@cyanheads/brapi-mcp-server 0.4.11 → 0.4.13

package/changelog/0.4.x/0.4.12.md

@@ -0,0 +1,29 @@
+---
+summary: "Built-in alias registry — `cassava`, `sweetpotato`, `wheat`, and `breedbase` resolve out-of-the-box without env vars; orientation envelope now carries CC-BY attribution metadata."
+breaking: false
+---
+
+# 0.4.12 — 2026-05-04
+
+`brapi_connect` now ships with a curated registry of public BrAPI v2 endpoints, so agents can call `brapi_connect({ alias: 'cassava' })` (or `sweetpotato`, `wheat`, `breedbase`) on a fresh deployment without any env-var setup. Each builtin was probed against the live upstream surface — anonymous reads return real data and the standard `/studies`, `/germplasm`, `/variables` endpoints respond with non-trivial totals. Two servers that brapi.org/servers still lists as no-auth (`musabase.org`, `solgenomics.net`) actually require login on every endpoint and are intentionally absent.
+
+## Added
+
+- **Built-in known-server registry** at `src/config/builtin-aliases.ts`. Frozen list with attribution metadata (license, citation, homepage, demo flag). Resolves between per-alias env vars and `BRAPI_DEFAULT_*` so operator overrides still win and credentialed connections still work as before.
+- **`attribution` block in the orientation envelope** — when a connection comes from a builtin, the envelope returned by `brapi_connect` and `brapi_server_info` includes `{ license, citation, homepage, isDemo? }`. CC-BY attribution propagates to the agent automatically; the formatted text output now renders an `## Attribution` section. Absent for custom env-only or agent-passed connections.
+- **`BRAPI_BUILTIN_ALIASES_DISABLED`** opt-out env var. Comma-separated alias names (case-insensitive, whitespace-tolerant) remove specific builtins from resolution and discovery for deployments that prefer a stripped surface.
+- **`origin: 'env' | 'builtin'`** field on `DiscoveredAlias`. The connect tool description now splits the two sources into separate sentences so agents can tell which aliases ship out-of-the-box vs which the operator pre-wired.
+
+## Changed
+
+- **`resolveConnectInput` precedence is four layers** (was three): agent input → per-alias env → builtin registry → default env. When the baseUrl comes from a builtin, `BRAPI_DEFAULT_*` credentials are no longer layered on top — those belong to the default server, not whatever upstream the builtin happens to point at. Per-alias credentials still apply.
+- **README** documents the new precedence, the four shipped aliases, override behavior (`BRAPI_<ALIAS>_BASE_URL` repoints, `BRAPI_<ALIAS>_USERNAME`+`_PASSWORD` attaches auth), and the opt-out env var.
+
+## Fixed
+
+- **`brapi_find_studies` and `brapi_get_study` tolerate `seasons: [null]`** — the breedbase.org demo deployment serves studies with a literal null inside the seasons array, which previously caused Zod to reject the entire response. Inner element type is now `string \| null`; the format renderers and distribution computation skip null entries. New sparse-payload test case covers the breedbase shape.
+
+## Notes
+
+- Hosted-deployment migration: operators currently setting `BRAPI_CASSAVA_BASE_URL=https://cassavabase.org/brapi/v2` can drop that env var — the builtin covers it. `BRAPI_CASSAVA_USERNAME` / `_PASSWORD` (if set for write access) continue to work unchanged.
+- Each Breedbase instance has its own user table — no SSO across `cassavabase.org`, `sweetpotatobase.org`, `wheat.triticeaetoolbox.org`. Write access still requires separate registration on each upstream.

