@cyanheads/brapi-mcp-server 0.3.5

package/dist/services/server-registry/server-registry.d.ts

@@ -0,0 +1,57 @@
+/**
+ * @fileoverview Session-scoped BrAPI connection registry. Maps named aliases
+ * to resolved connection state (base URL, auth header) within a tenant's
+ * `ctx.state`. Multi-server workflows register distinct aliases; tools read
+ * the alias from input (defaulting to `default`) and pull the base URL +
+ * auth header for routing. Auth modes that require a token exchange
+ * (`sgn`, `oauth2`) perform the exchange at registration time.
+ *
+ * @module services/server-registry/server-registry
+ */
+import type { Context } from '@cyanheads/mcp-ts-core';
+import type { ServerConfig } from '../../config/server-config.js';
+import type { AuthMode, ConnectAuth, RegisteredServer } from './types.js';
+export declare const DEFAULT_ALIAS = "default";
+export interface RegisterInput {
+    alias?: string;
+    auth?: ConnectAuth;
+    baseUrl: string;
+}
+export declare class ServerRegistry {
+    private readonly serverConfig;
+    private readonly tokenFetcher;
+    constructor(serverConfig: ServerConfig, tokenFetcher?: TokenFetcher);
+    /**
+     * Register a connection under an alias. Resolves the auth mode to a
+     * ready-to-use header (performing token exchange for `sgn` / `oauth2`) and
+     * persists the result in `ctx.state`.
+     */
+    register(ctx: Context, input: RegisterInput): Promise<RegisteredServer>;
+    /** Fetch a registered connection or throw `NotFound`. */
+    get(ctx: Context, alias?: string): Promise<RegisteredServer>;
+    /** Non-throwing variant of `get`. */
+    getOptional(ctx: Context, alias?: string): Promise<RegisteredServer | null>;
+    list(ctx: Context): Promise<RegisteredServer[]>;
+    unregister(ctx: Context, alias?: string): Promise<void>;
+    private resolveAuth;
+    private exchangeSgnToken;
+}
+/**
+ * Swappable token-exchange fetcher. Production uses `fetchWithTimeout`; tests
+ * inject a stub to avoid real network calls.
+ */
+export type TokenFetcher = (url: string, body: Record<string, unknown>, ctx: Context, options: {
+    timeoutMs: number;
+    rejectPrivateIPs: boolean;
+}) => Promise<TokenResponse>;
+interface TokenResponse {
+    access_token?: string;
+    expires_in?: number;
+    token_type?: string;
+    [key: string]: unknown;
+}
+export declare function initServerRegistry(serverConfig: ServerConfig): void;
+export declare function getServerRegistry(): ServerRegistry;
+export declare function resetServerRegistry(): void;
+export type { AuthMode, ConnectAuth, RegisteredServer };
+//# sourceMappingURL=server-registry.d.ts.map

package/dist/services/server-registry/server-registry.d.ts.map

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package/dist/services/server-registry/server-registry.js

