@cyanheads/brapi-mcp-server 0.3.5

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

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+/**
+ * @fileoverview `brapi_find_variants` — find variant records by variant set,
+ * reference, or genomic region. Standard find_* pattern — distributions +
+ * dataset spillover. Note: the BrAPI filter catalog uses `start` / `end` as
+ * single scalars (1-based inclusive / exclusive) per the spec.
+ *
+ * @module mcp-server/tools/definitions/brapi-find-variants.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { getServerConfig } from '../../../config/server-config.js';
+import { getBrapiClient } from '../../../services/brapi-client/index.js';
+import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { getDatasetStore } from '../../../services/dataset-store/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+import { AliasInput, asString, buildRefinementHint, computeDistribution, DatasetHandleSchema, ExtraFiltersInput, LoadLimitInput, loadInitialPage, maybeSpill, mergeFilters, renderDatasetHandle, renderDistributions, } from '../shared/find-helpers.js';
+const VariantRowSchema = z
+    .object({
+    variantDbId: z.string().describe('Server-side identifier for the variant.'),
+    variantNames: z
+        .array(z.string().describe('Variant name or alias.'))
+        .optional()
+        .describe('Known names / aliases for this variant.'),
+    variantSetDbId: z
+        .union([
+        z.string().describe('Single variant-set FK (older BrAPI servers).'),
+        z
+            .array(z.string().describe('One variant-set FK.'))
+            .describe('Variant-set FK array — a variant may belong to multiple sets.'),
+    ])
+        .optional()
+        .describe('FK to the variant set(s) this variant belongs to. May be a string or string[] depending on server.'),
+    variantSetDbIds: z
+        .array(z.string().describe('Variant-set FK.'))
+        .optional()
+        .describe('Plural-form FK array per BrAPI v2.1 spec, when the server uses it.'),
+    variantType: z.string().nullish().describe('Variant type (e.g. "SNP", "INDEL", "DUP").'),
+    referenceBases: z
+        .string()
+        .nullish()
+        .describe('Reference allele sequence at the variant position.'),
+    alternateBases: z
+        .array(z.string().describe('Alternate allele sequence.'))
+        .nullish()
+        .describe('Alternate alleles observed at this position.'),
+    referenceName: z.string().nullish().describe('Reference sequence name (e.g. "chr01").'),
+    start: z.number().nullish().describe('1-based inclusive start position.'),
+    end: z.number().nullish().describe('1-based exclusive end position.'),
+    filtersPassed: z.boolean().nullish().describe('True when the variant passed all QC filters.'),
+    filtersApplied: z
+        .boolean()
+        .nullish()
+        .describe('True when QC filters were evaluated on this variant.'),
+    filtersFailed: z
+        .array(z.string().describe('Filter ID that failed.'))
+        .nullish()
+        .describe('IDs of QC filters this variant failed, when any.'),
+})
+    .passthrough()
+    .describe('One BrAPI variant record.');
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    results: z
+        .array(VariantRowSchema)
+        .describe('Variant rows returned in-context (up to loadLimit).'),
+    returnedCount: z.number().int().nonnegative().describe('Length of `results[]`.'),
+    totalCount: z.number().int().nonnegative().describe('Total rows reported by the server.'),
+    hasMore: z.boolean().describe('True when more rows exist beyond the returned set.'),
+    distributions: z
+        .object({
+        variantType: z
+            .record(z.string(), z.number())
+            .describe('Variant type → count of variants of that type.'),
+        referenceName: z
+            .record(z.string(), z.number())
+            .describe('Reference sequence name → count of variants on that reference.'),
+        variantSetDbId: z
+            .record(z.string(), z.number())
+            .describe('Variant set ID → count of variants in that set.'),
+    })
+        .describe('Value frequency per field across the full result set.'),
+    refinementHint: z
+        .string()
+        .optional()
+        .describe('Suggested next-step query refinement when the result set is large.'),
+    dataset: DatasetHandleSchema.optional().describe('Dataset handle when the full result set was persisted to DatasetStore.'),
+    warnings: z
+        .array(z.string())
+        .describe('Advisory messages (filter overrides, partial data, capability gaps, etc.).'),
+    appliedFilters: z
+        .record(z.string(), z.unknown())
+        .describe('The final filter map sent to the server (named + extraFilters).'),
+});
+export const brapiFindVariants = tool('brapi_find_variants', {
+    description: 'Find variant records by variant set, reference sequence, or genomic region (start/end, 1-based inclusive / exclusive). Returns a dataset handle when the upstream total exceeds loadLimit.',
+    annotations: { readOnlyHint: true, openWorldHint: true },
+    input: z.object({
+        alias: AliasInput,
+        variantSets: z.array(z.string()).optional().describe('Filter by variantSetDbIds.'),
