@cyanheads/brapi-mcp-server 0.3.5

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

@@ -0,0 +1,323 @@
+/**
+ * @fileoverview `brapi_get_study` — fetch a single study by DbId, resolve
+ * program/trial/location FKs via ReferenceDataCache, and attach cheap
+ * `pageSize=0` counts (observations, observation units, variables) as
+ * response companions so the agent can decide where to drill next.
+ *
+ * @module mcp-server/tools/definitions/brapi-get-study.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 { getReferenceDataCache } from '../../../services/reference-data-cache/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+import { AliasInput, buildRequestOptions, isUpstreamNotFound } from '../shared/find-helpers.js';
+const StudySchema = z
+    .object({
+    studyDbId: z.string().describe('Server-side identifier for the study.'),
+    studyName: z.string().nullish().describe('Display name.'),
+    studyType: z.string().nullish().describe('E.g. "Yield Trial", "Phenotyping".'),
+    studyDescription: z.string().nullish().describe('Free-form description.'),
+    programDbId: z.string().nullish().describe('FK to the owning program.'),
+    programName: z.string().nullish().describe('Display name of the owning program.'),
+    trialDbId: z.string().nullish().describe('FK to the owning trial.'),
+    trialName: z.string().nullish().describe('Display name of the owning trial.'),
+    locationDbId: z.string().nullish().describe('FK to the study site.'),
+    locationName: z.string().nullish().describe('Display name of the study site.'),
+    commonCropName: z.string().nullish().describe('Common crop name (e.g. "Maize", "Wheat").'),
+    seasons: z
+        .array(z.string().describe('Season identifier — typically a year like "2022".'))
+        .nullish()
+        .describe('Season identifiers this study spans.'),
+    active: z.boolean().nullish().describe('True while the study is open for data capture.'),
+    startDate: z.string().nullish().describe('ISO 8601 start date.'),
+    endDate: z.string().nullish().describe('ISO 8601 end date.'),
+    studyCode: z.string().nullish().describe('Short code or alias for the study.'),
+    studyPUI: z.string().nullish().describe('Persistent unique identifier (URI).'),
+})
+    .passthrough();
+const ProgramSchema = z
+    .object({
+    programDbId: z.string().describe('Server-side identifier for the program.'),
+    programName: z.string().nullish().describe('Display name.'),
+    commonCropName: z.string().nullish().describe('Common crop name this program targets.'),
+    abbreviation: z.string().nullish().describe('Short abbreviation.'),
+    leadPersonName: z.string().nullish().describe('Name of the program lead.'),
+    documentationURL: z.string().nullish().describe('URL pointing at program documentation.'),
+})
+    .passthrough();
+const TrialSchema = z
+    .object({
+    trialDbId: z.string().describe('Server-side identifier for the trial.'),
+    trialName: z.string().nullish().describe('Display name.'),
+    programDbId: z.string().nullish().describe('FK to the owning program.'),
+    programName: z.string().nullish().describe('Display name of the owning program.'),
+    commonCropName: z.string().nullish().describe('Common crop name.'),
+    startDate: z.string().nullish().describe('ISO 8601 start date.'),
+    endDate: z.string().nullish().describe('ISO 8601 end date.'),
+    active: z.boolean().nullish().describe('True while the trial is ongoing.'),
+    trialDescription: z.string().nullish().describe('Free-form description.'),
+})
+    .passthrough();
+const LocationSchema = z
+    .object({
+    locationDbId: z.string().describe('Server-side identifier for the location.'),
+    locationName: z.string().nullish().describe('Display name.'),
+    abbreviation: z.string().nullish().describe('Short abbreviation.'),
+    countryCode: z.string().nullish().describe('ISO 3166-1 alpha-3 country code.'),
+    countryName: z.string().nullish().describe('Display name of the country.'),
+    locationType: z
+        .string()
+        .nullish()
+        .describe('Type of location (e.g. "Research Station", "Field").'),
+    latitude: z.number().nullish().describe('WGS84 latitude in decimal degrees.'),
+    longitude: z.number().nullish().describe('WGS84 longitude in decimal degrees.'),
+    altitude: z.number().nullish().describe('Altitude in meters above sea level.'),
+})
+    .passthrough();
+const OutputSchema = z.object({
+    alias: z.string().describe('Alias of the registered BrAPI connection the call used.'),
+    study: StudySchema.describe('Canonical study record as returned by `/studies/{id}`.'),
+    program: ProgramSchema.optional().describe('Resolved program record (when the study has a programDbId and the FK lookup succeeded).'),
+    trial: TrialSchema.optional().describe('Resolved trial record (when the study has a trialDbId and the FK lookup succeeded).'),
+    location: LocationSchema.optional().describe('Resolved location record (when the study has a locationDbId and the FK lookup succeeded).'),
+    observationCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Total observations recorded against this study.'),