package/changelog/0.4.x/0.4.13.md

@@ -0,0 +1,42 @@
+---
+summary: "Built-in alias rename — source-prefixed handles (`bti-*`, `t3-*`); adds T3/Oat and T3/Barley; fixes hyphenated-builtin env shadow."
+breaking: false
+---
+
+# 0.4.13 — 2026-05-04
+
+Source-prefixed alias rename across the built-in registry, plus two new T3 small-grains servers. Tool schemas refresh on next connect, so agents reading the current connect tool description pick up the new handles automatically. Operators with per-alias credential env vars (e.g. `BRAPI_CASSAVA_USERNAME`) need to rename to the new prefix (`BRAPI_BTI_CASSAVA_USERNAME`) — see Migration below.
+
+## Added
+
+- **`t3-oat` and `t3-barley` built-ins** — Triticeae Toolbox (T3) hosts three sibling Breedbase instances at `*.triticeaetoolbox.org`; only wheat shipped before. Live probes confirm anonymous reads return real data: T3/Oat advertises 2,564 studies / 59,780 germplasm / 288 variables, T3/Barley 1,574 / 63,859 / 208. Same Breedbase platform underneath, same CC-BY posture, same Morales et al. 2022 citation as the existing entries.
+
+## Changed
+
+- **Built-in aliases renamed to source-prefixed handles** so the hosting source is visible at the call site:
+
+  | Before | After |
+  |:-------|:------|
+  | `cassava` | `bti-cassava` |
+  | `sweetpotato` | `bti-sweetpotato` |
+  | `wheat` | `t3-wheat` |
+  | `breedbase` | `bti-breedbase-demo` |
+
+  Tool input schema is unchanged (alias is still a free-form `z.string().regex(...)`), and the connect tool description lists current builtins dynamically — fresh agent sessions read the new handles and use them. Custom env-only aliases under the old short names (`cassava`, `sweetpotato`, `wheat`, `breedbase`) are now valid free-form names that resolve via `BRAPI_<ALIAS>_*` env vars only — they no longer shadow a built-in.
+
+## Fixed
+
+- **`discoverConfiguredAliases` reverse-maps env var keys against hyphenated builtins.** The regex extracted alias names from `BRAPI_<X>_BASE_URL` keys but couldn't tell whether an underscore in the captured group should map back to a hyphen, so an env var like `BRAPI_BTI_CASSAVA_BASE_URL` was reported as a separate `bti_cassava` alias instead of shadowing the built-in `bti-cassava`. Discovery now consults the registry's underscored-name map and uses the canonical hyphenated alias when one matches. `resolveConnectInput` was unaffected — it derives the env prefix from the alias the agent passed.
+
+## Migration
+
+Operators who attached per-alias credentials to a built-in via env vars need to rename:
+
+| Old env var | New env var |
+|:------------|:------------|
+| `BRAPI_CASSAVA_*` | `BRAPI_BTI_CASSAVA_*` |
+| `BRAPI_SWEETPOTATO_*` | `BRAPI_BTI_SWEETPOTATO_*` |
+| `BRAPI_WHEAT_*` | `BRAPI_T3_WHEAT_*` |
+| `BRAPI_BREEDBASE_*` | `BRAPI_BTI_BREEDBASE_DEMO_*` |
+
+`BRAPI_BUILTIN_ALIASES_DISABLED` values follow the same rename. Hardcoded `alias: 'cassava'` (etc.) in agent system prompts or saved scripts also need updating to the new handles.