+        variants: z.array(z.string()).optional().describe('Filter by variantDbIds.'),
+        references: z.array(z.string()).optional().describe('Filter by referenceDbIds.'),
+        referenceName: z.string().optional().describe('Reference display name (e.g. "chr01", "chr1").'),
+        start: z.number().int().nonnegative().optional().describe('Inclusive 1-based start.'),
+        end: z.number().int().positive().optional().describe('Exclusive 1-based end.'),
+        loadLimit: LoadLimitInput,
+        extraFilters: ExtraFiltersInput,
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const registry = getServerRegistry();
+        const capabilities = getCapabilityRegistry();
+        const client = getBrapiClient();
+        const datasetStore = getDatasetStore();
+        const config = getServerConfig();
+        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const capabilityLookup = {};
+        if (connection.resolvedAuth)
+            capabilityLookup.auth = connection.resolvedAuth;
+        await capabilities.ensure(connection.baseUrl, { service: 'variants', method: 'GET' }, ctx, capabilityLookup);
+        const warnings = [];
+        if (input.start !== undefined && input.end !== undefined && input.start >= input.end) {
+            warnings.push('start >= end; upstream will likely return an empty result set.');
+        }
+        const filters = mergeFilters({
+            variantSetDbIds: input.variantSets,
+            variantDbIds: input.variants,
+            referenceDbIds: input.references,
+            referenceName: input.referenceName,
+            start: input.start,
+            end: input.end,
+        }, input.extraFilters, warnings);
+        const loadLimit = input.loadLimit ?? config.loadLimit;
+        const firstPage = await loadInitialPage(client, connection, '/variants', filters, loadLimit, ctx);
+        const { fullRows, dataset: datasetMeta } = await maybeSpill({
+            firstPage,
+            client,
+            connection,
+            path: '/variants',
+            filters,
+            source: 'find_variants',
+            loadLimit,
+            ctx,
+            store: datasetStore,
+        });
+        const distributions = {
+            variantType: computeDistribution(fullRows, (r) => asString(r.variantType)),
+            referenceName: computeDistribution(fullRows, (r) => asString(r.referenceName)),
+            variantSetDbId: computeDistribution(fullRows, (r) => collectVariantSetIds(r)),
+        };
+        const totalCount = firstPage.totalCount ?? firstPage.rows.length;
+        const refinementHint = buildRefinementHint(totalCount, loadLimit, distributions);
+        const result = {
+            alias: connection.alias,
+            results: firstPage.rows,
+            returnedCount: firstPage.rows.length,
+            totalCount,
+            hasMore: firstPage.hasMore,
+            distributions,
+            warnings,
+            appliedFilters: filters,
+        };
+        if (refinementHint)
+            result.refinementHint = refinementHint;
+        if (datasetMeta)
+            result.dataset = datasetMeta;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# ${result.returnedCount} of ${result.totalCount} variants — \`${result.alias}\``);
+        lines.push('');
+        if (result.hasMore) {
+            lines.push(`⚠ More rows exist beyond the returned set. ${result.dataset ? `Full set persisted as dataset \`${result.dataset.datasetId}\`.` : 'Narrow filters or raise loadLimit.'}`);
+            lines.push('');
+        }
+        if (result.refinementHint) {
+            lines.push(`**Refinement hint:** ${result.refinementHint}`);
+            lines.push('');
+        }
+        lines.push(`Applied filters: \`${JSON.stringify(result.appliedFilters)}\``);
+        lines.push('');
+        lines.push('## Distributions');
+        lines.push(renderDistributions(result.distributions) || '_No values to summarize._');
+        lines.push('');
+        lines.push('## Variants');
+        if (result.results.length === 0) {
+            lines.push('_No rows returned._');
+        }
+        else {
+            for (const v of result.results) {
+                const label = v.variantNames?.[0] ?? v.variantDbId;
+                const parts = [`**${label}**`];
+                parts.push(`id=\`${v.variantDbId}\``);
+                if (v.variantType)
+                    parts.push(`type=${v.variantType}`);
+                const setIds = collectVariantSetIds(v);
+                if (setIds && setIds.length > 0)
+                    parts.push(`set=${setIds.join(',')}`);
+                if (v.referenceName)
+                    parts.push(`ref=${v.referenceName}`);
+                if (v.start != null)
+                    parts.push(`start=${v.start}`);
+                if (v.end != null)
+                    parts.push(`end=${v.end}`);
+                if (v.referenceBases)
+                    parts.push(`refBases=${v.referenceBases}`);
+                if (v.alternateBases?.length)
+                    parts.push(`altBases=${v.alternateBases.join(',')}`);
+                if (v.filtersApplied != null)
+                    parts.push(`filtersApplied=${v.filtersApplied}`);
+                if (v.filtersPassed != null)
