AgentMode + JetBrains AI Assistant: Complete MCP Integration

AgentMode is a MCP server that Connect to dozens of databases, data warehouses, Github & more, from a single MCP server. Run the Docker image locally, in the cloud, or on-premise..

When integrated with JetBrains AI Assistant, you can:

• Execute SQL queries across connected databases
• Interact with GitHub repositories and issues
• Connect to data warehouses like Snowflake, BigQuery

This guide provides step-by-step instructions to set up AgentMode in JetBrains AI Assistant, including configuration, examples, and troubleshooting.

What You'll Achieve

After completing this setup:

• AgentMode will be fully integrated and operational
• You can use AgentMode tools directly in JetBrains AI Assistant
• All AgentMode capabilities will be available for your workflows
• Access to 3 different tools

Prerequisites

Before starting, ensure you have:

• API key from AgentMode dashboard
• Workspace identifier
• JetBrains AI Assistant installed and configured
• Compatible operating system (Windows, macOS, Linux)

Installation

Step 1: Install AgentMode

Configuration

Step 2: Configure JetBrains AI Assistant

1. Locate your configuration file:

   • Windows: Settings > Tools > AI Assistant > Model Context Protocol (MCP)
   • macOS: Preferences > Tools > AI Assistant > Model Context Protocol (MCP)
   • Linux: Settings > Tools > AI Assistant > Model Context Protocol (MCP)

2. Add server configuration:

{
  "mcpServers": {
    "agentmode": {
      "command": "npx",
      "args": ["-y", "agentmode"],
      "env": {
        "AGENTMODE_API_KEY": "am_1234567890abcdef",
        "AGENTMODE_WORKSPACE": "my-team-workspace"
      }
    }
  }
}

3. Restart JetBrains AI Assistant

Completely quit and restart JetBrains AI Assistant to load the new configuration.

Examples

Once configured, you can use AgentMode in JetBrains AI Assistant:

Multi-Database Analytics

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Ask JetBrains AI Assistant: "Show me user engagement metrics from both databases"

Expected Result: undefined

GitHub Issue Management

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Ask JetBrains AI Assistant: "Create issues for users with failed payments"

Expected Result: undefined

Data Pipeline Monitoring

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Ask JetBrains AI Assistant: "Check status of yesterday's data pipeline runs"

Expected Result: undefined

Testing Your Setup

1. Start a new conversation in JetBrains AI Assistant
2. Ask JetBrains AI Assistant to list available tools
3. Try using AgentMode functionality

Test prompts:

• "Type / and look for AgentMode tools in the command list"
• "Ask AI Assistant to use AgentMode for a specific task"
• "Check the MCP settings page for connection status indicator"

Troubleshooting

Common Issues

MCP Server Not Connecting

Symptoms: Server status shows disconnected, Tools not appearing in chat, Connection timeout

Cause: Server configuration incorrect or server not starting

Solution:

• Verify server command is correct and executable
• Check environment variables are set properly
• View MCP logs: Help > Show Log in Explorer > mcp folder
• Test server command in terminal manually

Remote Server Not Supported

Symptoms: HTTP server not connecting, SSE transport errors

Cause: AI Assistant only supports stdio transport for client connections

Solution:

• Use mcp-remote proxy for remote servers
• Configuration: npx -y mcp-remote@latest https://server-url/endpoint
• This wraps HTTP/SSE in stdio transport

Import from Claude Not Working

Symptoms: No servers imported, Configuration empty after import

Cause: Claude Desktop config file not found or in unexpected location

Solution:

• Verify Claude Desktop is installed
• Check config exists at ~/Library/Application Support/Claude/claude_desktop_config.json (macOS)
• Or %APPDATA%/Claude/claude_desktop_config.json (Windows)
• Manually copy configuration if auto-import fails

External Client Cannot Connect to IDE Server

Symptoms: Client shows MCP server unavailable, Connection refused

Cause: IDE MCP server not enabled or client not configured

Solution:

• Enable MCP Server in Settings > Tools > MCP Server
• Use Auto-Configure for supported clients
• Restart both IDE and external client
• Check firewall allows local connections

Brave Mode Commands Not Running

Symptoms: Terminal commands require confirmation, Workflow interrupted by prompts

Cause: Brave mode not enabled

Solution:

• Enable in Settings > Tools > MCP Server
• Check "Run shell commands without confirmation (brave mode)"
• Use with caution - commands run without confirmation

AgentMode not appearing in JetBrains AI Assistant

Symptoms: Server not listed, Tools not available

Cause: Configuration or installation issue

Solution:

• Verify configuration syntax
• Check AgentMode installation
• Restart JetBrains AI Assistant
• Check logs for error messages

Next Steps

Now that AgentMode is integrated with JetBrains AI Assistant:

• Explore all AgentMode capabilities through JetBrains AI Assistant
• Check out other MCP servers that work with JetBrains AI Assistant
• Join the MCP community for tips and support
• Consider contributing to AgentMode development

Need Help?

• Search for AgentMode documentation
• Check the JetBrains AI Assistant MCP guide
• Join the MCP community discussions