@elnora-ai/mcp-server 0.1.0

package/CHANGELOG.md

@@ -0,0 +1,20 @@
+# Changelog
+
+All notable changes to the Elnora MCP Server will be documented in this file.
+
+The format is based on [Keep a Changelog](https://keepachangelog.com/),
+and this project adheres to [Semantic Versioning](https://semver.org/).
+
+## [Unreleased]
+
+## [0.1.0] - 2026-02-27
+
+### Added
+
+- Initial release of Elnora MCP Server
+- 8 MCP tools: `elnora_create_task`, `elnora_list_tasks`, `elnora_get_task_messages`,
+  `elnora_send_message`, `elnora_list_files`, `elnora_get_file_content`,
+  `elnora_upload_file`, `elnora_generate_protocol`
+- HTTP transport (Streamable HTTP) with OAuth 2.1 and API key authentication
+- Protected Resource Metadata endpoint (RFC 9728)
+- Health check endpoint

package/LICENSE

@@ -0,0 +1,201 @@
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package/README.md

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+# Elnora MCP Server
+
+Connect AI agents to the [Elnora](https://elnora.ai) bioprotocol optimization platform via the [Model Context Protocol](https://modelcontextprotocol.io).
+
+[![License](https://img.shields.io/badge/license-Apache%202.0-blue.svg)](LICENSE)
+
+## What is Elnora?
+
+Elnora is an AI-powered platform that helps researchers generate, optimize, and manage bioprotocols for wet-lab experiments. With this MCP server, you can interact with Elnora directly from AI coding assistants like Claude Code, Codex, Cursor, VS Code, and ChatGPT.
+
+## Quick Start
+
+Add the Elnora MCP server to your AI client. No installation required — just point to the remote URL.
+
+### Claude Code
+
+```bash
+claude mcp add elnora --transport streamable-http https://mcp.elnora.ai/mcp
+```
+
+### Cursor
+
+Add to your Cursor MCP settings (Settings > MCP Servers):
+
+```json
+{
+  "mcpServers": {
+    "elnora": {
+      "url": "https://mcp.elnora.ai/mcp"
+    }
+  }
+}
+```
+
+### VS Code (Copilot)
+
+Add to your `.vscode/mcp.json`:
+
+```json
+{
+  "servers": {
+    "elnora": {
+      "type": "streamable-http",
+      "url": "https://mcp.elnora.ai/mcp"
+    }
+  }
+}
+```
+
+### Codex
+
+```bash
+codex --mcp-config mcp.json
+```
+
+With `mcp.json`:
+
+```json
+{
+  "mcpServers": {
+    "elnora": {
+      "url": "https://mcp.elnora.ai/mcp"
+    }
+  }
+}
+```
+
+### ChatGPT
+
+Add as a remote MCP server in ChatGPT settings using the URL `https://mcp.elnora.ai/mcp`.
+
+---
+
+On first connection, a browser window will open for OAuth login. Subsequent requests use the issued token automatically.
+
+## Available Tools
+
+### Tasks
+
+| Tool | Description |
+|------|-------------|
+| `elnora_create_task` | Create a new task (conversation thread) for interacting with Elnora's AI |
+| `elnora_list_tasks` | List tasks in your workspace with optional status filter |
+| `elnora_get_task_messages` | Get the message history for a specific task |
+
+### Messages
+
+| Tool | Description |
+|------|-------------|
+| `elnora_send_message` | Send a message to a task and receive an AI response (30-120s for complex requests) |
+
+### Files
+
+| Tool | Description |
+|------|-------------|
+| `elnora_list_files` | List files in your workspace with optional project filter |
+| `elnora_get_file_content` | Retrieve the content of a specific file |
+| `elnora_upload_file` | Upload a text file to your workspace |
+
+### Protocols
+
+| Tool | Description |
+|------|-------------|
+| `elnora_generate_protocol` | Generate a bioprotocol — creates a task, sends your description, and returns the result |
+
+## Authentication
+
+### OAuth 2.1 (Recommended)
+
+Most MCP clients handle OAuth automatically. On first connection:
+
+1. A browser window opens for login
+2. You authenticate with your Elnora account
+3. The client receives a token and uses it for subsequent requests
+
+No manual configuration needed.
+
+### API Key
+
+Alternatively, create an API key in your [Elnora dashboard](https://platform.elnora.ai) and pass it as a Bearer token:
+
+```json
+{
+  "mcpServers": {
+    "elnora": {
+      "url": "https://mcp.elnora.ai/mcp",
+      "headers": {
+        "Authorization": "Bearer YOUR_API_KEY"
+      }
+    }
+  }
+}
+```
+
+**Security best practices:**
+- Never commit API keys to version control
+- Use environment variables or a secrets manager
+- Rotate keys periodically via the Elnora dashboard
+- Use OAuth when possible — it handles token refresh automatically
+
+## Examples
+
+### Generate a bioprotocol
+
+Ask your AI assistant:
+
+> "Use Elnora to generate a HEK 293 cell maintenance protocol"
+
+The assistant will call `elnora_generate_protocol` with your description and return the generated protocol.
+
+### Search and read files
+
+> "List my files in Elnora, then show me the content of the most recent protocol"
+
+The assistant will call `elnora_list_files` followed by `elnora_get_file_content`.
+
+### Manage tasks
+
+> "Show me my active Elnora tasks and get the messages from the latest one"
+
+The assistant will call `elnora_list_tasks` and then `elnora_get_task_messages`.
+
+## Troubleshooting
+
+| Error | Cause | Solution |
+|-------|-------|----------|
+| 401 Unauthorized | Missing or expired token | Re-authenticate via OAuth or check your API key |
+| 403 Forbidden | Insufficient permissions | Verify your account has access to the requested resource |
+| 408 / Timeout | Complex operation taking too long | Protocol generation can take up to 120s — try again or simplify the request |
+| Connection refused | Server unreachable | Check your internet connection; verify `https://mcp.elnora.ai/health` is accessible |
+
+If you encounter persistent issues, please [open a GitHub issue](https://github.com/Elnora-AI/elnora-mcp-server/issues).
+
+## Security
+
+We take security seriously. If you discover a vulnerability, please report it responsibly — see our [security policy](.github/SECURITY.md).
+
+## Changelog
+
+See [CHANGELOG.md](CHANGELOG.md) for version history.
+
+## Contributing
+
+See [CONTRIBUTING.md](.github/CONTRIBUTING.md) for contribution guidelines.
+
+## License
+
+This project is licensed under the [Apache License 2.0](LICENSE).
+
+## Support
+
+- **Bug reports and feature requests:** [GitHub Issues](https://github.com/Elnora-AI/elnora-mcp-server/issues)
+- **Account and billing questions:** [support@elnora.ai](mailto:support@elnora.ai)
+- **Security vulnerabilities:** [security@elnora.ai](mailto:security@elnora.ai)