+                    parts.push(`filtersPassed=${v.filtersPassed}`);
+                if (v.filtersFailed?.length)
+                    parts.push(`filtersFailed=${v.filtersFailed.join(',')}`);
+                if (v.variantNames?.length)
+                    parts.push(`names=${v.variantNames.join(',')}`);
+                lines.push(`- ${parts.join(' · ')}`);
+            }
+        }
+        if (result.dataset) {
+            lines.push('');
+            lines.push('## Dataset handle');
+            lines.push(...renderDatasetHandle(result.dataset));
+        }
+        if (result.warnings.length > 0) {
+            lines.push('');
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function collectVariantSetIds(row) {
+    const ids = new Set();
+    const collect = (value) => {
+        if (typeof value === 'string' && value.length > 0)
+            ids.add(value);
+        else if (Array.isArray(value)) {
+            for (const v of value)
+                if (typeof v === 'string' && v.length > 0)
+                    ids.add(v);
+        }
+    };
+    collect(row.variantSetDbId);
+    collect(row.variantSetDbIds);
+    return ids.size > 0 ? Array.from(ids) : undefined;
+}
+//# sourceMappingURL=brapi-find-variants.tool.js.map

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package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts

@@ -0,0 +1,59 @@
+/**
+ * @fileoverview `brapi_get_germplasm` — fetch a single germplasm with
+ * attributes and direct parents, plus companion counts (studies the
+ * germplasm has appeared in, direct parents, direct descendants) to signal
+ * where to drill next.
+ *
+ * @module mcp-server/tools/definitions/brapi-get-germplasm.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const brapiGetGermplasm: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    germplasmDbId: z.ZodString;
+    alias: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    germplasm: z.ZodObject<{
+        germplasmDbId: z.ZodString;
+        germplasmName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        germplasmPUI: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        commonCropName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        accessionNumber: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        genus: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        species: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        subtaxa: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        defaultDisplayName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        pedigree: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        biologicalStatusOfAccessionDescription: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        germplasmOrigin: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{}, z.core.$loose>>>>;
+        countryOfOriginCode: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        collection: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        instituteCode: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        instituteName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        synonyms: z.ZodOptional<z.ZodNullable<z.ZodArray<z.ZodObject<{
+            synonym: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+            type: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        }, z.core.$loose>>>>;
+    }, z.core.$loose>;
+    parents: z.ZodArray<z.ZodObject<{
+        germplasmDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        germplasmName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        parentType: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$loose>>;
+    attributes: z.ZodArray<z.ZodObject<{
+        attributeDbId: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        attributeName: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        attributeValue: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+        determinedDate: z.ZodOptional<z.ZodNullable<z.ZodString>>;
+    }, z.core.$loose>>;
+    studyCount: z.ZodOptional<z.ZodNumber>;
+    directParentCount: z.ZodNumber;
+    directDescendantCount: z.ZodOptional<z.ZodNumber>;
+    warnings: z.ZodArray<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "germplasm_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Upstream returned no germplasm record for the requested DbId";
+    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+}]>;
+//# sourceMappingURL=brapi-get-germplasm.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"brapi-get-germplasm.tool.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/tools/definitions/brapi-get-germplasm.tool.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAQ,CAAC,EAAE,MAAM,wBAAwB,CAAC;AACjD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AAkGjE,eAAO,MAAM,iBAAiB;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;;GA8M5B,CAAC"}

package/dist/mcp-server/tools/definitions/brapi-get-germplasm.tool.js

@@ -0,0 +1,306 @@
+/**
+ * @fileoverview `brapi_get_germplasm` — fetch a single germplasm with
+ * attributes and direct parents, plus companion counts (studies the
+ * germplasm has appeared in, direct parents, direct descendants) to signal
+ * where to drill next.
