npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.9 → 0.7.11 - Mend

@cyanheads/brapi-mcp-server 0.7.9 → 0.7.11

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 (105) hide show

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts CHANGED Viewed

@@ -24,14 +24,14 @@ export declare const brapiBuildPhenotypeMatrix: import("@cyanheads/mcp-ts-core")
     variables: z.ZodOptional<z.ZodArray<z.ZodString>>;
     germplasm: z.ZodOptional<z.ZodArray<z.ZodString>>;
     shape: z.ZodDefault<z.ZodEnum<{
-        wide: "wide";
         long: "long";
+        wide: "wide";
     }>>;
     aggregate: z.ZodDefault<z.ZodEnum<{
         all: "all";
+        first: "first";
         mean: "mean";
         median: "median";
-        first: "first";
     }>>;
     loadLimit: z.ZodOptional<z.ZodNumber>;
     extraFilters: z.ZodOptional<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
@@ -39,14 +39,14 @@ export declare const brapiBuildPhenotypeMatrix: import("@cyanheads/mcp-ts-core")
     alias: z.ZodString;
     studies: z.ZodArray<z.ZodString>;
     shape: z.ZodEnum<{
-        wide: "wide";
         long: "long";
+        wide: "wide";
     }>;
     aggregate: z.ZodEnum<{
         all: "all";
+        first: "first";
         mean: "mean";
         median: "median";
-        first: "first";
     }>;
     observationCount: z.ZodNumber;
     germplasmCount: z.ZodNumber;
@@ -65,19 +65,24 @@ export declare const brapiBuildPhenotypeMatrix: import("@cyanheads/mcp-ts-core")
     }, z.core.$strip>>;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    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_build_phenotype_matrix.";
+    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_build_phenotype_matrix.';
 }, {
-    readonly reason: "all_filters_dropped";
+    readonly reason: 'all_filters_dropped';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline";
-    readonly recovery: "Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.";
+    readonly when: 'The active dialect dropped every filter supplied — the call would silently widen to the unfiltered baseline';
+    readonly recovery: 'Drop unsupported filters or use studies / germplasm / variables to scope the query to supported filter paths on the active dialect.';
 }, {
-    readonly reason: "no_observation_path";
+    readonly reason: 'no_observation_path';
     readonly code: JsonRpcErrorCode.ServiceUnavailable;
-    readonly when: "Neither /observations nor /observationunits returned data for any requested study after probing both paths";
-    readonly recovery: "Verify the studyDbIds exist and the BrAPI server exposes /observations or /observationunits. Use brapi_server_info to inspect the capability list.";
-}], undefined>;
+    readonly when: 'Neither /observations nor /observationunits returned data for any requested study after probing both paths';
+    readonly recovery: 'Verify the studyDbIds exist and the BrAPI server exposes /observations or /observationunits. Use brapi_server_info to inspect the capability list.';
+}], {
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-build-phenotype-matrix.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-build-phenotype-matrix.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;GAiBG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,yBAAyB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMxB,eAAe;;mBAEjB,6DAA6D;uBAEjE,gIAAgI;;qBAG1H,qBAAqB;;mBAEvB,6GAA6G;uBAEjH,qIAAqI;;qBAG/H,qBAAqB;;mBAEvB,4GAA4G;uBAEhH,oJAAoJ;;;;;;EA6P1J,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js CHANGED Viewed

