npm - @cyanheads/brapi-mcp-server - Versions diffs - 0.6.3 → 0.7.0 - Mend

@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0

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Files changed (106) hide show

package/dist/mcp-server/tools/definitions/index.js CHANGED Viewed

@@ -10,12 +10,14 @@
  *
  * @module mcp-server/tools/definitions/index
  */
+import { brapiBuildPhenotypeMatrix } from './brapi-build-phenotype-matrix.tool.js';
 import { brapiConnect } from './brapi-connect.tool.js';
 import { brapiDataframeDescribe } from './brapi-dataframe-describe.tool.js';
 import { brapiDataframeDrop } from './brapi-dataframe-drop.tool.js';
 import { brapiDataframeExport } from './brapi-dataframe-export.tool.js';
 import { brapiDataframeQuery } from './brapi-dataframe-query.tool.js';
 import { brapiDescribeFilters } from './brapi-describe-filters.tool.js';
+import { brapiExportGenotypeMatrix } from './brapi-export-genotype-matrix.tool.js';
 import { brapiFindGenotypeCalls } from './brapi-find-genotype-calls.tool.js';
 import { brapiFindGermplasm } from './brapi-find-germplasm.tool.js';
 import { brapiFindImages } from './brapi-find-images.tool.js';
@@ -24,6 +26,7 @@ import { brapiFindObservations } from './brapi-find-observations.tool.js';
 import { brapiFindStudies } from './brapi-find-studies.tool.js';
 import { brapiFindVariables } from './brapi-find-variables.tool.js';
 import { brapiFindVariants } from './brapi-find-variants.tool.js';
+import { brapiGermplasmPerformance } from './brapi-germplasm-performance.tool.js';
 import { brapiGetGermplasm } from './brapi-get-germplasm.tool.js';
 import { brapiGetImage } from './brapi-get-image.tool.js';
 import { brapiGetStudy } from './brapi-get-study.tool.js';
@@ -39,6 +42,7 @@ import { brapiWalkPedigree } from './brapi-walk-pedigree.tool.js';
  */
 export const readOnlyToolDefinitions = [
     brapiConnect,
+    brapiBuildPhenotypeMatrix,
     brapiServerInfo,
     brapiDescribeFilters,
     brapiFindStudies,
@@ -46,6 +50,7 @@ export const readOnlyToolDefinitions = [
     brapiFindGermplasm,
     brapiGetGermplasm,
     brapiWalkPedigree,
+    brapiGermplasmPerformance,
     brapiFindVariables,
     brapiFindObservations,
     brapiFindImages,
@@ -53,6 +58,7 @@ export const readOnlyToolDefinitions = [
     brapiFindLocations,
     brapiFindVariants,
     brapiFindGenotypeCalls,
+    brapiExportGenotypeMatrix,
     brapiDataframeDescribe,
     brapiDataframeQuery,
     brapiRawGet,

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

	@@ -1 +1 @@
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package/dist/mcp-server/tools/shared/canvas-columns.d.ts ADDED Viewed

@@ -0,0 +1,32 @@
+/**
+ * @fileoverview Shared canvas column-name sanitizer. The two matrix-building
+ * tools (`brapi_build_phenotype_matrix`, `brapi_export_genotype_matrix`) pivot
+ * upstream IDs (`observationVariableDbId`, `variantDbId`) into dataframe column
+ * names. The framework's canvas registers tables through `assertValidIdentifier`,
+ * which rejects any column whose name fails `/^[A-Za-z_][A-Za-z0-9_]{0,62}$/` or
+ * matches a reserved SQL keyword. BrAPI DbIds are routinely numeric (Breedbase
+ * uses integers) or collide with reserved words, so column names must be
+ * sanitized to SQL-safe identifiers before registration — paired with a legend
+ * mapping the safe name back to the original ID so the correlation is never lost.
+ *
+ * @module mcp-server/tools/shared/canvas-columns
+ */
+/**
+ * Sanitize an arbitrary upstream ID into a valid DuckDB column identifier.
+ * Mirrors the framework's `CANVAS_IDENTIFIER_REGEX` (`/^[A-Za-z_][A-Za-z0-9_]{0,62}$/`):
+ * replace illegal characters with `_`, prefix `v_` when the result would start
+ * with a digit, truncate to 63 chars, and suffix `_` when the result collides
+ * with a reserved SQL keyword.
+ */
+export declare function sanitizeColumnName(raw: string): string;
+/**
+ * Sanitize a list of IDs into unique column names, preserving input order. When
+ * two IDs sanitize to the same name, later collisions get a numeric suffix
+ * (`_2`, `_3`, …). Returns the column names in order plus a legend mapping each
+ * safe column name back to its original ID.
+ */
+export declare function buildUniqueColumns(ids: readonly string[]): {
+    columns: string[];
+    toOriginal: Record<string, string>;
+};
+//# sourceMappingURL=canvas-columns.d.ts.map

