@djmima/pubmed-mcp 0.0.0-stage → 1.0.0

package/dist/auth.d.ts

@@ -0,0 +1,39 @@
+/**
+ * OAuth 2.0 resource-server enforcement for HTTP mode.
+ *
+ * The MCP server acts as an OAuth 2.0 *resource server* (RFC 9728 /
+ * MCP authorization spec 2025-06-18). A managed authorization server
+ * (WorkOS AuthKit) runs Dynamic Client Registration (so claude.ai can register
+ * itself) and issues signed JWT access tokens. This module:
+ *
+ *   1. Advertises the authorization server via Protected Resource Metadata at
+ *      /.well-known/oauth-protected-resource
+ *   2. Validates the Bearer JWT on every /mcp request against the provider's
+ *      JWKS (signature, issuer, audience, expiry).
+ *   3. Restricts access to an allowlist of token subjects — since DCR lets
+ *      anyone register a client, this is what makes the server *yours only*.
+ *      With the allowlist empty, any valid token is accepted.
+ *
+ * Required environment variables (copy issuer/jwks from the provider's
+ *   https://<your-authkit-domain>/.well-known/oauth-authorization-server ):
+ *   OAUTH_ISSUER      — `issuer` from that document
+ *   OAUTH_JWKS_URL    — `jwks_uri` from that document
+ *   MCP_RESOURCE_URL  — public URL of this server's MCP endpoint, exactly as
+ *                       clients connect to it (e.g.
+ *                       https://pubmed-mcp-PROJECT_NUMBER.asia-northeast1.run.app/mcp);
+ *                       used as the expected token `aud` and as the resource
+ *                       identifier
+ *
+ * Optional:
+ *   ALLOWED_SUBJECTS  — comma-separated token `sub` values (user IDs) permitted
+ *                       to connect. When empty, nothing is logged, so to find
+ *                       your own id deploy with a placeholder value first:
+ *                       rejected subjects are logged as
+ *                       "[auth] forbidden subject: <sub>". Then set the real
+ *                       value with `gcloud run services update --update-env-vars`.
+ */
+import type { Request, Response, NextFunction } from 'express';
+/** Tells the client which authorization server to use for this resource. */
+export declare function protectedResourceMetadata(_req: Request, res: Response): void;
+export declare function requireAuth(req: Request, res: Response, next: NextFunction): Promise<void>;
+//# sourceMappingURL=auth.d.ts.map

package/dist/auth.d.ts.map

@@ -0,0 +1 @@
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package/dist/auth.js

