@cyanheads/brapi-mcp-server 0.3.5

package/dist/config/server-config.d.ts

@@ -0,0 +1,39 @@
+/**
+ * @fileoverview Server-specific configuration for brapi-mcp-server. Covers
+ * default connection details, HTTP client behavior (timeouts, retries,
+ * concurrency), async-search polling, dataset lifecycle, and reference-data
+ * cache tuning. Lazy-parsed via `parseEnvConfig` so env-var names appear in
+ * validation errors.
+ *
+ * @module config/server-config
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+declare const ServerConfigSchema: z.ZodObject<{
+    defaultBaseUrl: z.ZodOptional<z.ZodString>;
+    defaultUsername: z.ZodOptional<z.ZodString>;
+    defaultPassword: z.ZodOptional<z.ZodString>;
+    defaultOauthClientId: z.ZodOptional<z.ZodString>;
+    defaultOauthClientSecret: z.ZodOptional<z.ZodString>;
+    defaultApiKey: z.ZodOptional<z.ZodString>;
+    defaultApiKeyHeader: z.ZodDefault<z.ZodString>;
+    datasetTtlSeconds: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    datasetStoreDir: z.ZodOptional<z.ZodString>;
+    loadLimit: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    maxConcurrentRequests: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    retryMaxAttempts: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    retryBaseDelayMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    referenceCacheTtlSeconds: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    requestTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    searchPollTimeoutMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    searchPollIntervalMs: z.ZodDefault<z.ZodCoercedNumber<unknown>>;
+    allowPrivateIps: z.ZodPipe<z.ZodDefault<z.ZodEnum<{
+        true: "true";
+        false: "false";
+    }>>, z.ZodTransform<boolean, "true" | "false">>;
+}, z.core.$strip>;
+export type ServerConfig = z.infer<typeof ServerConfigSchema>;
+export declare function getServerConfig(): ServerConfig;
+/** Test-only — reset the lazy cache between suites. */
+export declare function resetServerConfig(): void;
+export {};
+//# sourceMappingURL=server-config.d.ts.map

package/dist/config/server-config.d.ts.map

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package/dist/config/server-config.js