+ *
+ * @module mcp-server/tools/definitions/brapi-get-germplasm.tool
+ */
+import { tool, z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+import { getBrapiClient } from '../../../services/brapi-client/index.js';
+import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+import { AliasInput, buildRequestOptions, isUpstreamNotFound } from '../shared/find-helpers.js';
+const GermplasmSchema = z
+    .object({
+    germplasmDbId: z.string().describe('Server-side identifier for the germplasm.'),
+    germplasmName: z.string().nullish().describe('Display name.'),
+    germplasmPUI: z.string().nullish().describe('Persistent unique identifier (URI).'),
+    commonCropName: z.string().nullish().describe('Common crop name.'),
+    accessionNumber: z.string().nullish().describe('Gene-bank catalog number.'),
+    genus: z.string().nullish().describe('Botanical genus.'),
+    species: z.string().nullish().describe('Botanical species.'),
+    subtaxa: z.string().nullish().describe('Botanical subtaxa.'),
+    defaultDisplayName: z.string().nullish().describe('Preferred display label.'),
+    pedigree: z.string().nullish().describe('Pedigree as a free-text string.'),
+    biologicalStatusOfAccessionDescription: z
+        .string()
+        .nullish()
+        .describe('MCPD biological-status label.'),
+    germplasmOrigin: z
+        .array(z
+        .object({})
+        .passthrough()
+        .describe('One origin record (collection coordinates and uncertainty per BrAPI v2).'))
+        .nullish()
+        .describe('Origin records — array of collection-site objects per BrAPI v2.'),
+    countryOfOriginCode: z.string().nullish().describe('ISO 3166-1 alpha-3 country code.'),
+    collection: z.string().nullish().describe('Collection name.'),
+    instituteCode: z.string().nullish().describe('FAO WIEWS institute code.'),
+    instituteName: z.string().nullish().describe('Display name of the holding institute.'),
+    synonyms: z
+        .array(z
+        .object({
+        synonym: z.string().nullish().describe('Synonym value.'),
+        type: z.string().nullish().describe('Synonym type (e.g. "COMMON", "SYNONYM").'),
+    })
+        .passthrough()
+        .describe('Registered synonym for this germplasm.'))
+        .nullish()
+        .describe('All registered synonyms.'),
+})
+    .passthrough();
+const ParentSchema = z
+    .object({
+    germplasmDbId: z.string().nullish().describe('FK to the parent germplasm.'),
+    germplasmName: z.string().nullish().describe('Display name of the parent germplasm.'),
+    parentType: z.string().nullish().describe('E.g. "MALE", "FEMALE", "SELF".'),
+})
+    .passthrough()
+    .describe('One direct parent of the germplasm.');
+const AttributeSchema = z
+    .object({
+    attributeDbId: z.string().nullish().describe('Attribute identifier.'),
+    attributeName: z.string().nullish().describe('Attribute display name.'),
+    attributeValue: z.string().nullish().describe('Recorded value (stringified).'),
+    determinedDate: z.string().nullish().describe('ISO 8601 date the attribute was determined.'),
+})
+    .passthrough()
+    .describe('One germplasm attribute record.');
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    germplasm: GermplasmSchema.describe('Canonical germplasm record as returned by `/germplasm/{id}`.'),
+    parents: z.array(ParentSchema).describe('Direct parents from /germplasm/{id}/pedigree.'),
+    attributes: z
+        .array(AttributeSchema)
+        .describe('Germplasm attributes from /germplasm/{id}/attributes.'),
+    studyCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('How many studies this germplasm has appeared in.'),
+    directParentCount: z.number().int().nonnegative().describe('Count of direct parents.'),
+    directDescendantCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Count of direct descendants from /germplasm/{id}/progeny.'),
+    warnings: z
+        .array(z.string())
+        .describe('Advisory messages — failed sub-endpoint lookups, missing counts.'),
+});
+export const brapiGetGermplasm = tool('brapi_get_germplasm', {
+    description: 'Fetch a single germplasm by DbId with attributes and direct parents. Response companions report study count, direct parent count, and direct descendant count — signals for pedigree depth and observation coverage.',
+    annotations: { readOnlyHint: true, idempotentHint: true },
+    errors: [
+        {
+            reason: 'germplasm_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Upstream returned no germplasm record for the requested DbId',
+            recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.',
+        },