package/dist/auth/middleware.d.ts

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+import { Request, Response, NextFunction } from "express";
+import { AuthContext, ElnoraConfig } from "../types.js";
+declare global {
+    namespace Express {
+        interface Request {
+            authContext?: AuthContext;
+            bearerToken?: string;
+        }
+    }
+}
+export declare function authMiddleware(config: ElnoraConfig): (req: Request, res: Response, next: NextFunction) => Promise<void>;
+//# sourceMappingURL=middleware.d.ts.map

package/dist/auth/middleware.d.ts.map

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package/dist/auth/middleware.js

@@ -0,0 +1,40 @@
+import { ElnoraApiClient } from "../services/elnora-api-client.js";
+export function authMiddleware(config) {
+    return async (req, res, next) => {
+        const authHeader = req.headers.authorization;
+        if (!authHeader || !authHeader.startsWith("Bearer ")) {
+            res.setHeader("WWW-Authenticate", `Bearer resource_metadata="${req.protocol}://${req.get("host")}/.well-known/oauth-protected-resource"`);
+            res.status(401).json({
+                error: "unauthorized",
+                error_description: "Bearer token required",
+            });
+            return;
+        }
+        const token = authHeader.slice(7); // Remove "Bearer "
+        try {
+            const validation = await ElnoraApiClient.validateToken(config.tokenValidationUrl, token);
+            if (!validation.valid || !validation.userId || !validation.organizationId) {
+                res.status(401).json({
+                    error: "invalid_token",
+                    error_description: "Token is invalid or expired",
+                });
+                return;
+            }
+            req.authContext = {
+                userId: validation.userId,
+                organizationId: validation.organizationId,
+                scopes: validation.scopes || "",
+                tokenType: validation.tokenType || "unknown",
+            };
+            req.bearerToken = token;
+            next();
+        }
+        catch {
+            res.status(401).json({
+                error: "invalid_token",
+                error_description: "Token validation failed",
+            });
+        }
+    };
+}
+//# sourceMappingURL=middleware.js.map