@@ -0,0 +1,128 @@
+/**
+ * @fileoverview Server-specific configuration for brapi-mcp-server. Covers
+ * default connection details, HTTP client behavior (timeouts, retries,
+ * concurrency), async-search polling, dataset lifecycle, and reference-data
+ * cache tuning. Lazy-parsed via `parseEnvConfig` so env-var names appear in
+ * validation errors.
+ *
+ * @module config/server-config
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
+const ServerConfigSchema = z.object({
+    defaultBaseUrl: z
+        .string()
+        .url()
+        .optional()
+        .describe('Default BrAPI v2 base URL if no connection is opened via brapi_connect.'),
+    defaultUsername: z
+        .string()
+        .optional()
+        .describe('Default SGN-family username for session-token auth.'),
+    defaultPassword: z
+        .string()
+        .optional()
+        .describe('Default SGN-family password for session-token auth.'),
+    defaultOauthClientId: z
+        .string()
+        .optional()
+        .describe('Default OAuth2 client ID (e.g. CGIAR-family servers).'),
+    defaultOauthClientSecret: z.string().optional().describe('Default OAuth2 client secret.'),
+    defaultApiKey: z.string().optional().describe('Default static API key.'),
+    defaultApiKeyHeader: z
+        .string()
+        .default('Authorization')
+        .describe('Header name to carry the static API key.'),
+    datasetTtlSeconds: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(86_400)
+        .describe('TTL for datasets held in DatasetStore (seconds).'),
+    datasetStoreDir: z
+        .string()
+        .optional()
+        .describe('Filesystem path for DatasetStore payloads when filesystem storage is active.'),
+    loadLimit: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(200)
+        .describe('Default row cap returned in-context before spilling to DatasetStore.'),
+    maxConcurrentRequests: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(4)
+        .describe('Per-connection concurrency cap for parallel upstream fan-out.'),
+    retryMaxAttempts: z.coerce
+        .number()
+        .int()
+        .min(0)
+        .default(3)
+        .describe('Max retries on 429/5xx before surfacing.'),
+    retryBaseDelayMs: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(500)
+        .describe('Base delay for exponential backoff in retry.'),
+    referenceCacheTtlSeconds: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(3_600)
+        .describe('TTL for ReferenceDataCache entries (programs, trials, locations, crops).'),
+    requestTimeoutMs: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(30_000)
+        .describe('Per-request HTTP timeout.'),
+    searchPollTimeoutMs: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(60_000)
+        .describe('Total wait budget for async /search/{noun}/{id} polling.'),
+    searchPollIntervalMs: z.coerce
+        .number()
+        .int()
+        .positive()
+        .default(1_000)
+        .describe('Poll interval between async-search status checks.'),
+    allowPrivateIps: z
+        .enum(['true', 'false'])
+        .default('false')
+        .transform((v) => v === 'true')
+        .describe('Allow connecting to RFC 1918 / loopback targets. Dev-only.'),
+});
+let _config;
+export function getServerConfig() {
+    _config ??= parseEnvConfig(ServerConfigSchema, {
+        defaultBaseUrl: 'BRAPI_DEFAULT_BASE_URL',
+        defaultUsername: 'BRAPI_DEFAULT_USERNAME',
+        defaultPassword: 'BRAPI_DEFAULT_PASSWORD',
+        defaultOauthClientId: 'BRAPI_DEFAULT_OAUTH_CLIENT_ID',
+        defaultOauthClientSecret: 'BRAPI_DEFAULT_OAUTH_CLIENT_SECRET',
+        defaultApiKey: 'BRAPI_DEFAULT_API_KEY',
+        defaultApiKeyHeader: 'BRAPI_DEFAULT_API_KEY_HEADER',
+        datasetTtlSeconds: 'BRAPI_DATASET_TTL_SECONDS',
+        datasetStoreDir: 'BRAPI_DATASET_STORE_DIR',
+        loadLimit: 'BRAPI_LOAD_LIMIT',
+        maxConcurrentRequests: 'BRAPI_MAX_CONCURRENT_REQUESTS',
+        retryMaxAttempts: 'BRAPI_RETRY_MAX_ATTEMPTS',
+        retryBaseDelayMs: 'BRAPI_RETRY_BASE_DELAY_MS',
+        referenceCacheTtlSeconds: 'BRAPI_REFERENCE_CACHE_TTL_SECONDS',
+        requestTimeoutMs: 'BRAPI_REQUEST_TIMEOUT_MS',
+        searchPollTimeoutMs: 'BRAPI_SEARCH_POLL_TIMEOUT_MS',
+        searchPollIntervalMs: 'BRAPI_SEARCH_POLL_INTERVAL_MS',
+        allowPrivateIps: 'BRAPI_ALLOW_PRIVATE_IPS',
+    });
+    return _config;
+}
+/** Test-only — reset the lazy cache between suites. */
+export function resetServerConfig() {
+    _config = undefined;
+}
+//# sourceMappingURL=server-config.js.map

package/dist/config/server-config.js.map

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package/dist/index.d.ts

@@ -0,0 +1,10 @@
+#!/usr/bin/env node
+/**
+ * @fileoverview brapi-mcp-server MCP server entry point. Registers the MCP
+ * surface (tools/resources/prompts) and initializes domain services in
+ * `setup()` before the transport starts.
+ *
+ * @module index
+ */
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../src/index.ts"],"names":[],"mappings":";AACA;;;;;;GAMG"}

