@cyanheads/brapi-mcp-server 0.7.13 → 0.8.0

package/changelog/0.8.x/0.8.0.md

@@ -0,0 +1,48 @@
+---
+summary: "Server-configured credentials are only sent to the base URL configured with them, and caller-supplied credentials are refused on session-less shared HTTP. The T3 built-ins are gone, auth walls fail brapi_connect with typed errors, and the orientation envelope names the finders the server supports."
+breaking: true
+security: true
+---
+
+# 0.8.0 — 2026-09-23
+
+## Added
+
+- **`nextToolSuggestions`** on the orientation envelope (`brapi_connect`, `brapi_server_info`, `brapi://server/info`) — the entry-point finders the server can serve (`brapi_find_studies`, `brapi_find_germplasm`, `brapi_find_variables`, `brapi_find_locations`, in that order), each with `args: { alias }`. A finder counts when its GET route or a POST `/search` route the active dialect doesn't disable is advertised ([#57](https://github.com/cyanheads/brapi-mcp-server/issues/57)).
+
+## Changed
+
+- **Auth walls fail `brapi_connect`** — an HTTP 401/403 on `/serverinfo` or `/calls` throws `upstream_unauthorized` (-32006) / `upstream_forbidden` (-32005) with a credentials hint and caches nothing, instead of registering an empty profile ([#52](https://github.com/cyanheads/brapi-mcp-server/issues/52)).
+- **Upstream 4xx carry an `upstream_*` reason** — 401/403/404 as `upstream_unauthorized` / `upstream_forbidden` / `upstream_not_found`, 429 as `upstream_rate_limited` (still retried), every other 4xx as `ValidationError` (-32007) `upstream_bad_request`. 408 and 425 stay `Timeout` and keep retrying ([#52](https://github.com/cyanheads/brapi-mcp-server/issues/52)).
+- **A failed `brapi_connect` registers nothing** — token exchange and a fresh capability fetch run before the connection is saved, so a failure leaves any previous registration under the alias and its cached profile intact. `ServerRegistry.register()` is now `resolve()` + `save()`.
+- **`baseUrl` with userinfo (`user:password@host`) is refused** with a `ValidationError` that does not echo the URL.
+- **`discoverConfiguredAliases`** reports the `authMode` an argument-free `brapi_connect` would resolve to under the pairing rules below, including default credentials for an alias on `BRAPI_DEFAULT_BASE_URL`.
+- **README reorganized** — one-line tool, resource, and prompt tables and a condensed capability reference; `.env.example` documents `BRAPI_<ALIAS>_DIALECT`, the `BRAPI_DEFAULT_*` credential fields, `BRAPI_BUILTIN_ALIASES_DISABLED`, and `BRAPI_COMPANION_TIMEOUT_MS`.
+
+## Removed
+
+- **Built-in aliases `t3-wheat`, `t3-oat`, `t3-barley`** — the Triticeae Toolbox hosts now require login. The registry keeps `bti-cassava`, `bti-sweetpotato`, and `bti-breedbase-demo` ([#52](https://github.com/cyanheads/brapi-mcp-server/issues/52)).
+
+## Fixed
+
+- **`brapi_describe_filters`** escapes backslashes in Description cells, so a backslash in a filter description renders literally instead of being consumed as a Markdown escape — `x\|y` and `a\*b` no longer render as `x|y` and `a*b`. Pipes in the code-span Name and Example cells are escaped too, since a bare `|` there split the row ([#55](https://github.com/cyanheads/brapi-mcp-server/issues/55)).
+- **Capability and reference-data cache keys** hash the base URL (SHA-256) instead of mapping punctuation to `-`, so servers whose URLs differ only in punctuation no longer share cached entries.
+- **Built-in attribution and the demo note** attach only when a built-in alias still points at its built-in URL.
+- **Built-in alias lookup** matches every spelling that shares the alias's `BRAPI_<ALIAS>_*` env prefix (case, `_` for `-`), including entries in `BRAPI_BUILTIN_ALIASES_DISABLED`.
+
+## Security
+
+- **Caller-supplied credentials are no longer shared across session-less callers** — on an HTTP deployment with `MCP_AUTH_MODE=none` and `BRAPI_SESSION_ISOLATION=true`, `brapi_connect` refuses caller `auth` from a request with no MCP session (`auth_session_required`, before any token exchange). Keyless connects and operator env credentials still work ([#49](https://github.com/cyanheads/brapi-mcp-server/issues/49)).
+- **Operator env credentials are only sent to the base URL configured with them** — per-alias credentials pair with `BRAPI_<ALIAS>_BASE_URL`, else the alias's enabled built-in URL; a caller `baseUrl` that differs is refused with `auth_base_url_mismatch` before any request. `BRAPI_DEFAULT_*` credentials attach only when the resolved URL is `BRAPI_DEFAULT_BASE_URL`. URLs compare after normalizing host case, default port, and trailing slashes.
+
+## Dependencies
+
+- `@types/node` ^26.5.1 → ^26.6.2
+
+## Migration
+
+- **T3 aliases** — set `BRAPI_<ALIAS>_BASE_URL` plus credentials for the host (e.g. `BRAPI_WHEAT_BASE_URL=https://wheat.triticeaetoolbox.org/brapi/v2` with `BRAPI_WHEAT_USERNAME` / `BRAPI_WHEAT_PASSWORD`), then connect with that alias.
+- **`BRAPI_DEFAULT_*` credentials** are no longer inherited by an alias whose URL points at another server — give that alias its own `BRAPI_<ALIAS>_*` credentials.
+- **Env credentials with no URL of their own** — per-alias ones without `BRAPI_<ALIAS>_BASE_URL` (including leftovers for a built-in disabled via `BRAPI_BUILTIN_ALIASES_DISABLED`), and `BRAPI_DEFAULT_*` ones without `BRAPI_DEFAULT_BASE_URL` — are refused with `alias_base_url_unset` (-32008) instead of being sent to a caller `baseUrl`; set the alias's `BASE_URL` or remove the credential variables.
+- **A caller `baseUrl` that differs from a credentialed alias's configured URL** is refused with `auth_base_url_mismatch` — omit `baseUrl`, or register the other server under a different alias.
+- **Upstream HTTP 4xx other than 401, 403, 404, 408, 425, and 429** now surface as -32007 `upstream_bad_request` — 400 was -32602, 402 was -32005, 409/423/424 were -32002, 422 is unchanged, the rest were -32600; clients routing on the code should switch to `data.reason`.