@@ -0,0 +1,210 @@
+/**
+ * @fileoverview Session-scoped BrAPI connection registry. Maps named aliases
+ * to resolved connection state (base URL, auth header) within a tenant's
+ * `ctx.state`. Multi-server workflows register distinct aliases; tools read
+ * the alias from input (defaulting to `default`) and pull the base URL +
+ * auth header for routing. Auth modes that require a token exchange
+ * (`sgn`, `oauth2`) perform the exchange at registration time.
+ *
+ * @module services/server-registry/server-registry
+ */
+import { forbidden, notFound, serviceUnavailable, validationError, } from '@cyanheads/mcp-ts-core/errors';
+import { fetchWithTimeout } from '@cyanheads/mcp-ts-core/utils';
+export const DEFAULT_ALIAS = 'default';
+const CONN_PREFIX = 'brapi/conn/';
+export class ServerRegistry {
+    serverConfig;
+    tokenFetcher;
+    constructor(serverConfig, tokenFetcher = defaultTokenFetcher) {
+        this.serverConfig = serverConfig;
+        this.tokenFetcher = tokenFetcher;
+    }
+    /**
+     * Register a connection under an alias. Resolves the auth mode to a
+     * ready-to-use header (performing token exchange for `sgn` / `oauth2`) and
+     * persists the result in `ctx.state`.
+     */
+    async register(ctx, input) {
+        const alias = input.alias?.trim() || DEFAULT_ALIAS;
+        validateAlias(alias);
+        validateBaseUrl(input.baseUrl);
+        const auth = input.auth ?? { mode: 'none' };
+        const registered = {
+            alias,
+            baseUrl: normalizeBaseUrl(input.baseUrl),
+            authMode: auth.mode,
+            registeredAt: new Date().toISOString(),
+        };
+        const resolvedAuth = await this.resolveAuth(auth, registered.baseUrl, ctx);
+        if (resolvedAuth)
+            registered.resolvedAuth = resolvedAuth;
+        await ctx.state.set(connKey(alias), registered);
+        return registered;
+    }
+    /** Fetch a registered connection or throw `NotFound`. */
+    async get(ctx, alias = DEFAULT_ALIAS) {
+        const entry = await ctx.state.get(connKey(alias));
+        if (!entry) {
+            throw notFound(`No BrAPI connection registered under alias '${alias}'. Call brapi_connect first.`, { alias, reason: 'unknown_alias' });
+        }
+        return entry;
+    }
+    /** Non-throwing variant of `get`. */
+    getOptional(ctx, alias = DEFAULT_ALIAS) {
+        return ctx.state.get(connKey(alias));
+    }
+    async list(ctx) {
+        const servers = [];
+        let cursor;
+        do {
+            const listOpts = { limit: 100 };
+            if (cursor !== undefined)
+                listOpts.cursor = cursor;
+            const page = await ctx.state.list(CONN_PREFIX, listOpts);
+            for (const item of page.items) {
+                if (isRegisteredServer(item.value))
+                    servers.push(item.value);
+            }
+            cursor = page.cursor;
+        } while (cursor);
+        return servers;
+    }
+    async unregister(ctx, alias = DEFAULT_ALIAS) {
+        await ctx.state.delete(connKey(alias));
+    }
+    async resolveAuth(auth, baseUrl, ctx) {
+        switch (auth.mode) {
+            case 'none':
+                return;
+            case 'bearer':
+                return { headerName: 'Authorization', headerValue: `Bearer ${auth.token}` };
+            case 'api_key':
+                return {
+                    headerName: auth.headerName ?? this.serverConfig.defaultApiKeyHeader,
+                    headerValue: auth.apiKey,
+                };
+            case 'sgn':
+                return await this.exchangeSgnToken(auth, baseUrl, ctx);
+            case 'oauth2':
+                throw validationError('OAuth2 auth is not yet implemented. Use mode="bearer" with a pre-obtained access token for now.', { mode: 'oauth2' });
+            default: {
+                const _exhaustive = auth;
+                throw validationError('Unknown auth mode', { received: _exhaustive });
+            }
+        }
+    }
+    async exchangeSgnToken(auth, baseUrl, ctx) {
+        const tokenUrl = joinUrl(baseUrl, '/token');
+        const payload = await this.tokenFetcher(tokenUrl, {
+            username: auth.username,
+            password: auth.password,
+            grant_type: 'password',
+        }, ctx, {
+            timeoutMs: this.serverConfig.requestTimeoutMs,
+            rejectPrivateIPs: !this.serverConfig.allowPrivateIps,
+        });
+        if (!payload.access_token) {
+            throw forbidden('SGN token exchange returned no access_token', {
+                tokenUrl,
+                payloadKeys: Object.keys(payload),
+                reason: 'auth_no_access_token',
+                ...ctx.recoveryFor('auth_no_access_token'),
+            });
+        }
+        const resolved = {
+            headerName: 'Authorization',
+            headerValue: `Bearer ${payload.access_token}`,
+        };
+        if (payload.expires_in && Number.isFinite(payload.expires_in)) {
+            resolved.expiresAt = new Date(Date.now() + payload.expires_in * 1000).toISOString();
+        }
+        return resolved;
+    }
+}
+const defaultTokenFetcher = async (url, body, ctx, options) => {
+    const form = new URLSearchParams();
+    for (const [key, value] of Object.entries(body)) {
+        if (value !== undefined && value !== null)
+            form.set(key, String(value));
+    }
+    let response;
+    try {
+        response = await fetchWithTimeout(url, options.timeoutMs, ctx, {
+            method: 'POST',
+            headers: {
+                'Content-Type': 'application/x-www-form-urlencoded',
+                Accept: 'application/json',
+            },
+            body: form.toString(),
+            signal: ctx.signal,
+            rejectPrivateIPs: options.rejectPrivateIPs,
+        });
+    }
+    catch (err) {
+        throw forbidden(`Token exchange failed at ${url}. Verify credentials and that the server exposes /token.`, {
+            tokenUrl: url,
+            reason: 'auth_token_exchange_failed',
+            ...ctx.recoveryFor('auth_token_exchange_failed'),
+        }, { cause: err });
+    }
+    const text = await response.text();
+    if (!text) {
+        throw serviceUnavailable('Token exchange returned an empty body', { tokenUrl: url });
+    }
+    try {
+        return JSON.parse(text);
+    }
+    catch (err) {
+        throw serviceUnavailable('Token exchange returned non-JSON response', { tokenUrl: url, bodyPreview: text.slice(0, 200) }, { cause: err });
+    }
+};
+function connKey(alias) {
+    return `${CONN_PREFIX}${alias}`;
+}
+function validateAlias(alias) {
+    if (!/^[a-zA-Z0-9_-]+$/.test(alias)) {
+        throw validationError(`Invalid connection alias '${alias}'. Use letters, digits, '_', or '-'.`, { alias });
+    }
+}
+function validateBaseUrl(baseUrl) {
+    let parsed;
+    try {
+        parsed = new URL(baseUrl);
+    }
+    catch {
+        throw validationError(`Invalid baseUrl '${baseUrl}' — not a valid URL.`, { baseUrl });
+    }
+    if (parsed.protocol !== 'http:' && parsed.protocol !== 'https:') {
+        throw validationError(`Invalid baseUrl protocol '${parsed.protocol}'. Use http or https.`, {
+            baseUrl,
+        });
+    }
+}
+function normalizeBaseUrl(baseUrl) {
+    return baseUrl.replace(/\/+$/, '');
+}
+function joinUrl(baseUrl, path) {
+    const trimmedBase = baseUrl.replace(/\/+$/, '');
+    const prefixedPath = path.startsWith('/') ? path : `/${path}`;
+    return `${trimmedBase}${prefixedPath}`;
+}
+function isRegisteredServer(value) {
+    if (typeof value !== 'object' || value === null)
+        return false;
+    const v = value;
+    return (typeof v.alias === 'string' && typeof v.baseUrl === 'string' && typeof v.authMode === 'string');
+}
+let _registry;
+export function initServerRegistry(serverConfig) {
+    _registry = new ServerRegistry(serverConfig);
+}
+export function getServerRegistry() {
+    if (!_registry) {
+        throw new Error('ServerRegistry not initialized — call initServerRegistry() in setup()');
+    }
+    return _registry;
+}
+export function resetServerRegistry() {
+    _registry = undefined;
+}
+//# sourceMappingURL=server-registry.js.map

