@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js

@@ -0,0 +1,494 @@
+/**
+ * @fileoverview `brapi_export_genotype_matrix` — pull genotype calls for a
+ * germplasm × variant set and pivot them into a matrix in the requested format.
+ *
+ * Three output formats:
+ *
+ * - `matrix-json`: Wide germplasm × variant table registered as a canvas
+ *   dataframe (`df_<uuid>`). One row per call-set (germplasm); one column per
+ *   variant. Column names are sanitized for DuckDB (SQL-safe identifiers); a
+ *   `variantColumnLegend` maps sanitized name → original variant ID.
+ *
+ * - `vcf-lite`: Standard VCF-subset text (`#CHROM POS ID REF ALT <sample…>`),
+ *   one row per variant, returned in the `vcf` output field. CHROM/POS/REF/ALT
+ *   come from a `/variants` metadata pull; `.` when the server doesn't provide
+ *   them (common — the BrAPI test server leaves them null). The wide matrix is
+ *   also registered as a dataframe for SQL follow-up.
+ *
+ * - `plink`: `.ped` and `.map` text returned in the `ped` / `map` output fields.
+ *   `.map` carries chromosome + base-pair position from the variant pull; `.ped`
+ *   carries biallelic genotype pairs split from each call's genotype string.
+ *   Alleles are passed through verbatim (numeric 0/1 codings are not recoded to
+ *   nucleotides). The wide matrix is also registered as a dataframe.
+ *
+ * The genotype-call pull infrastructure is shared with `brapi_find_genotype_calls`
+ * via `src/mcp-server/tools/shared/genotype-calls.ts`; column sanitization is
+ * shared via `src/mcp-server/tools/shared/canvas-columns.ts`.
+ *
+ * @module mcp-server/tools/definitions/brapi-export-genotype-matrix.tool
+ */
+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 { resolveDialect } from '../../../services/brapi-dialect/index.js';
+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, asString, buildRequestOptions, DataframeHandleSchema, extractRows, renderDataframeHandle, requireRegisteredConnection, toDataframeHandle, } from '../shared/find-helpers.js';
+import { buildCallsSearchBody, collectCalls, renderGenotypeString, } from '../shared/genotype-calls.js';
+/** Max variant records scanned when pulling coordinate metadata for vcf/plink. */
+const MAX_VARIANT_METADATA_ROWS = 50_000;
+const VARIANT_METADATA_PAGE_SIZE = 1_000;
+/** Lines of format text shown inline in content[]; full text lives in structuredContent. */
+const FORMAT_PREVIEW_LINES = 25;
+// ---------------------------------------------------------------------------
+// Output schema
+// ---------------------------------------------------------------------------
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection used.'),
+    format: z
+        .enum(['plink', 'vcf-lite', 'matrix-json'])
+        .describe('The output format that was produced.'),
+    rowCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of call-set (germplasm) rows in the matrix.'),
+    columnCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of variant columns in the matrix (excluding the germplasm ID column).'),
+    variantColumnLegend: z
+        .record(z.string(), z.string())
+        .describe('Map of sanitized column name → original variantDbId. Dataframe column names are SQL-safe identifiers; use this legend to correlate them back to the original variant IDs.'),
+    callFormatting: z
+        .object({
+        expandHomozygotes: z.boolean().nullish().describe('Homozygous allele expansion flag.'),
+        unknownString: z.string().nullish().describe('String used for unknown/missing calls.'),
+        sepPhased: z.string().nullish().describe('Phased allele separator.'),
+        sepUnphased: z.string().nullish().describe('Unphased allele separator.'),
+    })
+        .describe('Genotype-encoding hints echoed by the server.'),
+    dataframe: DataframeHandleSchema.describe('Canvas dataframe handle for the wide germplasm × variant matrix (registered for every format). Query with brapi_dataframe_query (SQL); export with brapi_dataframe_export. The vcf/ped/map text fields are the format-specific serialization of the same data.'),
+    vcf: z
+        .string()
+        .optional()
+        .describe('VCF-lite text — header `#CHROM POS ID REF ALT` plus one genotype column per sample, one row per variant. Present only when format="vcf-lite". CHROM/POS/REF/ALT come from /variants metadata; "." when the server does not provide them.'),
+    ped: z
+        .string()
+        .optional()
+        .describe('PLINK .ped text — FID IID PAT MAT SEX PHENO placeholders (all 0) followed by biallelic genotype pairs per variant, one row per sample. Present only when format="plink". Alleles are passed through verbatim; PLINK missing is `0`.'),
+    map: z
+        .string()
+        .optional()
+        .describe('PLINK .map text — chromosome, variant-id, genetic-distance (0 placeholder), base-pair position, one row per variant. Present only when format="plink". Chromosome/position come from /variants metadata; `0` when absent.'),
