@cyanheads/brapi-mcp-server 0.6.4 → 0.7.0

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

@@ -1 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.d.ts

@@ -0,0 +1,60 @@
+/**
+ * @fileoverview `brapi_germplasm_performance` — aggregate a single germplasm's
+ * observations across the studies it appears in, returning per-variable summary
+ * statistics (n, mean, median, sd, min, max) plus the contributing studies and
+ * seasons. Answers the breeder's primary question — "how does line X perform
+ * across the pool's history?" — in one call.
+ *
+ * Study-anchored by design: a naked `/observations?germplasmDbId=…` pull stalls
+ * on SGN/Breedbase deployments (the count-probe bailout). Instead the tool
+ * discovers the germplasm's studies via `/studies?germplasmDbIds=…` (with a
+ * dialect-honor cross-check, since some servers silently drop that filter and
+ * return the global list), then pulls observations per study through the shared
+ * `pullStudyObservations` machinery — the same `/observations` →
+ * `/observationunits` fallback chain `brapi_build_phenotype_matrix` uses.
+ *
+ * Returned rows are filtered to the iterated study and the target germplasm, so
+ * the aggregate stays correct even on servers that ignore the studyDbId filter
+ * on `/observations` (the BrAPI Community Test Server does) or over-return from
+ * the germplasm-anchored fallback.
+ *
+ * @module mcp-server/tools/definitions/brapi-germplasm-performance.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const brapiGermplasmPerformance: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    alias: z.ZodOptional<z.ZodString>;
+    germplasmDbId: z.ZodString;
+    variables: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strip>, z.ZodObject<{
+    alias: z.ZodString;
+    germplasmDbId: z.ZodString;
+    germplasmName: z.ZodOptional<z.ZodString>;
+    studyCount: z.ZodNumber;
+    studyDbIds: z.ZodArray<z.ZodString>;
+    perVariable: z.ZodArray<z.ZodObject<{
+        observationVariableDbId: z.ZodString;
+        observationVariableName: z.ZodOptional<z.ZodString>;
+        n: z.ZodNumber;
+        mean: z.ZodOptional<z.ZodNumber>;
+        median: z.ZodOptional<z.ZodNumber>;
+        sd: z.ZodOptional<z.ZodNumber>;
+        min: z.ZodOptional<z.ZodString>;
+        max: z.ZodOptional<z.ZodString>;
+        studyCount: z.ZodNumber;
+        studyDbIds: z.ZodArray<z.ZodString>;
+        seasons: z.ZodArray<z.ZodString>;
+    }, z.core.$strip>>;
+    warnings: z.ZodArray<z.ZodString>;
+}, z.core.$strip>, readonly [{
+    readonly reason: "unknown_alias";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "No connection has been registered under the requested alias";
+    readonly recovery: "Run brapi_connect with this alias (or omit `alias` to use the default connection) before calling brapi_germplasm_performance.";
+}, {
+    readonly reason: "germplasm_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Upstream returned no germplasm record for the requested germplasmDbId";
+    readonly recovery: "Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.";
+}], undefined>;
+//# sourceMappingURL=brapi-germplasm-performance.tool.d.ts.map

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

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/definitions/brapi-germplasm-performance.tool.js

@@ -0,0 +1,416 @@
+/**
+ * @fileoverview `brapi_germplasm_performance` — aggregate a single germplasm's
+ * observations across the studies it appears in, returning per-variable summary
+ * statistics (n, mean, median, sd, min, max) plus the contributing studies and
+ * seasons. Answers the breeder's primary question — "how does line X perform
+ * across the pool's history?" — in one call.
+ *
+ * Study-anchored by design: a naked `/observations?germplasmDbId=…` pull stalls
+ * on SGN/Breedbase deployments (the count-probe bailout). Instead the tool
+ * discovers the germplasm's studies via `/studies?germplasmDbIds=…` (with a
+ * dialect-honor cross-check, since some servers silently drop that filter and
+ * return the global list), then pulls observations per study through the shared
+ * `pullStudyObservations` machinery — the same `/observations` →
+ * `/observationunits` fallback chain `brapi_build_phenotype_matrix` uses.