package/dist/config/alias-credentials.d.ts

@@ -39,44 +39,56 @@ export interface ResolvedConnectInput {
     baseUrl: string;
 }
 /**
- * Layer agent input over alias env over default env. Returns the resolved
- * baseUrl + auth. Throws when no baseUrl is resolvable from any layer.
+ * Layer agent input over alias env over the builtin registry over default env.
+ * Returns the resolved baseUrl + auth. Throws when no baseUrl is resolvable
+ * from any layer.
  *
  * Precedence:
  *   1. Explicit agent input (`baseUrl`, `auth`) wins.
  *   2. Per-alias env vars (`BRAPI_<ALIAS>_*`).
- *   3. Default env vars (`BRAPI_DEFAULT_*`) — only when alias differs.
- *   4. `auth` falls through to `{ mode: 'none' }`; `baseUrl` has no fallback.
+ *   3. Built-in known-server registry — see `config/builtin-aliases.ts`.
+ *   4. Default env vars (`BRAPI_DEFAULT_*`) — only when alias differs.
+ *   5. `auth` falls through to `{ mode: 'none' }`; `baseUrl` has no fallback.
+ *
+ * When the baseUrl is satisfied by a builtin, default-env auth is NOT used —
+ * default credentials belong to the default server, not whatever upstream the
+ * builtin happens to point at. Per-alias creds still apply, since those were
+ * explicitly set for this alias.
  */
 export declare function resolveConnectInput(alias: string, agent: {
     baseUrl?: string | undefined;
     auth?: ConnectAuth | undefined;
 }, env?: NodeJS.ProcessEnv): ResolvedConnectInput;
 /**
- * Summary of an alias discovered from env vars — what the operator pre-wired
- * for this deployment. Surfaced to the LLM via the connect tool description so
- * agents can pick a shortcut without the human having to enumerate them.
+ * Summary of an alias the agent can call out-of-the-box. Either pre-wired by
+ * the operator via `BRAPI_<ALIAS>_BASE_URL` (`origin: 'env'`) or shipped in the
+ * built-in known-server registry (`origin: 'builtin'`). Surfaced to the LLM
+ * via the connect tool description so agents can pick a shortcut without the
+ * human having to enumerate them.
  */
 export interface DiscoveredAlias {
     alias: string;
     authMode: AuthMode;
     baseUrl: string;
+    origin: 'env' | 'builtin';
 }
 /**
- * Scan env for `BRAPI_<X>_BASE_URL` keys and derive the alias inventory the
- * operator has pre-configured. Each alias resolves its credential family via
- * the same logic `resolveConnectInput` uses; ambiguous families fall back to
- * `none` so the alias is still surfaced (the connect call will then raise the
- * same `ValidationError` the agent would have hit anyway).
+ * Inventory of aliases the agent can call without specifying a baseUrl. Merges
+ * env-driven entries (operator-set `BRAPI_<X>_BASE_URL`) with the built-in
+ * known-server registry. Env-set aliases win when both are present, since the
+ * resolver gives env precedence; their `origin` reflects that. Per-alias
+ * credentials still derive auth in either case, so a builtin alias with
+ * `BRAPI_<ALIAS>_USERNAME` set surfaces with the right `authMode`.
  *
  * Default-alias entries land first; the rest are alphabetical.
  */
 export declare function discoverConfiguredAliases(env?: NodeJS.ProcessEnv): DiscoveredAlias[];
 /**
  * Render the discovered alias list as a sentence appended to the connect
- * tool's description. Empty when nothing is pre-configured — the original
- * description stands alone in that case. Phrased so that absent aliases are
- * never read as restricted servers: any BrAPI v2 URL stays connectable.
+ * tool's description. Empty when nothing is configured. Splits builtins from
+ * env-driven aliases so the LLM understands which work out-of-the-box vs
+ * which the operator pre-wired. Phrased so that absent aliases are never read
+ * as restricted servers: any BrAPI v2 URL stays connectable.
  */
 export declare function formatConfiguredAliasesHint(aliases: DiscoveredAlias[]): string;
 //# sourceMappingURL=alias-credentials.d.ts.map

package/dist/config/alias-credentials.d.ts.map

@@ -1 +1 @@
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package/dist/config/alias-credentials.js