+    truncated: z
+        .boolean()
+        .describe('True when the call pull was capped before exhausting upstream data.'),
+    warnings: z.array(z.string()).describe('Advisory messages (truncation, missing fields, etc.).'),
+});
+// ---------------------------------------------------------------------------
+// Tool definition
+// ---------------------------------------------------------------------------
+export const brapiExportGenotypeMatrix = tool('brapi_export_genotype_matrix', {
+    description: 'Pull genotype calls for a germplasm × variant set and pivot them into a matrix. `format` controls the output: `matrix-json` registers a wide germplasm × variant canvas dataframe for SQL analysis; `vcf-lite` returns VCF-subset text (in the `vcf` field) and also registers the dataframe; `plink` returns .ped/.map text (in the `ped`/`map` fields) and also registers the dataframe. vcf-lite/plink pull /variants metadata for CHROM/POS/REF/ALT (`.`/`0` when the server lacks them). Column names are SQL-safe identifiers; `variantColumnLegend` maps them back to original variant IDs.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    errors: [
+        {
+            reason: 'unknown_alias',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'No connection has been registered under the requested alias',
+            recovery: 'Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_export_genotype_matrix.',
+        },
+        {
+            reason: 'no_filters',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'No variantSetDbId was provided',
+            recovery: 'Provide variantSetDbId before retrying — unfiltered genotype-call pulls are too expensive.',
+        },
+        {
+            reason: 'search_endpoint_disabled',
+            code: JsonRpcErrorCode.ValidationError,
+            when: 'The active dialect declares POST /search/calls as known-dead on this server',
+            recovery: 'Connect to a different BrAPI server that exposes a working /search/calls route — genotype-call workflows are not viable here.',
+        },
+    ],
+    input: z.object({
+        alias: AliasInput,
+        germplasmDbIds: z
+            .array(z.string())
+            .optional()
+            .describe('Restrict to these germplasm. Omit to pull all germplasm in the variant set (use with caution on large sets).'),
+        variantSetDbId: z.string().min(1).describe('Variant set to pull calls for. Required.'),
+        format: z
+            .enum(['plink', 'vcf-lite', 'matrix-json'])
+            .describe('Output format. `matrix-json` registers a wide canvas dataframe only. `vcf-lite` returns VCF-subset text and registers the dataframe. `plink` returns .ped/.map text and registers the dataframe.'),
+        maxCalls: z
+            .number()
+            .int()
+            .positive()
+            .optional()
+            .describe('Override the deployment-level pull cap (BRAPI_GENOTYPE_CALLS_MAX_PULL). Useful for large panels where the default is too low.'),
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const capabilities = getCapabilityRegistry();
+        const client = getBrapiClient();
+        const bridge = getCanvasBridge();
+        const connection = await requireRegisteredConnection(ctx, input.alias);
+        const capabilityLookup = {};
+        if (connection.resolvedAuth)
+            capabilityLookup.auth = connection.resolvedAuth;
+        await capabilities.ensure(connection.baseUrl, { service: 'search/calls', method: 'POST' }, ctx, capabilityLookup);
+        const dialect = await resolveDialect(connection, ctx, capabilityLookup);
+        if (dialect.disabledSearchEndpoints?.has('calls')) {
+            throw ctx.fail('search_endpoint_disabled', `Dialect '${dialect.id}' marks POST /search/calls as known-dead on this server. Genotype-call workflows are not viable here.`, { dialectId: dialect.id, ...ctx.recoveryFor('search_endpoint_disabled') });
+        }
+        const config = getServerConfig();
+        const maxCalls = input.maxCalls ?? config.genotypeCallsMaxPull;
+        const searchOpts = {
+            variantSetDbId: input.variantSetDbId,
+        };
+        if (input.germplasmDbIds !== undefined)
+            searchOpts.germplasmDbIds = input.germplasmDbIds;
+        const searchBody = buildCallsSearchBody(searchOpts);
+        if (!searchBody.variantSetDbIds) {
+            throw ctx.fail('no_filters', 'variantSetDbId is required — unfiltered genotype-call pulls are prohibitively expensive.', { ...ctx.recoveryFor('no_filters') });
+        }
+        const warnings = [];
+        const collected = await collectCalls({
+            client,
+            connection,
+            ctx,
+            body: searchBody,
+            maxCalls,
+            warnings,
+        });
+        // Build the pivot matrix plus the structured data the text encoders need.