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package/dist/auth/protected-resource.d.ts

@@ -0,0 +1,4 @@
+import { Request, Response } from "express";
+import { ElnoraConfig } from "../types.js";
+export declare function protectedResourceMetadataHandler(config: ElnoraConfig): (req: Request, res: Response) => void;
+//# sourceMappingURL=protected-resource.d.ts.map

package/dist/auth/protected-resource.d.ts.map

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package/dist/auth/protected-resource.js

@@ -0,0 +1,19 @@
+export function protectedResourceMetadataHandler(config) {
+    return (req, res) => {
+        const resource = process.env.RESOURCE_URL || `${req.protocol}://${req.get("host")}`;
+        res.json({
+            resource,
+            authorization_servers: [config.authUrl],
+            scopes_supported: [
+                "tasks:read",
+                "tasks:write",
+                "files:read",
+                "files:write",
+                "messages:read",
+                "messages:write",
+            ],
+            bearer_methods_supported: ["header"],
+        });
+    };
+}
+//# sourceMappingURL=protected-resource.js.map

package/dist/auth/protected-resource.js.map

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package/dist/constants.d.ts

@@ -0,0 +1,6 @@
+export declare const CHARACTER_LIMIT = 25000;
+export declare const DEFAULT_PAGE_SIZE = 20;
+export declare const MAX_PAGE_SIZE = 100;
+export declare const REQUEST_TIMEOUT_MS = 30000;
+export declare const LONG_REQUEST_TIMEOUT_MS = 120000;
+//# sourceMappingURL=constants.d.ts.map

package/dist/constants.d.ts.map

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

@@ -0,0 +1,6 @@
+export const CHARACTER_LIMIT = 25000;
+export const DEFAULT_PAGE_SIZE = 20;
+export const MAX_PAGE_SIZE = 100;
+export const REQUEST_TIMEOUT_MS = 30000;
+export const LONG_REQUEST_TIMEOUT_MS = 120000;
+//# sourceMappingURL=constants.js.map

package/dist/constants.js.map

@@ -0,0 +1 @@
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package/dist/index.d.ts

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=index.d.ts.map

package/dist/index.d.ts.map

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

package/dist/index.js

@@ -0,0 +1,65 @@
+import { StreamableHTTPServerTransport } from "@modelcontextprotocol/sdk/server/streamableHttp.js";
+import express from "express";
+import { ElnoraApiClient } from "./services/elnora-api-client.js";
+import { authMiddleware } from "./auth/middleware.js";
+import { protectedResourceMetadataHandler } from "./auth/protected-resource.js";
+import { createElnoraServer } from "./server.js";
+function requireEnv(name) {
+    const value = process.env[name];
+    if (!value) {
+        throw new Error(`Required environment variable ${name} is not set`);
+    }
+    return value;
+}
+function loadConfig() {
+    return {
+        apiUrl: requireEnv("ELNORA_API_URL"),
+        authUrl: requireEnv("ELNORA_AUTH_URL"),
+        tokenValidationUrl: requireEnv("ELNORA_TOKEN_VALIDATION_URL"),
+        port: parseInt(process.env.PORT || "3000", 10),
+    };
+}
+async function main() {
+    const config = loadConfig();
+    const app = express();
+    app.use(express.json());
+    // Health check
+    app.get("/health", (_req, res) => {
+        res.json({ status: "ok", service: "elnora-mcp-server" });
+    });
+    // OAuth Protected Resource Metadata (per MCP spec, RFC 9728)
+    app.get("/.well-known/oauth-protected-resource", protectedResourceMetadataHandler(config));
+    // MCP endpoint with auth
+    app.post("/mcp", authMiddleware(config), async (req, res) => {
+        try {
+            // Create per-request MCP server and API client
+            const client = new ElnoraApiClient(config, req.bearerToken);
+            const getClient = () => client;
+            const server = createElnoraServer(config, getClient);
+            // Stateless transport — new transport per request
+            const transport = new StreamableHTTPServerTransport({
+                sessionIdGenerator: undefined,
+                enableJsonResponse: true,
+            });
+            res.on("close", () => transport.close());
+            await server.connect(transport);
+            await transport.handleRequest(req, res, req.body);
+        }
+        catch (error) {
+            console.error("MCP request error:", error);
+            if (!res.headersSent) {
+                res.status(500).json({ error: "internal_error", error_description: "MCP request failed" });
+            }
+        }
+    });
+    app.listen(config.port, () => {
+        console.error(`Elnora MCP server running on http://localhost:${config.port}/mcp`);
+        console.error(`Protected Resource Metadata: http://localhost:${config.port}/.well-known/oauth-protected-resource`);
+        console.error(`Health check: http://localhost:${config.port}/health`);
+    });
+}
+main().catch((error) => {
+    console.error("Server error:", error);
+    process.exit(1);
+});
+//# sourceMappingURL=index.js.map