@@ -9,6 +9,7 @@
  * @module config/alias-credentials
  */
 import { validationError } from '@cyanheads/mcp-ts-core/errors';
+import { findBuiltinAlias, listBuiltinAliases } from '../config/builtin-aliases.js';
 const FIELD_SUFFIXES = [
     ['baseUrl', 'BASE_URL'],
     ['username', 'USERNAME'],
@@ -21,6 +22,7 @@ const FIELD_SUFFIXES = [
     ['oauthTokenUrl', 'OAUTH_TOKEN_URL'],
 ];
 const DEFAULT_ALIAS = 'default';
+const NONE_AUTH = { mode: 'none' };
 /** Compute the env-var prefix for an alias. `my-server` → `BRAPI_MY_SERVER_`. */
 export function aliasEnvPrefix(alias) {
     return `BRAPI_${alias.replace(/-/g, '_').toUpperCase()}_`;
@@ -81,59 +83,85 @@ export function deriveAuthFromCredentials(creds, alias) {
     return;
 }
 /**
- * Layer agent input over alias env over default env. Returns the resolved
- * baseUrl + auth. Throws when no baseUrl is resolvable from any layer.
+ * Layer agent input over alias env over the builtin registry over default env.
+ * Returns the resolved baseUrl + auth. Throws when no baseUrl is resolvable
+ * from any layer.
  *
  * Precedence:
  *   1. Explicit agent input (`baseUrl`, `auth`) wins.
  *   2. Per-alias env vars (`BRAPI_<ALIAS>_*`).
- *   3. Default env vars (`BRAPI_DEFAULT_*`) — only when alias differs.
- *   4. `auth` falls through to `{ mode: 'none' }`; `baseUrl` has no fallback.
+ *   3. Built-in known-server registry — see `config/builtin-aliases.ts`.
+ *   4. Default env vars (`BRAPI_DEFAULT_*`) — only when alias differs.
+ *   5. `auth` falls through to `{ mode: 'none' }`; `baseUrl` has no fallback.
+ *
+ * When the baseUrl is satisfied by a builtin, default-env auth is NOT used —
+ * default credentials belong to the default server, not whatever upstream the
+ * builtin happens to point at. Per-alias creds still apply, since those were
+ * explicitly set for this alias.
  */
 export function resolveConnectInput(alias, agent, env = process.env) {
     const aliasCreds = readAliasCredentials(alias, env);
     const defaultCreds = alias === DEFAULT_ALIAS ? aliasCreds : readAliasCredentials(DEFAULT_ALIAS, env);
-    const baseUrl = agent.baseUrl ?? aliasCreds.baseUrl ?? defaultCreds.baseUrl;
+    const builtin = !agent.baseUrl && !aliasCreds.baseUrl ? findBuiltinAlias(alias, env) : undefined;
+    const baseUrl = agent.baseUrl ?? aliasCreds.baseUrl ?? builtin?.baseUrl ?? defaultCreds.baseUrl;
     if (!baseUrl) {
         throw validationError(`No baseUrl provided. Pass \`baseUrl\` explicitly, or set ${aliasEnvPrefix(alias)}BASE_URL${alias === DEFAULT_ALIAS ? '' : ` or ${aliasEnvPrefix(DEFAULT_ALIAS)}BASE_URL`}.`, { alias });
     }
+    const allowDefaultAuthFallback = !builtin && alias !== DEFAULT_ALIAS;
     const auth = agent.auth ??
         deriveAuthFromCredentials(aliasCreds, alias) ??
-        (alias === DEFAULT_ALIAS
-            ? undefined
-            : deriveAuthFromCredentials(defaultCreds, DEFAULT_ALIAS)) ??
-        { mode: 'none' };
+        (allowDefaultAuthFallback
+            ? deriveAuthFromCredentials(defaultCreds, DEFAULT_ALIAS)
+            : undefined) ??
+        NONE_AUTH;
     return { baseUrl, auth };
 }
 const ALIAS_BASE_URL_PATTERN = /^BRAPI_([A-Z0-9_]+)_BASE_URL$/;
 /**
- * Scan env for `BRAPI_<X>_BASE_URL` keys and derive the alias inventory the
- * operator has pre-configured. Each alias resolves its credential family via
- * the same logic `resolveConnectInput` uses; ambiguous families fall back to
- * `none` so the alias is still surfaced (the connect call will then raise the
- * same `ValidationError` the agent would have hit anyway).
+ * Inventory of aliases the agent can call without specifying a baseUrl. Merges
+ * env-driven entries (operator-set `BRAPI_<X>_BASE_URL`) with the built-in
+ * known-server registry. Env-set aliases win when both are present, since the
+ * resolver gives env precedence; their `origin` reflects that. Per-alias
+ * credentials still derive auth in either case, so a builtin alias with
+ * `BRAPI_<ALIAS>_USERNAME` set surfaces with the right `authMode`.
  *
  * Default-alias entries land first; the rest are alphabetical.
  */
 export function discoverConfiguredAliases(env = process.env) {
     const result = [];
+    const seen = new Set();