+        const matrix = buildMatrix(collected.rows, collected.callFormatting);
+        // Register the wide matrix as a canvas dataframe (used by all three formats).
+        const registerInput = {
+            source: 'export_genotype_matrix',
+            baseUrl: connection.baseUrl,
+            query: searchBody,
+            rows: matrix.matrixRows,
+        };
+        if (collected.truncated) {
+            registerInput.truncated = true;
+            registerInput.maxRows = maxCalls;
+        }
+        const dfResult = await bridge.registerDataframe(ctx, registerInput);
+        const dataframeHandle = toDataframeHandle(dfResult);
+        // For text formats, pull variant coordinate metadata and render the text.
+        let vcf;
+        let ped;
+        let map;
+        if (input.format === 'vcf-lite' || input.format === 'plink') {
+            const variantMeta = await collectVariantMetadata({
+                client,
+                connection,
+                dialect,
+                variantSetDbId: input.variantSetDbId,
+                neededIds: new Set(matrix.variantIdOrder),
+                ctx,
+                warnings,
+            });
+            if (input.format === 'vcf-lite') {
+                vcf = buildVcfText(matrix, variantMeta, collected.callFormatting);
+            }
+            else {
+                ped = buildPedText(matrix, collected.callFormatting);
+                map = buildMapText(matrix, variantMeta);
+                warnings.push('PLINK alleles are passed through verbatim from the genotype calls; numeric (0/1) codings are not recoded to nucleotides and `0` denotes PLINK missing. Supply letter-coded genotypes or recode downstream if a true biallelic .ped is required.');
+            }
+        }
+        const result = {
+            alias: connection.alias,
+            format: input.format,
+            rowCount: matrix.matrixRows.length,
+            columnCount: matrix.columnCount,
+            variantColumnLegend: matrix.variantColumnLegend,
+            callFormatting: collected.callFormatting,
+            dataframe: dataframeHandle,
+            truncated: collected.truncated,
+            warnings,
+        };
+        if (vcf !== undefined)
+            result.vcf = vcf;
+        if (ped !== undefined)
+            result.ped = ped;
+        if (map !== undefined)
+            result.map = map;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# Genotype matrix — ${result.format} — ${result.rowCount} germplasm × ${result.columnCount} variants — \`${result.alias}\``);
+        if (result.truncated)
+            lines.push('> **Truncated** at pull cap. See `warnings` for details.');
+        lines.push('');
+        lines.push('## Dataframe');
+        lines.push(...renderDataframeHandle(result.dataframe));
+        lines.push('');
+        lines.push('## Call formatting');
+        const f = result.callFormatting;
+        lines.push(`- expandHomozygotes: ${f.expandHomozygotes ?? '—'}`);
+        lines.push(`- unknownString: ${f.unknownString ?? '—'}`);
+        lines.push(`- sepPhased: ${f.sepPhased ?? '—'}`);
+        lines.push(`- sepUnphased: ${f.sepUnphased ?? '—'}`);
+        lines.push('');
+        const legendEntries = Object.entries(result.variantColumnLegend);
+        if (legendEntries.length > 0) {
+            const remapped = legendEntries.filter(([col, orig]) => col !== orig);
+            if (remapped.length > 0) {
+                lines.push('## Column name remappings (sanitized → original)');
+                for (const [col, orig] of remapped.slice(0, 20)) {
+                    lines.push(`- \`${col}\` → \`${orig}\``);
+                }
+                if (remapped.length > 20)
+                    lines.push(`- …and ${remapped.length - 20} more`);
+                lines.push('');
+            }
+        }
+        // Render the format text (preview-capped; full text is in structuredContent).