+    observationUnitCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Total observation units (plots, plants, samples) in this study.'),
+    variableCount: z
+        .number()
+        .int()
+        .nonnegative()
+        .optional()
+        .describe('Total observation variables (traits) measured in this study.'),
+    warnings: z.array(z.string()).describe('Advisory messages — failed FK lookups, missing counts.'),
+});
+export const brapiGetStudy = tool('brapi_get_study', {
+    description: 'Fetch a single study by DbId with program, trial, and location fully resolved. Response includes cheap observation/observation-unit/variable counts as drill-down signals.',
+    annotations: { readOnlyHint: true, idempotentHint: true },
+    errors: [
+        {
+            reason: 'study_not_found',
+            code: JsonRpcErrorCode.NotFound,
+            when: 'Upstream returned no study record for the requested DbId',
+            recovery: 'Verify the studyDbId on the target server, or run brapi_find_studies to discover valid IDs.',
+        },
+    ],
+    input: z.object({
+        studyDbId: z.string().min(1).describe('Study identifier.'),
+        alias: AliasInput,
+    }),
+    output: OutputSchema,
+    async handler(input, ctx) {
+        const registry = getServerRegistry();
+        const capabilities = getCapabilityRegistry();
+        const client = getBrapiClient();
+        const referenceData = getReferenceDataCache();
+        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: 'studies', method: 'GET' }, ctx, capabilityLookup);
+        const warnings = [];
+        const referenceLookup = {};
+        if (connection.resolvedAuth)
+            referenceLookup.auth = connection.resolvedAuth;
+        let studyEnv;
+        try {
+            studyEnv = await client.get(connection.baseUrl, `/studies/${encodeURIComponent(input.studyDbId)}`, ctx, buildRequestOptions(connection));
+        }
+        catch (err) {
+            if (isUpstreamNotFound(err)) {
+                throw ctx.fail('study_not_found', `Study '${input.studyDbId}' not found on ${connection.baseUrl}.`, {
+                    studyDbId: input.studyDbId,
+                    baseUrl: connection.baseUrl,
+                    ...ctx.recoveryFor('study_not_found'),
+                });
+            }
+            throw err;
+        }
+        const study = studyEnv.result;
+        if (!study || typeof study !== 'object' || !study.studyDbId) {
+            throw ctx.fail('study_not_found', `Study '${input.studyDbId}' not found on ${connection.baseUrl}.`, {
+                studyDbId: input.studyDbId,
+                baseUrl: connection.baseUrl,
+                ...ctx.recoveryFor('study_not_found'),
+            });
+        }
+        const profile = await capabilities.profile(connection.baseUrl, ctx, capabilityLookup);
+        const supportsObservations = profile.supported.observations?.methods?.includes('GET') ?? false;
+        const supportsObservationUnits = profile.supported.observationunits?.methods?.includes('GET') ?? false;
+        const supportsVariables = profile.supported.variables?.methods?.includes('GET') ?? false;
+        const programDbId = asString(study.programDbId);
+        const trialDbId = asString(study.trialDbId);
+        const locationDbId = asString(study.locationDbId);
+        const [programs, trials, locations, obsCount, obsUnitCount, variableCount] = await Promise.all([
+            programDbId
+                ? referenceData
+                    .getPrograms(connection.baseUrl, [programDbId], ctx, referenceLookup)
+                    .catch((err) => recordWarning(warnings, 'program FK lookup failed', err))
+                : Promise.resolve(undefined),
+            trialDbId
+                ? referenceData
+                    .getTrials(connection.baseUrl, [trialDbId], ctx, referenceLookup)
+                    .catch((err) => recordWarning(warnings, 'trial FK lookup failed', err))
+                : Promise.resolve(undefined),
+            locationDbId
+                ? referenceData
+                    .getLocations(connection.baseUrl, [locationDbId], ctx, referenceLookup)
+                    .catch((err) => recordWarning(warnings, 'location FK lookup failed', err))
+                : Promise.resolve(undefined),
+            supportsObservations
+                ? fetchTotalCount(client, connection.baseUrl, '/observations', ctx, buildRequestOptions(connection, {
+                    studyDbIds: [input.studyDbId],
+                    pageSize: 1,
+                })).catch((err) => recordWarning(warnings, 'observation count probe failed', err))
+                : Promise.resolve(undefined),
+            supportsObservationUnits
+                ? fetchTotalCount(client, connection.baseUrl, '/observationunits', ctx, buildRequestOptions(connection, {
+                    studyDbIds: [input.studyDbId],
+                    pageSize: 1,
+                })).catch((err) => recordWarning(warnings, 'observation-unit count probe failed', err))
+                : Promise.resolve(undefined),
+            supportsVariables
+                ? fetchTotalCount(client, connection.baseUrl, '/variables', ctx, buildRequestOptions(connection, {
+                    studyDbId: input.studyDbId,