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

@@ -38,6 +38,8 @@ export interface ResolvedConnectInput {
     auth: ConnectAuth;
     baseUrl: string;
 }
+/** Recovery hint for the `auth_base_url_mismatch` refusal; shared with the `brapi_connect` contract. */
+export declare const AUTH_BASE_URL_MISMATCH_RECOVERY = "Omit `baseUrl` to connect to the server configured for this alias, or register the other server under a different alias.";
 /**
  * Layer agent input over alias env over the builtin registry over default env.
  * Returns the resolved baseUrl + auth. Throws when no baseUrl is resolvable
@@ -50,15 +52,31 @@ export interface ResolvedConnectInput {
  *   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.
+ * Env credentials only travel to the server configured alongside them:
+ * - Per-alias credentials pair with the alias's own URL: its env base URL,
+ *   else its enabled builtin URL (for `default`, `BRAPI_DEFAULT_BASE_URL`).
+ *   A caller `baseUrl` that differs from it is refused with
+ *   `auth_base_url_mismatch`. Credentials with no URL of their own pair with
+ *   nothing and are refused with `alias_base_url_unset` — they never fall
+ *   back to `BRAPI_DEFAULT_BASE_URL`. Both refusals precede any request.
+ * - Default credentials pair with `BRAPI_DEFAULT_BASE_URL` only. For another
+ *   alias they attach when the resolved URL is that one and are otherwise
+ *   left off, so auth falls through to `none`.
+ *
+ * URLs compare after normalization (host case, default port, trailing
+ * slashes). Caller-supplied `auth` bypasses env credentials entirely.
  */
 export declare function resolveConnectInput(alias: string, agent: {
     baseUrl?: string | undefined;
     auth?: ConnectAuth | undefined;
 }, env?: NodeJS.ProcessEnv): ResolvedConnectInput;
+/**
+ * True when both URLs parse, carry no userinfo, and name the same BrAPI base:
+ * scheme, host (case-insensitive), port (default port elided), path with
+ * trailing slashes dropped, query, and fragment. A URL with userinfo never
+ * matches — `brapi_connect` refuses it as a baseUrl.
+ */
+export declare function sameBaseUrl(a: string, b: string | undefined): boolean;
 /**
  * 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
@@ -76,9 +94,12 @@ export interface DiscoveredAlias {
  * 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`.
+ * resolver gives env precedence; their `origin` reflects that. `authMode` is
+ * what an argument-free `brapi_connect` for the alias resolves to, so the
+ * pairing rules apply: a builtin with `BRAPI_<ALIAS>_USERNAME` set reports
+ * `sgn`, and default credentials count only on `BRAPI_DEFAULT_BASE_URL`.
+ * Credentials with no URL of their own have nothing to connect to, so they
+ * never surface an alias.
  *
  * Default-alias entries land first; the rest are alphabetical.
  */