+    const builtins = listBuiltinAliases(env);
+    // Reverse-map for hyphen → underscore env-var translation: a builtin named
+    // `bti-cassava` exposes BRAPI_BTI_CASSAVA_*, but the regex below only sees
+    // the underscored form. Without this map, an env var that shadows a
+    // hyphenated builtin would be reported as a separate `bti_cassava` alias.
+    const builtinByUnderscoredName = new Map(builtins.map((b) => [b.alias.replace(/-/g, '_'), b]));
     for (const [key, value] of Object.entries(env)) {
         const match = key.match(ALIAS_BASE_URL_PATTERN);
         const captured = match?.[1];
         if (!captured || !value)
             continue;
-        const alias = captured.toLowerCase();
+        const lowerCaptured = captured.toLowerCase();
+        const alias = builtinByUnderscoredName.get(lowerCaptured)?.alias ?? lowerCaptured;
         const creds = readAliasCredentials(alias, env);
-        let authMode = 'none';
-        try {
-            const auth = deriveAuthFromCredentials(creds, alias);
-            if (auth)
-                authMode = auth.mode;
-        }
-        catch {
-            // Ambiguous credential family — surface the alias anyway.
-        }
-        result.push({ alias, authMode, baseUrl: value });
+        result.push({
+            alias,
+            authMode: deriveModeForDiscovery(creds, alias),
+            baseUrl: value,
+            origin: 'env',
+        });
+        seen.add(alias);
+    }
+    for (const builtin of builtins) {
+        if (seen.has(builtin.alias))
+            continue;
+        const creds = readAliasCredentials(builtin.alias, env);
+        result.push({
+            alias: builtin.alias,
+            authMode: deriveModeForDiscovery(creds, builtin.alias),
+            baseUrl: builtin.baseUrl,
+            origin: 'builtin',
+        });
     }
     result.sort((a, b) => {
         if (a.alias === DEFAULT_ALIAS)
@@ -144,16 +172,37 @@ export function discoverConfiguredAliases(env = process.env) {
     });
     return result;
 }
+function deriveModeForDiscovery(creds, alias) {
+    try {
+        const auth = deriveAuthFromCredentials(creds, alias);
+        return auth?.mode ?? 'none';
+    }
+    catch {
+        // Ambiguous credential family — surface the alias as `none` so the agent
+        // still sees it; the connect call will raise the same ValidationError.
+        return 'none';
+    }
+}
 /**
  * Render the discovered alias list as a sentence appended to the connect
- * tool's description. Empty when nothing is pre-configured — the original
- * description stands alone in that case. Phrased so that absent aliases are
- * never read as restricted servers: any BrAPI v2 URL stays connectable.
+ * tool's description. Empty when nothing is configured. Splits builtins from
+ * env-driven aliases so the LLM understands which work out-of-the-box vs
+ * which the operator pre-wired. Phrased so that absent aliases are never read
+ * as restricted servers: any BrAPI v2 URL stays connectable.
  */
 export function formatConfiguredAliasesHint(aliases) {
     if (aliases.length === 0)
         return '';
-    const names = aliases.map((a) => `\`${a.alias}\``).join(', ');
-    return `Pre-configured aliases on this deployment (callable without \`baseUrl\` or \`auth\` — credentials are read from server env vars): ${names}. Aliases are shortcuts only; any other BrAPI v2 server is reachable by passing \`baseUrl\` directly.`;
+    const builtin = aliases.filter((a) => a.origin === 'builtin').map((a) => `\`${a.alias}\``);
+    const env = aliases.filter((a) => a.origin === 'env').map((a) => `\`${a.alias}\``);
+    const parts = [];
+    if (builtin.length > 0) {
+        parts.push(`Built-in known servers (callable with no \`baseUrl\` or \`auth\` — public BrAPI v2 endpoints): ${builtin.join(', ')}.`);
+    }
+    if (env.length > 0) {
+        parts.push(`Operator-configured aliases on this deployment (credentials and/or baseUrl read from server env vars): ${env.join(', ')}.`);
+    }
+    parts.push('Aliases are shortcuts only; any other BrAPI v2 server is reachable by passing `baseUrl` directly.');
+    return parts.join(' ');
 }
 //# sourceMappingURL=alias-credentials.js.map