@@ -25,7 +25,7 @@ import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
 import { buildUniqueColumns } from '../shared/canvas-columns.js';
 import { AliasInput, DataframeHandleSchema, ExtraFiltersInput, LoadLimitInput, renderDataframeHandle, requireRegisteredConnection, } from '../shared/find-helpers.js';
-import { pullStudyObservations } from '../shared/observations.js';
+import { pullObservationsForStudies } from '../shared/observations.js';
 // ---------------------------------------------------------------------------
 // Output schema
 // ---------------------------------------------------------------------------
@@ -113,6 +113,28 @@ export const brapiBuildPhenotypeMatrix = tool('brapi_build_phenotype_matrix', {
         extraFilters: ExtraFiltersInput,
     }),
     output: OutputSchema,
+    enrichment: {
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when at least one study saturated the per-study loadLimit.'),
+        shown: z
+            .number()
+            .int()
+            .nonnegative()
+            .optional()
+            .describe('Observations collected across all studies after filtering.'),
+        cap: z
+            .number()
+            .int()
+            .positive()
+            .optional()
+            .describe('Per-study observation cap that was applied.'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance for reaching the observations this call left out.'),
+    },
     async handler(input, ctx) {
         const client = getBrapiClient();
         const bridge = getCanvasBridge();
@@ -125,25 +147,36 @@ export const brapiBuildPhenotypeMatrix = tool('brapi_build_phenotype_matrix', {
         const loadLimit = input.loadLimit ?? config.loadLimit;
         const warnings = [];
         const allObs = [];
-        // Collect observations study-by-study. Isolation per study avoids
-        // unbounded queries and preserves studyDbId on each row.
-        for (const studyDbId of input.studies) {
-            const studyObs = await pullStudyObservations({
-                studyDbId,
-                input,
-                client,
-                connection,
-                profile: profile.supported,
-                dialect,
-                config,
-                loadLimit,
-                warnings,
-                ctx,
-            });
-            if (studyObs === null) {
-                throw ctx.fail('no_observation_path', `Neither /observations nor /observationunits returned a usable path for study '${studyDbId}'. Check brapi_server_info for the capability list.`, { ...ctx.recoveryFor('no_observation_path'), studyDbId });
+        // Collect observations across the studies with bounded concurrency,
+        // reassembled in input order so the wide-matrix column/row layout (derived
+        // from study encounter order below) stays deterministic across identical
+        // runs. Fail-fast: aborts the whole call on the first study with no
+        // observation path or a hard error, preserving studyDbId on each row.
+        const outcomes = await pullObservationsForStudies({
+            studyDbIds: input.studies,
+            input,
+            client,
+            connection,
+            profile: profile.supported,
+            dialect,
+            config,
+            loadLimit,
+            failFast: true,
+            ctx,
+        });
+        const cappedStudies = [];
+        for (const outcome of outcomes) {
+            if (outcome.error !== undefined)
+                throw outcome.error;
+            warnings.push(...outcome.warnings);
+            // Each study's pull is bounded at loadLimit, so a saturated count means
+            // the upstream had more rows than this call collected.
+            if ((outcome.observations?.length ?? 0) >= loadLimit)
+                cappedStudies.push(outcome.studyDbId);
+            if (outcome.observations === null) {
+                throw ctx.fail('no_observation_path', `Neither /observations nor /observationunits returned a usable path for study '${outcome.studyDbId}'. Check brapi_server_info for the capability list.`, { ...ctx.recoveryFor('no_observation_path'), studyDbId: outcome.studyDbId });
             }
-            allObs.push(...studyObs);
+            allObs.push(...outcome.observations);
         }
         // Apply variable and germplasm filters if requested
         const filteredObs = filterObservations(allObs, input.variables, input.germplasm);
@@ -216,6 +249,13 @@ export const brapiBuildPhenotypeMatrix = tool('brapi_build_phenotype_matrix', {
                 expiresAt: dataframe.expiresAt,
             };
         }
+        if (cappedStudies.length > 0) {
+            ctx.enrich.truncated({
+                shown: filteredObs.length,
+                cap: loadLimit,
+                guidance: `Per-study collection hit loadLimit (${loadLimit}) for ${cappedStudies.join(', ')} — the matrix covers a partial set. Raise loadLimit, or narrow with variables / germplasm / fewer studies.`,
+            });
+        }
         return result;
     },
     format: (result) => {

package/dist/mcp-server/tools/definitions/brapi-build-phenotype-matrix.tool.js.map CHANGED Viewed

