruneEmptyNestedObjects(row) {
+    let changed = false;
+    const out = {};
+    for (const [key, value] of Object.entries(row)) {
+        if (value && typeof value === 'object' && !Array.isArray(value)) {
+            const inner = value;
+            const meaningful = Object.values(inner).some((v) => v !== null && v !== undefined && v !== '');
+            if (!meaningful) {
+                changed = true;
+                continue;
+            }
+        }
+        out[key] = value;
+    }
+    return changed ? out : row;
+}
 //# sourceMappingURL=brapi-find-variables.tool.js.map

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

@@ -1,7 +1,7 @@
 /**
  * @fileoverview `brapi_find_variants` — find variant records by variant set,
  * reference, or genomic region. Standard find_* pattern — distributions +
- * dataset spillover. Note: the BrAPI filter catalog uses `start` / `end` as
+ * dataframe spillover. Note: the BrAPI filter catalog uses `start` / `end` as
  * single scalars (1-based inclusive / exclusive) per the spec.
  *
  * @module mcp-server/tools/definitions/brapi-find-variants.tool
@@ -44,16 +44,14 @@ export declare const brapiFindVariants: import("@cyanheads/mcp-ts-core").ToolDef
         variantSetDbId: z.ZodRecord<z.ZodString, z.ZodNumber>;
     }, z.core.$strip>;
     refinementHint: z.ZodOptional<z.ZodString>;
-    dataset: z.ZodOptional<z.ZodObject<{
-        datasetId: z.ZodString;
+    dataframe: z.ZodOptional<z.ZodObject<{
+        tableName: z.ZodString;
         rowCount: z.ZodNumber;
-        sizeBytes: z.ZodNumber;
         columns: z.ZodArray<z.ZodString>;
         createdAt: z.ZodString;
         expiresAt: z.ZodString;
         truncated: z.ZodOptional<z.ZodBoolean>;
         maxRows: z.ZodOptional<z.ZodNumber>;
-        dataframe: z.ZodOptional<z.ZodString>;
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
     appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;

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

	@@ -1 +1 @@
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;AA+HjE,eAAO,MAAM,iBAAiB~~;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;~~GAkM5B,CAAC"}
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;AA+HjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GAkM5B,CAAC"}

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

@@ -1,7 +1,7 @@
 /**
  * @fileoverview `brapi_find_variants` — find variant records by variant set,
  * reference, or genomic region. Standard find_* pattern — distributions +
- * dataset spillover. Note: the BrAPI filter catalog uses `start` / `end` as
+ * dataframe spillover. Note: the BrAPI filter catalog uses `start` / `end` as
  * single scalars (1-based inclusive / exclusive) per the spec.
  *
  * @module mcp-server/tools/definitions/brapi-find-variants.tool
@@ -11,10 +11,10 @@ import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
 import { getServerConfig } from '../../../config/server-config.js';
 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 { getDatasetStore } from '../../../services/dataset-store/index.js';
 import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, collectPassthroughParts, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDatasetHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildRefinementHint, collectPassthroughParts, computeDistribution, DataframeHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderAppliedFilters, renderDataframeHandle, renderDistributions, renderFindHeader, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariantRowSchema = z
     .object({
     variantDbId: z.string().describe('Server-side identifier for the variant.'),
@@ -84,7 +84,7 @@ const OutputSchema = z.object({
         .string()
         .optional()
         .describe('Suggested next-step query refinement when the result set is large.'),
-    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
+    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.).'),
@@ -107,7 +107,7 @@ const SERVER_TO_USER = {
     end: 'end',
 };
 export const brapiFindVariants = tool('brapi_find_variants', {
-    description: 'Find variant records by variant set, reference sequence, or genomic region (start/end, 1-based inclusive / exclusive). Returns a dataset handle when the upstream total exceeds loadLimit.',
+    description: 'Find variant records by variant set, reference sequence, or genomic region (start/end, 1-based inclusive / exclusive). When the upstream total exceeds loadLimit, the full result set is materialized as a dataframe — query it with brapi_dataframe_query (SQL).',
     annotations: { readOnlyHint: true, openWorldHint: true },
     errors: [
         {
@@ -133,7 +133,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         const registry = getServerRegistry();
         const capabilities = getCapabilityRegistry();
         const client = getBrapiClient();
-        const datasetStore = getDatasetStore();
+        const bridge = getCanvasBridge();
         const config = getServerConfig();
         const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
         const capabilityLookup = {};
@@ -164,7 +164,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         });
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const firstPage = await loadInitialFindPage(client, connection, route, loadLimit, ctx);
-        const { fullRows, dataset: datasetMeta } = await maybeSpill({
+        const { fullRows, dataframe } = await maybeSpill({
             firstPage,
             client,
             connection,
@@ -174,7 +174,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             source: 'find_variants',
             loadLimit,
             ctx,
-            store: datasetStore,
+            bridge,
         });
         const distributions = {
             variantType: computeDistribution(fullRows, (r) => asString(r.variantType)),
@@ -197,8 +197,8 @@ export const brapiFindVariants = tool('brapi_find_variants', {
         };
         if (refinementHint)
             result.refinementHint = refinementHint;
-        if (datasetMeta)
-            result.dataset = datasetMeta;
+        if (dataframe)
+            result.dataframe = dataframe;
         return result;
     },
     format: (result) => {
@@ -208,11 +208,11 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             alias: result.alias,
             returnedCount: result.returnedCount,
             totalCount: result.totalCount,
-            dataset: result.dataset,
+            dataframe: result.dataframe,
         }));
         lines.push('');
         if (result.hasMore) {
-            lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
+            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) {
@@ -275,10 +275,10 @@ export const brapiFindVariants = tool('brapi_find_variants', {
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }
-        if (result.dataset) {
+        if (result.dataframe) {
             lines.push('');
-            lines.push('## Dataset handle');
-            lines.push(...renderDatasetHandle(result.dataset));
+            lines.push('## Dataframe handle');
+            lines.push(...renderDataframeHandle(result.dataframe));
         }
         if (result.warnings.length > 0) {
             lines.push('');