atlassian-mcp-server 0.4.3
MCP server for Atlassian Cloud (Confluence & Jira) with seamless OAuth 2.0 authentication
License: MIT
Requires Python: >=3.10
Keywords: mcp, atlassian, jira, confluence, oauth, ai, assistant

# Atlassian MCP Server

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MCP server for Atlassian Cloud (Confluence & Jira) with seamless OAuth 2.0 authentication. This server enables AI agents to help users document work in Confluence, manage Jira issues, and understand project context.

## Features

- **Seamless OAuth 2.0 Flow**: Automatic browser-based authentication with PKCE security
- **Modular Architecture**: Specialized client classes for Jira, Confluence, and Service Desk operations
- **Selective Module Loading**: Configure which modules to load using environment variables
- **Jira Integration**: Search, create, and update issues; add comments; manage work
- **Confluence Integration**: Search and read content for context understanding
- **Service Management**: Access support tickets and requests
- **Automatic Token Management**: Handles token refresh automatically
- **Minimal Permissions**: Follows least privilege principle with only required scopes

## Architecture

The server uses a modular architecture with specialized client classes:

- **BaseAtlassianClient**: Core OAuth 2.0 authentication and HTTP request handling
- **JiraClient**: Jira-specific operations (issues, projects, comments)
- **ConfluenceClient**: Confluence-specific operations (pages, spaces, search)
- **ServiceDeskClient**: Service Management operations (requests, approvals, Assets CMDB)

Each module can be independently enabled/disabled for optimal performance and security.

## Use Cases

This MCP server is designed to help AI agents assist users with:

- **Work Documentation**: Help document work progress and decisions in Confluence
- **Issue Management**: Create, update, and track Jira issues based on conversations
- **Context Understanding**: Read Confluence pages to understand project background
- **Time & Activity Logging**: Track work activities and time spent on tasks
- **Service Requests**: Access service management tickets for support context
- **Project Coordination**: Search across Jira and Confluence for project information

## OAuth App Setup

### 1. Create OAuth App

1. Go to [Atlassian Developer Console](https://developer.atlassian.com/console/myapps/)
2. Click **Create** → **OAuth 2.0 integration**
3. Enter your app name and accept the terms
4. Set **Callback URL** to: `http://localhost:8080/callback`

### 2. Configure Required Scopes

**IMPORTANT**: You must add these exact scopes to your OAuth app before the MCP server can function properly.

#### Jira API Scopes
Navigate to **Permissions** → **Jira API** and add:
- `read:jira-work` - Read issues, projects, and search
- `read:jira-user` - Read user information  
- `write:jira-work` - Create and update issues

#### Confluence API Scopes
Navigate to **Permissions** → **Confluence API** and add:
- `read:page:confluence` - Read page content (granular scope for v2 API)
- `read:space:confluence` - Read space information (granular scope for v2 API)  
- `write:page:confluence` - Create and update pages (granular scope for v2 API)

#### Service Management API Scopes
Navigate to **Permissions** → **Jira Service Management API** and add:
- `read:servicedesk-request` - Read service management requests
- `write:servicedesk-request` - Create and update service management requests  
- `manage:servicedesk-customer` - Manage service desk customers and participants
- `read:knowledgebase:jira-service-management` - Search knowledge base articles

#### User Identity API Scopes
Navigate to **Permissions** → **User identity API** and add:
- `read:me` - User profile information

#### Core Scopes
These are typically available by default:
- `offline_access` - Token refresh capability

### 3. Install App to Your Atlassian Site

After configuring scopes, you need to install the app to your Atlassian site:

1. In your OAuth app, go to **Authorization** tab
2. Use the **Authorization URL generator** to create an installation URL:
   - Select your configured scopes
   - Choose your Atlassian site from the dropdown
   - Click **Generate URL**
3. **Visit the generated URL** in your browser to install the app to your site
4. **Grant permissions** when prompted by Atlassian

**Note**: This step is required before the MCP server can access your Atlassian data. The app must be installed and authorized for your specific site.

