@cyanheads/brapi-mcp-server 0.6.3 → 0.7.0

package/dist/mcp-server/tools/shared/genotype-calls.js

@@ -0,0 +1,172 @@
+/**
+ * @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 { z } from '@cyanheads/mcp-ts-core';
+import { buildRequestOptions } from './find-helpers.js';
+const PAGE_SIZE = 10_000;
+export const CallRowSchema = z
+    .object({
+    callSetDbId: z
+        .string()
+        .nullish()
+        .describe('FK to the call set (one germplasm × one variant set = one call set).'),
+    callSetName: z.string().nullish().describe('Display name of the call set.'),
+    variantDbId: z.string().nullish().describe('FK to the variant being called.'),
+    variantName: z.string().nullish().describe('Display name / alias of the variant.'),
+    variantSetDbId: z.string().nullish().describe('FK to the variant set the call belongs to.'),
+    genotype: z
+        .object({
+        values: z
+            .array(z.string().describe('Per-allele value string.'))
+            .nullish()
+            .describe('Encoded allele values — interpret using top-level `callFormatting`.'),
+    })
+        .passthrough()
+        .nullish()
+        .describe('Structured genotype payload (array of allele values plus server-specific fields).'),
+    genotypeValue: z
+        .string()
+        .nullish()
+        .describe('Legacy flat string form of the call (provided by some servers instead of `genotype`).'),
+    phaseSet: z
+        .string()
+        .nullish()
+        .describe('Phase-set identifier linking calls that share a haplotype phase.'),
+})
+    .passthrough()
+    .describe('One genotype call row.');
+/**
+ * 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 function buildCallsSearchBody(input) {
+    const body = {};
+    if (input.variantSetDbId)
+        body.variantSetDbIds = [input.variantSetDbId];
+    if (input.variantSetDbIds?.length) {
+        body.variantSetDbIds = Array.from(new Set([...(body.variantSetDbIds ?? []), ...input.variantSetDbIds]));
+    }
+    if (input.germplasmDbIds?.length)
+        body.germplasmDbIds = input.germplasmDbIds;
+    if (input.callSetDbIds?.length)
+        body.callSetDbIds = input.callSetDbIds;
+    if (input.variantDbIds?.length)
+        body.variantDbIds = input.variantDbIds;
+    if (input.callFormat)
+        body.callFormat = input.callFormat;
+    body.pageSize = PAGE_SIZE;
+    return body;
+}
+/**
+ * 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 async function collectCalls(input) {
+    const rows = [];
+    let callFormatting = {};
+    let truncated = false;
+    const firstBody = { ...input.body, page: 0 };
+    const first = await input.client.postSearch(input.connection.baseUrl, 'calls', firstBody, input.ctx, buildRequestOptions(input.connection));
+    let envelope;
+    let searchResultsDbId;
+    if (first.kind === 'sync') {
+        envelope = first.envelope;
+    }
+    else {
+        searchResultsDbId = first.searchResultsDbId;
+        envelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', first.searchResultsDbId, input.ctx, buildRequestOptions(input.connection));
+    }
+    consumePage(envelope, rows, (cf) => {
+        callFormatting = cf;
+    });
+    const totalPages = envelope.metadata?.pagination?.totalPages;
+    for (let page = 1; page < (totalPages ?? 1); page++) {
+        if (rows.length >= input.maxCalls) {
+            truncated = true;
+            break;
+        }
+        if (input.ctx.signal.aborted)
+            break;
+        let pageEnvelope;
+        if (searchResultsDbId) {
+            pageEnvelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', searchResultsDbId, input.ctx, buildRequestOptions(input.connection, { page, pageSize: PAGE_SIZE }));
+        }
+        else {
+            const nextSearch = await input.client.postSearch(input.connection.baseUrl, 'calls', { ...input.body, page }, input.ctx, buildRequestOptions(input.connection));
+            if (nextSearch.kind === 'sync') {
+                pageEnvelope = nextSearch.envelope;
+            }
+            else {
+                pageEnvelope = await input.client.getSearchResults(input.connection.baseUrl, 'calls', nextSearch.searchResultsDbId, input.ctx, buildRequestOptions(input.connection));
+            }
+        }
+        consumePage(pageEnvelope, rows, (cf) => {
+            callFormatting = cf;
+        });
+    }
+    if (rows.length > input.maxCalls) {
+        rows.length = input.maxCalls;
+        truncated = true;
+        input.warnings.push(`Truncated at the deployment pull limit (${input.maxCalls} rows). Narrow the filters and re-pull; the captured slice is preserved in the spilled dataframe.`);
+    }
+    return { rows, callFormatting, truncated };
+}
+/**
+ * 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 function consumePage(envelope, rows, setCallFormatting) {
+    const result = envelope.result;
+    if (!result || typeof result !== 'object')
+        return;
+    const record = result;
+    const cf = {};
+    if (typeof record.expandHomozygotes === 'boolean')
+        cf.expandHomozygotes = record.expandHomozygotes;
+    if (typeof record.unknownString === 'string')
+        cf.unknownString = record.unknownString;
+    if (typeof record.sepPhased === 'string')
+        cf.sepPhased = record.sepPhased;
+    if (typeof record.sepUnphased === 'string')
+        cf.sepUnphased = record.sepUnphased;
+    setCallFormatting(cf);
+    const data = record.data;
+    if (!Array.isArray(data))
+        return;
+    for (const entry of data) {
+        if (typeof entry === 'object' && entry !== null) {
+            rows.push(entry);
+        }
+    }
+}
+/**
+ * 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 function renderGenotypeString(row, callFormatting, phased) {
+    const unknown = callFormatting.unknownString ?? '.';
+    const values = row.genotype?.values;
+    if (values && values.length > 0) {
+        const sep = phased ? (callFormatting.sepPhased ?? '|') : (callFormatting.sepUnphased ?? '/');
+        return values.join(sep);
+    }
+    if (row.genotypeValue)
+        return row.genotypeValue;
+    return unknown;
+}
+//# sourceMappingURL=genotype-calls.js.map