+    ],
+    input: z.object({
+        germplasmDbId: z.string().min(1).describe('Germplasm identifier.'),
+        alias: AliasInput,
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const registry = getServerRegistry();
+        const capabilities = getCapabilityRegistry();
+        const client = getBrapiClient();
+        const connection = await registry.get(ctx, input.alias ?? DEFAULT_ALIAS);
+        const capabilityLookup = {};
+        if (connection.resolvedAuth)
+            capabilityLookup.auth = connection.resolvedAuth;
+        await capabilities.ensure(connection.baseUrl, { service: 'germplasm', method: 'GET' }, ctx, capabilityLookup);
+        const id = encodeURIComponent(input.germplasmDbId);
+        const warnings = [];
+        let germplasmEnv;
+        try {
+            germplasmEnv = await client.get(connection.baseUrl, `/germplasm/${id}`, ctx, buildRequestOptions(connection));
+        }
+        catch (err) {
+            if (isUpstreamNotFound(err)) {
+                throw ctx.fail('germplasm_not_found', `Germplasm '${input.germplasmDbId}' not found on ${connection.baseUrl}.`, {
+                    germplasmDbId: input.germplasmDbId,
+                    baseUrl: connection.baseUrl,
+                    ...ctx.recoveryFor('germplasm_not_found'),
+                });
+            }
+            throw err;
+        }
+        const germplasm = germplasmEnv.result;
+        if (!germplasm || typeof germplasm !== 'object' || !germplasm.germplasmDbId) {
+            throw ctx.fail('germplasm_not_found', `Germplasm '${input.germplasmDbId}' not found on ${connection.baseUrl}.`, {
+                germplasmDbId: input.germplasmDbId,
+                baseUrl: connection.baseUrl,
+                ...ctx.recoveryFor('germplasm_not_found'),
+            });
+        }
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const supportsPedigree = Boolean(profile.supported['germplasm/{germplasmDbId}/pedigree']);
+        const supportsAttributes = Boolean(profile.supported['germplasm/{germplasmDbId}/attributes']);
+        const supportsProgeny = Boolean(profile.supported['germplasm/{germplasmDbId}/progeny']);
+        const supportsStudies = profile.supported.studies?.methods?.includes('GET') ?? false;
+        const [pedigree, attributes, studyCount, progenyCount] = await Promise.all([
+            supportsPedigree
+                ? fetchPedigree(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'pedigree lookup failed', err))
+                : Promise.resolve(undefined),
+            supportsAttributes
+                ? fetchAttributes(client, connection.baseUrl, id, ctx, buildRequestOptions(connection)).catch((err) => recordWarning(warnings, 'attributes lookup failed', err))
+                : Promise.resolve(undefined),
+            supportsStudies
+                ? fetchTotalCount(client, connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, {
+                    germplasmDbIds: [input.germplasmDbId],
+                    pageSize: 1,
+                })).catch((err) => recordWarning(warnings, 'study count probe failed', err))
+                : Promise.resolve(undefined),
+            supportsProgeny
+                ? fetchTotalCount(client, connection.baseUrl, `/germplasm/${id}/progeny`, ctx, buildRequestOptions(connection, { pageSize: 1 })).catch((err) => recordWarning(warnings, 'progeny count probe failed', err))
+                : Promise.resolve(undefined),
+        ]);
+        const parents = pedigree?.parents ?? [];
+        const attrList = attributes ?? [];
+        const result = {
+            alias: connection.alias,
+            germplasm: germplasm,
+            parents,
+            attributes: attrList,
+            directParentCount: parents.length,
+            warnings,
+        };
+        if (typeof studyCount === 'number')
+            result.studyCount = studyCount;
+        if (typeof progenyCount === 'number')
+            result.directDescendantCount = progenyCount;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        const g = result.germplasm;
+        lines.push(`# ${g.germplasmName ?? g.defaultDisplayName ?? g.germplasmDbId}`);
+        lines.push('');
+        lines.push(`- **germplasmDbId:** \`${g.germplasmDbId}\``);
+        if (g.germplasmName)
+            lines.push(`- **germplasmName:** ${g.germplasmName}`);
+        if (g.germplasmPUI)
+            lines.push(`- **germplasmPUI:** ${g.germplasmPUI}`);
+        if (g.commonCropName)
+            lines.push(`- **commonCropName:** ${g.commonCropName}`);
+        if (g.accessionNumber)
+            lines.push(`- **accessionNumber:** ${g.accessionNumber}`);