### 4. Get Your Credentials

After installing the app:
1. Go to **Settings** tab in your OAuth app
2. Copy your **Client ID** and **Client Secret**
3. Set the environment variables (see Configuration section below)

### 5. Scope Configuration Summary

**Minimal Required (12 scopes):**
```
read:jira-work
read:jira-user  
write:jira-work
read:page:confluence
read:space:confluence
write:page:confluence
read:servicedesk-request
write:servicedesk-request
manage:servicedesk-customer
read:knowledgebase:jira-service-management
read:me
offline_access
```

**Optional (add only if needed):**
```
write:servicedesk-request      # Only if creating service tickets
manage:* scopes                # Only for administrative operations
```

### 6. Troubleshooting Scopes

If you get scope-related errors:
- **"scope does not match"**: The scope isn't added to your OAuth app in Developer Console
- **"Current user not permitted"**: User lacks product-level permissions (contact your Atlassian admin)
- **"Unauthorized"**: Check that all required scopes are properly configured

**Note**: After adding new scopes to your OAuth app, you must re-authenticate using the `authenticate_atlassian` tool to get fresh tokens with the new permissions.

## Installation

### Prerequisites

- Python 3.8 or higher
- pip3 package manager
- Access to an Atlassian Cloud site
- OAuth app configured (see OAuth App Setup above)

### Install from PyPI (Recommended)

```bash
pip3 install atlassian-mcp-server
```

### Install from GitHub Repository

```bash
# Install directly from GitHub repository
pip3 install git+https://github.com/rorymcmahon/atlassian-mcp-server.git
```

### Install from Source

```bash
# Clone the repository
git clone https://github.com/rorymcmahon/atlassian-mcp-server.git
cd atlassian-mcp-server

# Install in development mode
pip3 install -e .
```

### Verify Installation

```bash
# Check that the command is available
atlassian-mcp-server --help

# Or check the Python module
python -m atlassian_mcp_server --help
```

## Configuration

Set the following environment variables:

```bash
export ATLASSIAN_SITE_URL="https://your-domain.atlassian.net"
export ATLASSIAN_CLIENT_ID="your-oauth-client-id"
export ATLASSIAN_CLIENT_SECRET="your-oauth-client-secret"
```

### Optional Configuration

**Module Selection**: Control which modules are loaded (default: all modules enabled):
```bash
export ATLASSIAN_MODULES="jira,confluence,service_desk"  # Enable specific modules
export ATLASSIAN_MODULES="jira,confluence"              # Enable only Jira and Confluence
export ATLASSIAN_MODULES="jira"                         # Enable only Jira
```

Available modules:
- `jira` - Jira issue management and project operations
- `confluence` - Confluence page and space operations  
- `service_desk` - Service Management and Assets CMDB operations

**Note**: Disabling unused modules reduces memory usage and improves startup time.

## Usage

```bash
# Start the MCP server
python -m atlassian_mcp_server

# Or run directly
python src/atlassian_mcp_server/server.py
```

## MCP Client Configuration

**Note**: All configuration examples below show the required environment variables. You can optionally add `"ATLASSIAN_MODULES": "jira,confluence,service_desk"` to any `env` section to control which modules are loaded.

### Claude Desktop

Add to your Claude Desktop configuration file:

**macOS**: `~/Library/Application Support/Claude/claude_desktop_config.json`
**Windows**: `%APPDATA%\Claude\claude_desktop_config.json`

```json
{
  "mcpServers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}
```

### Amazon Q Developer CLI

Create an agent configuration file:

**File**: `~/.aws/amazonq/cli-agents/atlassian.json`

```json
{
  "$schema": "https://raw.githubusercontent.com/aws/amazon-q-developer-cli/refs/heads/main/schemas/agent-v1.json",
  "name": "atlassian",
  "description": "Atlassian Jira and Confluence integration agent",
  "prompt": "You are an AI assistant with access to Atlassian Jira and Confluence. Help users manage issues, search content, and document their work.",
  "mcpServers": {
    "atlassian-mcp-server": {
      "command": "atlassian-mcp-server",
      "args": [],
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      },
      "autoApprove": ["*"],
      "disabled": false,
      "timeout": 60000,
      "initTimeout": 120000
    }
  },
  "tools": [
    "@atlassian-mcp-server/*"
  ],
  "allowedTools": [
    "@atlassian-mcp-server/*"
  ]
}
```