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package/dist/services/server-registry/types.d.ts

@@ -0,0 +1,43 @@
+/**
+ * @fileoverview Types for ServerRegistry — session-scoped connection aliases.
+ * A `RegisteredServer` holds everything tools need to route a request: the
+ * base URL, the resolved auth header, and the declared auth mode (so tools
+ * can surface meaningful re-auth guidance).
+ *
+ * @module services/server-registry/types
+ */
+import type { ResolvedAuth } from '../../services/brapi-client/index.js';
+export type AuthMode = 'none' | 'sgn' | 'oauth2' | 'api_key' | 'bearer';
+export interface RegisteredServer {
+    alias: string;
+    authMode: AuthMode;
+    baseUrl: string;
+    registeredAt: string;
+    /** Resolved header to attach to outbound requests. Omitted for `none`. */
+    resolvedAuth?: ResolvedAuth;
+}
+/**
+ * Input accepted by `ServerRegistry.register`. Discriminated by `mode`.
+ * Optional fields allow `undefined` explicitly so Zod-parsed values (which
+ * carry optional-as-undefined) assign cleanly under `exactOptionalPropertyTypes`.
+ */
+export type ConnectAuth = {
+    mode: 'none';
+} | {
+    mode: 'sgn';
+    username: string;
+    password: string;
+} | {
+    mode: 'oauth2';
+    clientId: string;
+    clientSecret: string;
+    tokenUrl?: string | undefined;
+} | {
+    mode: 'api_key';
+    apiKey: string;
+    headerName?: string | undefined;
+} | {
+    mode: 'bearer';
+    token: string;
+};
+//# sourceMappingURL=types.d.ts.map