+        if (result.vcf !== undefined) {
+            lines.push(...renderTextPreview('VCF-lite', 'vcf', result.vcf));
+        }
+        if (result.map !== undefined) {
+            lines.push(...renderTextPreview('PLINK .map', 'map', result.map));
+        }
+        if (result.ped !== undefined) {
+            lines.push(...renderTextPreview('PLINK .ped', 'ped', result.ped));
+        }
+        if (result.warnings.length > 0) {
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+            lines.push('');
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+// ---------------------------------------------------------------------------
+// content[] text preview
+// ---------------------------------------------------------------------------
+function renderTextPreview(label, field, text) {
+    const allLines = text.split('\n');
+    const preview = allLines.slice(0, FORMAT_PREVIEW_LINES);
+    const out = [`## ${label}`, '```', ...preview];
+    if (allLines.length > FORMAT_PREVIEW_LINES) {
+        out.push(`… ${allLines.length - FORMAT_PREVIEW_LINES} more line(s) — full text in structuredContent.${field}`);
+    }
+    out.push('```', '');
+    return out;
+}
+/**
+ * Pivot the flat call rows into a wide germplasm × variant matrix and capture
+ * the ordered structures the VCF/PLINK encoders consume.
+ *
+ * Row identity: `callSetDbId` (preferred) or `callSetName`, else `'unknown'`.
+ * Variant identity: `variantDbId` (preferred) or `variantName`.
+ */
+function buildMatrix(rows, callFormatting) {
+    const variantSeen = new Set();
+    const variantIdOrder = [];
+    const sampleSeen = new Set();
+    const sampleOrder = [];
+    const sampleLabels = {};
+    const genotypeAt = new Map();
+    for (const row of rows) {
+        const vid = row.variantDbId ?? row.variantName ?? 'unknown_variant';
+        if (!variantSeen.has(vid)) {
+            variantSeen.add(vid);
+            variantIdOrder.push(vid);
+        }
+        const sampleKey = row.callSetDbId ?? row.callSetName ?? 'unknown';
+        if (!sampleSeen.has(sampleKey)) {
+            sampleSeen.add(sampleKey);
+            sampleOrder.push(sampleKey);
+            sampleLabels[sampleKey] = row.callSetName ?? sampleKey;
+        }
+        const gt = renderGenotypeString(row, callFormatting);
+        let byVariant = genotypeAt.get(sampleKey);
+        if (!byVariant) {
+            byVariant = new Map();
+            genotypeAt.set(sampleKey, byVariant);
+        }
+        byVariant.set(vid, gt);
+    }
+    const { columns: sanitizedCols, toOriginal: variantColumnLegend } = buildUniqueColumns(variantIdOrder);
+    const matrixRows = sampleOrder.map((sampleKey) => {
+        const row = { germplasmDbId: sampleKey };
+        const byVariant = genotypeAt.get(sampleKey);
+        variantIdOrder.forEach((vid, i) => {
+            const col = sanitizedCols[i] ?? `v_${i}`;
+            row[col] = byVariant?.get(vid) ?? null;
+        });
+        return row;
+    });
+    return {
+        matrixRows,
+        variantColumnLegend,
+        columnCount: variantIdOrder.length,
+        variantIdOrder,
+        sampleOrder,
+        sampleLabels,