package/dist/mcp-server/tools/shared/canvas-columns.d.ts.map ADDED Viewed

@@ -0,0 +1 @@

+ {"version":3,"file":"canvas-columns.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/shared/canvas-columns.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AA+CH;;;;;;GAMG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,MAAM,GAAG,MAAM,CAStD;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,GAAG,EAAE,SAAS,MAAM,EAAE,GAAG;IAC1D,OAAO,EAAE,MAAM,EAAE,CAAC;IAClB,UAAU,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CACpC,CAaA"}

package/dist/mcp-server/tools/shared/canvas-columns.js ADDED Viewed

@@ -0,0 +1,98 @@
+/**
+ * @fileoverview Shared canvas column-name sanitizer. The two matrix-building
+ * tools (`brapi_build_phenotype_matrix`, `brapi_export_genotype_matrix`) pivot
+ * upstream IDs (`observationVariableDbId`, `variantDbId`) into dataframe column
+ * names. The framework's canvas registers tables through `assertValidIdentifier`,
+ * which rejects any column whose name fails `/^[A-Za-z_][A-Za-z0-9_]{0,62}$/` or
+ * matches a reserved SQL keyword. BrAPI DbIds are routinely numeric (Breedbase
+ * uses integers) or collide with reserved words, so column names must be
+ * sanitized to SQL-safe identifiers before registration — paired with a legend
+ * mapping the safe name back to the original ID so the correlation is never lost.
+ *
+ * @module mcp-server/tools/shared/canvas-columns
+ */
+/**
+ * Reserved SQL keywords rejected by the framework canvas gate
+ * (`assertValidIdentifier`, reason `identifierReserved`). Kept in sync with the
+ * framework's `RESERVED_IDENTIFIERS` set — a sanitized name matching one of
+ * these (case-insensitive) is suffixed with `_` to clear the gate.
+ */
+const RESERVED_IDENTIFIERS = new Set([
+    'select',
+    'from',
+    'where',
+    'order',
+    'group',
+    'having',
+    'limit',
+    'offset',
+    'union',
+    'intersect',
+    'except',
+    'all',
+    'distinct',
+    'as',
+    'and',
+    'or',
+    'not',
+    'null',
+    'true',
+    'false',
+    'case',
+    'when',
+    'then',
+    'else',
+    'end',
+    'join',
+    'inner',
+    'outer',
+    'left',
+    'right',
+    'full',
+    'cross',
+    'on',
+    'using',
+    'with',
+    'recursive',
+]);
+/**
+ * Sanitize an arbitrary upstream ID into a valid DuckDB column identifier.
+ * Mirrors the framework's `CANVAS_IDENTIFIER_REGEX` (`/^[A-Za-z_][A-Za-z0-9_]{0,62}$/`):
+ * replace illegal characters with `_`, prefix `v_` when the result would start
+ * with a digit, truncate to 63 chars, and suffix `_` when the result collides
+ * with a reserved SQL keyword.
+ */
+export function sanitizeColumnName(raw) {
+    let name = raw.replace(/[^A-Za-z0-9_]/g, '_');
+    if (/^[0-9]/.test(name))
+        name = `v_${name}`;
+    if (name.length > 63)
+        name = name.slice(0, 63);
+    if (name.length === 0)
+        name = 'v_unknown';
+    if (RESERVED_IDENTIFIERS.has(name.toLowerCase())) {
+        name = name.length >= 63 ? `${name.slice(0, 62)}_` : `${name}_`;
+    }
+    return name;
+}
+/**
+ * Sanitize a list of IDs into unique column names, preserving input order. When
+ * two IDs sanitize to the same name, later collisions get a numeric suffix
+ * (`_2`, `_3`, …). Returns the column names in order plus a legend mapping each
+ * safe column name back to its original ID.
+ */
+export function buildUniqueColumns(ids) {
+    const used = new Map();
+    const columns = [];
+    const toOriginal = {};
+    for (const id of ids) {
+        const base = sanitizeColumnName(id);
+        const count = (used.get(base) ?? 0) + 1;
+        used.set(base, count);
+        const colName = count === 1 ? base : `${base}_${count}`;
+        columns.push(colName);
+        toOriginal[colName] = id;
+    }
+    return { columns, toOriginal };
+}
+//# sourceMappingURL=canvas-columns.js.map

package/dist/mcp-server/tools/shared/canvas-columns.js.map ADDED Viewed

@@ -0,0 +1 @@

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

@@ -131,7 +131,7 @@ export declare function renderFindHeader(opts: {
     noun: string;
     alias: string;
     returnedCount: number;
-    totalCount: number;
+    totalCount?: number;
     dataframe?: {
         rowCount: number;
         expiresAt?: string;