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

@@ -1 +1 @@
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+{"version":3,"file":"alias-credentials.d.ts","sourceRoot":"","sources":["../../src/config/alias-credentials.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAMH,OAAO,KAAK,EAAE,QAAQ,EAAE,WAAW,EAAE,MAAM,qCAAqC,CAAC;AAEjF;;;GAGG;AACH,MAAM,WAAW,gBAAgB;IAC/B,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,YAAY,CAAC,EAAE,MAAM,CAAC;IACtB,OAAO,CAAC,EAAE,MAAM,CAAC;IACjB,WAAW,CAAC,EAAE,MAAM,CAAC;IACrB,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,iBAAiB,CAAC,EAAE,MAAM,CAAC;IAC3B,aAAa,CAAC,EAAE,MAAM,CAAC;IACvB,QAAQ,CAAC,EAAE,MAAM,CAAC;IAClB,QAAQ,CAAC,EAAE,MAAM,CAAC;CACnB;AA6BD,iFAAiF;AACjF,wBAAgB,cAAc,CAAC,KAAK,EAAE,MAAM,GAAG,MAAM,CAEpD;AAED,sFAAsF;AACtF,wBAAgB,oBAAoB,CAClC,KAAK,EAAE,MAAM,EACb,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,gBAAgB,CAalB;AAED;;;;GAIG;AACH,wBAAgB,yBAAyB,CACvC,KAAK,EAAE,gBAAgB,EACvB,KAAK,EAAE,MAAM,GACZ,WAAW,GAAG,SAAS,CAwCzB;AAED,MAAM,WAAW,oBAAoB;IACnC,IAAI,EAAE,WAAW,CAAC;IAClB,OAAO,EAAE,MAAM,CAAC;CACjB;AAED,wGAAwG;AACxG,eAAO,MAAM,+BAA+B,6HACgF,CAAC;AAE7H;;;;;;;;;;;;;;;;;;;;;;;;;GAyBG;AACH,wBAAgB,mBAAmB,CACjC,KAAK,EAAE,MAAM,EACb,KAAK,EAAE;IAAE,OAAO,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;IAAC,IAAI,CAAC,EAAE,WAAW,GAAG,SAAS,CAAA;CAAE,EACvE,GAAG,GAAE,MAAM,CAAC,UAAwB,GACnC,oBAAoB,CAwDtB;AAED;;;;;GAKG;AACH,wBAAgB,WAAW,CAAC,CAAC,EAAE,MAAM,EAAE,CAAC,EAAE,MAAM,GAAG,SAAS,GAAG,OAAO,CAIrE;AAcD;;;;;;GAMG;AACH,MAAM,WAAW,eAAe;IAC9B,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,QAAQ,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,MAAM,EAAE,KAAK,GAAG,SAAS,CAAC;CAC3B;AAID;;;;;;;;;;;;GAYG;AACH,wBAAgB,yBAAyB,CAAC,GAAG,GAAE,MAAM,CAAC,UAAwB,GAAG,eAAe,EAAE,CA2CjG;AAYD;;;;;;GAMG;AACH,wBAAgB,2BAA2B,CAAC,OAAO,EAAE,eAAe,EAAE,GAAG,MAAM,CAmB9E"}