+                    pageSize: 1,
+                })).catch((err) => recordWarning(warnings, 'variable count probe failed', err))
+                : Promise.resolve(undefined),
+        ]);
+        const result = {
+            alias: connection.alias,
+            study: study,
+            warnings,
+        };
+        if (programDbId && programs instanceof Map) {
+            const program = programs.get(programDbId);
+            if (program)
+                result.program = program;
+        }
+        if (trialDbId && trials instanceof Map) {
+            const trial = trials.get(trialDbId);
+            if (trial)
+                result.trial = trial;
+        }
+        if (locationDbId && locations instanceof Map) {
+            const location = locations.get(locationDbId);
+            if (location)
+                result.location = location;
+        }
+        if (typeof obsCount === 'number')
+            result.observationCount = obsCount;
+        if (typeof obsUnitCount === 'number')
+            result.observationUnitCount = obsUnitCount;
+        if (typeof variableCount === 'number')
+            result.variableCount = variableCount;
+        return result;
+    },
+    format: (result) => {
+        const lines = [];
+        const study = result.study;
+        lines.push(`# ${study.studyName ?? study.studyDbId}`);
+        lines.push('');
+        lines.push(`- **studyDbId:** \`${study.studyDbId}\``);
+        if (study.studyName)
+            lines.push(`- **studyName:** ${study.studyName}`);
+        if (study.studyType)
+            lines.push(`- **studyType:** ${study.studyType}`);
+        if (study.studyDescription)
+            lines.push(`- **studyDescription:** ${study.studyDescription}`);
+        if (study.programDbId)
+            lines.push(`- **programDbId:** ${study.programDbId}`);
+        if (study.programName)
+            lines.push(`- **programName:** ${study.programName}`);
+        if (study.trialDbId)
+            lines.push(`- **trialDbId:** ${study.trialDbId}`);
+        if (study.trialName)
+            lines.push(`- **trialName:** ${study.trialName}`);
+        if (study.locationDbId)
+            lines.push(`- **locationDbId:** ${study.locationDbId}`);
+        if (study.locationName)
+            lines.push(`- **locationName:** ${study.locationName}`);
+        if (study.commonCropName)
+            lines.push(`- **commonCropName:** ${study.commonCropName}`);
+        if (study.seasons?.length)
+            lines.push(`- **seasons:** ${study.seasons.join(', ')}`);
+        if (study.active != null)
+            lines.push(`- **active:** ${study.active}`);
+        if (study.startDate)
+            lines.push(`- **startDate:** ${study.startDate}`);
+        if (study.endDate)
+            lines.push(`- **endDate:** ${study.endDate}`);
+        if (study.studyCode)
+            lines.push(`- **studyCode:** ${study.studyCode}`);
+        if (study.studyPUI)
+            lines.push(`- **studyPUI:** ${study.studyPUI}`);
+        lines.push(`- **alias:** ${result.alias}`);
+        if (result.program) {
+            lines.push('');
+            lines.push('## Program');
+            renderKeyValues(lines, result.program);
+        }
+        if (result.trial) {
+            lines.push('');
+            lines.push('## Trial');
+            renderKeyValues(lines, result.trial);
+        }
+        if (result.location) {
+            lines.push('');
+            lines.push('## Location');
+            renderKeyValues(lines, result.location);
+        }
+        lines.push('');
+        lines.push('## Drill-down signals');
+        lines.push(`- observationCount: ${result.observationCount ?? '—'}`);
+        lines.push(`- observationUnitCount: ${result.observationUnitCount ?? '—'}`);
+        lines.push(`- variableCount: ${result.variableCount ?? '—'}`);
+        if (result.warnings.length > 0) {
+            lines.push('');
+            lines.push('## Warnings');
+            for (const w of result.warnings)
+                lines.push(`- ${w}`);
+        }
+        return [{ type: 'text', text: lines.join('\n') }];
+    },
+});
+function asString(value) {
+    return typeof value === 'string' && value.length > 0 ? value : undefined;
+}
+function recordWarning(warnings, label, err) {
+    warnings.push(`${label}: ${err instanceof Error ? err.message : String(err)}`);
+    return;
+}
+async function fetchTotalCount(client, baseUrl, path, ctx, options) {
+    const env = await client.get(baseUrl, path, ctx, options);
+    const total = env.metadata?.pagination?.totalCount;
+    return typeof total === 'number' ? total : undefined;
+}
+function renderKeyValues(lines, record) {
+    for (const [key, value] of Object.entries(record)) {
+        if (value === undefined || value === null)
+            continue;
+        if (Array.isArray(value)) {
+            if (value.length === 0)
+                continue;
+            lines.push(`- **${key}:** ${value.join(', ')}`);
+        }
+        else if (typeof value === 'object') {
+        }
+        else {
+            lines.push(`- **${key}:** ${value}`);
+        }
+    }
+}
+//# sourceMappingURL=brapi-get-study.tool.js.map

