@cyanheads/brapi-mcp-server 0.7.5 → 0.7.7

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

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

@@ -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;AAuHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA2P5B,CAAC"}
+{"version":3,"file":"brapi-find-variants.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-variants.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAsHjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EA4P5B,CAAC"}

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

@@ -13,7 +13,7 @@ import { getBrapiClient } from '../../../services/brapi-client/index.js';
 import { resolveDialect } from '../../../services/brapi-dialect/index.js';
 import { getCanvasBridge } from '../../../services/canvas-bridge/index.js';
 import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
-import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, truncationMeta, } from '../shared/find-helpers.js';
+import { AliasInput, applyDialectFiltersOrFail, asString, buildExtraFilterChecks, buildRefinementHint, checkFilterMatchRates, collectPassthroughParts, computeDistribution, DataframeHandleSchema, dialectRowMapper, ExtraFiltersInput, LoadLimitInput, loadInitialFindPage, maybeSpill, mergeFilters, renderDataframeHandle, renderDistributions, renderFindHeader, requireRegisteredConnection, resolveFindRoute, } from '../shared/find-helpers.js';
 const VariantRowSchema = z
     .object({
     variantDbId: z.string().describe('Server-side identifier for the variant.'),
@@ -261,8 +261,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
             lines.push('');
         }
         lines.push('## Distributions');
-        lines.push(renderDistributions(result.distributions, truncationMeta(result.dataframe)) ||
-            '_No values to summarize._');
+        lines.push(renderDistributions(result.distributions, result.dataframe) || '_No values to summarize._');
         lines.push('');
         lines.push('## Variants');
         if (result.results.length === 0) {
@@ -311,7 +310,7 @@ export const brapiFindVariants = tool('brapi_find_variants', {
                     parts.push(`filtersFailed=${v.filtersFailed.join(',')}`);
                 if (v.variantNames?.length)
                     parts.push(`names=${v.variantNames.join(',')}`);
-                parts.push(...collectPassthroughParts(v, RENDERED));
+                parts.push(...collectPassthroughParts(v, RENDERED, result.dataframe));
                 lines.push(`- ${parts.join(' · ')}`);
             }
         }