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

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

@@ -247,9 +247,13 @@ export function renderFindHeader(opts) {
         const expiry = opts.dataframe.expiresAt
             ? ` (${formatExpiresIn(opts.dataframe.expiresAt)})`
             : '';
-        return `# ${opts.returnedCount} returned · ${opts.dataframe.rowCount} in dataframe${expiry} · ${opts.totalCount} total ${opts.noun} — \`${opts.alias}\``;
+        const totalPart = opts.totalCount !== undefined ? ` · ${opts.totalCount} total ${opts.noun}` : '';
+        return `# ${opts.returnedCount} returned · ${opts.dataframe.rowCount} in dataframe${expiry}${totalPart} — \`${opts.alias}\``;
     }
-    return `# ${opts.returnedCount} of ${opts.totalCount} ${opts.noun} — \`${opts.alias}\``;
+    if (opts.totalCount !== undefined) {
+        return `# ${opts.returnedCount} of ${opts.totalCount} ${opts.noun} — \`${opts.alias}\``;
+    }
+    return `# ${opts.returnedCount} ${opts.noun} — \`${opts.alias}\``;
 }
 /**
  * Render the filters-sent-to-server block, optionally translating

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

	@@ -1 +1 @@
1	- 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package/dist/mcp-server/tools/shared/genotype-calls.d.ts ADDED Viewed

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+/**
+ * @fileoverview Shared genotype-call pull logic — the async-search machinery
+ * (`POST /search/calls` → poll → page-walk) and the `CallRow` schema extracted
+ * from `brapi-find-genotype-calls.tool.ts` so that `brapi_export_genotype_matrix`
+ * can reuse the same pull infrastructure without duplicating it.
+ *
+ * This module owns: the `CallRowSchema`, `CallFormatting` type, and the
+ * `collectCalls` / `consumePage` helpers. It does NOT contain `spillCalls` or
+ * any tool-level concerns — those stay in the consuming tool files.
+ *
+ * @module mcp-server/tools/shared/genotype-calls
+ */
+import { type Context, z } from '@cyanheads/mcp-ts-core';
+import type { BrapiClient } from '../../../services/brapi-client/index.js';
+import type { RegisteredServer } from '../../../services/server-registry/types.js';
+export declare const CallRowSchema: z.ZodObject<{
+    callSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    callSetName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    variantDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    variantName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    variantSetDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    genotype: z.ZodOptional<z.ZodNullable<z.ZodObject<{
+        values: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodString>>>;
+    }, z.core.$loose>>>;
+    genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+}, z.core.$loose>;
+export type CallRow = z.infer<typeof CallRowSchema>;
+export interface CallFormatting {
+    expandHomozygotes?: boolean | null;
+    sepPhased?: string | null;
+    sepUnphased?: string | null;
+    unknownString?: string | null;
+}
+export interface CollectCallsInput {
+    body: Record<string, unknown>;
+    client: BrapiClient;
+    connection: RegisteredServer;
+    ctx: Context;
+    maxCalls: number;
+    warnings: string[];
+}
+export interface CollectCallsResult {
+    callFormatting: CallFormatting;
+    rows: CallRow[];
+    truncated: boolean;
+}
+/**
+ * Build the POST /search/calls body from named filter params. Handles both the
+ * singular `variantSetDbId` convenience and the plural `variantSetDbIds` array,
+ * merging and deduplicating them.
+ */
+export declare function buildCallsSearchBody(input: {
+    variantSetDbId?: string | undefined;
+    variantSetDbIds?: string[] | undefined;
+    germplasmDbIds?: string[] | undefined;
+    callSetDbIds?: string[] | undefined;
+    variantDbIds?: string[] | undefined;
+    callFormat?: string | undefined;
+}): Record<string, unknown>;
+/**
+ * Pull all genotype call pages for a given search body, capping at `maxCalls`.
+ * Uses BrAPI's async-search pattern: `POST /search/calls` → `GET /search/calls/{id}`
+ * with 202-retry. Pages are collected until all results are fetched or `maxCalls`
+ * is reached.
+ */
+export declare function collectCalls(input: CollectCallsInput): Promise<CollectCallsResult>;
+/**
+ * Extract call rows and `callFormatting` hints from one BrAPI envelope page.
+ * Mutates `rows` in-place; invokes `setCallFormatting` when formatting hints
+ * are present so the caller can merge across pages.
+ */
+export declare function consumePage(envelope: Awaited<ReturnType<BrapiClient['get']>>, rows: CallRow[], setCallFormatting: (f: CallFormatting) => void): void;
+/**
+ * Render the genotype string for one call row given the server's callFormatting
+ * hints. Prefers `genotype.values` joined with the appropriate separator;
+ * falls back to `genotypeValue`; returns the `unknownString` (or ".") when
+ * no data is available.
+ */
+export declare function renderGenotypeString(row: CallRow, callFormatting: CallFormatting, phased?: boolean): string;
+//# sourceMappingURL=genotype-calls.d.ts.map

package/dist/mcp-server/tools/shared/genotype-calls.d.ts.map ADDED Viewed

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