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

@@ -45,11 +45,11 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
     }, z.core.$strip>;
     auth: z.ZodObject<{
         mode: z.ZodEnum<{
-            none: "none";
-            sgn: "sgn";
-            oauth2: "oauth2";
             api_key: "api_key";
             bearer: "bearer";
+            none: "none";
+            oauth2: "oauth2";
+            sgn: "sgn";
         }>;
         headerName: z.ZodOptional<z.ZodString>;
         expiresAt: z.ZodOptional<z.ZodString>;
@@ -63,10 +63,10 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
         id: z.ZodString;
         source: z.ZodEnum<{
             "env-override": "env-override";
-            "url-pattern": "url-pattern";
-            "server-name": "server-name";
-            "organization-name": "organization-name";
             fallback: "fallback";
+            "organization-name": "organization-name";
+            "server-name": "server-name";
+            "url-pattern": "url-pattern";
         }>;
         envVar: z.ZodString;
         disabledSearchEndpoints: z.ZodArray<z.ZodString>;
@@ -90,14 +90,14 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
     notes: z.ZodArray<z.ZodString>;
     fetchedAt: z.ZodString;
 }, z.core.$strip>, readonly [{
-    readonly reason: "auth_token_exchange_failed";
+    readonly reason: 'auth_token_exchange_failed';
     readonly code: JsonRpcErrorCode.Forbidden;
-    readonly when: "SGN or OAuth token exchange against the BrAPI /token endpoint failed";
-    readonly recovery: "Verify the credentials and that the server exposes /token before retrying.";
+    readonly when: 'SGN or OAuth token exchange against the BrAPI /token endpoint failed';
+    readonly recovery: 'Verify the credentials and that the server exposes /token before retrying.';
 }, {
-    readonly reason: "auth_no_access_token";
+    readonly reason: 'auth_no_access_token';
     readonly code: JsonRpcErrorCode.Forbidden;
-    readonly when: "Token endpoint responded but did not return an access_token";
-    readonly recovery: "Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.";
+    readonly when: 'Token endpoint responded but did not return an access_token';
+    readonly recovery: 'Confirm the credentials are valid and the upstream IdP issues access tokens for this grant.';
 }], undefined>;
 //# sourceMappingURL=brapi-connect.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-connect.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-connect.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAqBjE,eAAO,MAAM,YAAY;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAWX,4BAA4B;;mBAE9B,sEAAsE;uBAClE,4EAA4E;;qBAG9E,sBAAsB;;mBAExB,6DAA6D;uBAEjE,6FAA6F;cAoEnG,CAAC"}

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

@@ -34,9 +34,9 @@ export declare const brapiDataframeDescribe: import("@cyanheads/mcp-ts-core").To
         }, z.core.$strip>>;
     }, z.core.$strip>>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "list_all_disabled_on_shared_http";
+    readonly reason: 'list_all_disabled_on_shared_http';
     readonly code: JsonRpcErrorCode.Forbidden;
     readonly when: "This server is running as a shared HTTP endpoint without per-caller auth — listing every dataframe would expose other concurrent clients' workspaces, since all callers resolve to one shared tenant.";
-    readonly recovery: "Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.";
+    readonly recovery: 'Pass `dataframe` with a specific name — either from a prior find_* spillover result (`result.dataframe.tableName`) or one you registered via `brapi_dataframe_query` with `registerAs`. Listing all dataframes is not available on this deployment.';
 }], undefined>;
 //# sourceMappingURL=brapi-dataframe-describe.tool.d.ts.map

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

	@@ -1 +1 @@
1	- {"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8CjE,eAAO,MAAM,sBAAsB~~;;;;;;;;;;;;;;;;;;;;;;;;;cAkCjC~~,CAAC"}
1	+ {"version":3,"file":"brapi-dataframe-describe.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-describe.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAEjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AA8CjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;qBAMrB,kCAAkC;;mBAEpC,uMAAuM;uBAE3M,qPAAqP;cAwB3P,CAAC"}

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

@@ -23,8 +23,8 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     dataframe: z.ZodString;
     format: z.ZodEnum<{
         csv: "csv";
-        parquet: "parquet";
         json: "json";
+        parquet: "parquet";
     }>;
     filename: z.ZodOptional<z.ZodString>;
     columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
@@ -33,8 +33,8 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     dataframe: z.ZodString;
     format: z.ZodEnum<{
         csv: "csv";
-        parquet: "parquet";
         json: "json";
+        parquet: "parquet";
     }>;
     path: z.ZodString;
     filename: z.ZodString;
@@ -46,24 +46,24 @@ export declare const brapiDataframeExport: import("@cyanheads/mcp-ts-core").Tool
     }, z.core.$strip>>;
     expiresAt: z.ZodString;
 }, z.core.$strip>, readonly [{
-    readonly reason: "export_dir_unset";
+    readonly reason: 'export_dir_unset';
     readonly code: JsonRpcErrorCode.ConfigurationError;
-    readonly when: "BRAPI_EXPORT_DIR is not configured (defensive — the registration gate normally hides the tool when this happens)";
-    readonly recovery: "Set BRAPI_EXPORT_DIR on the server before retrying.";
+    readonly when: 'BRAPI_EXPORT_DIR is not configured (defensive — the registration gate normally hides the tool when this happens)';
+    readonly recovery: 'Set BRAPI_EXPORT_DIR on the server before retrying.';
 }, {
-    readonly reason: "dataframe_not_found";
+    readonly reason: 'dataframe_not_found';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "No dataframe with this name exists on the canvas (expired, dropped, or typo)";
-    readonly recovery: "Call brapi_dataframe_describe to list available dataframes.";
+    readonly when: 'No dataframe with this name exists on the canvas (expired, dropped, or typo)';
+    readonly recovery: 'Call brapi_dataframe_describe to list available dataframes.';
 }, {
-    readonly reason: "invalid_filename";
+    readonly reason: 'invalid_filename';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "filename contains path separators or traversal segments";
-    readonly recovery: "Provide a filename without \"/\", \"\\\", or \"..\" — leave it unset to use the default.";
+    readonly when: 'filename contains path separators or traversal segments';
+    readonly recovery: 'Provide a filename without "/", "\\", or ".." — leave it unset to use the default.';
 }, {
-    readonly reason: "mutually_exclusive_projection";
+    readonly reason: 'mutually_exclusive_projection';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "Both `columns` and `sql` were supplied";
-    readonly recovery: "Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.";
+    readonly when: 'Both `columns` and `sql` were supplied';
+    readonly recovery: 'Pass either `columns` for a thin projection or `sql` for filtering/aggregation, not both.';
 }], undefined>;
 //# sourceMappingURL=brapi-dataframe-export.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-dataframe-export.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-export.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAIH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAE/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAoEjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;;;;qBAMnB,kBAAkB;;mBAEpB,kHAAkH;uBAC9G,qDAAqD;;qBAGvD,qBAAqB;;mBAEvB,8EAA8E;uBAC1E,6DAA6D;;qBAG/D,kBAAkB;;mBAEpB,yDAAyD;uBAE7D,oFAAoF;;qBAG9E,+BAA+B;;mBAEjC,wCAAwC;uBAE5C,2FAA2F;cAqFjG,CAAC"}