package/dist/index.js.map

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package/dist/server.d.ts

@@ -0,0 +1,5 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ElnoraApiClient } from "./services/elnora-api-client.js";
+import { ElnoraConfig } from "./types.js";
+export declare function createElnoraServer(config: ElnoraConfig, getClient: () => ElnoraApiClient): McpServer;
+//# sourceMappingURL=server.d.ts.map

package/dist/server.d.ts.map

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

@@ -0,0 +1,17 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { registerTaskTools } from "./tools/tasks.js";
+import { registerMessageTools } from "./tools/messages.js";
+import { registerFileTools } from "./tools/files.js";
+import { registerProtocolTools } from "./tools/protocols.js";
+export function createElnoraServer(config, getClient) {
+    const server = new McpServer({
+        name: "elnora-mcp-server",
+        version: "0.1.0",
+    });
+    registerTaskTools(server, getClient);
+    registerMessageTools(server, getClient);
+    registerFileTools(server, getClient);
+    registerProtocolTools(server, getClient);
+    return server;
+}
+//# sourceMappingURL=server.js.map

package/dist/server.js.map

@@ -0,0 +1 @@
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package/dist/services/elnora-api-client.d.ts

@@ -0,0 +1,29 @@
+import { ElnoraConfig, ElnoraTask, ElnoraMessage, ElnoraFile, TokenValidationResult } from "../types.js";
+export declare class ElnoraApiClient {
+    private bearerToken;
+    private client;
+    private tokenValidationUrl;
+    constructor(config: ElnoraConfig, bearerToken: string);
+    static validateToken(tokenValidationUrl: string, token: string): Promise<TokenValidationResult>;
+    createTask(title?: string): Promise<ElnoraTask>;
+    listTasks(status?: string, limit?: number, offset?: number): Promise<{
+        items: ElnoraTask[];
+        totalCount: number;
+    }>;
+    getTaskMessages(taskId: string, limit?: number, offset?: number): Promise<{
+        items: ElnoraMessage[];
+        totalCount: number;
+    }>;
+    sendMessage(taskId: string, content: string, fileIds?: string[]): Promise<ElnoraMessage>;
+    listFiles(projectId?: string, limit?: number, offset?: number): Promise<{
+        items: ElnoraFile[];
+        totalCount: number;
+    }>;
+    getFileContent(fileId: string): Promise<{
+        content: string;
+        name: string;
+        fileType: string;
+    }>;
+    uploadFile(name: string, content: string, fileType?: string): Promise<ElnoraFile>;
+}
+//# sourceMappingURL=elnora-api-client.d.ts.map

package/dist/services/elnora-api-client.d.ts.map

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package/dist/services/elnora-api-client.js