package/dist/index.js

@@ -0,0 +1,85 @@
+#!/usr/bin/env node
+/**
+ * @fileoverview brapi-mcp-server MCP server entry point. Registers the MCP
+ * surface (tools/resources/prompts) and initializes domain services in
+ * `setup()` before the transport starts.
+ *
+ * @module index
+ */
+import { createApp } from '@cyanheads/mcp-ts-core';
+import { getServerConfig } from './config/server-config.js';
+import { initBrapiClient } from './services/brapi-client/index.js';
+import { initCapabilityRegistry } from './services/capability-registry/index.js';
+import { initDatasetStore } from './services/dataset-store/index.js';
+import { initOntologyResolver } from './services/ontology-resolver/index.js';
+import { initReferenceDataCache } from './services/reference-data-cache/index.js';
+import { initServerRegistry } from './services/server-registry/index.js';
+import { brapiEdaStudy } from './mcp-server/prompts/definitions/brapi-eda-study.prompt.js';
+import { brapiMetaAnalysis } from './mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js';
+import { brapiCallsResource } from './mcp-server/resources/definitions/brapi-calls.resource.js';
+import { brapiDatasetResource } from './mcp-server/resources/definitions/brapi-dataset.resource.js';
+import { brapiFiltersResource } from './mcp-server/resources/definitions/brapi-filters.resource.js';
+import { brapiGermplasmResource } from './mcp-server/resources/definitions/brapi-germplasm.resource.js';
+import { brapiServerInfoResource } from './mcp-server/resources/definitions/brapi-server-info.resource.js';
+import { brapiStudyResource } from './mcp-server/resources/definitions/brapi-study.resource.js';
+import { brapiConnect } from './mcp-server/tools/definitions/brapi-connect.tool.js';
+import { brapiDescribeFilters } from './mcp-server/tools/definitions/brapi-describe-filters.tool.js';
+import { brapiFindGenotypeCalls } from './mcp-server/tools/definitions/brapi-find-genotype-calls.tool.js';
+import { brapiFindGermplasm } from './mcp-server/tools/definitions/brapi-find-germplasm.tool.js';
+import { brapiFindImages } from './mcp-server/tools/definitions/brapi-find-images.tool.js';
+import { brapiFindLocations } from './mcp-server/tools/definitions/brapi-find-locations.tool.js';
+import { brapiFindObservations } from './mcp-server/tools/definitions/brapi-find-observations.tool.js';
+import { brapiFindStudies } from './mcp-server/tools/definitions/brapi-find-studies.tool.js';
+import { brapiFindVariables } from './mcp-server/tools/definitions/brapi-find-variables.tool.js';
+import { brapiFindVariants } from './mcp-server/tools/definitions/brapi-find-variants.tool.js';
+import { brapiGetGermplasm } from './mcp-server/tools/definitions/brapi-get-germplasm.tool.js';
+import { brapiGetImage } from './mcp-server/tools/definitions/brapi-get-image.tool.js';
+import { brapiGetStudy } from './mcp-server/tools/definitions/brapi-get-study.tool.js';
+import { brapiManageDataset } from './mcp-server/tools/definitions/brapi-manage-dataset.tool.js';
+import { brapiRawGet } from './mcp-server/tools/definitions/brapi-raw-get.tool.js';
+import { brapiRawSearch } from './mcp-server/tools/definitions/brapi-raw-search.tool.js';
+import { brapiServerInfo } from './mcp-server/tools/definitions/brapi-server-info.tool.js';
+import { brapiSubmitObservations } from './mcp-server/tools/definitions/brapi-submit-observations.tool.js';
+import { brapiWalkPedigree } from './mcp-server/tools/definitions/brapi-walk-pedigree.tool.js';
+await createApp({
+    tools: [
+        brapiConnect,
+        brapiServerInfo,
+        brapiDescribeFilters,
+        brapiFindStudies,
+        brapiGetStudy,
+        brapiFindGermplasm,
+        brapiGetGermplasm,
+        brapiWalkPedigree,
+        brapiFindVariables,
+        brapiFindObservations,
+        brapiFindImages,
+        brapiGetImage,
+        brapiFindLocations,
+        brapiFindVariants,
+        brapiFindGenotypeCalls,
+        brapiManageDataset,
+        brapiSubmitObservations,
+        brapiRawGet,
+        brapiRawSearch,
+    ],
+    resources: [
+        brapiServerInfoResource,
+        brapiCallsResource,
+        brapiStudyResource,
+        brapiGermplasmResource,
+        brapiDatasetResource,
+        brapiFiltersResource,
+    ],
+    prompts: [brapiEdaStudy, brapiMetaAnalysis],
+    setup() {
+        const serverConfig = getServerConfig();
+        initBrapiClient(serverConfig);
+        initCapabilityRegistry(serverConfig);
+        initReferenceDataCache(serverConfig);
+        initDatasetStore(serverConfig);
+        initServerRegistry(serverConfig);
+        initOntologyResolver();
+    },
+});
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.d.ts