package/dist/services/server-registry/types.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.d.ts","sourceRoot":"","sources":["../../../src/services/server-registry/types.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EAAE,YAAY,EAAE,MAAM,kCAAkC,CAAC;AAErE,MAAM,MAAM,QAAQ,GAAG,MAAM,GAAG,KAAK,GAAG,QAAQ,GAAG,SAAS,GAAG,QAAQ,CAAC;AAExE,MAAM,WAAW,gBAAgB;IAC/B,KAAK,EAAE,MAAM,CAAC;IACd,QAAQ,EAAE,QAAQ,CAAC;IACnB,OAAO,EAAE,MAAM,CAAC;IAChB,YAAY,EAAE,MAAM,CAAC;IACrB,0EAA0E;IAC1E,YAAY,CAAC,EAAE,YAAY,CAAC;CAC7B;AAED;;;;GAIG;AACH,MAAM,MAAM,WAAW,GACnB;IAAE,IAAI,EAAE,MAAM,CAAA;CAAE,GAChB;IAAE,IAAI,EAAE,KAAK,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAC;IAAC,QAAQ,EAAE,MAAM,CAAA;CAAE,GACnD;IACE,IAAI,EAAE,QAAQ,CAAC;IACf,QAAQ,EAAE,MAAM,CAAC;IACjB,YAAY,EAAE,MAAM,CAAC;IACrB,QAAQ,CAAC,EAAE,MAAM,GAAG,SAAS,CAAC;CAC/B,GACD;IAAE,IAAI,EAAE,SAAS,CAAC;IAAC,MAAM,EAAE,MAAM,CAAC;IAAC,UAAU,CAAC,EAAE,MAAM,GAAG,SAAS,CAAA;CAAE,GACpE;IAAE,IAAI,EAAE,QAAQ,CAAC;IAAC,KAAK,EAAE,MAAM,CAAA;CAAE,CAAC"}

package/dist/services/server-registry/types.js

@@ -0,0 +1,10 @@
+/**
+ * @fileoverview Types for ServerRegistry — session-scoped connection aliases.
+ * A `RegisteredServer` holds everything tools need to route a request: the
+ * base URL, the resolved auth header, and the declared auth mode (so tools
+ * can surface meaningful re-auth guidance).
+ *
+ * @module services/server-registry/types
+ */
+export {};
+//# sourceMappingURL=types.js.map

package/dist/services/server-registry/types.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"types.js","sourceRoot":"","sources":["../../../src/services/server-registry/types.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG"}

package/package.json

@@ -0,0 +1,86 @@
+{
+  "name": "@cyanheads/brapi-mcp-server",
+  "mcpName": "io.github.cyanheads/brapi-mcp-server",
+  "version": "0.3.5",
+  "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
+  "author": "Casey Hand @cyanheads (https://github.com/cyanheads/brapi-mcp-server#readme)",
+  "type": "module",
+  "main": "dist/index.js",
+  "types": "dist/index.d.ts",
+  "bin": {
+    "brapi-mcp-server": "dist/index.js"
+  },
+  "files": [
+    "changelog/",
+    "dist/",
+    "README.md",
+    "LICENSE",
+    "CLAUDE.md",
+    "Dockerfile",
+    "server.json"
+  ],
+  "scripts": {
+    "build": "tsx scripts/build.ts",
+    "rebuild": "tsx scripts/clean.ts && tsx scripts/build.ts",
+    "clean": "tsx scripts/clean.ts",
+    "devcheck": "tsx scripts/devcheck.ts",
+    "tree": "tsx scripts/tree.ts",
+    "format": "biome check --write --unsafe .",
+    "lint:mcp": "tsx scripts/lint-mcp.ts",
+    "changelog:build": "tsx scripts/build-changelog.ts",
+    "changelog:check": "tsx scripts/build-changelog.ts --check",
+    "test": "bunx --bun vitest run",
+    "start": "node dist/index.js",
+    "start:stdio": "MCP_TRANSPORT_TYPE=stdio node dist/index.js",
+    "start:http": "MCP_TRANSPORT_TYPE=http node dist/index.js"
+  },
+  "keywords": [
+    "mcp",
+    "mcp-server",
+    "model-context-protocol",
+    "claude",
+    "brapi",
+    "breedbase",
+    "plant-breeding",
+    "bioinformatics",
+    "agriculture",
+    "phenotyping",
+    "genotyping",
+    "germplasm",
+    "pedigree",
+    "observations",
+    "llm-tools",
+    "typescript"
+  ],
+  "repository": {
+    "type": "git",
+    "url": "git+https://github.com/cyanheads/brapi-mcp-server.git"
+  },
+  "homepage": "https://github.com/cyanheads/brapi-mcp-server#readme",
+  "bugs": {
+    "url": "https://github.com/cyanheads/brapi-mcp-server/issues"
+  },
+  "license": "Apache-2.0",
+  "engines": {
+    "node": ">=22.0.0",
+    "bun": ">=1.2.0"
+  },
+  "packageManager": "bun@1.3.11",
+  "publishConfig": {
+    "access": "public"
+  },
+  "dependencies": {
+    "@cyanheads/mcp-ts-core": "^0.8.7",
+    "pino-pretty": "^13.1.3"
+  },
+  "devDependencies": {
+    "@biomejs/biome": "^2.4.13",
+    "@types/node": "^25.6.0",
+    "depcheck": "^1.4.7",
+    "ignore": "^7.0.5",
+    "tsc-alias": "^1.8.16",
+    "tsx": "^4.21.0",
+    "typescript": "^6.0.3",
+    "vitest": "^4.1.5"
+  }
+}