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

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

@@ -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

@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/find-helpers.js

@@ -345,43 +345,78 @@ export function renderAppliedFilters(filters, serverToUser = {}) {
     return lines.join('\n');
 }
 /**
- * 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.
+ * Character budget for one rendered comma-joined list line before it caps.
+ *
+ * Sized by rendered width rather than a fixed entry count so a line adapts to
+ * its data: the common case (a distribution over a 26-study server, a `find_*`
+ * dataframe's ~18 columns) renders complete, while a pathological one (a
+ * spilled set whose `fullRows` reach {@link MAX_SPILLOVER_ROWS}; a genotype
+ * matrix's 500,000 variant columns) caps instead of emitting megabytes into
+ * `content[]`. Mirrors {@link MAX_INLINE_JSON}'s size-aware philosophy; a
+ * hardcoded top-N did neither job well.
+ *
+ * Applied only to lines whose omitted entries stay retrievable elsewhere —
+ * never to a line that is the sole carrier of a mapping (see
+ * `renderDataframeHandle`'s `renamedColumns`).
+ */
+const MAX_LIST_LINE = 400;
+/**
+ * Join `parts` with `, ` until `budget` characters are consumed. Always emits
+ * at least one part — a line naming no value carries less than one that
+ * overruns the budget slightly. Returns the rendered prefix plus how many parts
+ * were left out, so callers can append their own recovery hint.
+ */
+function joinWithinBudget(parts, budget) {
+    const shown = [];
+    let remaining = budget;
+    for (const part of parts) {
+        if (shown.length > 0 && part.length + 2 > remaining)
+            break;
+        shown.push(part);
+        remaining -= part.length + 2;
+    }
+    return { text: shown.join(', '), omitted: parts.length - shown.length };
+}
+/**
+ * Name where a capped distribution's remaining entries can actually be read.
+ * When the result spilled, the dataframe holds every row the distribution was
+ * computed from, so aggregating there reconstructs it in full — a path a
+ * content-only client can take. Without a dataframe there is nothing to point
+ * at but `structuredContent`, which those clients cannot read; that residual
+ * is only reachable when a small result set carries a very high-cardinality
+ * field.
+ *
+ * Deliberately does not emit a `GROUP BY` snippet: distribution accessors may
+ * explode array-valued fields (`find_studies.seasons`), so a per-field
+ * `GROUP BY` would return per-array-literal counts rather than the exploded
+ * distribution it claims to reconstruct.
+ */
+function distributionRecoveryHint(dataframe) {
+    return dataframe
+        ? ` — aggregate dataframe \`${dataframe.tableName}\` with brapi_dataframe_query for the full distribution`
+        : ' (see structuredContent.distributions)';
+}
+/**
+ * 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 function renderDistributions(distributions, truncated) {
+export function renderDistributions(distributions, dataframe) {
     const lines = [];
-    if (truncated?.truncated) {
-        lines.push(`_Computed over ${truncated.rowCount} of ${truncated.totalCount} upstream rows — narrow filters or raise loadLimit for a representative sample._`);
+    if (dataframe?.truncated) {
+        lines.push(`_Computed over ${dataframe.rowCount} of ${dataframe.totalCount ?? dataframe.rowCount} upstream rows — narrow filters or raise loadLimit for a representative sample._`);
     }
     for (const [field, counts] of Object.entries(distributions)) {
         const entries = Object.entries(counts);
         if (entries.length === 0)
             continue;
-        const summary = entries
-            .slice(0, 5)
-            .map(([value, count]) => `${value} (${count})`)
-            .join(', ');
-        const suffix = entries.length > 5 ? `, …+${entries.length - 5} more` : '';
-        lines.push(`- **${field}:** ${summary}${suffix}`);
+        const { text, omitted } = joinWithinBudget(entries.map(([value, count]) => `${value} (${count})`), MAX_LIST_LINE);
+        const suffix = omitted > 0 ? `, …+${omitted} more${distributionRecoveryHint(dataframe)}` : '';
+        lines.push(`- **${field}:** ${text}${suffix}`);
     }
     return lines.join('\n');
 }
-/**
- * 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 function truncationMeta(dataframe) {
-    if (!dataframe?.truncated)
-        return;
-    return {
-        truncated: true,
-        rowCount: dataframe.rowCount,
-        totalCount: dataframe.totalCount ?? dataframe.rowCount,
-    };
-}
 /**
  * Build a row mapper that runs `dialect.normalizeRow` per row, when the
  * dialect declares one. Returns `undefined` on dialects with no normalizer
@@ -487,12 +522,26 @@ export const DataframeHandleSchema = z.object({
  * 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 function renderDataframeHandle(handle) {
+    const { text: columns, omitted } = joinWithinBudget(handle.columns, MAX_LIST_LINE);