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

@@ -38,9 +38,14 @@ export declare const brapiDataframeQuery: import("@cyanheads/mcp-ts-core").ToolD
     rows: z.ZodArray<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
     dataframe: z.ZodOptional<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "sql_rejected";
+    readonly reason: 'sql_rejected';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)";
-    readonly recovery: "Submit a single SELECT statement using only registered dataframes. For changes, use `registerAs` in this tool to materialize a result, or brapi_dataframe_drop to remove a dataframe.";
-}], undefined>;
+    readonly when: 'SQL violated read-only rules (multi-statement, non-SELECT, or disallowed operation)';
+    readonly recovery: 'Submit a single SELECT statement using only registered dataframes. For changes, use `registerAs` in this tool to materialize a result, or brapi_dataframe_drop to remove a dataframe.';
+}], {
+    readonly truncated: z.ZodOptional<z.ZodBoolean>;
+    readonly shown: z.ZodOptional<z.ZodNumber>;
+    readonly cap: z.ZodOptional<z.ZodNumber>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-dataframe-query.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-dataframe-query.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-dataframe-query.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;;;GAuBG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAO/D,OAAO,EAAE,gBAAgB,EAAY,MAAM,+BAA+B,CAAC;AAmH3E,eAAO,MAAM,mBAAmB;;;;;;;;;;;;;;qBAMlB,cAAc;;mBAEhB,qFAAqF;uBAEzF,uLAAuL;;;;;;EA2F7L,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js CHANGED Viewed

@@ -119,6 +119,23 @@ export const brapiDataframeQuery = tool('brapi_dataframe_query', {
     ],
     input: InputSchema,
     output: OutputSchema,
+    enrichment: {
+        truncated: z
+            .boolean()
+            .optional()
+            .describe('True when the response carries fewer rows than the query produced.'),
+        shown: z.number().int().nonnegative().optional().describe('Rows materialized into `rows`.'),
+        cap: z
+            .number()
+            .int()
+            .positive()
+            .optional()
+            .describe('Row ceiling that bound the response (the smaller of preview and rowLimit).'),
+        notice: z
+            .string()
+            .optional()
+            .describe('Guidance for reaching the rows this response left out.'),
+    },
     async handler(input, ctx) {
         const bridge = getCanvasBridge();
         const userRegisterAs = input.registerAs;
@@ -165,6 +182,20 @@ export const brapiDataframeQuery = tool('brapi_dataframe_query', {
         };
         if (userRegisterAs !== undefined)
             out.dataframe = userRegisterAs;
+        if (out.rows.length < out.rowCount) {
+            // Two ceilings can bind here — `preview` and the (config-clamped)
+            // `rowLimit` — and the rows that came back are exactly the one that did,
+            // so report that count as the cap and name the lever that produced it.
+            const shown = out.rows.length;
+            const lever = input.preview !== undefined && shown === input.preview ? 'preview' : 'rowLimit';
+            ctx.enrich.truncated({
+                shown,
+                cap: shown,
+                guidance: `\`${lever}\` bound the response at ${shown} of ${out.rowCount} rows. ${userRegisterAs
+                    ? `Query \`${userRegisterAs}\` with LIMIT/OFFSET to walk the remainder, or aggregate instead of materializing it.`
+                    : 'Re-run with `registerAs` to keep the full result queryable, then page it with LIMIT/OFFSET.'}`,
+            });
+        }
         return out;
     },
     format: (result) => [{ type: 'text', text: renderQuery(result) }],

package/dist/mcp-server/tools/definitions/brapi-dataframe-query.tool.js.map CHANGED Viewed