package/dist/mcp-server/tools/shared/genotype-calls.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/tools/shared/observations.d.ts

@@ -0,0 +1,87 @@
+/**
+ * @fileoverview Shared observation-pull logic for the phenotype tools
+ * (`brapi_build_phenotype_matrix`, `brapi_germplasm_performance`). Owns the
+ * study-anchored observation collection strategy and the raw/normalized row
+ * shapes, so both tools pull observations identically without duplicating the
+ * server-dependent fallback chain.
+ *
+ * Observation pull strategy (server-dependent), per study:
+ *   1. Prefer `/observations?studyDbId=…` (BrAPI spec path).
+ *   2. Fall back to `/observationunits?studyDbId=…` with embedded
+ *      `observations[]` arrays when `/observations` returns empty or the dialect
+ *      drops the study filter — required for the BrAPI Community Test Server,
+ *      where `/observations?studyDbId` is not honored.
+ *   3. When units carry `germplasmDbId`s but no embedded observations, pull
+ *      `/observations?germplasmDbId=…` per germplasm and filter back to the
+ *      study — stays study-anchored without an unbounded scan.
+ *
+ * `pullStudyObservations` returns `null` only when no usable observation path
+ * exists for the study (caller throws its typed `no_observation_path` error);
+ * an empty array means the paths exist but yielded no rows.
+ *
+ * @module mcp-server/tools/shared/observations
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import type { ServerConfig } from '../../../config/server-config.js';
+import { type BrapiClient } from '../../../services/brapi-client/index.js';
+import type { BrapiDialect } from '../../../services/brapi-dialect/index.js';
+import type { CallDescriptor } from '../../../services/capability-registry/types.js';
+import type { RegisteredServer } from '../../../services/server-registry/index.js';
+/** Raw BrAPI `/observations` row shape (passthrough). */
+export interface RawObservationRow {
+    germplasmDbId?: string | null;
+    germplasmName?: string | null;
+    observationDbId?: string | null;
+    observationVariableDbId?: string | null;
+    observationVariableName?: string | null;
+    season?: unknown;
+    seasonDbId?: string | null;
+    studyDbId?: string | null;
+    value?: string | null;
+    [key: string]: unknown;
+}
+/** Normalized observation — required fields are non-empty strings after extraction. */
+export interface NormObs {
+    germplasmDbId: string;
+    germplasmName: string;
+    observationVariableDbId: string;
+    observationVariableName: string;
+    /** Human season label (`"spring 2013"` / seasonDbId), when the row carries one. */
+    season?: string;
+    studyDbId: string;
+    value: string;
+}
+/** Filters that scope an observation pull beyond the study anchor. */
+export interface ObservationPullFilters {
+    extraFilters?: Record<string, unknown> | undefined;
+    germplasm?: string[] | undefined;
+    variables?: string[] | undefined;
+}
+export interface PullStudyObservationsArgs {
+    client: BrapiClient;
+    config: ServerConfig;
+    connection: RegisteredServer;
+    ctx: Context;
+    dialect: BrapiDialect;
+    input: ObservationPullFilters;
+    loadLimit: number;
+    profile: Record<string, CallDescriptor>;
+    studyDbId: string;
+    warnings: string[];
+}
+/**
+ * Collect observations for a single study, trying `/observations` first and
+ * falling back to `/observationunits` (embedded, then germplasm-anchored).
+ * Returns `null` when no usable path exists; `[]` when paths exist but are
+ * empty.
+ */
+export declare function pullStudyObservations(args: PullStudyObservationsArgs): Promise<NormObs[] | null>;
+/** Normalise a raw /observations row; drops rows missing any required field. */
+export declare function normalizeObsRow(row: RawObservationRow): NormObs | null;
+/**
+ * Derive a human season label from a BrAPI observation row. Servers carry
+ * season either as a nested object (`{ seasonName, year, seasonDbId }`) or a
+ * flat `seasonDbId` string. Returns undefined when neither is present.
+ */
+export declare function seasonLabel(row: RawObservationRow): string | undefined;
+//# sourceMappingURL=observations.d.ts.map