package/dist/config/alias-credentials.js

@@ -10,7 +10,7 @@
  */
 import { z } from '@cyanheads/mcp-ts-core';
 import { parseEnvConfig } from '@cyanheads/mcp-ts-core/config';
-import { validationError } from '@cyanheads/mcp-ts-core/errors';
+import { configurationError, forbidden, validationError } from '@cyanheads/mcp-ts-core/errors';
 import { findBuiltinAlias, listBuiltinAliases } from './builtin-aliases.js';
 const FIELD_SUFFIXES = [
     ['baseUrl', 'BASE_URL'],
@@ -96,6 +96,8 @@ export function deriveAuthFromCredentials(creds, alias) {
     }
     return;
 }
+/** Recovery hint for the `auth_base_url_mismatch` refusal; shared with the `brapi_connect` contract. */
+export const AUTH_BASE_URL_MISMATCH_RECOVERY = 'Omit `baseUrl` to connect to the server configured for this alias, or register the other server under a different alias.';
 /**
  * Layer agent input over alias env over the builtin registry over default env.
  * Returns the resolved baseUrl + auth. Throws when no baseUrl is resolvable
@@ -108,36 +110,103 @@ export function deriveAuthFromCredentials(creds, alias) {
  *   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.
+ * Env credentials only travel to the server configured alongside them:
+ * - Per-alias credentials pair with the alias's own URL: its env base URL,
+ *   else its enabled builtin URL (for `default`, `BRAPI_DEFAULT_BASE_URL`).
+ *   A caller `baseUrl` that differs from it is refused with
+ *   `auth_base_url_mismatch`. Credentials with no URL of their own pair with
+ *   nothing and are refused with `alias_base_url_unset` — they never fall
+ *   back to `BRAPI_DEFAULT_BASE_URL`. Both refusals precede any request.
+ * - Default credentials pair with `BRAPI_DEFAULT_BASE_URL` only. For another
+ *   alias they attach when the resolved URL is that one and are otherwise
+ *   left off, so auth falls through to `none`.
+ *
+ * URLs compare after normalization (host case, default port, trailing
+ * slashes). Caller-supplied `auth` bypasses env credentials entirely.
  */
 export function resolveConnectInput(alias, agent, env = process.env) {
     const aliasCreds = readAliasCredentials(alias, env);
     const defaultCreds = alias === DEFAULT_ALIAS ? aliasCreds : readAliasCredentials(DEFAULT_ALIAS, env);
-    const builtin = !agent.baseUrl && !aliasCreds.baseUrl ? findBuiltinAlias(alias, env) : undefined;
-    const baseUrl = agent.baseUrl ?? aliasCreds.baseUrl ?? builtin?.baseUrl ?? defaultCreds.baseUrl;
+    const ownBaseUrl = aliasCreds.baseUrl ?? findBuiltinAlias(alias, env)?.baseUrl;
+    const aliasAuth = agent.auth ? undefined : deriveAuthFromCredentials(aliasCreds, alias);
+    if (aliasAuth && ownBaseUrl === undefined) {
+        const envVar = `${aliasEnvPrefix(alias)}BASE_URL`;
+        throw configurationError(`Alias '${alias}' has server-configured credentials but no base URL of its own, so they are not sent anywhere. Set ${envVar} on the server, or remove the alias's credential variables. No request was made.`, {
+            reason: 'alias_base_url_unset',
+            alias,
+            envVar,
+            retryable: false,
+            recovery: {
+                hint: `Set ${envVar} on the server for alias '${alias}', or remove its credential variables, before retrying.`,
+            },
+        });
+    }
+    const baseUrl = agent.baseUrl ?? ownBaseUrl ?? defaultCreds.baseUrl;
     if (!baseUrl) {
         throw validationError(`No baseUrl provided. Pass \`baseUrl\` explicitly, or set ${aliasEnvPrefix(alias)}BASE_URL${alias === DEFAULT_ALIAS ? '' : ` or ${aliasEnvPrefix(DEFAULT_ALIAS)}BASE_URL`}.`, { alias });
     }
-    const allowDefaultAuthFallback = !builtin && alias !== DEFAULT_ALIAS;
-    const auth = agent.auth ??
-        deriveAuthFromCredentials(aliasCreds, alias) ??
-        (allowDefaultAuthFallback
-            ? deriveAuthFromCredentials(defaultCreds, DEFAULT_ALIAS)
-            : undefined) ??
-        NONE_AUTH;
-    return { baseUrl, auth };