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

@@ -19,13 +19,13 @@ export declare const brapiDescribeFilters: import("@cyanheads/mcp-ts-core").Tool
     filters: z.ZodArray<z.ZodObject<{
         name: z.ZodString;
         type: z.ZodEnum<{
-            string: "string";
-            number: "number";
             boolean: "boolean";
             date: "date";
             integer: "integer";
-            "string[]": "string[]";
             "integer[]": "integer[]";
+            number: "number";
+            string: "string";
+            "string[]": "string[]";
         }>;
         description: z.ZodString;
         example: z.ZodString;
@@ -33,9 +33,9 @@ export declare const brapiDescribeFilters: import("@cyanheads/mcp-ts-core").Tool
     specReference: z.ZodOptional<z.ZodString>;
     availableEndpoints: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_endpoint";
+    readonly reason: 'unknown_endpoint';
     readonly code: JsonRpcErrorCode.NotFound;
-    readonly when: "No filter catalog is registered for the requested endpoint";
-    readonly recovery: "Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).";
+    readonly when: 'No filter catalog is registered for the requested endpoint';
+    readonly recovery: 'Pick an endpoint from data.availableEndpoints — same set as the input enum (studies, germplasm, observations, variables, images, variants, locations).';
 }], undefined>;
 //# sourceMappingURL=brapi-describe-filters.tool.d.ts.map

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

	@@ -1 +1 @@
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1	+ {"version":3,"file":"brapi-describe-filters.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-describe-filters.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;GAQG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgBjE,eAAO,MAAM,oBAAoB;;;;;;;;;;;;;;;;;;;;;;;;qBAMnB,kBAAkB;;mBAEpB,4DAA4D;uBAEhE,wJAAwJ;cAiE9J,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts CHANGED Viewed

@@ -34,18 +34,18 @@ export declare const brapiExportGenotypeMatrix: import("@cyanheads/mcp-ts-core")
     germplasmDbIds: z.ZodOptional<z.ZodArray<z.ZodString>>;
     variantSetDbId: z.ZodString;
     format: z.ZodEnum<{
+        "matrix-json": "matrix-json";
         plink: "plink";
         "vcf-lite": "vcf-lite";
-        "matrix-json": "matrix-json";
     }>;
     maxCalls: z.ZodOptional<z.ZodNumber>;
     maxColumns: z.ZodOptional<z.ZodNumber>;
 }, z.core.$strip>, z.ZodObject<{
     alias: z.ZodString;
     format: z.ZodEnum<{
+        "matrix-json": "matrix-json";
         plink: "plink";
         "vcf-lite": "vcf-lite";
-        "matrix-json": "matrix-json";
     }>;
     rowCount: z.ZodNumber;
     columnCount: z.ZodNumber;
@@ -73,19 +73,19 @@ export declare const brapiExportGenotypeMatrix: import("@cyanheads/mcp-ts-core")
     truncated: z.ZodBoolean;
     warnings: z.ZodArray<z.ZodString>;
 }, z.core.$strip>, readonly [{
-    readonly reason: "unknown_alias";
+    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_export_genotype_matrix.";
+    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_export_genotype_matrix.';
 }, {
-    readonly reason: "no_filters";
+    readonly reason: 'no_filters';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "No variantSetDbId was provided";
-    readonly recovery: "Provide variantSetDbId before retrying — unfiltered genotype-call pulls are too expensive.";
+    readonly when: 'No variantSetDbId was provided';
+    readonly recovery: 'Provide variantSetDbId before retrying — unfiltered genotype-call pulls are too expensive.';
 }, {
-    readonly reason: "search_endpoint_disabled";
+    readonly reason: 'search_endpoint_disabled';
     readonly code: JsonRpcErrorCode.ValidationError;
-    readonly when: "The active dialect declares POST /search/calls as known-dead on this server";
-    readonly recovery: "Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.";
+    readonly when: 'The active dialect declares POST /search/calls as known-dead on this server';
+    readonly recovery: 'Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.';
 }], undefined>;
 //# sourceMappingURL=brapi-export-genotype-matrix.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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