package/dist/mcp-server/tools/shared/observations.d.ts.map

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package/dist/mcp-server/tools/shared/observations.js

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+/**
+ * @fileoverview Shared observation-pull logic for the phenotype tools
+ * (`brapi_build_phenotype_matrix`, `brapi_germplasm_performance`). Owns the
+ * study-anchored observation collection strategy and the raw/normalized row
+ * shapes, so both tools pull observations identically without duplicating the
+ * server-dependent fallback chain.
+ *
+ * Observation pull strategy (server-dependent), per study:
+ *   1. Prefer `/observations?studyDbId=…` (BrAPI spec path).
+ *   2. Fall back to `/observationunits?studyDbId=…` with embedded
+ *      `observations[]` arrays when `/observations` returns empty or the dialect
+ *      drops the study filter — required for the BrAPI Community Test Server,
+ *      where `/observations?studyDbId` is not honored.
+ *   3. When units carry `germplasmDbId`s but no embedded observations, pull
+ *      `/observations?germplasmDbId=…` per germplasm and filter back to the
+ *      study — stays study-anchored without an unbounded scan.
+ *
+ * `pullStudyObservations` returns `null` only when no usable observation path
+ * exists for the study (caller throws its typed `no_observation_path` error);
+ * an empty array means the paths exist but yielded no rows.
+ *
+ * @module mcp-server/tools/shared/observations
+ */
+import { isDialectAllDropped } from '../../../services/brapi-client/index.js';
+import { companionRequestOptions, extractRows, mergeFilters, } from './find-helpers.js';
+/**
+ * Collect observations for a single study, trying `/observations` first and
+ * falling back to `/observationunits` (embedded, then germplasm-anchored).
+ * Returns `null` when no usable path exists; `[]` when paths exist but are
+ * empty.
+ */
+export async function pullStudyObservations(args) {
+    const { studyDbId, input, client, connection, dialect, config, loadLimit, warnings, ctx } = args;
+    // Build named filters for observations endpoint
+    const namedFilters = {
+        studyDbIds: [studyDbId],
+    };
+    if (input.variables?.length)
+        namedFilters.observationVariableDbIds = input.variables;
+    if (input.germplasm?.length)
+        namedFilters.germplasmDbIds = input.germplasm;
+    const merged = mergeFilters(namedFilters, input.extraFilters, warnings);
+    // Apply dialect (plurals → singulars on SGN-family servers)
+    const adapted = dialect.adaptGetFilters('observations', merged);
+    warnings.push(...adapted.warnings);
+    // When the dialect drops ALL filters for /observations (known case: the
+    // brapi-test server doesn't honor studyDbId on /observations at all), skip
+    // the observations path entirely and go straight to the observationunits
+    // fallback rather than making an unscoped request.
+    const obsFiltersDropped = adapted.dropped.length > 0 && Object.keys(adapted.filters).length === 0;
+    const obsFilters = adapted.filters;
+    // ---- Path 1: /observations ----
+    const supportsObservations = supportsGet(args.profile, 'observations') && !obsFiltersDropped;
+    if (supportsObservations) {
+        const obs = await fetchObservationsPath(client, connection, dialect, config, obsFilters, loadLimit, ctx);
+        if (obs !== null && obs.length > 0) {
+            return obs;
+        }
+        if (obs !== null && obs.length === 0) {
+            // Server responded with empty for this study — note it and try fallback
+            warnings.push(`Study '${studyDbId}': /observations returned 0 rows — trying /observationunits fallback.`);
+        }
+    }
+    else if (obsFiltersDropped) {
+        warnings.push(`Study '${studyDbId}': dialect '${dialect.id}' drops all study filters for /observations — using /observationunits fallback.`);
+    }
+    // ---- Path 2: /observationunits fallback ----
+    // Two sub-strategies:
+    //   2a. Units embed observations[] arrays — extract directly.
+    //   2b. Units carry germplasmDbIds but observations[] is null — pull
+    //       /observations?germplasmDbId=X per germplasm found in the study.
+    const supportsObsUnits = supportsGet(args.profile, 'observationunits');
+    if (supportsObsUnits) {
+        const unitResult = await fetchObservationUnitsRaw(client, connection, dialect, config, studyDbId, loadLimit, ctx);
+        if (unitResult !== null) {
+            // 2a: check for embedded observations
