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MCP Integration Guide

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Overview

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Table of Contents

1. Prerequisites
2. Step 1: Create an Integration
3. Step 2: Configure MCP Server
4. Step 3: Create a Connection
5. Step 4: Use MCP Tools in YAML
6. Provider-Specific Setup
7. Troubleshooting

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Prerequisites

• Access credentials for your MCP provider (OAuth credentials or API key)
• The MCP server URL (base URL where the MCP server is running)

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Step 1: Create an Integration

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For OAuth2 Providers (e.g., Microsoft, Atlassian)

1. Navigate to Settings → Integrations
2. Click “Add Integration”
3. Fill in the form:
   • Provider: Select your provider (e.g., Microsoft, Atlassian)
   • Name: Give your integration a descriptive name (e.g., “Company Atlassian”)
   • Description: Optional description
   • OAuth Client ID: Your OAuth application’s client ID
   • OAuth Client Secret: Your OAuth application’s client secret
   • Scopes: Required OAuth scopes (comma-separated), e.g:
     • For Atlassian: read:jira-work, write:jira-work
     • For Microsoft: Mail.Read, Mail.Send, offline_access
4. Click “Create Integration”
5. Set the integration as default one (at least one default integration is needed for a provider)

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For API Key Providers (e.g., Lexware)

1. Navigate to Settings → Integrations
2. Click “Add Integration”
3. Fill in the form:
   • Provider: Select your API key provider (e.g., Lexware)
   • Name: Give your integration a descriptive name (e.g., “Company Lexware”)
   • Description: Optional description
4. Click “Create Integration”
5. Set the integration as default one (at least one default integration is needed for a provider)

Note: For API key providers, you don’t need to provide credentials at the integration level. The API key will be provided when creating a connection.

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Step 2: Configure MCP Server

1. Navigate to Tools → MCP Servers
2. Click “Add MCP”
3. Fill in the configuration:
   • Name: Descriptive name for this MCP server (e.g., “Atlassian Jira MCP”)
   • Base URL: The MCP server endpoint
     • Example: http://localhost:8008/mcp (for local development)
     • Example: https://mcp-atlassian.yourcompany.com/mcp (for production)
   • Authentication Type: Select the auth type
     • No Authentication: For public MCP servers
     • OAuth 2.0: For OAuth-based providers
     • API Key: For API key-based providers
   • Provider: Select the provider which is linked to your created integration in Step 1
4. Click “Create MCP Server”

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Step 3: Create a Connection

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For OAuth2 Providers

1. Navigate to the MCP server configured in step 2
2. Click “Connect” or View Details -> “Add Connection”
3. Give the connection a unique name not used in other MCPs as well (set it as default, at least 1 default connection is needed)
4. You’ll be redirected to the provider’s OAuth consent screen
5. Grant the requested permissions
6. You’ll be redirected back to Atthene with an active connection

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For API Key Providers

1. Navigate to the MCP server configured in step 2
2. Click “Connect” or View Details -> “Add Connection”
3. Give the connection a unique name not used in other MCPs as well (set it as default, at least 1 default connection is needed)
4. You’ll be redirected to the provider’s consent screen
   • API Key: Enter your API key from the provider
5. Click “Connect”
6. You’ll be redirected back to Atthene with an active connection

Important: Each user needs to create their own connection to use MCP tools. The integration is shared at the company level, but connections are per-user.

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Step 4: Retrieve tools

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Step 5: Use MCP Tools in YAML

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Tool Naming Convention

mcp__<mcp_configuration_name>

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Example YAML Configuration

name: Atlassian Helper
description: AI assistant with atlassian mcp tools
save_messages: true
persistent_state: true
agents:
- name: atlassian_tool_agent
  tools:
  - mcp__my_atlassian_mcp
  agent_type: react_agent
  llm_config:
    max_tokens: 2000
    temperature: 0.1
  description: AI assistant with Atlassian tool calling capabilities
  prompt_config:
    system_prompt: 'You are a helpful AI assistant with access to Atlassian various tools.
      When you need to use a tool, think step by step about what information you need
      '
  streaming_config:
    enable_streaming: true
    show_output_to_user: true
edges:
- to: atlassian_tool_agent
  from: START
- to: END
  from: atlassian_tool_agent
entry_point: START
architecture: workflow

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Provider-Specific Setup

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Atlassian (Jira/Confluence)

• read:jira-work - Read Jira issues
• write:jira-work - Create/update Jira issues

Note: You can have a look at the client you have configured at the atlassian admin for more scopes

• The system automatically fetches your Atlassian Cloud ID
• If you have multiple Atlassian sites, you’ll need to configure the Cloud ID manually (Still under development)

• list_issues - List Jira issues with filters
• create_issue - Create new Jira issues
• update_issue - Update existing issues
• get_issue - Get details of a specific issue

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Lexware Office

• Uses custom header Lexware-API-Key for authentication
• No OAuth setup required

• get_invoices - List invoices with filters
• get_invoice - Get invoice details by ID
• get_contacts - List contacts
• get_posting_categories - Get posting categories
• get_countries - Get country tax classifications

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Troubleshooting

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”No connection found” Error

1. Ensure you’ve created a connection (Step 3)
2. Check that the connection is set as default (if you have multiple)

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“Multiple Atlassian sites found” Error

1. This occurs when your Atlassian account has access to multiple sites
2. You need to manually configure the Cloud ID
3. Contact your administrator to set the specific Cloud ID for your organization

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Advanced Configuration

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Multiple MCP Servers for Same Provider

# MCP Config 1: "jira-engineering"
tools:
  - mcp__jira_engineering

# MCP Config 2: "jira-marketing"  
tools:
  - mcp__jira_marketing

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Custom MCP Servers

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If you’re running your own MCP server with some custom provider for authentication please communicate to the administrator to set up the MCP.