+    const columnsSuffix = omitted > 0 ? `, …+${omitted} more — brapi_dataframe_describe lists the full schema` : '';
     const lines = [
         `- tableName: \`${handle.tableName}\` (query via brapi_dataframe_query)`,
         `- rowCount: ${handle.rowCount}`,
-        `- columns: ${handle.columns.join(', ')}`,
+        `- columns: ${columns}${columnsSuffix}`,
         `- createdAt: ${handle.createdAt}`,
         `- expiresAt: ${handle.expiresAt} (${formatExpiresIn(handle.expiresAt)})`,
     ];
@@ -1005,32 +1054,44 @@ export function buildRefinementHint(totalCount, loadLimit, distributions, option
     return `${totalCount} rows exceed loadLimit=${loadLimit}. Add more specific filters or raise loadLimit.`;
 }
 /**
- * Inline JSON over this many characters renders as a `<N keys, Xkb — see
- * structuredContent>` placeholder instead of the raw stringified value. Picked
- * to keep a single bulleted row under one display line while still showing
- * small objects (`{traitDbId: "...", traitName: "..."}`) inline. Structured
- * clients (Codex Desktop) still receive the full object via
- * `structuredContent.results[]`; this cap only affects the `content[]` text
- * surface that Claude Desktop reads.
+ * Inline JSON over this many characters renders as a `<N keys, Xkb — …>`
+ * placeholder instead of the raw stringified value. Picked to keep a single
+ * bulleted row under one display line while still showing small objects
+ * (`{traitDbId: "...", traitName: "..."}`) inline. Rendering every oversized
+ * value in full is not an option at the row scale these helpers run at — a
+ * `loadLimit`-sized page of GeoJSON-heavy rows reaches megabytes, and
+ * `content[]` carries it a second time on top of `structuredContent`.
  */
 const MAX_INLINE_JSON = 240;
 /**
  * Render a value for the row/line passthrough surface. Scalars are stringified
  * via `String(value)`; objects/arrays are JSON-encoded and replaced with a
- * size-aware placeholder when they exceed `MAX_INLINE_JSON`.
+ * size-aware placeholder when they exceed {@link MAX_INLINE_JSON}.
+ *
+ * When the caller's result spilled, the placeholder names the dataframe rather
+ * than `structuredContent`. That matters for correctness, not just wording:
+ * the dataframe stores the value untruncated (object-shaped columns register
+ * as DuckDB `JSON` and round-trip through `JSON.stringify`), and
+ * `brapi_dataframe_query` reaches it from a content-only client — which
+ * `structuredContent` never does. Callers whose rows are not in a dataframe
+ * (the `get_*` detail tools, `get_germplasm`'s parent/attribute companions)
+ * must pass nothing: pointing those at a dataframe would name a table that
+ * does not contain the record.
  */
-function renderPassthroughValue(value) {
+function renderPassthroughValue(value, dataframe) {
     if (typeof value !== 'object')
         return String(value);
     const json = JSON.stringify(value);
     if (json.length <= MAX_INLINE_JSON)
         return json;
     const kb = (json.length / 1024).toFixed(1);
-    if (Array.isArray(value)) {
-        return `<${value.length} entries, ${kb}KB — see structuredContent>`;
-    }
-    const keyCount = Object.keys(value).length;
-    return `<${keyCount} keys, ${kb}KB — see structuredContent>`;
+    const size = Array.isArray(value)
+        ? `${value.length} entries`
+        : `${Object.keys(value).length} keys`;
+    const where = dataframe
+        ? `query \`${dataframe.tableName}\` via brapi_dataframe_query`
+        : 'see structuredContent';
+    return `<${size}, ${kb}KB — ${where}>`;
 }
 /**
  * Collect `key=value` strings for every top-level key in a passthrough row
@@ -1038,14 +1099,19 @@ function renderPassthroughValue(value) {
  * structuredContent parity — server fields beyond the declared schema are
  * still emitted to text-only clients (Claude Desktop sees content[] only).
  * Large nested objects (over `MAX_INLINE_JSON` chars when stringified) collapse
- * to a size-aware placeholder; the full payload remains in `structuredContent`.
+ * to a size-aware placeholder.
+ *
+ * `dataframe` is the calling `find_*` result's handle, when it spilled — the
+ * rows rendered inline are a prefix of the rows it holds, so the placeholder
+ * can name it as the retrieval path. Omit it for records the dataframe does
+ * not contain.
  */
-export function collectPassthroughParts(row, renderedKeys) {
+export function collectPassthroughParts(row, renderedKeys, dataframe) {
     const parts = [];
     for (const [key, value] of Object.entries(row)) {
         if (renderedKeys.has(key) || value === undefined || value === null)
             continue;
-        parts.push(`${key}=${renderPassthroughValue(value)}`);
+        parts.push(`${key}=${renderPassthroughValue(value, dataframe)}`);
     }
     return parts;
 }
@@ -1055,6 +1121,15 @@ export function collectPassthroughParts(row, renderedKeys) {
  * `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 function appendPassthroughLines(lines, record, renderedKeys) {
     for (const [key, value] of Object.entries(record)) {