+    if (agent.auth)
+        return { baseUrl, auth: agent.auth };
+    if (aliasAuth) {
+        if (agent.baseUrl === undefined || sameBaseUrl(agent.baseUrl, ownBaseUrl)) {
+            return { baseUrl, auth: aliasAuth };
+        }
+        // An unparsable or userinfo-bearing caller URL fails baseUrl validation
+        // downstream, which does not echo it; it just gets no credentials.
+        if (comparableBaseUrl(agent.baseUrl) === undefined)
+            return { baseUrl, auth: NONE_AUTH };
+        throw forbidden(`Alias '${alias}' has server-configured credentials that are only sent to the server configured for it, and the supplied baseUrl points elsewhere. No request was made.`, {
+            reason: 'auth_base_url_mismatch',
+            alias,
+            baseUrl: agent.baseUrl,
+            retryable: false,
+            recovery: { hint: AUTH_BASE_URL_MISMATCH_RECOVERY },
+        });
+    }
+    if (alias !== DEFAULT_ALIAS && sameBaseUrl(baseUrl, defaultCreds.baseUrl)) {
+        const defaultAuth = deriveAuthFromCredentials(defaultCreds, DEFAULT_ALIAS);
+        if (defaultAuth)
+            return { baseUrl, auth: defaultAuth };
+    }
+    return { baseUrl, auth: NONE_AUTH };
+}
+/**
+ * True when both URLs parse, carry no userinfo, and name the same BrAPI base:
+ * scheme, host (case-insensitive), port (default port elided), path with
+ * trailing slashes dropped, query, and fragment. A URL with userinfo never
+ * matches — `brapi_connect` refuses it as a baseUrl.
+ */
+export function sameBaseUrl(a, b) {
+    if (b === undefined)
+        return false;
+    const left = comparableBaseUrl(a);
+    return left !== undefined && left === comparableBaseUrl(b);
+}
+function comparableBaseUrl(value) {
+    if (!URL.canParse(value))
+        return;
+    const url = new URL(value);
+    if (url.username || url.password)
+        return;
+    // Read `pathname` once: the getter re-serializes on every access.
+    const { pathname } = url;
+    let end = pathname.length;
+    while (end > 0 && pathname[end - 1] === '/')
+        end--;
+    const path = pathname.slice(0, end);
+    return `${url.protocol}//${url.host}${path}${url.search}${url.hash}`;
 }
 const ALIAS_BASE_URL_PATTERN = /^BRAPI_([A-Z0-9_]+)_BASE_URL$/;
 /**
  * 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`.
+ * resolver gives env precedence; their `origin` reflects that. `authMode` is
+ * what an argument-free `brapi_connect` for the alias resolves to, so the
+ * pairing rules apply: a builtin with `BRAPI_<ALIAS>_USERNAME` set reports
+ * `sgn`, and default credentials count only on `BRAPI_DEFAULT_BASE_URL`.
+ * Credentials with no URL of their own have nothing to connect to, so they
+ * never surface an alias.
  *
  * Default-alias entries land first; the rest are alphabetical.
  */
@@ -162,7 +231,7 @@ export function discoverConfiguredAliases(env = process.env) {
             continue;
         result.push({
             alias,
-            authMode: deriveModeForDiscovery(creds, alias),
+            authMode: deriveModeForDiscovery(alias, env),
             baseUrl: creds.baseUrl,
             origin: 'env',
         });
@@ -171,10 +240,9 @@ export function discoverConfiguredAliases(env = process.env) {
     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),
+            authMode: deriveModeForDiscovery(builtin.alias, env),
             baseUrl: builtin.baseUrl,
             origin: 'builtin',
         });
@@ -188,10 +256,9 @@ export function discoverConfiguredAliases(env = process.env) {
     });
     return result;
 }
-function deriveModeForDiscovery(creds, alias) {
+function deriveModeForDiscovery(alias, env) {
     try {
-        const auth = deriveAuthFromCredentials(creds, alias);
-        return auth?.mode ?? 'none';
+        return resolveConnectInput(alias, {}, env).auth.mode;
     }
     catch {
         // Ambiguous credential family — surface the alias as `none` so the agent