package/dist/config/alias-credentials.js.map

@@ -1 +1 @@
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package/dist/config/builtin-aliases.d.ts

@@ -0,0 +1,51 @@
+/**
+ * @fileoverview Built-in known-server registry. Curated list of public BrAPI v2
+ * endpoints that ship as default connection aliases — operators can call
+ * `brapi_connect({ alias: 'cassava' })` (or any other entry) without setting
+ * `BRAPI_<ALIAS>_BASE_URL`. Each entry carries CC-BY attribution metadata so
+ * the orientation envelope can surface license + citation alongside the data.
+ *
+ * Override behavior: env-set `BRAPI_<ALIAS>_BASE_URL` always wins over the
+ * builtin URL — the builtin is a fallback, not a lock. Per-alias credentials
+ * (`BRAPI_<ALIAS>_USERNAME` / `_PASSWORD` / etc.) layer on top of any selected
+ * baseUrl, so write workflows still need a separate registration on each
+ * upstream instance.
+ *
+ * Opt-out: comma-separated alias names in `BRAPI_BUILTIN_ALIASES_DISABLED`
+ * remove specific builtins from resolution and discovery (matched
+ * case-insensitively).
+ *
+ * @module config/builtin-aliases
+ */
+export interface BuiltinAlias {
+    readonly alias: string;
+    readonly baseUrl: string;
+    readonly citation: string;
+    readonly cropFocus: string;
+    readonly homepage: string;
+    readonly isDemo?: boolean;
+    readonly license: 'CC-BY';
+    readonly organizationName: string;
+}
+/**
+ * Frozen registry of known public BrAPI v2 servers. Each entry was verified
+ * against the live upstream surface — anonymous reads return real data and
+ * the standard `/studies`, `/germplasm`, `/variables` endpoints respond with
+ * non-trivial totals. Servers that flipped to an auth wall (musabase,
+ * solgenomics) are intentionally absent.
+ */
+export declare const BUILTIN_ALIASES: ReadonlyArray<BuiltinAlias>;
+/**
+ * Resolve a builtin entry by alias. Case-insensitive lookup; respects the
+ * `BRAPI_BUILTIN_ALIASES_DISABLED` opt-out list. Returns `undefined` when the
+ * alias is unknown or disabled — callers fall through to the next baseUrl
+ * source (default env, then a thrown ValidationError).
+ */
+export declare function findBuiltinAlias(alias: string, env?: NodeJS.ProcessEnv): BuiltinAlias | undefined;
+/**
+ * Active builtins — the registry minus any aliases listed in
+ * `BRAPI_BUILTIN_ALIASES_DISABLED`. Used by alias discovery so the connect
+ * tool description can advertise what's available out-of-the-box.
+ */
+export declare function listBuiltinAliases(env?: NodeJS.ProcessEnv): ReadonlyArray<BuiltinAlias>;
+//# sourceMappingURL=builtin-aliases.d.ts.map