+        if (g.genus)
+            lines.push(`- **genus:** ${g.genus}`);
+        if (g.species)
+            lines.push(`- **species:** ${g.species}`);
+        if (g.subtaxa)
+            lines.push(`- **subtaxa:** ${g.subtaxa}`);
+        if (g.defaultDisplayName)
+            lines.push(`- **defaultDisplayName:** ${g.defaultDisplayName}`);
+        if (g.pedigree)
+            lines.push(`- **pedigree (string):** ${g.pedigree}`);
+        if (g.biologicalStatusOfAccessionDescription)
+            lines.push(`- **biologicalStatus:** ${g.biologicalStatusOfAccessionDescription}`);
+        if (g.germplasmOrigin?.length)
+            lines.push(`- **germplasmOrigin:** ${g.germplasmOrigin.length} record(s)`);
+        if (g.countryOfOriginCode)
+            lines.push(`- **countryOfOriginCode:** ${g.countryOfOriginCode}`);
+        if (g.collection)
+            lines.push(`- **collection:** ${g.collection}`);
+        if (g.instituteCode)
+            lines.push(`- **instituteCode:** ${g.instituteCode}`);
+        if (g.instituteName)
+            lines.push(`- **instituteName:** ${g.instituteName}`);
+        if (g.synonyms?.length) {
+            const synStr = g.synonyms
+                .map((s) => `${s.synonym ?? '?'}${s.type ? ` (${s.type})` : ''}`)
+                .join(', ');
+            lines.push(`- **synonyms:** ${synStr}`);
+        }
+        lines.push(`- **alias:** ${result.alias}`);
+        lines.push('');
+        lines.push(`## Parents (${result.directParentCount})`);
+        if (result.parents.length === 0) {
+            lines.push('_No parents recorded._');
+        }
+        else {
+            for (const p of result.parents) {
+                const parts = [];
+                if (p.germplasmName)
+                    parts.push(p.germplasmName);
+                if (p.germplasmDbId)
+                    parts.push(`id=\`${p.germplasmDbId}\``);
+                if (p.parentType)
+                    parts.push(`type=${p.parentType}`);
+                lines.push(`- ${parts.join(' · ')}`);
+            }
+        }
+        lines.push('');
+        lines.push(`## Attributes (${result.attributes.length})`);
+        if (result.attributes.length === 0) {
+            lines.push('_No attributes recorded._');
+        }
+        else {
+            for (const a of result.attributes) {
+                const parts = [];
+                if (a.attributeName)
+                    parts.push(a.attributeName);
+                if (a.attributeDbId)
+                    parts.push(`(id=\`${a.attributeDbId}\`)`);
+                if (a.attributeValue != null)
+                    parts.push(`= ${a.attributeValue}`);
+                if (a.determinedDate)
+                    parts.push(`[determined ${a.determinedDate}]`);
+                lines.push(`- ${parts.join(' ')}`);
+            }
+        }
+        lines.push('');
+        lines.push('## Drill-down signals');
+        lines.push(`- studyCount: ${result.studyCount ?? '—'}`);
+        lines.push(`- directParentCount: ${result.directParentCount}`);
+        lines.push(`- directDescendantCount: ${result.directDescendantCount ?? '—'}`);
+        if (result.warnings.length > 0) {
+            lines.push('');
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function recordWarning(warnings, label, err) {
+    warnings.push(`${label}: ${err instanceof Error ? err.message : String(err)}`);
+    return;
+}
+async function fetchPedigree(client, baseUrl, id, ctx, options) {
+    const env = await client.get(baseUrl, `/germplasm/${id}/pedigree`, ctx, options);
+    const result = env.result;
+    if (!result || typeof result !== 'object')
+        return { parents: [] };
+    const rawParents = result.parents;
+    if (!Array.isArray(rawParents))
+        return { parents: [] };
+    return {
+        parents: rawParents.filter((p) => typeof p === 'object' && p !== null),
+    };
+}
+async function fetchAttributes(client, baseUrl, id, ctx, options) {
+    const env = await client.get(baseUrl, `/germplasm/${id}/attributes`, ctx, options);
+    const result = env.result;
+    const rows = Array.isArray(result)
+        ? result
+        : Array.isArray(result?.data)
+            ? result.data
+            : [];
+    return rows.filter((r) => typeof r === 'object' && r !== null);
+}
+async function fetchTotalCount(client, baseUrl, path, ctx, options) {
+    const env = await client.get(baseUrl, path, ctx, options);
+    const total = env.metadata?.pagination?.totalCount;
+    return typeof total === 'number' ? total : undefined;
+}
+//# sourceMappingURL=brapi-get-germplasm.tool.js.map