@@ -0,0 +1,97 @@
+/**
+ * OAuth 2.0 resource-server enforcement for HTTP mode.
+ *
+ * The MCP server acts as an OAuth 2.0 *resource server* (RFC 9728 /
+ * MCP authorization spec 2025-06-18). A managed authorization server
+ * (WorkOS AuthKit) runs Dynamic Client Registration (so claude.ai can register
+ * itself) and issues signed JWT access tokens. This module:
+ *
+ *   1. Advertises the authorization server via Protected Resource Metadata at
+ *      /.well-known/oauth-protected-resource
+ *   2. Validates the Bearer JWT on every /mcp request against the provider's
+ *      JWKS (signature, issuer, audience, expiry).
+ *   3. Restricts access to an allowlist of token subjects — since DCR lets
+ *      anyone register a client, this is what makes the server *yours only*.
+ *      With the allowlist empty, any valid token is accepted.
+ *
+ * Required environment variables (copy issuer/jwks from the provider's
+ *   https://<your-authkit-domain>/.well-known/oauth-authorization-server ):
+ *   OAUTH_ISSUER      — `issuer` from that document
+ *   OAUTH_JWKS_URL    — `jwks_uri` from that document
+ *   MCP_RESOURCE_URL  — public URL of this server's MCP endpoint, exactly as
+ *                       clients connect to it (e.g.
+ *                       https://pubmed-mcp-PROJECT_NUMBER.asia-northeast1.run.app/mcp);
+ *                       used as the expected token `aud` and as the resource
+ *                       identifier
+ *
+ * Optional:
+ *   ALLOWED_SUBJECTS  — comma-separated token `sub` values (user IDs) permitted
+ *                       to connect. When empty, nothing is logged, so to find
+ *                       your own id deploy with a placeholder value first:
+ *                       rejected subjects are logged as
+ *                       "[auth] forbidden subject: <sub>". Then set the real
+ *                       value with `gcloud run services update --update-env-vars`.
+ */
+import { createRemoteJWKSet, jwtVerify } from 'jose';
+const ISSUER = requireEnv('OAUTH_ISSUER');
+const JWKS_URL = requireEnv('OAUTH_JWKS_URL');
+const RESOURCE = requireEnv('MCP_RESOURCE_URL');
+const ALLOWED_SUBJECTS = (process.env.ALLOWED_SUBJECTS ?? '')
+    .split(',')
+    .map((s) => s.trim())
+    .filter(Boolean);
+// Metadata lives at the well-known path on the same origin as the resource.
+const RESOURCE_METADATA_URL = `${originOf(RESOURCE)}/.well-known/oauth-protected-resource`;
+const jwks = createRemoteJWKSet(new URL(JWKS_URL));
+// ── Protected Resource Metadata (RFC 9728) ──────────────────────────────────
+/** Tells the client which authorization server to use for this resource. */
+export function protectedResourceMetadata(_req, res) {
+    res.json({
+        resource: RESOURCE,
+        authorization_servers: [ISSUER],
+        bearer_methods_supported: ['header'],
+    });
+}
+// ── Bearer token enforcement ────────────────────────────────────────────────
+export async function requireAuth(req, res, next) {
+    const header = req.headers.authorization;
+    if (!header?.startsWith('Bearer ')) {
+        unauthorized(res, 'missing_token');
+        return;
+    }
+    const token = header.slice('Bearer '.length).trim();
+    try {
+        const { payload } = await jwtVerify(token, jwks, {
+            issuer: ISSUER,
+            audience: RESOURCE,
+        });
+        if (ALLOWED_SUBJECTS.length > 0 && !ALLOWED_SUBJECTS.includes(payload.sub ?? '')) {
+            // Valid token, but not you. Log the subject so you can allowlist yourself.
+            process.stderr.write(`[auth] forbidden subject: ${payload.sub ?? '(none)'}\n`);
+            res.status(403).json({ error: 'forbidden' });
+            return;
+        }
+        next();
+    }
+    catch (err) {
+        process.stderr.write(`[auth] token rejected: ${String(err)}\n`);
+        unauthorized(res, 'invalid_token');
+    }
+}
+// ── Helpers ─────────────────────────────────────────────────────────────────
+/** 401 with the RFC 9728 pointer so the client can discover how to authorize. */
+function unauthorized(res, error) {
+    res.setHeader('WWW-Authenticate', `Bearer resource_metadata="${RESOURCE_METADATA_URL}", error="${error}"`);
+    res.status(401).json({ error });
+}
+function originOf(url) {
+    return new URL(url).origin;
+}
+function requireEnv(name) {
+    const value = process.env[name];
+    if (!value) {
+        throw new Error(`Missing required environment variable: ${name}`);
+    }
+    return value;
+}
+//# sourceMappingURL=auth.js.map

package/dist/auth.js.map

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package/dist/cli/commands.d.ts

@@ -0,0 +1,42 @@
+/**
+ * Command table for the pubmed CLI.
+ *
+ * Each command runs one MCP tool: it turns command-line input into the tool's
+ * parameters, validates them with the tool's zod schema (as the MCP server
+ * does), and calls the same tool function, so the JSON output is the same.
+ * Lists longer than a tool's per-request limit are split into batches that
+ * run one after another through the shared client and its rate limiter; the
+ * batch results are merged into one response of the same shape.
+ */
+import type { NcbiClient } from '../pubmed/client.js';
+/** Invalid command-line input. The CLI exits with status 2 instead of 1. */
+export declare class UsageError extends Error {
+    constructor(message: string);
+}
+export interface CommandInput {
+    /** Option values by long name (e.g. "max-results"); unset options are undefined. */
+    values: Record<string, string | undefined>;
+    positionals: string[];
+    /** Read a file, or stdin when path is "-". */
+    readText(path: string): Promise<string>;
+}
+export interface CommandResult {
+    output: unknown;
+    /** Short description of the output, e.g. "20 articles". */
+    summary: string;
+}
+export interface Command {
+    name: string;
+    /** The MCP tool this command runs. */
+    tool: string;
+    /** One line for the command list in `pubmed --help`. */
+    description: string;
+    help: string;
+    options: Record<string, {
+        type: 'string';
+    }>;
+    execute(input: CommandInput, client: NcbiClient): Promise<CommandResult>;
+}
+export declare const COMMANDS: Command[];
+export declare function errorMessage(err: unknown): string;
+//# sourceMappingURL=commands.d.ts.map

package/dist/cli/commands.d.ts.map

@@ -0,0 +1 @@
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