+            const embeddedObs = extractEmbeddedObservations(unitResult, studyDbId);
+            if (embeddedObs.length > 0) {
+                warnings.push(`Study '${studyDbId}': Using /observationunits embedded observations[] fallback.`);
+                return embeddedObs;
+            }
+            // 2b: germplasm-anchored pull — units have germplasmDbIds, use them
+            let germplasmIds = [
+                ...new Set(unitResult
+                    .map((u) => u.germplasmDbId)
+                    .filter((id) => typeof id === 'string' && id.length > 0)),
+            ];
+            // When the caller scoped to specific germplasm, pull only those — avoids
+            // an O(all-germplasm-in-study) fan-out for single-germplasm callers (#9).
+            if (input.germplasm?.length) {
+                const want = new Set(input.germplasm);
+                germplasmIds = germplasmIds.filter((g) => want.has(g));
+            }
+            if (germplasmIds.length > 0) {
+                const germObs = await fetchObservationsByGermplasm(client, connection, dialect, config, germplasmIds, studyDbId, loadLimit, ctx);
+                if (germObs !== null && germObs.length > 0) {
+                    warnings.push(`Study '${studyDbId}': Used /observationunits → /observations?germplasmDbId fallback because studyDbId filter is not honored on /observations.`);
+                    return germObs;
+                }
+            }
+        }
+    }
+    // Neither path yielded data. Distinguish "no path" from "empty".
+    if (!supportsObservations && !obsFiltersDropped && !supportsObsUnits) {
+        return null; // caller throws typed error
+    }
+    // Paths exist but all returned empty — treat as empty (not an error)
+    warnings.push(`Study '${studyDbId}': No observations found via /observations or /observationunits.`);
+    return [];
+}
+function supportsGet(profile, service) {
+    const descriptor = profile[service];
+    if (!descriptor)
+        return false;
+    if (!descriptor.methods || descriptor.methods.length === 0)
+        return true;
+    return descriptor.methods.includes('GET');
+}
+/** Fetch from /observations with study-anchored filters. Returns null on error. */
+async function fetchObservationsPath(client, connection, dialect, config, filters, pageSize, ctx) {
+    try {
+        const opts = companionRequestOptions(connection, dialect, config, [], {
+            ...filters,
+            pageSize,
+        });
+        const envelope = await client.get(connection.baseUrl, '/observations', ctx, opts);
+        const rows = extractRows(envelope.result);
+        return rows.flatMap(normalizeObsRow).filter(Boolean);
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Fetch raw observationunit records (without extracting observations). Returns null on error. */
+async function fetchObservationUnitsRaw(client, connection, dialect, config, studyDbId, pageSize, ctx) {
+    try {
+        const rawFilters = { studyDbIds: [studyDbId] };
+        const adapted = dialect.adaptGetFilters('observationunits', rawFilters);
+        const obsUnitFilters = adapted.filters;
+        const opts = companionRequestOptions(connection, dialect, config, [], {
+            ...obsUnitFilters,
+            pageSize,
+        });
+        const envelope = await client.get(connection.baseUrl, '/observationunits', ctx, opts);
+        return extractRows(envelope.result);
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Extract embedded observations[] from observationunit records (strategy 2a). */
+function extractEmbeddedObservations(units, studyDbId) {
+    const obs = [];
+    for (const unit of units) {
+        const unitStudyDbId = unit.studyDbId ?? studyDbId;
+        const unitGermplasmDbId = unit.germplasmDbId ?? 'unknown';
+        const unitGermplasmName = typeof unit.germplasmName === 'string' && unit.germplasmName.length > 0
+            ? unit.germplasmName
+            : unitGermplasmDbId;
+        const embedded = unit.observations;
+        if (!Array.isArray(embedded))
+            continue;
+        for (const raw of embedded) {
+            if (!raw || typeof raw !== 'object')
+                continue;
+            const r = raw;
+            const varId = r.observationVariableDbId ?? null;
+            const val = r.value ?? null;
+            if (!varId || val === null || val === undefined)
+                continue;
+            const season = seasonLabel(r);
+            obs.push({
+                germplasmDbId: unitGermplasmDbId,