@@ -0,0 +1,71 @@
+import axios from "axios";
+import { REQUEST_TIMEOUT_MS, LONG_REQUEST_TIMEOUT_MS } from "../constants.js";
+export class ElnoraApiClient {
+    bearerToken;
+    client;
+    tokenValidationUrl;
+    constructor(config, bearerToken) {
+        this.bearerToken = bearerToken;
+        this.client = axios.create({
+            baseURL: config.apiUrl,
+            timeout: REQUEST_TIMEOUT_MS,
+            headers: {
+                "Content-Type": "application/json",
+                Accept: "application/json",
+                Authorization: `Bearer ${bearerToken}`,
+            },
+        });
+        this.tokenValidationUrl = config.tokenValidationUrl;
+    }
+    // --- Token Validation ---
+    static async validateToken(tokenValidationUrl, token) {
+        const response = await axios.post(tokenValidationUrl, { token }, { timeout: REQUEST_TIMEOUT_MS });
+        return response.data;
+    }
+    // --- Tasks ---
+    async createTask(title) {
+        const response = await this.client.post("/tasks", {
+            title: title || "New Task",
+        });
+        return response.data;
+    }
+    async listTasks(status, limit = 20, offset = 0) {
+        const params = { limit, offset };
+        if (status)
+            params.status = status;
+        const response = await this.client.get("/tasks", { params });
+        return response.data;
+    }
+    async getTaskMessages(taskId, limit = 50, offset = 0) {
+        const response = await this.client.get(`/tasks/${taskId}/messages`, {
+            params: { limit, offset },
+        });
+        return response.data;
+    }
+    // --- Messages ---
+    async sendMessage(taskId, content, fileIds) {
+        const response = await this.client.post(`/tasks/${taskId}/messages`, { content, fileIds }, { timeout: LONG_REQUEST_TIMEOUT_MS });
+        return response.data;
+    }
+    // --- Files ---
+    async listFiles(projectId, limit = 20, offset = 0) {
+        const params = { limit, offset };
+        if (projectId)
+            params.projectId = projectId;
+        const response = await this.client.get("/files", { params });
+        return response.data;
+    }
+    async getFileContent(fileId) {
+        const response = await this.client.get(`/files/${fileId}/content`);
+        return response.data;
+    }
+    async uploadFile(name, content, fileType) {
+        const response = await this.client.post("/files", {
+            name,
+            content,
+            fileType: fileType || "text/markdown",
+        });
+        return response.data;
+    }
+}
+//# sourceMappingURL=elnora-api-client.js.map

package/dist/services/elnora-api-client.js.map

@@ -0,0 +1 @@
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package/dist/services/error-handler.d.ts

@@ -0,0 +1,2 @@
+export declare function handleApiError(error: unknown): string;
+//# sourceMappingURL=error-handler.d.ts.map

package/dist/services/error-handler.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"error-handler.d.ts","sourceRoot":"","sources":["../../src/services/error-handler.ts"],"names":[],"mappings":"AAEA,wBAAgB,cAAc,CAAC,KAAK,EAAE,OAAO,GAAG,MAAM,CA6BrD"}

package/dist/services/error-handler.js

@@ -0,0 +1,33 @@
+import axios from "axios";
+export function handleApiError(error) {
+    if (axios.isAxiosError(error)) {
+        const axiosErr = error;
+        if (axiosErr.response) {
+            const status = axiosErr.response.status;
+            const data = axiosErr.response.data;
+            const messages = data?.messages?.join(", ") || "";
+            switch (status) {
+                case 400:
+                    return `Error: Invalid request. ${messages || "Check your parameters."}`;
+                case 401:
+                    return "Error: Authentication failed. Your token may have expired — re-authenticate.";
+                case 403:
+                    return "Error: Permission denied. You don't have access to this resource.";
+                case 404:
+                    return `Error: Resource not found. ${messages || "Check the ID is correct."}`;
+                case 429:
+                    return "Error: Rate limit exceeded. Please wait before making more requests.";
+                default:
+                    return `Error: API request failed (${status}). ${messages}`;
+            }
+        }
+        else if (axiosErr.code === "ECONNABORTED") {
+            return "Error: Request timed out. The operation may still be in progress.";
+        }
+        else if (axiosErr.code === "ECONNREFUSED") {
+            return "Error: Service temporarily unavailable. Please try again later.";
+        }
+    }
+    return `Error: Unexpected error: ${error instanceof Error ? error.message : String(error)}`;
+}
+//# sourceMappingURL=error-handler.js.map

package/dist/services/error-handler.js.map

@@ -0,0 +1 @@
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package/dist/tools/files.d.ts