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

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

@@ -7,13 +7,16 @@
  *
  * 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.
+ * (`BRAPI_<ALIAS>_USERNAME` / `_PASSWORD` / etc.) layer on top of the alias's
+ * configured URL (env base URL, else the builtin one) and are never sent to a
+ * caller-supplied baseUrl that points elsewhere, 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).
+ * case-insensitively). Credentials left set for a disabled builtin have no URL
+ * to pair with, so `brapi_connect` refuses that alias until
+ * `BRAPI_<ALIAS>_BASE_URL` is set.
  *
  * @module config/builtin-aliases
  */
@@ -32,11 +35,13 @@ export interface BuiltinAlias {
  * 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.
+ * solgenomics, the Triticeae Toolbox hosts) are intentionally absent; they
+ * stay reachable through `BRAPI_<ALIAS>_BASE_URL` plus credentials.
  */
 export declare const BUILTIN_ALIASES: ReadonlyArray<BuiltinAlias>;
 /**
- * Resolve a builtin entry by alias. Case-insensitive lookup; respects the
+ * Resolve a builtin entry by alias. Matches every spelling that shares the
+ * builtin's env prefix (case-insensitive, `_` for `-`); 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).

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

@@ -1 +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"}
+{"version":3,"file":"builtin-aliases.d.ts","sourceRoot":"","sources":["../../src/config/builtin-aliases.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;;GAqBG;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;;;;;;;GAOG;AACH,eAAO,MAAM,eAAe,EAAE,aAAa,CAAC,YAAY,CA6BtD,CAAC;AA4BH;;;;;;GAMG;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

@@ -7,13 +7,16 @@
  *
  * 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.
+ * (`BRAPI_<ALIAS>_USERNAME` / `_PASSWORD` / etc.) layer on top of the alias's
+ * configured URL (env base URL, else the builtin one) and are never sent to a
+ * caller-supplied baseUrl that points elsewhere, 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).
+ * case-insensitively). Credentials left set for a disabled builtin have no URL
+ * to pair with, so `brapi_connect` refuses that alias until
+ * `BRAPI_<ALIAS>_BASE_URL` is set.
  *
  * @module config/builtin-aliases
  */
@@ -23,7 +26,8 @@ const BREEDBASE_CITATION = 'Morales et al. 2022. "Breedbase: a digital ecosystem
  * 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.
+ * solgenomics, the Triticeae Toolbox hosts) are intentionally absent; they
+ * stay reachable through `BRAPI_<ALIAS>_BASE_URL` plus credentials.
  */
 export const BUILTIN_ALIASES = Object.freeze([
     Object.freeze({
@@ -44,33 +48,6 @@ export const BUILTIN_ALIASES = Object.freeze([
         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',
@@ -83,9 +60,17 @@ export const BUILTIN_ALIASES = Object.freeze([
     }),
 ]);
 const DISABLED_ENV_VAR = 'BRAPI_BUILTIN_ALIASES_DISABLED';
+/**
+ * Canonical builtin key for an alias spelling. Spellings that share a
+ * `BRAPI_<ALIAS>_*` env prefix (case, `-` vs `_`) read the same credentials,
+ * so they must resolve to the same builtin — and so the same paired URL.
+ */
+function builtinKey(alias) {
+    return alias.toLowerCase().replace(/_/g, '-');
+}
 /**
  * Parse the comma-separated disabled list from env. Whitespace tolerant,
- * case-insensitive — entries are lowercased to match alias keys.
+ * case-insensitive — entries are canonicalized to match alias keys.
  */
 function readDisabledSet(env) {
     const raw = env[DISABLED_ENV_VAR];
@@ -93,20 +78,21 @@ function readDisabledSet(env) {
         return new Set();
     const out = new Set();
     for (const part of raw.split(',')) {
-        const trimmed = part.trim().toLowerCase();
+        const trimmed = part.trim();
         if (trimmed)
-            out.add(trimmed);
+            out.add(builtinKey(trimmed));
     }
     return out;
 }
 /**
- * Resolve a builtin entry by alias. Case-insensitive lookup; respects the
+ * Resolve a builtin entry by alias. Matches every spelling that shares the
+ * builtin's env prefix (case-insensitive, `_` for `-`); 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 key = builtinKey(alias);
     const disabled = readDisabledSet(env);
     if (disabled.has(key))
         return;

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

@@ -1 +1 @@
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package/dist/index.js