@@ -0,0 +1,14 @@
+/**
+ * @fileoverview `brapi_eda_study` — exploratory-data-analysis playbook for a
+ * single BrAPI study. Walks the agent through structure, variables, coverage,
+ * outliers, and missing-data checks using the curated `brapi_*` tool surface.
+ * Pure prompt template: no Context, no auth, no side effects.
+ *
+ * @module mcp-server/prompts/definitions/brapi-eda-study.prompt
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const brapiEdaStudy: import("@cyanheads/mcp-ts-core").PromptDefinition<z.ZodObject<{
+    studyDbId: z.ZodString;
+    alias: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>>;
+//# sourceMappingURL=brapi-eda-study.prompt.d.ts.map

package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.d.ts.map

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package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.js

@@ -0,0 +1,75 @@
+/**
+ * @fileoverview `brapi_eda_study` — exploratory-data-analysis playbook for a
+ * single BrAPI study. Walks the agent through structure, variables, coverage,
+ * outliers, and missing-data checks using the curated `brapi_*` tool surface.
+ * Pure prompt template: no Context, no auth, no side effects.
+ *
+ * @module mcp-server/prompts/definitions/brapi-eda-study.prompt
+ */
+import { prompt, z } from '@cyanheads/mcp-ts-core';
+export const brapiEdaStudy = prompt('brapi_eda_study', {
+    description: 'Run an exploratory-data-analysis pass over a single BrAPI study — structure, variables, coverage, outliers, missing data — using the curated brapi_* tools.',
+    args: z.object({
+        studyDbId: z
+            .string()
+            .min(1)
+            .describe('Target studyDbId. Locate via brapi_find_studies if unknown.'),
+        alias: z
+            .string()
+            .regex(/^[a-zA-Z0-9_-]+$/)
+            .optional()
+            .describe('Connection alias registered via brapi_connect. Omit to use the default connection.'),
+    }),
+    generate: (args) => {
+        const aliasArg = args.alias ? `, alias: "${args.alias}"` : '';
+        const text = [
+            `You are running an exploratory data analysis (EDA) on BrAPI study \`${args.studyDbId}\`. Work through the steps below and produce a written report at the end. Use the curated \`brapi_*\` tools — do not hand-roll HTTP. If a step requires a capability the server does not advertise, note the gap and continue.`,
+            '',
+            '## Step 1 — Orient',
+            `1. Call \`brapi_get_study\` with \`studyDbId: "${args.studyDbId}"${aliasArg}\` to pull the study record, resolved program/trial/location, and companion counts (\`observationCount\`, \`observationUnitCount\`, \`variableCount\`).`,
+            '2. Note the season(s), crop, and active state. Capture the three companion counts — they bound everything that follows.',
+            '',
+            '## Step 2 — Variables',
+            `1. Call \`brapi_find_variables\` with \`studies: ["${args.studyDbId}"]${aliasArg}\` to enumerate the observation variables measured in this study.`,
+            '2. For each variable record the trait name, trait class, scale data type (numerical / categorical / date / text), and unit/scale name.',
+            '3. Group variables by trait class and by scale data type — the breakdown drives which downstream checks make sense (numerical → outlier checks; categorical → distribution checks).',
+            '',
+            '## Step 3 — Observation coverage',
+            `1. Call \`brapi_find_observations\` with \`studies: ["${args.studyDbId}"]${aliasArg}\` and a \`loadLimit\` large enough to materialize the full study in one shot if \`observationCount\` from Step 1 fits, otherwise spill to a dataset and read it back via \`brapi_manage_dataset\` (mode: \`load\`).`,
+            '2. From the response `distributions`, capture: observations per variable, observations per germplasm, observations per observation level (plot / plant / field), and observations per season.',