package/server.json

@@ -0,0 +1,99 @@
+{
+  "$schema": "https://static.modelcontextprotocol.io/schemas/2025-12-11/server.schema.json",
+  "name": "io.github.cyanheads/brapi-mcp-server",
+  "description": "BrAPI v2.1 MCP server — studies, germplasm, observations, genotypes, images, and pedigrees.",
+  "repository": {
+    "url": "https://github.com/cyanheads/brapi-mcp-server",
+    "source": "github"
+  },
+  "version": "0.3.5",
+  "packages": [
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/brapi-mcp-server",
+      "runtimeHint": "node",
+      "version": "0.3.5",
+      "packageArguments": [
+        { "type": "positional", "value": "run" },
+        { "type": "positional", "value": "start:stdio" }
+      ],
+      "environmentVariables": [
+        {
+          "name": "BRAPI_DEFAULT_BASE_URL",
+          "description": "Default BrAPI v2 base URL. Optional — connections can be opened at runtime via the brapi_connect tool instead.",
+          "format": "string",
+          "isRequired": false
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "stdio"
+      }
+    },
+    {
+      "registryType": "npm",
+      "registryBaseUrl": "https://registry.npmjs.org",
+      "identifier": "@cyanheads/brapi-mcp-server",
+      "runtimeHint": "node",
+      "version": "0.3.5",
+      "packageArguments": [
+        { "type": "positional", "value": "run" },
+        { "type": "positional", "value": "start:http" }
+      ],
+      "environmentVariables": [
+        {
+          "name": "BRAPI_DEFAULT_BASE_URL",
+          "description": "Default BrAPI v2 base URL. Optional — connections can be opened at runtime via the brapi_connect tool instead.",
+          "format": "string",
+          "isRequired": false
+        },
+        {
+          "name": "MCP_HTTP_HOST",
+          "description": "The hostname for the HTTP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "127.0.0.1"
+        },
+        {
+          "name": "MCP_HTTP_PORT",
+          "description": "The port to run the HTTP server on.",
+          "format": "string",
+          "isRequired": false,
+          "default": "3010"
+        },
+        {
+          "name": "MCP_HTTP_ENDPOINT_PATH",
+          "description": "The endpoint path for the MCP server.",
+          "format": "string",
+          "isRequired": false,
+          "default": "/mcp"
+        },
+        {
+          "name": "MCP_AUTH_MODE",
+          "description": "Authentication mode to use: 'none', 'jwt', or 'oauth'.",
+          "format": "string",
+          "isRequired": false,
+          "default": "none"
+        },
+        {
+          "name": "MCP_LOG_LEVEL",
+          "description": "Sets the minimum log level for output (e.g., 'debug', 'info', 'warn').",
+          "format": "string",
+          "isRequired": false,
+          "default": "info"
+        }
+      ],
+      "transport": {
+        "type": "streamable-http",
+        "url": "http://localhost:3010/mcp"
+      }
+    }
+  ]
+}