+ *
+ * Returned rows are filtered to the iterated study and the target germplasm, so
+ * the aggregate stays correct even on servers that ignore the studyDbId filter
+ * on `/observations` (the BrAPI Community Test Server does) or over-return from
+ * the germplasm-anchored fallback.
+ *
+ * @module mcp-server/tools/definitions/brapi-germplasm-performance.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 { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { AliasInput, asString, buildRequestOptions, extractRows, isUpstreamNotFound, requireRegisteredConnection, } from '../shared/find-helpers.js';
+import { pullStudyObservations } from '../shared/observations.js';
+/** Upper bound on studies discovered per germplasm (guards the filter-ignored case). */
+const STUDY_DISCOVERY_CAP = 200;
+const STUDY_DISCOVERY_PAGE_SIZE = 100;
+// ---------------------------------------------------------------------------
+// Output schema
+// ---------------------------------------------------------------------------
+const PerVariableSchema = z
+    .object({
+    observationVariableDbId: z.string().describe('Observation variable identifier.'),
+    observationVariableName: z.string().optional().describe('Display name of the variable.'),
+    n: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of observations of this variable for the germplasm.'),
+    mean: z
+        .number()
+        .optional()
+        .describe('Arithmetic mean of numeric values (omitted for non-numeric traits).'),
+    median: z
+        .number()
+        .optional()
+        .describe('Median of numeric values (omitted for non-numeric traits).'),
+    sd: z
+        .number()
+        .optional()
+        .describe('Sample standard deviation (n−1) of numeric values; omitted when n < 2 or non-numeric.'),
+    min: z
+        .string()
+        .optional()
+        .describe('Minimum value — numeric min when numeric, else lexical min.'),
+    max: z
+        .string()
+        .optional()
+        .describe('Maximum value — numeric max when numeric, else lexical max.'),
+    studyCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of distinct studies contributing observations of this variable.'),
+    studyDbIds: z
+        .array(z.string())
+        .describe('Distinct studyDbIds contributing observations of this variable.'),
+    seasons: z
+        .array(z.string())
+        .describe('Distinct season labels across the observations (empty when the server carries no season).'),
+})
+    .describe('Aggregated statistics for one observation variable across the studies the germplasm appears in.');
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection used.'),
+    germplasmDbId: z.string().describe('The germplasm that was analyzed.'),
+    germplasmName: z
+        .string()
+        .optional()
+        .describe('Display name of the germplasm, when the server provides one.'),
+    studyCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .describe('Number of distinct studies that contributed any observation.'),
+    studyDbIds: z.array(z.string()).describe('Distinct studyDbIds that contributed observations.'),
+    perVariable: z
+        .array(PerVariableSchema)
+        .describe('Per-variable aggregates, sorted by observationVariableDbId.'),
+    warnings: z
+        .array(z.string())
+        .describe('Advisory messages (study-discovery limits, dropped filters, fallback paths, per-study failures).'),
+});
+// ---------------------------------------------------------------------------
+// Tool definition
+// ---------------------------------------------------------------------------
+export const brapiGermplasmPerformance = tool('brapi_germplasm_performance', {
+    description: "Aggregate a single germplasm's observations across every study it appears in, returning per-variable summary statistics (n, mean, median, sd, min, max), the contributing studies, and seasons. Study-anchored: discovers the germplasm's studies first (with a dialect-honor cross-check), then pulls observations per study — avoids the unanchored germplasm-only pull that stalls on SGN/Breedbase. For the underlying observation matrix, use brapi_build_phenotype_matrix.",
+    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_germplasm_performance.',
+        },
+        {
+            reason: 'germplasm_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Upstream returned no germplasm record for the requested germplasmDbId',
+            recovery: 'Verify the germplasmDbId on the target server, or run brapi_find_germplasm to discover valid IDs.',
+        },
+    ],
+    input: z.object({
+        alias: AliasInput,
+        germplasmDbId: z.string().min(1).describe('The germplasmDbId to summarize performance for.'),
+        variables: z
+            .array(z.string())
+            .optional()
+            .describe('Optional subset of observationVariableDbIds to aggregate. Omit to include every variable observed for the germplasm.'),
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const client = getBrapiClient();
+        const config = getServerConfig();
+        const capabilities = getCapabilityRegistry();
+        const connection = await requireRegisteredConnection(ctx, input.alias);
+        const capabilityLookup = {};
+        if (connection.resolvedAuth)
+            capabilityLookup.auth = connection.resolvedAuth;
+        await capabilities.ensure(connection.baseUrl, { service: 'germplasm', method: 'GET' }, ctx, capabilityLookup);
+        // 1. Confirm the germplasm exists and capture its display name.