package/dist/config/builtin-aliases.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"builtin-aliases.d.ts","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAKH,MAAM,WAAW,YAAY;IAC3B,QAAQ,CAAC,KAAK,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,OAAO,EAAE,MAAM,CAAC;IACzB,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,SAAS,EAAE,MAAM,CAAC;IAC3B,QAAQ,CAAC,QAAQ,EAAE,MAAM,CAAC;IAC1B,QAAQ,CAAC,MAAM,CAAC,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,OAAO,EAAE,OAAO,CAAC;IAC1B,QAAQ,CAAC,gBAAgB,EAAE,MAAM,CAAC;CACnC;AAED;;;;;;GAMG;AACH,eAAO,MAAM,eAAe,EAAE,aAAa,CAAC,YAAY,CAwDtD,CAAC;AAmBH;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAC9B,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,YAAY,GAAG,SAAS,CAK1B;AAED;;;;GAIG;AACH,wBAAgB,kBAAkB,CAChC,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,aAAa,CAAC,YAAY,CAAC,CAI7B"}

package/dist/config/builtin-aliases.js

@@ -0,0 +1,126 @@
+/**
+ * @fileoverview Built-in known-server registry. Curated list of public BrAPI v2
+ * endpoints that ship as default connection aliases — operators can call
+ * `brapi_connect({ alias: 'cassava' })` (or any other entry) without setting
+ * `BRAPI_<ALIAS>_BASE_URL`. Each entry carries CC-BY attribution metadata so
+ * the orientation envelope can surface license + citation alongside the data.
+ *
+ * Override behavior: env-set `BRAPI_<ALIAS>_BASE_URL` always wins over the
+ * builtin URL — the builtin is a fallback, not a lock. Per-alias credentials
+ * (`BRAPI_<ALIAS>_USERNAME` / `_PASSWORD` / etc.) layer on top of any selected
+ * baseUrl, so write workflows still need a separate registration on each
+ * upstream instance.
+ *
+ * Opt-out: comma-separated alias names in `BRAPI_BUILTIN_ALIASES_DISABLED`
+ * remove specific builtins from resolution and discovery (matched
+ * case-insensitively).
+ *
+ * @module config/builtin-aliases
+ */
+const BREEDBASE_CITATION = 'Morales et al. 2022. "Breedbase: a digital ecosystem for modern plant breeding." G3 12(7): jkac078. https://doi.org/10.1093/g3journal/jkac078';
+/**
+ * Frozen registry of known public BrAPI v2 servers. Each entry was verified
+ * against the live upstream surface — anonymous reads return real data and
+ * the standard `/studies`, `/germplasm`, `/variables` endpoints respond with
+ * non-trivial totals. Servers that flipped to an auth wall (musabase,
+ * solgenomics) are intentionally absent.
+ */
+export const BUILTIN_ALIASES = Object.freeze([
+    Object.freeze({
+        alias: 'bti-cassava',
+        baseUrl: 'https://cassavabase.org/brapi/v2',
+        homepage: 'https://cassavabase.org/',
+        organizationName: 'Boyce Thompson Institute',
+        cropFocus: 'Cassava',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 'bti-sweetpotato',
+        baseUrl: 'https://sweetpotatobase.org/brapi/v2',
+        homepage: 'https://sweetpotatobase.org/',
+        organizationName: 'Boyce Thompson Institute',
+        cropFocus: 'SweetPotato',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 't3-wheat',
+        baseUrl: 'https://wheat.triticeaetoolbox.org/brapi/v2',
+        homepage: 'https://wheat.triticeaetoolbox.org/',
+        organizationName: 'Triticeae Toolbox (T3)',
+        cropFocus: 'Wheat',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 't3-oat',
+        baseUrl: 'https://oat.triticeaetoolbox.org/brapi/v2',
+        homepage: 'https://oat.triticeaetoolbox.org/',
+        organizationName: 'Triticeae Toolbox (T3)',
+        cropFocus: 'Oat',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 't3-barley',
+        baseUrl: 'https://barley.triticeaetoolbox.org/brapi/v2',
+        homepage: 'https://barley.triticeaetoolbox.org/',
+        organizationName: 'Triticeae Toolbox (T3)',
+        cropFocus: 'Barley',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+    }),
+    Object.freeze({
+        alias: 'bti-breedbase-demo',
+        baseUrl: 'https://breedbase.org/brapi/v2',
+        homepage: 'https://breedbase.org/',
+        organizationName: 'Boyce Thompson Institute',
+        cropFocus: 'Demo (sample data)',
+        license: 'CC-BY',
+        citation: BREEDBASE_CITATION,
+        isDemo: true,
+    }),
+]);
+const DISABLED_ENV_VAR = 'BRAPI_BUILTIN_ALIASES_DISABLED';
+/**
+ * Parse the comma-separated disabled list from env. Whitespace tolerant,
+ * case-insensitive — entries are lowercased to match alias keys.
+ */
+function readDisabledSet(env) {
+    const raw = env[DISABLED_ENV_VAR];
+    if (!raw)
+        return new Set();
+    const out = new Set();
+    for (const part of raw.split(',')) {
+        const trimmed = part.trim().toLowerCase();
+        if (trimmed)
+            out.add(trimmed);
+    }
+    return out;
+}
+/**
+ * Resolve a builtin entry by alias. Case-insensitive lookup; respects the
+ * `BRAPI_BUILTIN_ALIASES_DISABLED` opt-out list. Returns `undefined` when the
+ * alias is unknown or disabled — callers fall through to the next baseUrl
+ * source (default env, then a thrown ValidationError).
+ */
+export function findBuiltinAlias(alias, env = process.env) {
+    const key = alias.toLowerCase();
+    const disabled = readDisabledSet(env);
+    if (disabled.has(key))
+        return;
+    return BUILTIN_ALIASES.find((entry) => entry.alias === key);
+}
+/**
+ * Active builtins — the registry minus any aliases listed in
+ * `BRAPI_BUILTIN_ALIASES_DISABLED`. Used by alias discovery so the connect
+ * tool description can advertise what's available out-of-the-box.
+ */
+export function listBuiltinAliases(env = process.env) {
+    const disabled = readDisabledSet(env);
+    if (disabled.size === 0)
+        return BUILTIN_ALIASES;
+    return BUILTIN_ALIASES.filter((entry) => !disabled.has(entry.alias));
+}
+//# sourceMappingURL=builtin-aliases.js.map