@@ -0,0 +1,4 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ElnoraApiClient } from "../services/elnora-api-client.js";
+export declare function registerFileTools(server: McpServer, getClient: () => ElnoraApiClient): void;
+//# sourceMappingURL=files.d.ts.map

package/dist/tools/files.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"files.d.ts","sourceRoot":"","sources":["../../src/tools/files.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AAInE,wBAAgB,iBAAiB,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,eAAe,GAAG,IAAI,CAwE3F"}

package/dist/tools/files.js

@@ -0,0 +1,64 @@
+import { z } from "zod";
+import { handleApiError } from "../services/error-handler.js";
+import { CHARACTER_LIMIT } from "../constants.js";
+export function registerFileTools(server, getClient) {
+    server.registerTool("elnora_list_files", {
+        title: "List Files",
+        description: "List files in your Elnora workspace. Returns file metadata including name, type, and visibility.",
+        inputSchema: {
+            project_id: z.string().uuid().optional().describe("Filter by project UUID"),
+            limit: z.number().int().min(1).max(100).default(20).describe("Max results"),
+            offset: z.number().int().min(0).default(0).describe("Pagination offset"),
+        },
+        annotations: { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
+    }, async ({ project_id, limit, offset }) => {
+        try {
+            const result = await getClient().listFiles(project_id, limit, offset);
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+    server.registerTool("elnora_get_file_content", {
+        title: "Get File Content",
+        description: "Retrieve the content of a specific file by its ID. Returns the file content as text along with metadata.",
+        inputSchema: {
+            file_id: z.string().uuid().describe("File UUID"),
+        },
+        annotations: { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
+    }, async ({ file_id }) => {
+        try {
+            const result = await getClient().getFileContent(file_id);
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+    server.registerTool("elnora_upload_file", {
+        title: "Upload File",
+        description: "Upload a text file to Elnora. Files are stored in the user's workspace and can be attached to task messages.",
+        inputSchema: {
+            name: z.string().min(1).max(255).describe("Filename"),
+            content: z.string().min(1).max(CHARACTER_LIMIT).describe("File content (max 25,000 chars)"),
+            file_type: z.string().optional().describe("MIME type (default: text/markdown)"),
+        },
+        annotations: { readOnlyHint: false, destructiveHint: false, idempotentHint: false, openWorldHint: true },
+    }, async ({ name, content, file_type }) => {
+        try {
+            const result = await getClient().uploadFile(name, content, file_type);
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+}
+//# sourceMappingURL=files.js.map

package/dist/tools/files.js.map

@@ -0,0 +1 @@
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package/dist/tools/messages.d.ts

@@ -0,0 +1,4 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ElnoraApiClient } from "../services/elnora-api-client.js";
+export declare function registerMessageTools(server: McpServer, getClient: () => ElnoraApiClient): void;
+//# sourceMappingURL=messages.d.ts.map

package/dist/tools/messages.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"messages.d.ts","sourceRoot":"","sources":["../../src/tools/messages.ts"],"names":[],"mappings":"AAAA,OAAO,EAAE,SAAS,EAAE,MAAM,yCAAyC,CAAC;AAEpE,OAAO,EAAE,eAAe,EAAE,MAAM,kCAAkC,CAAC;AAGnE,wBAAgB,oBAAoB,CAAC,MAAM,EAAE,SAAS,EAAE,SAAS,EAAE,MAAM,eAAe,GAAG,IAAI,CA8B9F"}

package/dist/tools/messages.js

@@ -0,0 +1,30 @@
+import { z } from "zod";
+import { handleApiError } from "../services/error-handler.js";
+export function registerMessageTools(server, getClient) {
+    server.registerTool("elnora_send_message", {
+        title: "Send Message",
+        description: "Send a message to an Elnora task and receive the AI response. The message is processed by Elnora's AI system, which handles protocol generation, research, and data analysis. This operation may take 30-120 seconds for complex requests.",
+        inputSchema: {
+            task_id: z.string().uuid().describe("Task UUID"),
+            message: z.string().min(1).max(10000).describe("Message content (markdown supported)"),
+            file_ids: z.array(z.string().uuid()).optional().describe("File IDs to attach"),
+        },
+        annotations: {
+            readOnlyHint: false,
+            destructiveHint: false,
+            idempotentHint: false,
+            openWorldHint: true,
+        },
+    }, async ({ task_id, message, file_ids }) => {
+        try {
+            const response = await getClient().sendMessage(task_id, message, file_ids);
+            return {
+                content: [{ type: "text", text: JSON.stringify(response, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+}
+//# sourceMappingURL=messages.js.map

package/dist/tools/messages.js.map

@@ -0,0 +1 @@
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package/dist/tools/protocols.d.ts