@@ -118,7 +118,7 @@ await createApp({
     // visitors even when MCP_AUTH_MODE is jwt/oauth. Framework default (0.9.13+)
     // gates the inventory behind auth; this override restores the open-catalog UX.
     landing: { requireAuth: false },
-    instructions: 'Bridges BrAPI v2 servers (Breeding API for plant/crop research). Call `brapi_connect` first to register a server under an alias and return the orientation envelope (capabilities, dialect, sample IDs). `brapi_find_*` tools page filtered lookups across studies, germplasm, observations, variables, locations, images, variants, and genotype calls; rows beyond the per-call cap spill to a canvas dataframe — query with `brapi_dataframe_query` (SELECT-only SQL). `brapi_get_*` fetch single records by `*DbId`. Use `brapi_raw_get` / `brapi_raw_search` only when no curated tool fits — responses route back to the right curated tool.',
+    instructions: 'Bridges BrAPI v2 servers (Breeding API for plant/crop research). Call `brapi_connect` first to register a server under an alias and return the orientation envelope (capabilities, dialect, content summary, the finders the server supports). `brapi_find_*` tools page filtered lookups across studies, germplasm, observations, variables, locations, images, variants, and genotype calls; rows beyond the per-call cap spill to a canvas dataframe — query with `brapi_dataframe_query` (SELECT-only SQL). `brapi_get_*` fetch single records by `*DbId`. Use `brapi_raw_get` / `brapi_raw_search` only when no curated tool fits — responses route back to the right curated tool.',
     setup(core) {
         if (!core.canvas) {
             throw configurationError('brapi-mcp-server requires the framework canvas service (DuckDB) for dataframe spillover. Set CANVAS_PROVIDER_TYPE=duckdb (the default) and ensure @duckdb/node-api is installed.', { canvasProviderType: process.env.CANVAS_PROVIDER_TYPE ?? 'duckdb' });

package/dist/index.js.map

@@ -1 +1 @@
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package/dist/mcp-server/resources/definitions/brapi-server-info.resource.js

@@ -11,7 +11,7 @@ import { brapiServerInfo } from '../../tools/definitions/brapi-server-info.tool.
 export const brapiServerInfoResource = resource('brapi://server/info', {
     name: 'brapi-server-info',
     title: 'BrAPI server orientation envelope',
-    description: 'Orientation envelope for the default BrAPI connection — identity, capabilities, content counts, notes. Same payload as the brapi_server_info tool.',
+    description: 'Orientation envelope for the default BrAPI connection — identity, capabilities, content counts, suggested finders, notes. Same payload as the brapi_server_info tool.',
     mimeType: 'application/json',
     errors: [
         {

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

@@ -1 +1 @@
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+{"version":3,"file":"brapi-server-info.resource.js","sourceRoot":"","sources":["../../../../src/mcp-server/resources/definitions/brapi-server-info.resource.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,QAAQ,EAAE,MAAM,wBAAwB,CAAC;AAClD,OAAO,EAAE,gBAAgB,EAAE,MAAM,+BAA+B,CAAC;AACjE,OAAO,EAAE,eAAe,EAAE,MAAM,0DAA0D,CAAC;AAE3F,MAAM,CAAC,MAAM,uBAAuB,GAAG,QAAQ,CAAC,qBAAqB,EAAE;IACrE,IAAI,EAAE,mBAAmB;IACzB,KAAK,EAAE,mCAAmC;IAC1C,WAAW,EACT,uKAAuK;IACzK,QAAQ,EAAE,kBAAkB;IAC5B,MAAM,EAAE;QACN;YACE,MAAM,EAAE,eAAe;YACvB,IAAI,EAAE,gBAAgB,CAAC,QAAQ;YAC/B,IAAI,EAAE,iDAAiD;YACvD,QAAQ,EACN,8FAA8F;YAChG,QAAQ,EAAE,SAAS;SACpB;KACO;IACV,KAAK,CAAC,OAAO,CAAC,OAAO,EAAE,GAAG;QACxB,OAAO,MAAM,eAAe,CAAC,OAAO,CAAC,eAAe,CAAC,KAAK,CAAC,KAAK,CAAC,EAAE,CAAC,EAAE,GAAG,CAAC,CAAC;IAC7E,CAAC;IACD,IAAI,EAAE,KAAK,IAAI,EAAE,CAAC,CAAC;QACjB,SAAS,EAAE;YACT;gBACE,GAAG,EAAE,qBAAqB;gBAC1B,IAAI,EAAE,mCAAmC;gBACzC,QAAQ,EAAE,kBAAkB;aAC7B;SACF;KACF,CAAC;CACH,CAAC,CAAC"}