+            '3. Compute coverage = `observationCount` ÷ (`observationUnitCount` × `variableCount`). Anything materially below 1.0 implies missing measurements.',
+            '',
+            '## Step 4 — Missing data',
+            '1. From the rows pulled in Step 3, count observations with `value == null`, `value == ""`, or values matching the unknown sentinel from the variable\'s scale (e.g. `.`, `NA`, `999`).',
+            '2. Cross-tab missing-rate by variable and by germplasm. Surface the top-3 worst offenders on each axis.',
+            '',
+            '## Step 5 — Outliers (numerical variables only)',
+            '1. For each numerical variable, parse `value` as a number (skip non-numeric).',
+            '2. Compute median and IQR. Flag values outside [Q1 − 1.5·IQR, Q3 + 1.5·IQR].',
+            "3. Cross-reference outliers with the scale's declared min/max if present — values outside the scale range are data-entry errors, values inside but outside IQR are biological outliers worth a second look.",
+            '',
+            '## Step 6 — Pedigree context (optional)',
+            `1. Pick the top-5 germplasm by observation count from Step 3. Call \`brapi_walk_pedigree\` with \`germplasmDbIds: [...]\`, \`direction: "ancestors"\`, \`maxDepth: 2${aliasArg}\` to surface immediate parentage.`,
+            '2. Note any common ancestors — they may explain trait covariance.',
+            '',
+            '## Report',
+            'Produce a markdown report with the following sections:',
+            '1. **Study summary** — name, crop, seasons, location, program, observation/unit/variable counts.',
+            '2. **Variables** — table grouped by trait class with scale type and unit.',
+            '3. **Coverage** — overall coverage ratio plus the per-variable and per-germplasm distributions.',
+            '4. **Missing data** — top-3 worst variables and germplasm by missing rate.',
+            '5. **Outliers** — per-variable outlier list (DbId, value, reason: out-of-range vs IQR).',
+            '6. **Pedigree notes** — common ancestors among top-observed germplasm.',
+            '7. **Recommended next steps** — concrete follow-ups (e.g. "re-measure variable X on germplasm Y", "expand pedigree walk to depth 4 on accession Z").',
+            '',
+            'Be honest about gaps — if the server lacks `/ontologies` and trait classes are sparse, say so. If `observationCount` is zero, stop after Step 1 and report that the study has no recorded observations yet.',
+        ].join('\n');
+        return [
+            {
+                role: 'user',
+                content: { type: 'text', text },
+            },
+        ];
+    },
+});
+//# sourceMappingURL=brapi-eda-study.prompt.js.map

package/dist/mcp-server/prompts/definitions/brapi-eda-study.prompt.js.map

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package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.d.ts

@@ -0,0 +1,16 @@
+/**
+ * @fileoverview `brapi_meta_analysis` — cross-study meta-analysis playbook.
+ * Given a germplasm set and a target trait, walks the agent through ontology
+ * resolution, study discovery, observation pull, harmonization, and
+ * across-study summarization using the curated `brapi_*` tool surface. Pure
+ * prompt template: no Context, no auth, no side effects.
+ *
+ * @module mcp-server/prompts/definitions/brapi-meta-analysis.prompt
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const brapiMetaAnalysis: import("@cyanheads/mcp-ts-core").PromptDefinition<z.ZodObject<{
+    germplasmDbIds: z.ZodString;
+    traitName: z.ZodString;
+    alias: z.ZodOptional<z.ZodString>;
+}, z.core.$strip>>;
+//# sourceMappingURL=brapi-meta-analysis.prompt.d.ts.map

package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.d.ts.map

@@ -0,0 +1 @@
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package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js