Then use: `q chat --agent atlassian`

### VS Code with Continue

Add to your Continue configuration:

**File**: `~/.continue/config.json`

```json
{
  "models": [...],
  "mcpServers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}
```

### VS Code with GitHub Copilot Chat

For GitHub Copilot Chat with MCP support, add to workspace settings:

**File**: `.vscode/settings.json`

```json
{
  "github.copilot.chat.mcp.servers": {
    "atlassian": {
      "command": "atlassian-mcp-server",
      "env": {
        "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
        "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
        "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
      }
    }
  }
}
```

### Cline (VS Code Extension)

Add to Cline's MCP configuration:

**File**: `~/.cline/mcp_servers.json`

```json
{
  "atlassian": {
    "command": "atlassian-mcp-server",
    "env": {
      "ATLASSIAN_SITE_URL": "https://your-domain.atlassian.net",
      "ATLASSIAN_CLIENT_ID": "your-oauth-client-id",
      "ATLASSIAN_CLIENT_SECRET": "your-oauth-client-secret"
    }
  }
}
```

### Environment Variables Setup

For security, set environment variables instead of hardcoding in config files:

```bash
# Add to your shell profile (.bashrc, .zshrc, etc.)
export ATLASSIAN_SITE_URL="https://your-domain.atlassian.net"
export ATLASSIAN_CLIENT_ID="your-oauth-client-id"
export ATLASSIAN_CLIENT_SECRET="your-oauth-client-secret"
```

Then use in configurations:
```json
{
  "env": {
    "ATLASSIAN_SITE_URL": "${ATLASSIAN_SITE_URL}",
    "ATLASSIAN_CLIENT_ID": "${ATLASSIAN_CLIENT_ID}",
    "ATLASSIAN_CLIENT_SECRET": "${ATLASSIAN_CLIENT_SECRET}"
  }
}
```

## Authentication Flow

1. Start the MCP server
2. Use the `authenticate_atlassian` tool to begin OAuth flow
3. Browser opens automatically to Atlassian login
4. After authorization, authentication completes automatically
5. Credentials are saved locally for future use

## Available Tools

### Authentication
- `authenticate_atlassian()` - Start seamless OAuth authentication flow

### Jira Operations
- `jira_search(jql, max_results=50)` - Search issues with JQL
- `jira_get_issue(issue_key)` - Get specific issue details
- `jira_create_issue(project_key, summary, description, issue_type="Task")` - Create new issue
- `jira_update_issue(issue_key, summary=None, description=None)` - Update existing issue
- `jira_add_comment(issue_key, comment)` - Add comment to issue

### Confluence Operations

#### Core Content Management
- `confluence_search(query, limit=10)` - Search Confluence content
- `confluence_get_page(page_id)` - Get specific page content
- `confluence_create_page(space_key, title, content, parent_id=None)` - Create new Confluence page
- `confluence_update_page(page_id, title, content, version)` - Update existing Confluence page

#### Space Management
- `confluence_list_spaces(limit=25, space_type=None, status="current")` - List available spaces
- `confluence_get_space(space_id, include_icon=False)` - Get detailed space information
- `confluence_get_space_pages(space_id, limit=25, status="current")` - Get pages in a space

#### Enhanced Search & Discovery
- `confluence_search_content(query, limit=25, space_id=None)` - Advanced content search
- `confluence_get_page_children(page_id, limit=25)` - Get child pages

#### Comments & Collaboration
- `confluence_get_page_comments(page_id, limit=25)` - Get page comments
- `confluence_add_comment(page_id, comment, parent_comment_id=None)` - Add comment to page
- `confluence_get_comment(comment_id)` - Get specific comment details