+                germplasmName: unitGermplasmName,
+                observationVariableDbId: String(varId),
+                observationVariableName: typeof r.observationVariableName === 'string' && r.observationVariableName.length > 0
+                    ? r.observationVariableName
+                    : String(varId),
+                studyDbId: unitStudyDbId,
+                value: String(val),
+                ...(season ? { season } : {}),
+            });
+        }
+    }
+    return obs;
+}
+/**
+ * Pull observations anchored by germplasmDbId (strategy 2b). Used when
+ * studyDbId filter is not honored on /observations but we know germplasmDbIds
+ * in the study from the observationunits response. Filters results to only
+ * observations for the target study.
+ */
+async function fetchObservationsByGermplasm(client, connection, dialect, config, germplasmIds, studyDbId, pageSize, ctx) {
+    try {
+        // Pull per germplasm to stay study-anchored. Bound by pageSize per call.
+        // For wide queries this is O(germplasmCount) requests but avoids an
+        // unbounded full-table scan on the observations endpoint.
+        const allObs = [];
+        for (const germId of germplasmIds) {
+            const rawFilters = { germplasmDbIds: [germId] };
+            const adapted = dialect.adaptGetFilters('observations', rawFilters);
+            // Skip if the germplasm filter is also dropped
+            if (adapted.dropped.length > 0 && Object.keys(adapted.filters).length === 0)
+                continue;
+            const opts = companionRequestOptions(connection, dialect, config, [], {
+                ...adapted.filters,
+                pageSize,
+            });
+            try {
+                const envelope = await client.get(connection.baseUrl, '/observations', ctx, opts);
+                const rows = extractRows(envelope.result);
+                // Filter to only observations for the target study
+                for (const row of rows) {
+                    if (row.studyDbId !== studyDbId)
+                        continue;
+                    const norm = normalizeObsRow(row);
+                    if (norm)
+                        allObs.push(norm);
+                }
+            }
+            catch { }
+        }
+        return allObs;
+    }
+    catch (err) {
+        if (isDialectAllDropped(err))
+            throw err;
+        return null;
+    }
+}
+/** Normalise a raw /observations row; drops rows missing any required field. */
+export function normalizeObsRow(row) {
+    const varId = row.observationVariableDbId ?? null;
+    const germId = row.germplasmDbId ?? null;
+    const studyId = row.studyDbId ?? null;
+    const val = row.value ?? null;
+    if (!varId || !germId || !studyId || val === null || val === undefined)
+        return null;
+    const norm = {
+        germplasmDbId: String(germId),
+        germplasmName: typeof row.germplasmName === 'string' && row.germplasmName.length > 0
+            ? row.germplasmName
+            : String(germId),
+        observationVariableDbId: String(varId),
+        observationVariableName: typeof row.observationVariableName === 'string' && row.observationVariableName.length > 0
+            ? row.observationVariableName
+            : String(varId),
+        studyDbId: String(studyId),
+        value: String(val),
+    };
+    const season = seasonLabel(row);
+    if (season)
+        norm.season = season;
+    return norm;
+}
+/**
+ * Derive a human season label from a BrAPI observation row. Servers carry
+ * season either as a nested object (`{ seasonName, year, seasonDbId }`) or a
+ * flat `seasonDbId` string. Returns undefined when neither is present.
+ */
+export function seasonLabel(row) {
+    const s = row.season;
+    if (s && typeof s === 'object') {
+        const so = s;
+        const name = typeof so.seasonName === 'string' && so.seasonName.length > 0 ? so.seasonName : undefined;
+        const year = typeof so.year === 'number' ? so.year : undefined;
+        if (name && year !== undefined)
+            return `${name} ${year}`;
+        if (name)
+            return name;
+        if (typeof so.seasonDbId === 'string' && so.seasonDbId.length > 0)
+            return so.seasonDbId;
+    }
+    else if (typeof s === 'string' && s.length > 0) {
+        return s;
+    }
+    if (typeof row.seasonDbId === 'string' && row.seasonDbId.length > 0)
+        return row.seasonDbId;
+    return;
+}
+//# sourceMappingURL=observations.js.map