@@ -0,0 +1,4 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ElnoraApiClient } from "../services/elnora-api-client.js";
+export declare function registerProtocolTools(server: McpServer, getClient: () => ElnoraApiClient): void;
+//# sourceMappingURL=protocols.d.ts.map

package/dist/tools/protocols.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/protocols.js

@@ -0,0 +1,45 @@
+import { z } from "zod";
+import { handleApiError } from "../services/error-handler.js";
+export function registerProtocolTools(server, getClient) {
+    server.registerTool("elnora_generate_protocol", {
+        title: "Generate Protocol",
+        description: `Generate a bioprotocol using Elnora's AI agents. This is a convenience tool that creates a task, sends the description as a message, and returns the generated protocol content. This is the primary tool for hackathon partners. The operation typically takes 30-120 seconds.
+
+Examples:
+  - "Generate a HEK 293 cell maintenance protocol"
+  - "Create a CRISPR guide RNA design protocol for BRCA1"
+  - "Write a western blot protocol for detecting p53 in HeLa cells"`,
+        inputSchema: {
+            description: z.string().min(10).max(5000).describe("Protocol description"),
+            title: z.string().max(200).optional().describe("Task title (defaults to description preview)"),
+        },
+        annotations: {
+            readOnlyHint: false,
+            destructiveHint: false,
+            idempotentHint: false,
+            openWorldHint: true,
+        },
+    }, async ({ description, title }) => {
+        try {
+            const client = getClient();
+            // 1. Create a task
+            const taskTitle = title || description.slice(0, 100);
+            const task = await client.createTask(taskTitle);
+            // 2. Send the description as a message
+            const response = await client.sendMessage(task.id, description);
+            // 3. Return the result
+            const result = {
+                task_id: task.id,
+                protocol_content: response.content,
+                message_id: response.id,
+            };
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+}
+//# sourceMappingURL=protocols.js.map

package/dist/tools/protocols.js.map

@@ -0,0 +1 @@
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package/dist/tools/tasks.d.ts

@@ -0,0 +1,4 @@
+import { McpServer } from "@modelcontextprotocol/sdk/server/mcp.js";
+import { ElnoraApiClient } from "../services/elnora-api-client.js";
+export declare function registerTaskTools(server: McpServer, getClient: () => ElnoraApiClient): void;
+//# sourceMappingURL=tasks.d.ts.map

package/dist/tools/tasks.d.ts.map

@@ -0,0 +1 @@
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package/dist/tools/tasks.js

@@ -0,0 +1,68 @@
+import { z } from "zod";
+import { handleApiError } from "../services/error-handler.js";
+export function registerTaskTools(server, getClient) {
+    server.registerTool("elnora_create_task", {
+        title: "Create Task",
+        description: "Create a new task (conversation) in Elnora. Tasks are the primary unit of interaction — each task is a chat thread where you can send messages and receive AI agent responses.",
+        inputSchema: {
+            title: z.string().max(200).optional().describe("Task title (e.g., 'HEK 293 protocol generation')"),
+        },
+        annotations: {
+            readOnlyHint: false,
+            destructiveHint: false,
+            idempotentHint: false,
+            openWorldHint: true,
+        },
+    }, async ({ title }) => {
+        try {
+            const task = await getClient().createTask(title);
+            return {
+                content: [{ type: "text", text: JSON.stringify(task, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+    server.registerTool("elnora_list_tasks", {
+        title: "List Tasks",
+        description: "List tasks in your Elnora workspace. Returns task summaries with status and timestamps.",
+        inputSchema: {
+            status: z.string().optional().describe("Filter by task status"),
+            limit: z.number().int().min(1).max(100).default(20).describe("Max results"),
+            offset: z.number().int().min(0).default(0).describe("Pagination offset"),
+        },
+        annotations: { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
+    }, async ({ status, limit, offset }) => {
+        try {
+            const result = await getClient().listTasks(status, limit, offset);
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+    server.registerTool("elnora_get_task_messages", {
+        title: "Get Task Messages",
+        description: "Get the message history for a specific task. Returns user and assistant messages in chronological order.",
+        inputSchema: {
+            task_id: z.string().uuid().describe("Task UUID"),
+            limit: z.number().int().min(1).max(100).default(50).describe("Max messages"),
+            offset: z.number().int().min(0).default(0).describe("Pagination offset"),
+        },
+        annotations: { readOnlyHint: true, destructiveHint: false, idempotentHint: true, openWorldHint: true },
+    }, async ({ task_id, limit, offset }) => {
+        try {
+            const result = await getClient().getTaskMessages(task_id, limit, offset);
+            return {
+                content: [{ type: "text", text: JSON.stringify(result, null, 2) }],
+            };
+        }
+        catch (error) {
+            return { content: [{ type: "text", text: handleApiError(error) }], isError: true };
+        }
+    });
+}
+//# sourceMappingURL=tasks.js.map