+        const germplasmName = await fetchGermplasmName(client, connection, input.germplasmDbId, ctx);
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const dialect = await resolveDialect(connection, ctx, capabilityLookup);
+        const loadLimit = config.loadLimit;
+        const warnings = [];
+        // 2. Discover the germplasm's studies (study-anchoring requirement).
+        const discovery = await discoverStudiesForGermplasm({
+            client,
+            connection,
+            dialect,
+            germplasmDbId: input.germplasmDbId,
+            ctx,
+            warnings,
+        });
+        if (discovery.studyDbIds.length === 0) {
+            warnings.push(`No studies discovered for germplasm '${input.germplasmDbId}'. It may not be associated with any study on this server, or /studies does not support a germplasm filter — use brapi_build_phenotype_matrix with explicit studies instead.`);
+        }
+        else if (discovery.studyDbIds.length >= STUDY_DISCOVERY_CAP) {
+            warnings.push(`Study discovery capped at ${STUDY_DISCOVERY_CAP} studies — aggregates may be incomplete. Narrow with brapi_build_phenotype_matrix on specific studies if needed.`);
+        }
+        // 3. Pull observations per study, scoped to the germplasm. Filter returned
+        //    rows to the iterated study + target germplasm so the aggregate stays
+        //    correct on servers that ignore the studyDbId filter or over-return.
+        const collected = [];
+        const wantVariables = input.variables?.length ? new Set(input.variables) : undefined;
+        for (const studyDbId of discovery.studyDbIds) {
+            let studyObs;
+            try {
+                studyObs = await pullStudyObservations({
+                    studyDbId,
+                    input: input.variables
+                        ? { germplasm: [input.germplasmDbId], variables: input.variables }
+                        : { germplasm: [input.germplasmDbId] },
+                    client,
+                    connection,
+                    profile: profile.supported,
+                    dialect,
+                    config,
+                    loadLimit,
+                    warnings,
+                    ctx,
+                });
+            }
+            catch (err) {
+                warnings.push(`Study '${studyDbId}': observation pull failed (${err instanceof Error ? err.message : String(err)}).`);
+                continue;
+            }
+            if (studyObs === null) {
+                warnings.push(`Study '${studyDbId}': no observation path (server exposes neither /observations nor /observationunits).`);
+                continue;
+            }
+            for (const o of studyObs) {
+                if (o.studyDbId !== studyDbId)
+                    continue;
+                if (o.germplasmDbId !== input.germplasmDbId)
+                    continue;
+                if (wantVariables && !wantVariables.has(o.observationVariableDbId))
+                    continue;
+                collected.push(o);
+            }
+        }
+        // 4. Aggregate per variable.