@@ -0,0 +1,109 @@
+/**
+ * @fileoverview `brapi_meta_analysis` — cross-study meta-analysis playbook.
+ * Given a germplasm set and a target trait, walks the agent through ontology
+ * resolution, study discovery, observation pull, harmonization, and
+ * across-study summarization using the curated `brapi_*` tool surface. Pure
+ * prompt template: no Context, no auth, no side effects.
+ *
+ * @module mcp-server/prompts/definitions/brapi-meta-analysis.prompt
+ */
+import { prompt, z } from '@cyanheads/mcp-ts-core';
+export const brapiMetaAnalysis = prompt('brapi_meta_analysis', {
+    description: 'Cross-study meta-analysis playbook for a germplasm × trait combination — resolve trait, find studies, pull observations, harmonize scales, summarize across studies.',
+    args: z.object({
+        germplasmDbIds: z
+            .string()
+            .min(1)
+            .describe('Comma-separated germplasmDbIds (e.g. "germplasm-1,germplasm-2"). The meta-analysis will collect every observation of the target trait on these germplasm across all reachable studies.'),
+        traitName: z
+            .string()
+            .min(1)
+            .describe('Target trait name or free-text query — e.g. "dry matter content", "Plant height". The agent will resolve it to one or more observation variables via brapi_find_variables.'),
+        alias: z
+            .string()
+            .regex(/^[a-zA-Z0-9_-]+$/)
+            .optional()
+            .describe('Connection alias registered via brapi_connect. Omit to use the default connection. For multi-server meta-analyses, run this prompt once per registered alias and merge.'),
+    }),
+    generate: (args) => {
+        const aliasArg = args.alias ? `, alias: "${args.alias}"` : '';
+        const ids = args.germplasmDbIds
+            .split(',')
+            .map((id) => id.trim())
+            .filter((id) => id.length > 0);
+        const idsLiteral = JSON.stringify(ids);
+        const text = [
+            `You are running a cross-study meta-analysis on the **${args.traitName}** trait across ${ids.length} germplasm: ${ids.map((id) => `\`${id}\``).join(', ')}. Use the curated \`brapi_*\` tools throughout. Reproducibility matters — record every dataset handle and query you generate.`,
+            '',
+            '## Step 1 — Resolve the trait to one or more observation variables',
+            `1. Call \`brapi_find_variables\` with \`text: "${args.traitName}"${aliasArg}\` to score candidates via the OntologyResolver.`,
+            '2. Inspect `ontologyCandidates`. If exactly one candidate has an unambiguous PUI / trait name match, use it. If multiple variables represent the same biological trait (e.g. "Dry Matter %" measured by gravimetric vs NIR methods), keep all of them and note the method differences — you will harmonize later.',
+            '3. Record the resulting `observationVariableDbId[]` and the scale `dataType` and `scaleName` for each. Numeric scales can be averaged across studies; categorical scales need a mapping table before pooling.',
+            '',
+            '## Step 2 — Discover studies that measured the trait on the target germplasm',
+            `1. Call \`brapi_find_observations\` with \`germplasm: ${idsLiteral}\` and \`variables: [<resolved variable DbIds from Step 1>]\`${aliasArg}, \`loadLimit: 200\`.`,
+            '2. From `distributions.studyName`, capture the distinct studies returning observations. If `hasMore` is true and a `dataset` handle is returned, page through with `brapi_manage_dataset` (mode: `load`) to materialize the full set.',
+            '3. For each study, call `brapi_get_study` to capture program, location, season, and trial context — these are the moderators in the meta-analysis.',
+            '',
+            '## Step 3 — Build the per-observation table',
+            'For each observation row, capture:',
+            '',
+            '| Column | Source |',
+            '|:-------|:-------|',
+            '| `germplasmDbId` / `germplasmName` | observation row |',
+            '| `studyDbId` / `studyName` | observation row + Step 2 |',
