npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.7.6 → 0.7.8 - Mend

@cyanheads/brapi-mcp-server 0.7.6 → 0.7.8

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 (74) hide show

package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js CHANGED Viewed

@@ -10,9 +10,11 @@
  */
 import { tool, z } from '@cyanheads/mcp-ts-core';
 import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getServerConfig } from '../../../config/server-config.js';
 import { getBrapiClient } from '../../../services/brapi-client/index.js';
+import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { AliasInput, buildRequestOptions, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { AliasInput, buildRequestOptions, DataframeHandleSchema, isUpstreamNotFound, LoadLimitInput, renderDataframeHandle, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
 const DEFAULT_MAX_DEPTH = 3;
 const MAX_NODES = 1_000;
 const NodeSchema = z
@@ -86,6 +88,8 @@ const OutputSchema = z.object({
     warnings: z
         .array(z.string())
         .describe('Advisory messages (capability gaps, per-node expansion failures).'),
+    nodesDataframe: DataframeHandleSchema.optional().describe('Canvas dataframe holding the full node set, present when the walk exceeds loadLimit — nodes[] is then a bounded preview. Query with brapi_dataframe_query (SQL); JOIN to the edges dataframe on germplasmDbId.'),
+    edgesDataframe: DataframeHandleSchema.optional().describe('Canvas dataframe holding the full edge set, present when the walk exceeds loadLimit — edges[] is then a bounded preview. Any edge field that is a reserved SQL word (e.g. `from` → `from_`) is renamed to a SQL-safe identifier; columnLegend maps it back. Query with brapi_dataframe_query (SQL).'),
 });
 export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
     description: 'Walk germplasm ancestry or descendancy as a deduplicated DAG, with multi-generation traversal, cycle detection, and depth limits. Returns nodes + edges plus traversal stats (depthReached, rootCount, leafCount, cycleCount, deadEndCount).',
@@ -115,6 +119,7 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
             .max(10)
             .default(DEFAULT_MAX_DEPTH)
             .describe(`Max generations to walk per direction (default ${DEFAULT_MAX_DEPTH}, cap 10).`),
+        loadLimit: LoadLimitInput,
         alias: AliasInput,
     }),
     output: OutputSchema,
@@ -238,12 +243,53 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         const nodes = Array.from(state.nodes.values()).sort((a, b) => a.depth - b.depth || a.germplasmDbId.localeCompare(b.germplasmDbId));
         const edges = Array.from(state.edges.values());
         const leafCount = computeLeafCount(nodes, edges, input.direction);
+        // Spillover: when the full graph exceeds loadLimit, materialize the node
+        // and edge sets as two canvas dataframes (JOINable on germplasmDbId) and
+        // return a bounded preview inline — mirrors the find_* pattern. The stats
+        // above still describe the full walk; small walks stay inline-only.
+        const loadLimit = input.loadLimit ?? getServerConfig().loadLimit;
+        let previewNodes = nodes;
+        let previewEdges = edges;
+        let nodesDataframe;
+        let edgesDataframe;
+        if (nodes.length > loadLimit || edges.length > loadLimit) {
+            const bridge = getCanvasBridge();
+            const query = {
+                germplasmDbIds: input.germplasmDbIds,
+                direction: input.direction,
+                maxDepth: input.maxDepth,
+            };
+            // Register sequentially, not in parallel: the first call resolves and
+            // caches the default canvas in ctx.state; a concurrent second call would
+            // race that cache and land the two tables on different canvases, breaking
+            // the JOIN. Both tables must share one canvas.
+            if (nodes.length > 0) {
+                const reg = await bridge.registerDataframe(ctx, {
+                    source: 'walk_pedigree_nodes',
+                    baseUrl: connection.baseUrl,
+                    query,
+                    rows: nodes,
+                });
+                nodesDataframe = toDataframeHandle(reg, nodes.length);
+                previewNodes = nodes.slice(0, loadLimit);
+            }
+            if (edges.length > 0) {
+                const reg = await bridge.registerDataframe(ctx, {
+                    source: 'walk_pedigree_edges',
+                    baseUrl: connection.baseUrl,
+                    query,
+                    rows: edges,
+                });
+                edgesDataframe = toDataframeHandle(reg, edges.length);
+                previewEdges = edges.slice(0, loadLimit);
+            }
+        }
         const result = {
             alias: connection.alias,
             direction: input.direction,
             maxDepth: input.maxDepth,
-            nodes,
-            edges,
+            nodes: previewNodes,
+            edges: previewEdges,
             depthReached,
             rootCount: input.germplasmDbIds.length,
             leafCount,
@@ -252,6 +298,10 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
             truncated,
             warnings,
         };
+        if (nodesDataframe)
+            result.nodesDataframe = nodesDataframe;
+        if (edgesDataframe)
+            result.edgesDataframe = edgesDataframe;
         return result;
     },
     format: (result) => {
@@ -268,7 +318,9 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         lines.push(`- truncated: ${result.truncated}`);
         if (result.nodes.length > 0) {
             lines.push('');
-            lines.push('## Nodes');
+            lines.push(result.nodesDataframe
+                ? `## Nodes (preview — ${result.nodes.length} of ${result.nodesDataframe.rowCount}; full set in dataframe \`${result.nodesDataframe.tableName}\`)`
+                : '## Nodes');
             for (const node of result.nodes) {
                 const parts = [`**${node.germplasmName ?? node.germplasmDbId}**`];
                 parts.push(`id=\`${node.germplasmDbId}\``);
@@ -279,13 +331,25 @@ export const brapiWalkPedigree = tool('brapi_walk_pedigree', {
         }
         if (result.edges.length > 0) {
             lines.push('');
-            lines.push('## Edges');
+            lines.push(result.edgesDataframe
+                ? `## Edges (preview — ${result.edges.length} of ${result.edgesDataframe.rowCount}; full set in dataframe \`${result.edgesDataframe.tableName}\`)`
+                : '## Edges');
             for (const edge of result.edges) {
                 const suffix = edge.parentType ? ` (${edge.parentType})` : '';
                 const arrow = edge.relationship === 'parent' ? '→' : '←';
                 lines.push(`- \`${edge.from}\` ${arrow} \`${edge.to}\` · ${edge.relationship}${suffix}`);
             }
         }
+        if (result.nodesDataframe) {
+            lines.push('');
+            lines.push('## Nodes dataframe');
+            lines.push(...renderDataframeHandle(result.nodesDataframe));
+        }
+        if (result.edgesDataframe) {
+            lines.push('');
+            lines.push('## Edges dataframe');
+            lines.push(...renderDataframeHandle(result.edgesDataframe));
+        }
         if (result.warnings.length > 0) {
             lines.push('');
             lines.push('## Warnings');