package/dist/tools/tasks.js.map

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package/dist/types.d.ts

@@ -0,0 +1,49 @@
+export interface ElnoraConfig {
+    apiUrl: string;
+    authUrl: string;
+    tokenValidationUrl: string;
+    port: number;
+}
+export interface AuthContext {
+    userId: number;
+    organizationId: string;
+    scopes: string;
+    tokenType: string;
+}
+export interface ElnoraTask {
+    id: string;
+    title: string;
+    status: string;
+    createdAt: string;
+    updatedAt: string;
+}
+export interface ElnoraMessage {
+    id: string;
+    taskId: string;
+    role: "user" | "assistant";
+    content: string;
+    createdAt: string;
+    agentName?: string;
+}
+export interface ElnoraFile {
+    id: string;
+    name: string;
+    fileType: string;
+    visibility: string;
+    createdAt: string;
+    latestVersionId?: string;
+}
+export interface TokenValidationResult {
+    valid: boolean;
+    userId?: number;
+    organizationId?: string;
+    scopes?: string;
+    tokenType?: string;
+}
+export interface PaginatedResponse<T> {
+    items: T[];
+    totalCount: number;
+    hasMore: boolean;
+    nextOffset?: number;
+}
+//# sourceMappingURL=types.d.ts.map

package/dist/types.d.ts.map

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

@@ -0,0 +1,2 @@
+export {};
+//# sourceMappingURL=types.js.map

package/dist/types.js.map

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

package/package.json

@@ -0,0 +1,54 @@
+{
+  "name": "@elnora-ai/mcp-server",
+  "version": "0.1.0",
+  "description": "MCP server for Elnora Platform — AI-powered bioprotocol optimization",
+  "type": "module",
+  "main": "dist/index.js",
+  "scripts": {
+    "start": "node dist/index.js",
+    "dev": "tsx watch src/index.ts",
+    "build": "tsc",
+    "clean": "rm -rf dist",
+    "test": "vitest run",
+    "test:watch": "vitest"
+  },
+  "license": "Apache-2.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/Elnora-AI/elnora-mcp-server.git"
+  },
+  "bugs": {
+    "url": "https://github.com/Elnora-AI/elnora-mcp-server/issues"
+  },
+  "homepage": "https://elnora.ai",
+  "keywords": [
+    "mcp",
+    "model-context-protocol",
+    "elnora",
+    "bioprotocol",
+    "ai-agent",
+    "lab-protocol"
+  ],
+  "files": [
+    "dist/",
+    "LICENSE",
+    "README.md",
+    "CHANGELOG.md"
+  ],
+  "engines": {
+    "node": ">=18"
+  },
+  "dependencies": {
+    "@modelcontextprotocol/sdk": "^1.12.0",
+    "express": "^5.1.0",
+    "zod": "^3.24.0",
+    "axios": "^1.8.0"
+  },
+  "devDependencies": {
+    "@types/express": "^5.0.0",
+    "@types/node": "^22.12.0",
+    "tsx": "^4.19.0",
+    "typescript": "^5.7.0",
+    "vitest": "^3.0.0"
+  }
+}