+            '| `season` | observation row |',
+            '| `locationDbId` / `locationName` | study record from Step 2 |',
+            '| `programDbId` / `programName` | study record from Step 2 |',
+            '| `observationVariableDbId` / `observationVariableName` | observation row |',
+            '| `methodName`, `scaleName`, `dataType` | variable record from Step 1 |',
+            '| `value` (raw) | observation row |',
+            '| `value_num` (parsed) | parse `value` as number for numeric scales |',
+            '| `observationTimeStamp` | observation row |',
+            '',
+            '## Step 4 — Harmonize',
+            '1. **Numeric scales** — confirm all observations use the same unit. If multiple scales appear (e.g. percent vs decimal fraction), normalize to a single canonical unit and document the conversion factor.',
+            "2. **Categorical scales** — build an explicit mapping table from each scale's category values to a shared ordinal or nominal scheme. Drop observations that cannot be mapped and report the count.",
+            '3. **Method differences** — note whether different `methodName` values are pooled together. If methods are biologically distinct (e.g. visual vs instrumented), keep them as separate strata in the summary, not merged.',
+            '',
+            '## Step 5 — Per-germplasm × per-study summary',
+            'Compute a wide table indexed by `germplasmDbId × studyDbId`:',
+            '',
+            '- Numeric variables: `n`, `mean`, `sd`, `min`, `max`, `cv = sd / mean`.',
+            '- Categorical variables: mode, modal-frequency, count-per-category.',
+            '',
+            'Flag cells where `n < 3` (insufficient replication) and cells with `cv > 0.30` (high within-study variability).',
+            '',
+            '## Step 6 — Across-study meta-summary',
+            'For each germplasm, summarize across studies:',
+            '',
+            "- **Numeric:** unweighted across-study mean, between-study variance (Cochran's Q proxy), grand min and max, study count.",
+            '- **Categorical:** dominant category and the share of studies in which that category was modal.',
+            '',
+            'Identify germplasm with high between-study variance (`Q proxy / mean^2 > 0.05`) — those are the candidates for genotype × environment interaction follow-up.',
+            '',
+            '## Step 7 — Pedigree side-quest',
+            `Optional: call \`brapi_walk_pedigree\` with \`germplasmDbIds: ${idsLiteral}\`, \`direction: "ancestors"\`, \`maxDepth: 2${aliasArg}\` to surface common parents. If the meta-analysis germplasm share a parent and exhibit similar trait values, that supports a heritability story; if they diverge, environment likely dominates.`,
+            '',
+            '## Report',
+            'Produce a markdown report with the following sections:',
+            '1. **Inputs** — verbatim trait name + germplasm IDs as supplied.',
+            '2. **Variable resolution** — the variable(s) selected and why; any ambiguity left unresolved.',
+            '3. **Studies** — table of contributing studies with program/location/season.',
+            '4. **Harmonization log** — every unit conversion, scale mapping, and method-stratification decision.',
+            '5. **Per-germplasm × per-study table** — Step 5 output.',
+            '6. **Across-study summary** — Step 6 output, sorted by between-study variance descending.',
+            '7. **Pedigree notes** — Step 7 if you ran it.',
+            '8. **Caveats** — missing data rates, dropped observations, sample-size warnings, capability gaps from the server (e.g. ontology endpoint missing).',
+            '',
+            'Reproducibility is non-negotiable: cite the dataset handle returned by every `find_*` call so a future agent can re-run with the same upstream snapshot.',
+        ].join('\n');
+        return [
+            {
+                role: 'user',
+                content: { type: 'text', text },
+            },
+        ];
+    },
+});
+//# sourceMappingURL=brapi-meta-analysis.prompt.js.map