package/dist/mcp-server/tools/definitions/brapi-walk-pedigree.tool.js.map CHANGED Viewed

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

@@ -700,6 +700,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     locations: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     locationNames: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     countryCodes: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
+    countryNames: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     locationTypes: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     abbreviations: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     bbox: import("zod").ZodOptional<import("zod").ZodObject<{
@@ -1055,6 +1056,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
 }> | import("@cyanheads/mcp-ts-core").ToolDefinition<import("zod").ZodObject<{
     alias: import("zod").ZodOptional<import("zod").ZodString>;
     germplasmDbId: import("zod").ZodString;
+    studyDbIds: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
     variables: import("zod").ZodOptional<import("zod").ZodArray<import("zod").ZodString>>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     alias: import("zod").ZodString;
@@ -1227,6 +1229,7 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
         descendants: "descendants";
     }>>;
     maxDepth: import("zod").ZodDefault<import("zod").ZodNumber>;
+    loadLimit: import("zod").ZodOptional<import("zod").ZodNumber>;
     alias: import("zod").ZodOptional<import("zod").ZodString>;
 }, import("zod/v4/core").$strip>, import("zod").ZodObject<{
     alias: import("zod").ZodString;
@@ -1264,6 +1267,28 @@ export declare const readOnlyToolDefinitions: (import("@cyanheads/mcp-ts-core").
     deadEndCount: import("zod").ZodNumber;
     truncated: import("zod").ZodBoolean;
     warnings: import("zod").ZodArray<import("zod").ZodString>;
+    nodesDataframe: import("zod").ZodOptional<import("zod").ZodObject<{
+        tableName: import("zod").ZodString;
+        rowCount: import("zod").ZodNumber;
+        columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
+        createdAt: import("zod").ZodString;
+        expiresAt: import("zod").ZodString;
+        truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
+        maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
+        totalCount: import("zod").ZodOptional<import("zod").ZodNumber>;
+    }, import("zod/v4/core").$strip>>;
+    edgesDataframe: import("zod").ZodOptional<import("zod").ZodObject<{
+        tableName: import("zod").ZodString;
+        rowCount: import("zod").ZodNumber;
+        columns: import("zod").ZodArray<import("zod").ZodString>;
+        columnLegend: import("zod").ZodOptional<import("zod").ZodRecord<import("zod").ZodString, import("zod").ZodString>>;
+        createdAt: import("zod").ZodString;
+        expiresAt: import("zod").ZodString;
+        truncated: import("zod").ZodOptional<import("zod").ZodBoolean>;
+        maxRows: import("zod").ZodOptional<import("zod").ZodNumber>;
+        totalCount: import("zod").ZodOptional<import("zod").ZodNumber>;
+    }, import("zod/v4/core").$strip>>;
 }, import("zod/v4/core").$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: import("@cyanheads/mcp-ts-core/errors").JsonRpcErrorCode.NotFound;

package/dist/mcp-server/tools/definitions/index.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.d.ts CHANGED Viewed