+        const perVariable = aggregatePerVariable(collected);
+        const allStudyDbIds = [...new Set(collected.map((o) => o.studyDbId))].sort();
+        const result = {
+            alias: connection.alias,
+            germplasmDbId: input.germplasmDbId,
+            studyCount: allStudyDbIds.length,
+            studyDbIds: allStudyDbIds,
+            perVariable,
+            warnings,
+        };
+        if (germplasmName)
+            result.germplasmName = germplasmName;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        lines.push(`# Germplasm performance — ${result.germplasmName ?? result.germplasmDbId} — \`${result.alias}\``);
+        lines.push('');
+        lines.push(`germplasmDbId: \`${result.germplasmDbId}\` · studies: ${result.studyCount} · variables: ${result.perVariable.length}`);
+        lines.push(`studyDbIds: ${result.studyDbIds.join(', ') || '—'}`);
+        lines.push('');
+        if (result.perVariable.length === 0) {
+            lines.push('_No observations found for this germplasm across the discovered studies._');
+        }
+        else {
+            lines.push('## Per-variable aggregates');
+            for (const v of result.perVariable) {
+                const stats = [`n=${v.n}`];
+                if (v.mean !== undefined)
+                    stats.push(`mean=${fmtNum(v.mean)}`);
+                if (v.median !== undefined)
+                    stats.push(`median=${fmtNum(v.median)}`);
+                if (v.sd !== undefined)
+                    stats.push(`sd=${fmtNum(v.sd)}`);
+                if (v.min !== undefined)
+                    stats.push(`min=${v.min}`);
+                if (v.max !== undefined)
+                    stats.push(`max=${v.max}`);
+                stats.push(`studies=${v.studyCount}`);
+                if (v.studyDbIds.length > 0)
+                    stats.push(`studyDbIds=${v.studyDbIds.join(',')}`);
+                if (v.seasons.length > 0)
+                    stats.push(`seasons=${v.seasons.join('/')}`);
+                lines.push(`- **${v.observationVariableName ?? v.observationVariableDbId}** (\`${v.observationVariableDbId}\`): ${stats.join(' · ')}`);
+            }
+        }
+        if (result.warnings.length > 0) {
+            lines.push('');
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+// ---------------------------------------------------------------------------
+// Germplasm existence
+// ---------------------------------------------------------------------------
+async function fetchGermplasmName(client, connection, germplasmDbId, ctx) {
+    const id = encodeURIComponent(germplasmDbId);
+    let env;
+    try {
+        env = await client.get(connection.baseUrl, `/germplasm/${id}`, ctx, buildRequestOptions(connection, undefined, { singleton: true }));
+    }
+    catch (err) {
+        if (isUpstreamNotFound(err))
+            throw germplasmNotFound(ctx, connection, germplasmDbId);
+        throw err;
+    }
+    const rec = env.result;
+    if (!rec || typeof rec !== 'object' || !rec.germplasmDbId) {
+        throw germplasmNotFound(ctx, connection, germplasmDbId);
+    }
+    return asString(rec.germplasmName);
+}
+function germplasmNotFound(ctx, connection, germplasmDbId) {
+    return ctx.fail('germplasm_not_found', `Germplasm '${germplasmDbId}' not found on ${connection.baseUrl}.`, {
+        germplasmDbId,
+        baseUrl: connection.baseUrl,
+        ...ctx.recoveryFor('germplasm_not_found'),
+    });
+}
+/**
+ * Discover the studies a germplasm appears in via `/studies?germplasmDbIds=…`,
+ * paging up to `STUDY_DISCOVERY_CAP`. Cross-checks the filtered total against an
+ * unfiltered baseline: when equal (and > 0) the server ignored the germplasm
+ * filter — the anchor set is over-broad, so it warns but still proceeds (the
+ * per-study observation pull remains germplasm-scoped). When the dialect drops
+ * the filter outright, returns an empty set with a warning.
+ */
+async function discoverStudiesForGermplasm(args) {
+    const { client, connection, dialect, germplasmDbId, ctx, warnings } = args;
+    const adapted = dialect.adaptGetFilters('studies', { germplasmDbIds: [germplasmDbId] });
+    warnings.push(...adapted.warnings);
+    if (Object.keys(adapted.filters).length === 0) {
+        warnings.push('Study discovery skipped: the active dialect dropped the germplasm filter for /studies (server does not honor it).');
+        return { studyDbIds: [] };
+    }
+    const studyDbIds = [];
+    const seen = new Set();
+    let page = 0;
+    let totalPages = 1;
+    let filteredTotal;
+    while (page < totalPages && studyDbIds.length < STUDY_DISCOVERY_CAP && !ctx.signal.aborted) {
+        const env = await client.get(connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, {
+            ...adapted.filters,
+            pageSize: STUDY_DISCOVERY_PAGE_SIZE,
+            page,
+        }));
+        const rows = extractRows(env.result);
+        for (const r of rows) {
+            const sid = asString(r.studyDbId);
+            if (sid && !seen.has(sid)) {
+                seen.add(sid);
+                studyDbIds.push(sid);
+            }
+            if (studyDbIds.length >= STUDY_DISCOVERY_CAP)
+                break;
+        }
+        if (page === 0) {
+            const tc = env.metadata?.pagination?.totalCount;
+            if (typeof tc === 'number')
+                filteredTotal = tc;
+        }
+        totalPages = env.metadata?.pagination?.totalPages ?? page + 1;
+        page++;
+        if (rows.length < STUDY_DISCOVERY_PAGE_SIZE)
+            break;
+    }
+    // Dialect-honor cross-check against an unfiltered baseline.