package/dist/mcp-server/prompts/definitions/brapi-meta-analysis.prompt.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts

@@ -0,0 +1,11 @@
+/**
+ * @fileoverview `brapi://calls` — capability profile (raw `/calls` data) for
+ * the default connection. Useful for clients that want the full descriptor
+ * map without the orientation-envelope wrapping.
+ *
+ * @module mcp-server/resources/definitions/brapi-calls.resource
+ */
+export declare const brapiCallsResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<import("zod").ZodObject<Readonly<{
+    [k: string]: import("zod/v4/core").$ZodType<unknown, unknown, import("zod/v4/core").$ZodTypeInternals<unknown, unknown>>;
+}>, import("zod/v4/core").$strip>, undefined, undefined>;
+//# sourceMappingURL=brapi-calls.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-calls.resource.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"brapi-calls.resource.d.ts","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-calls.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAuBH,eAAO,MAAM,kBAAkB;;wDAkB7B,CAAC"}

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js

@@ -0,0 +1,46 @@
+/**
+ * @fileoverview `brapi://calls` — capability profile (raw `/calls` data) for
+ * the default connection. Useful for clients that want the full descriptor
+ * map without the orientation-envelope wrapping.
+ *
+ * @module mcp-server/resources/definitions/brapi-calls.resource
+ */
+import { resource } from '@cyanheads/mcp-ts-core';
+import { getCapabilityRegistry } from '../../../services/capability-registry/index.js';
+import { DEFAULT_ALIAS, getServerRegistry } from '../../../services/server-registry/index.js';
+async function loadCallsProfile(ctx) {
+    const registry = getServerRegistry();
+    const capabilities = getCapabilityRegistry();
+    const connection = await registry.get(ctx, DEFAULT_ALIAS);
+    const lookup = {};
+    if (connection.resolvedAuth)
+        lookup.auth = connection.resolvedAuth;
+    const profile = await capabilities.profile(connection.baseUrl, ctx, lookup);
+    return {
+        alias: connection.alias,
+        baseUrl: connection.baseUrl,
+        server: profile.server,
+        crops: profile.crops,
+        supported: profile.supported,
+        fetchedAt: profile.fetchedAt,
+    };
+}
+export const brapiCallsResource = resource('brapi://calls', {
+    name: 'brapi-calls',
+    title: 'BrAPI capability profile',
+    description: 'Capability profile for the default BrAPI connection — supported services, their HTTP methods, declared versions, and crops list. Mirrors what /serverinfo + /calls returned at the last load.',
+    mimeType: 'application/json',
+    handler(_params, ctx) {
+        return loadCallsProfile(ctx);
+    },
+    list: () => ({
+        resources: [
+            {
+                uri: 'brapi://calls',
+                name: 'BrAPI capability profile',
+                mimeType: 'application/json',
+            },
+        ],
+    }),
+});
+//# sourceMappingURL=brapi-calls.resource.js.map

package/dist/mcp-server/resources/definitions/brapi-calls.resource.js.map

@@ -0,0 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-dataset.resource.d.ts

@@ -0,0 +1,13 @@
+/**
+ * @fileoverview `brapi://dataset/{datasetId}` — metadata + provenance for a
+ * persisted dataset (rows omitted; use `brapi_manage_dataset` mode `load` to
+ * page through rows). Dataset IDs are unbounded and tenant-scoped — clients
+ * obtain them from a `find_*` tool's spillover handle, then read this URI.
+ *
+ * @module mcp-server/resources/definitions/brapi-dataset.resource
+ */
+import { z } from '@cyanheads/mcp-ts-core';
+export declare const brapiDatasetResource: import("@cyanheads/mcp-ts-core").ResourceDefinition<z.ZodObject<{
+    datasetId: z.ZodString;
+}, z.core.$strip>, undefined, undefined>;
+//# sourceMappingURL=brapi-dataset.resource.d.ts.map

package/dist/mcp-server/resources/definitions/brapi-dataset.resource.d.ts.map

@@ -0,0 +1 @@
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