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

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package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts

@@ -0,0 +1,87 @@
+/**
+ * @fileoverview `brapi_manage_dataset` — consolidated lifecycle tool for
+ * datasets created by `find_*` spillovers. Four modes discriminated by
+ * `mode`: list (enumerate with provenance), summary (metadata only), load
+ * (paged rows with optional column projection), delete (drop metadata +
+ * payload). Export (CSV/Parquet) is deferred until storage backends for the
+ * write path are wired up.
+ *
+ * @module mcp-server/tools/definitions/brapi-manage-dataset.tool
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { JsonRpcErrorCode } from '@cyanheads/mcp-ts-core/errors';
+export declare const brapiManageDataset: import("@cyanheads/mcp-ts-core").ToolDefinition<z.ZodObject<{
+    mode: z.ZodEnum<{
+        delete: "delete";
+        list: "list";
+        summary: "summary";
+        load: "load";
+    }>;
+    datasetId: z.ZodOptional<z.ZodString>;
+    cursor: z.ZodOptional<z.ZodString>;
+    limit: z.ZodOptional<z.ZodNumber>;
+    page: z.ZodOptional<z.ZodNumber>;
+    pageSize: z.ZodOptional<z.ZodNumber>;
+    columns: z.ZodOptional<z.ZodArray<z.ZodString>>;
+}, z.core.$strip>, z.ZodObject<{
+    result: z.ZodDiscriminatedUnion<[z.ZodObject<{
+        mode: z.ZodLiteral<"list">;
+        datasets: z.ZodArray<z.ZodObject<{
+            datasetId: z.ZodString;
+            source: z.ZodString;
+            baseUrl: z.ZodString;
+            query: z.ZodUnknown;
+            rowCount: z.ZodNumber;
+            columns: z.ZodArray<z.ZodString>;
+            sizeBytes: z.ZodNumber;
+            createdAt: z.ZodString;
+            expiresAt: z.ZodString;
+            truncated: z.ZodOptional<z.ZodBoolean>;
+            maxRows: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strip>>;
+        cursor: z.ZodOptional<z.ZodString>;
+    }, z.core.$strip>, z.ZodObject<{
+        mode: z.ZodLiteral<"summary">;
+        dataset: z.ZodObject<{
+            datasetId: z.ZodString;
+            source: z.ZodString;
+            baseUrl: z.ZodString;
+            query: z.ZodUnknown;
+            rowCount: z.ZodNumber;
+            columns: z.ZodArray<z.ZodString>;
+            sizeBytes: z.ZodNumber;
+            createdAt: z.ZodString;
+            expiresAt: z.ZodString;
+            truncated: z.ZodOptional<z.ZodBoolean>;
+            maxRows: z.ZodOptional<z.ZodNumber>;
+        }, z.core.$strip>;
+    }, z.core.$strip>, z.ZodObject<{
+        mode: z.ZodLiteral<"load">;
+        datasetId: z.ZodString;
+        page: z.ZodNumber;
+        pageSize: z.ZodNumber;
+        totalRows: z.ZodNumber;
+        totalPages: z.ZodNumber;
+        rows: z.ZodArray<z.ZodRecord<z.ZodString, z.ZodUnknown>>;
+    }, z.core.$strip>, z.ZodObject<{
+        mode: z.ZodLiteral<"delete">;
+        datasetId: z.ZodString;
+        deleted: z.ZodLiteral<true>;
+    }, z.core.$strip>], "mode">;
+}, z.core.$strip>, readonly [{
+    readonly reason: "datasetid_required";
+    readonly code: JsonRpcErrorCode.ValidationError;
+    readonly when: "Mode summary, load, or delete was selected without a datasetId";
+    readonly recovery: "Call mode=list first to discover available dataset IDs, then retry with one.";
+}, {
+    readonly reason: "dataset_not_found";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Requested dataset is not present in the store (never existed or already expired)";
+    readonly recovery: "Run mode=list to confirm available datasets, or rerun the find_* tool that produced it.";
+}, {
+    readonly reason: "dataset_rows_missing";
+    readonly code: JsonRpcErrorCode.NotFound;
+    readonly when: "Dataset metadata is present but the row payload was lost or partially expired";
+    readonly recovery: "Delete the stale dataset via mode=delete and rerun the find_* tool that produced it.";
+}]>;
+//# sourceMappingURL=brapi-manage-dataset.tool.d.ts.map

package/dist/mcp-server/tools/definitions/brapi-manage-dataset.tool.d.ts.map

@@ -0,0 +1 @@
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