@@ -196,26 +196,12 @@ export declare function renderFindHeader(opts: {
  */
 export declare function renderAppliedFilters(filters: Record<string, unknown>, serverToUser?: Record<string, string>): string;
 /**
- * Render a distributions block in markdown. When `truncated` metadata is
- * supplied and `truncated.truncated` is true, a caveat line is prepended so
- * readers know the distribution covers only the fetched subset.
+ * Render a distributions block in markdown. Pass the `find_*` result's
+ * dataframe handle (when it spilled): a truncation caveat is prepended when the
+ * dataframe hit a row cap, and capped lines point at the dataframe as the
+ * content-visible path to the remaining entries.
  */
-export declare function renderDistributions(distributions: Record<string, Record<string, number>>, truncated?: {
-    truncated: boolean;
-    rowCount: number;
-    totalCount: number;
-}): string;
-/**
- * Project a `DataframeHandle | undefined` to the `truncated` metadata shape
- * expected by `renderDistributions`. Returns `undefined` when no dataframe is
- * present or when the dataframe was not truncated, so the caller doesn't need
- * to guard — just pass the result straight through.
- */
-export declare function truncationMeta(dataframe: DataframeHandle | undefined): {
-    truncated: boolean;
-    rowCount: number;
-    totalCount: number;
-} | undefined;
+export declare function renderDistributions(distributions: Record<string, Record<string, number>>, dataframe?: DataframeHandle): string;
 export interface LoadedRows<T> {
     /** True when we pulled a single page and the server has more. */
     hasMore: boolean;
@@ -319,6 +305,18 @@ export type DataframeHandle = z.infer<typeof DataframeHandleSchema>;
  * format. Centralized so the truncated/maxRows fields surface consistently.
  * `expiresAt` is paired with a human-readable `expires in Xh / Xd` so the
  * agent doesn't have to subtract dates to know when the handle goes stale.
+ *
+ * This is a *summary* surface — it is not the authoritative carrier of the
+ * schema, so `columns` is budgeted: it costs megabytes on a wide pivot (a
+ * genotype matrix reaches 500,000 variant columns) while
+ * `brapi_dataframe_describe` lists the full schema on demand, uncapped, from
+ * `content[]`. `renamedColumns` is deliberately NOT budgeted — it is the only
+ * mapping from a sanitized column back to its upstream key, with no describe
+ * or re-call path behind it, and capping the sole decoder is the same defect as
+ * capping the tool-level variant legend. It stays bounded in practice anyway:
+ * real upstream rows carry at most a key or two needing a rename, and the two
+ * matrix pivots pre-sanitize their keys before registration, so the field never
+ * populates for them at all.
  */
 export declare function renderDataframeHandle(handle: DataframeHandle): string[];
 /**
@@ -533,15 +531,29 @@ export declare function buildRefinementHint(totalCount: number, loadLimit: numbe
  * structuredContent parity — server fields beyond the declared schema are
  * still emitted to text-only clients (Claude Desktop sees content[] only).
  * Large nested objects (over `MAX_INLINE_JSON` chars when stringified) collapse
- * to a size-aware placeholder; the full payload remains in `structuredContent`.
+ * to a size-aware placeholder.
+ *
+ * `dataframe` is the calling `find_*` result's handle, when it spilled — the
+ * rows rendered inline are a prefix of the rows it holds, so the placeholder
+ * can name it as the retrieval path. Omit it for records the dataframe does
+ * not contain.
  */
-export declare function collectPassthroughParts(row: Record<string, unknown>, renderedKeys: ReadonlySet<string>): string[];
+export declare function collectPassthroughParts(row: Record<string, unknown>, renderedKeys: ReadonlySet<string>, dataframe?: DataframeHandle): string[];
 /**
  * Append `- **key:** value` lines for every top-level key in a passthrough
  * record that was not explicitly rendered. Companion to
  * `collectPassthroughParts` for detail-view (get_*) tools that use a
  * line-per-field layout instead of bullet-part lists. Honors the same inline
  * JSON cap.
+ *
+ * Takes no dataframe: its three callers (`get_study`, `get_germplasm`,
+ * `get_image`) fetch a single record by ID and never register one, so an
+ * oversized field on those tools still resolves only to `structuredContent`.
+ * Re-calling the sibling `get_*` tool is not a recovery path for a `find_*`
+ * row either — that lands back on this helper and re-renders the same
+ * placeholder. Closing that gap needs a mechanism these helpers do not have
+ * (see the `outline-on-overflow` technique, which suits the single-document
+ * shape of the `get_*` tools).
  */
 export declare function appendPassthroughLines(lines: string[], record: Record<string, unknown>, renderedKeys: ReadonlySet<string>): void;
 export type { BrapiEnvelope, BrapiPagination, ResolvedAuth, ServerConfig };

package/dist/mcp-server/tools/shared/find-helpers.d.ts.map CHANGED Viewed

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