package/dist/config/builtin-aliases.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"builtin-aliases.js","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;GAkBG;AAEH,MAAM,kBAAkB,GACtB,+IAA+I,CAAC;AAalJ;;;;;;GAMG;AACH,MAAM,CAAC,MAAM,eAAe,GAAgC,MAAM,CAAC,MAAM,CAAC;IACxE,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,aAAa;QACpB,OAAO,EAAE,kCAAkC;QAC3C,QAAQ,EAAE,0BAA0B;QACpC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,SAAS;QACpB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,iBAAiB;QACxB,OAAO,EAAE,sCAAsC;QAC/C,QAAQ,EAAE,8BAA8B;QACxC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,aAAa;QACxB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,UAAU;QACjB,OAAO,EAAE,6CAA6C;QACtD,QAAQ,EAAE,qCAAqC;QAC/C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,OAAO;QAClB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,QAAQ;QACf,OAAO,EAAE,2CAA2C;QACpD,QAAQ,EAAE,mCAAmC;QAC7C,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,KAAK;QAChB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,WAAW;QAClB,OAAO,EAAE,8CAA8C;QACvD,QAAQ,EAAE,sCAAsC;QAChD,gBAAgB,EAAE,wBAAwB;QAC1C,SAAS,EAAE,QAAQ;QACnB,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;KAC7B,CAAC;IACF,MAAM,CAAC,MAAM,CAAC;QACZ,KAAK,EAAE,oBAAoB;QAC3B,OAAO,EAAE,gCAAgC;QACzC,QAAQ,EAAE,wBAAwB;QAClC,gBAAgB,EAAE,0BAA0B;QAC5C,SAAS,EAAE,oBAAoB;QAC/B,OAAO,EAAE,OAAO;QAChB,QAAQ,EAAE,kBAAkB;QAC5B,MAAM,EAAE,IAAI;KACb,CAAC;CACH,CAAC,CAAC;AAEH,MAAM,gBAAgB,GAAG,gCAAgC,CAAC;AAE1D;;;GAGG;AACH,SAAS,eAAe,CAAC,GAAsB;IAC7C,MAAM,GAAG,GAAG,GAAG,CAAC,gBAAgB,CAAC,CAAC;IAClC,IAAI,CAAC,GAAG;QAAE,OAAO,IAAI,GAAG,EAAE,CAAC;IAC3B,MAAM,GAAG,GAAG,IAAI,GAAG,EAAU,CAAC;IAC9B,KAAK,MAAM,IAAI,IAAI,GAAG,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;QAClC,MAAM,OAAO,GAAG,IAAI,CAAC,IAAI,EAAE,CAAC,WAAW,EAAE,CAAC;QAC1C,IAAI,OAAO;YAAE,GAAG,CAAC,GAAG,CAAC,OAAO,CAAC,CAAC;IAChC,CAAC;IACD,OAAO,GAAG,CAAC;AACb,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,gBAAgB,CAC9B,KAAa,EACb,MAAyB,OAAO,CAAC,GAAG;IAEpC,MAAM,GAAG,GAAG,KAAK,CAAC,WAAW,EAAE,CAAC;IAChC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,GAAG,CAAC,GAAG,CAAC;QAAE,OAAO;IAC9B,OAAO,eAAe,CAAC,IAAI,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,KAAK,CAAC,KAAK,KAAK,GAAG,CAAC,CAAC;AAC9D,CAAC;AAED;;;;GAIG;AACH,MAAM,UAAU,kBAAkB,CAChC,MAAyB,OAAO,CAAC,GAAG;IAEpC,MAAM,QAAQ,GAAG,eAAe,CAAC,GAAG,CAAC,CAAC;IACtC,IAAI,QAAQ,CAAC,IAAI,KAAK,CAAC;QAAE,OAAO,eAAe,CAAC;IAChD,OAAO,eAAe,CAAC,MAAM,CAAC,CAAC,KAAK,EAAE,EAAE,CAAC,CAAC,QAAQ,CAAC,GAAG,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC,CAAC;AACvE,CAAC"}

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

@@ -9,7 +9,7 @@
  */
 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.',
+    description: 'Run a cross-study meta-analysis on a germplasm × trait combination — resolve trait, find studies, pull observations, harmonize scales, summarize across studies.',
     args: z.object({
         germplasmDbIds: z
             .string()
@@ -18,7 +18,7 @@ export const brapiMetaAnalysis = prompt('brapi_meta_analysis', {
         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.'),
+            .describe('Target trait name or free-text query — e.g. "dry matter content", "Plant height". Resolved to one or more observation variables via brapi_find_variables.'),
         alias: z
             .string()
             .regex(/^[a-zA-Z0-9_-]+$/)
@@ -36,7 +36,7 @@ export const brapiMetaAnalysis = prompt('brapi_meta_analysis', {
             `You are running a cross-study meta-analysis on the **${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.`,
+            `1. Call \`brapi_find_variables\` with \`text: "${args.traitName}"${aliasArg}\` to rank candidates against ontology terms.`,
             '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.',
             '',
@@ -97,7 +97,7 @@ export const brapiMetaAnalysis = prompt('brapi_meta_analysis', {
             '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.',
+            'Reproducibility is non-negotiable: cite the dataset handle returned by every `find_*` call so a future run can reproduce the same upstream snapshot.',
         ].join('\n');
         return [
             {

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

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

@@ -79,6 +79,12 @@ export declare const brapiConnect: import("@cyanheads/mcp-ts-core").ToolDefiniti
         programCount: z.ZodOptional<z.ZodNumber>;
         locationCount: z.ZodOptional<z.ZodNumber>;
     }, z.core.$strip>;
+    attribution: z.ZodOptional<z.ZodObject<{
+        homepage: z.ZodString;
+        license: z.ZodString;
+        citation: z.ZodString;
+        isDemo: z.ZodOptional<z.ZodBoolean>;
+    }, z.core.$strip>>;
     notes: z.ZodArray<z.ZodString>;
     fetchedAt: z.ZodString;
 }, z.core.$strip>, readonly [{

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

@@ -1 +1 @@
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