+        genotypeAt,
+    };
+}
+// ---------------------------------------------------------------------------
+// VCF-lite / PLINK text encoders
+// ---------------------------------------------------------------------------
+/** Tab-join a row of cells. */
+function tsv(cells) {
+    return cells.map(String).join('\t');
+}
+function buildVcfText(matrix, variantMeta, callFormatting) {
+    const missing = callFormatting.unknownString ?? '.';
+    const header = [
+        '#CHROM',
+        'POS',
+        'ID',
+        'REF',
+        'ALT',
+        ...matrix.sampleOrder.map((s) => matrix.sampleLabels[s] ?? s),
+    ];
+    const lines = [tsv(header)];
+    for (const vid of matrix.variantIdOrder) {
+        const m = variantMeta.get(vid) ?? {};
+        const genotypes = matrix.sampleOrder.map((s) => matrix.genotypeAt.get(s)?.get(vid) ?? missing);
+        lines.push(tsv([m.chrom ?? '.', m.pos ?? '.', vid, m.ref ?? '.', m.alt ?? '.', ...genotypes]));
+    }
+    return lines.join('\n');
+}
+function buildMapText(matrix, variantMeta) {
+    // chromosome, variant-id, genetic-distance (0 placeholder), base-pair position
+    return matrix.variantIdOrder
+        .map((vid) => {
+        const m = variantMeta.get(vid) ?? {};
+        return tsv([m.chrom ?? '0', vid, '0', m.pos ?? '0']);
+    })
+        .join('\n');
+}
+function buildPedText(matrix, callFormatting) {
+    // FID IID PAT MAT SEX PHENO (all 0 placeholders) + biallelic genotype pairs.
+    return matrix.sampleOrder
+        .map((sampleKey) => {
+        const fields = [
+            '0',
+            matrix.sampleLabels[sampleKey] ?? sampleKey,
+            '0',
+            '0',
+            '0',
+            '0',
+        ];
+        const byVariant = matrix.genotypeAt.get(sampleKey);
+        for (const vid of matrix.variantIdOrder) {
+            const [a1, a2] = splitAlleles(byVariant?.get(vid), callFormatting);
+            fields.push(a1, a2);
+        }
+        return fields.join('\t');
+    })
+        .join('\n');
+}
+/**
+ * Split a rendered genotype string into a biallelic pair for PLINK .ped. Splits
+ * on `/` or `|`; a single allele is treated as homozygous; unknown/missing maps
+ * to PLINK's `0` sentinel. Polyploid calls keep the first two alleles.
+ */
+function splitAlleles(gt, callFormatting) {
+    const unknown = callFormatting.unknownString ?? '.';
+    if (!gt || gt === unknown)
+        return ['0', '0'];
+    const norm = (t) => (t === unknown || t === '.' ? '0' : t);
+    const tokens = gt
+        .split(/[/|]/)
+        .map((t) => t.trim())
+        .filter((t) => t.length > 0);
+    if (tokens.length === 0)
+        return ['0', '0'];
+    if (tokens.length === 1) {
+        const a = norm(tokens[0]);
+        return [a, a];
+    }
+    return [norm(tokens[0]), norm(tokens[1])];
+}
+/**
+ * Page `/variants?variantSetDbId=…` and build a `variantDbId → VariantMeta` map
+ * (CHROM/POS/REF/ALT) for the variants in the matrix. Best-effort: a dropped
+ * filter, missing endpoint, or fetch error degrades to placeholders plus a
+ * warning rather than failing the export. Stops early once every needed variant
+ * is covered.