+    if (typeof filteredTotal === 'number') {
+        const baseline = await fetchStudyTotal(client, connection, ctx).catch(() => undefined);
+        if (typeof baseline === 'number' && baseline > 0 && filteredTotal === baseline) {
+            warnings.push(`/studies returned the same total (${baseline}) for the germplasm-filtered probe and an unfiltered baseline — the server appears to ignore the germplasm filter on /studies. Proceeding with the ${studyDbIds.length} discovered studies (per-study observation pulls remain germplasm-scoped), but coverage may be over-broad.`);
+        }
+    }
+    return { studyDbIds };
+}
+async function fetchStudyTotal(client, connection, ctx) {
+    const env = await client.get(connection.baseUrl, '/studies', ctx, buildRequestOptions(connection, { pageSize: 1 }));
+    const total = env.metadata?.pagination?.totalCount;
+    return typeof total === 'number' ? total : undefined;
+}
+// ---------------------------------------------------------------------------
+// Aggregation
+// ---------------------------------------------------------------------------
+function aggregatePerVariable(obs) {
+    const byVar = new Map();
+    for (const o of obs) {
+        const arr = byVar.get(o.observationVariableDbId);
+        if (arr)
+            arr.push(o);
+        else
+            byVar.set(o.observationVariableDbId, [o]);
+    }
+    const out = [];
+    for (const [varId, rows] of byVar) {
+        const values = rows.map((r) => r.value);
+        const nums = values.map(Number).filter((n) => !Number.isNaN(n));
+        const studyDbIds = [...new Set(rows.map((r) => r.studyDbId))].sort();
+        const seasons = [
+            ...new Set(rows.map((r) => r.season).filter((s) => typeof s === 'string')),
+        ].sort();
+        const pv = {
+            observationVariableDbId: varId,
+            observationVariableName: rows[0]?.observationVariableName ?? varId,
+            n: rows.length,
+            studyCount: studyDbIds.length,
+            studyDbIds,
+            seasons,
+        };
+        if (nums.length > 0) {
+            pv.mean = mean(nums);
+            pv.median = median(nums);
+            pv.min = String(Math.min(...nums));
+            pv.max = String(Math.max(...nums));
+            if (nums.length >= 2)
+                pv.sd = sampleStdDev(nums);
+        }
+        else {
+            const sorted = [...values].sort();
+            const first = sorted[0];
+            const last = sorted[sorted.length - 1];
+            if (first !== undefined)
+                pv.min = first;
+            if (last !== undefined)
+                pv.max = last;
+        }
+        out.push(pv);
+    }
+    out.sort((a, b) => a.observationVariableDbId.localeCompare(b.observationVariableDbId));
+    return out;
+}
+function mean(nums) {
+    return nums.reduce((a, b) => a + b, 0) / nums.length;
+}
+function median(nums) {
+    const s = [...nums].sort((a, b) => a - b);
+    const mid = Math.floor(s.length / 2);
+    const hi = s[mid];
+    if (hi === undefined)
+        throw new Error('median of empty array');
+    if (s.length % 2 !== 0)
+        return hi;
+    const lo = s[mid - 1];
+    return lo === undefined ? hi : (lo + hi) / 2;
+}
+function sampleStdDev(nums) {
+    const m = mean(nums);
+    const variance = nums.reduce((a, b) => a + (b - m) ** 2, 0) / (nums.length - 1);
+    return Math.sqrt(variance);
+}
+/** Render a number compactly — integers bare, else rounded to 3 decimals. */
+function fmtNum(n) {
+    return Number.isInteger(n) ? String(n) : String(Math.round(n * 1000) / 1000);
+}
+//# sourceMappingURL=brapi-germplasm-performance.tool.js.map

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