package/dist/mcp-server/tools/shared/observations.js.map

@@ -0,0 +1 @@
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package/manifest.json

@@ -1,7 +1,7 @@
 {
   "manifest_version": "0.3",
   "name": "brapi-mcp-server",
-  "version": "0.6.3",
+  "version": "0.7.0",
   "description": "Collaborative BrAPI v2.1 MCP workspace — studies, germplasm, genotypes across Breedbase, T3, more.",
   "author": {
     "name": "cyanheads"

package/package.json

@@ -1,7 +1,7 @@
 {
   "name": "@cyanheads/brapi-mcp-server",
   "mcpName": "io.github.cyanheads/brapi-mcp-server",
-  "version": "0.6.3",
+  "version": "0.7.0",
   "description": "A collaborative BrAPI v2.1 workspace for multi-agent research via MCP. Search studies, germplasm, genotypes, & more - across Breedbase, T3, Sweetpotatobase, & any BrAPI v2-compliant server.",
   "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
   "type": "module",
@@ -26,7 +26,8 @@
     "clean": "bun run scripts/clean.ts",
     "devcheck": "bun run scripts/devcheck.ts",
     "tree": "bun run scripts/tree.ts",
-    "format": "biome check --write --unsafe .",
+    "format": "biome check --write .",
+    "format:unsafe": "biome check --write --unsafe .",
     "lint:mcp": "bun run scripts/lint-mcp.ts",
     "lint:packaging": "bun run scripts/lint-packaging.ts",
     "list-skills": "bun run scripts/list-skills.ts",
@@ -79,8 +80,8 @@
     "access": "public"
   },
   "dependencies": {
-    "@cyanheads/mcp-ts-core": "^0.9.13",
-    "@duckdb/node-api": "^1.5.3-r.2",
+    "@cyanheads/mcp-ts-core": "^0.9.16",
+    "@duckdb/node-api": "^1.5.3-r.3",
     "pino-pretty": "^13.1.3",
     "zod": "^4.4.3"
   },
@@ -91,6 +92,6 @@
     "ignore": "^7.0.5",
     "tsc-alias": "^1.8.17",
     "typescript": "^6.0.3",
-    "vitest": "^4.1.7"
+    "vitest": "^4.1.8"
   }
 }

package/server.json

@@ -6,14 +6,14 @@
     "url": "https://github.com/cyanheads/brapi-mcp-server",
     "source": "github"
   },
-  "version": "0.6.3",
+  "version": "0.7.0",
   "packages": [
     {
       "registryType": "npm",
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.6.3",
+      "version": "0.7.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:stdio" }
@@ -49,7 +49,7 @@
       "registryBaseUrl": "https://registry.npmjs.org",
       "identifier": "@cyanheads/brapi-mcp-server",
       "runtimeHint": "bun",
-      "version": "0.6.3",
+      "version": "0.7.0",
       "packageArguments": [
         { "type": "positional", "value": "run" },
         { "type": "positional", "value": "start:http" }