+ */
+async function collectVariantMetadata(args) {
+    const { client, connection, dialect, variantSetDbId, neededIds, ctx, warnings } = args;
+    const meta = new Map();
+    try {
+        const adapted = dialect.adaptGetFilters('variants', { variantSetDbIds: [variantSetDbId] });
+        if (adapted.dropped.length > 0 && Object.keys(adapted.filters).length === 0) {
+            warnings.push(`Variant metadata pull skipped: dialect '${dialect.id}' dropped the variantSetDbId filter on /variants. CHROM/POS/REF/ALT use placeholders.`);
+            return meta;
+        }
+        let page = 0;
+        let totalPages = 1;
+        let scanned = 0;
+        while (page < totalPages && scanned < MAX_VARIANT_METADATA_ROWS && !ctx.signal.aborted) {
+            const opts = buildRequestOptions(connection, {
+                ...adapted.filters,
+                pageSize: VARIANT_METADATA_PAGE_SIZE,
+                page,
+            });
+            const envelope = await client.get(connection.baseUrl, '/variants', ctx, opts);
+            const rows = extractRows(envelope.result);
+            for (const r of rows) {
+                scanned++;
+                const vid = asString(r.variantDbId);
+                if (!vid)
+                    continue;
+                meta.set(vid, extractVariantMeta(r));
+            }
+            totalPages = envelope.metadata?.pagination?.totalPages ?? page + 1;
+            page++;
+            if (neededIds.size > 0 && [...neededIds].every((id) => meta.has(id)))
+                break;
+            if (rows.length < VARIANT_METADATA_PAGE_SIZE)
+                break;
+        }
+    }
+    catch (err) {
+        warnings.push(`Variant metadata pull failed (${err instanceof Error ? err.message : String(err)}). CHROM/POS/REF/ALT use placeholders.`);
+    }
+    return meta;
+}
+function extractVariantMeta(r) {
+    const meta = {};
+    const chrom = asString(r.referenceName);
+    if (chrom)
+        meta.chrom = chrom;
+    const start = r.start;
+    if (typeof start === 'number')
+        meta.pos = String(start);
+    else {
+        const startStr = asString(start);
+        if (startStr)
+            meta.pos = startStr;
+    }
+    const ref = asString(r.referenceBases);
+    if (ref)
+        meta.ref = ref;
+    const altRaw = r.alternateBases;
+    if (Array.isArray(altRaw)) {
+        const alts = altRaw.filter((a) => typeof a === 'string' && a.length > 0);
+        if (alts.length > 0)
+            meta.alt = alts.join(',');
+    }
+    else {
+        const alt = asString(altRaw);
+        if (alt)
+            meta.alt = alt;
+    }
+    return meta;
+}
+//# sourceMappingURL=brapi-export-genotype-matrix.tool.js.map

package/dist/mcp-server/tools/definitions/brapi-export-genotype-matrix.tool.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts

@@ -41,8 +41,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         genotypeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
         phaseSet: z.ZodOptional<z.ZodNullable<z.ZodString>>;
     }, z.core.$loose>>;
-    returnedCount: z.ZodNumber;
-    totalCount: z.ZodNumber;
     hasMore: z.ZodBoolean;
     callFormatting: z.ZodObject<{
         expandHomozygotes: z.ZodOptional<z.ZodNullable<z.ZodBoolean>>;
@@ -65,8 +63,6 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
         maxRows: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>>;
     truncated: z.ZodBoolean;
-    warnings: z.ZodArray<z.ZodString>;
-    searchBody: z.ZodRecord<z.ZodString, z.ZodUnknown>;
 }, z.core.$strip>, readonly [{
     readonly reason: "unknown_alias";
     readonly code: JsonRpcErrorCode.NotFound;
@@ -82,5 +78,11 @@ export declare const brapiFindGenotypeCalls: import("@cyanheads/mcp-ts-core").To
     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 totalCount: z.ZodNumber;
+    readonly returnedCount: z.ZodNumber;
+    readonly appliedFilters: z.ZodRecord<z.ZodString, z.ZodUnknown>;
+    readonly notice: z.ZodOptional<z.ZodString>;
+    readonly warnings: z.ZodArray<z.ZodString>;
+}>;
 //# sourceMappingURL=brapi-find-genotype-calls.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"brapi-find-genotype-calls.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-find-genotype-calls.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;GAYG;AAEH,OAAO,EAAsB,CAAC,EAAE,MAAM,wBAAwB,CAAC;AAC/D,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAgHjE,eAAO,MAAM,sBAAsB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;EAqQjC,CAAC"}