#### Labels & Organization
- `confluence_get_page_labels(page_id, limit=25)` - Get labels for a page
- `confluence_search_by_label(label_id, limit=25)` - Find pages with specific label
- `confluence_list_labels(limit=25, prefix=None)` - List all available labels

#### Attachments
- `confluence_get_page_attachments(page_id, limit=25)` - Get page attachments
- `confluence_get_attachment(attachment_id)` - Get attachment details

#### Version History
- `confluence_get_page_versions(page_id, limit=25)` - Get page version history
- `confluence_get_page_version(page_id, version_number)` - Get specific page version

### Service Management Operations

#### Discovery Tools (Essential for AI Agents)
- `servicedesk_check_availability()` - Check if Jira Service Management is configured
- `servicedesk_list_service_desks(limit=50)` - List available service desks for creating requests
- `servicedesk_get_service_desk(service_desk_id)` - Get detailed service desk information
- `servicedesk_list_request_types(service_desk_id=None, limit=50)` - List available request types
- `servicedesk_get_request_type(service_desk_id, request_type_id)` - Get detailed request type information
- `servicedesk_get_request_type_fields(service_desk_id, request_type_id)` - Get required/optional fields for request type

#### Request Management
- `servicedesk_get_requests(service_desk_id=None, limit=50)` - Get service desk requests
- `servicedesk_get_request(issue_key)` - Get specific service desk request details
- `servicedesk_create_request(service_desk_id, request_type_id, summary, description)` - Create new service request
- `servicedesk_add_comment(issue_key, comment, public=True)` - Add comment to service request
- `servicedesk_get_request_comments(issue_key, limit=50)` - Get comments for a service request
- `servicedesk_get_request_status(issue_key)` - Get service request status
- `servicedesk_get_request_transitions(issue_key)` - Get available status transitions for request
- `servicedesk_transition_request(issue_key, transition_id, comment=None)` - Transition request to new status

#### Approval & Participant Management
- `servicedesk_get_approvals(issue_key)` - Get approval information for request
- `servicedesk_approve_request(issue_key, approval_id, decision)` - Approve or decline request approval
- `servicedesk_get_participants(issue_key)` - Get participants for request
- `servicedesk_add_participants(issue_key, usernames)` - Add participants to request (with confirmation prompts)
- `servicedesk_manage_notifications(issue_key, subscribe)` - Subscribe/unsubscribe from request notifications

## Troubleshooting

### Authentication Issues
- Ensure redirect URI matches exactly: `http://localhost:8080/callback`
- Check that all required scopes are configured in Atlassian Developer Console
- Verify environment variables are set correctly

### Permission Issues
- Ensure your user has appropriate Jira and Confluence access
- Check that OAuth app has all required scopes enabled
- Verify user is in correct groups (e.g., confluence-users)

### API Errors
- Check that your Atlassian site URL is correct
- Ensure you have proper permissions for the resources you're accessing
- Run the test scripts to verify functionality

## Scope Requirements

This MCP server uses **minimal required scopes** following the principle of least privilege:

### Essential Scopes (16 total)
- **Jira**: `read:jira-work`, `read:jira-user`, `write:jira-work`
- **Confluence**: `read:page:confluence`, `read:space:confluence`, `write:page:confluence`, `read:comment:confluence`, `write:comment:confluence`, `read:label:confluence`, `read:attachment:confluence`
- **Service Management**: `read:servicedesk-request`, `write:servicedesk-request`, `manage:servicedesk-customer`, `read:knowledgebase:jira-service-management`
- **Core**: `read:me`, `offline_access`

### Optional Scopes (add only if needed)
- `manage:*` scopes - Only for administrative operations

## Important: Granular Scopes for v2 API

This MCP server uses **granular scopes** for Confluence operations to ensure compatibility with Confluence v2 API endpoints. The v2 API provides better performance and future-proofing compared to the deprecated v1 REST API.

**Granular vs Classic Scopes:**
- **Granular** (recommended): `read:page:confluence`, `write:page:confluence` - Works with v2 API
- **Classic** (deprecated): `read:confluence-content.all`, `write:confluence-content` - Only works with v1 API

If you previously configured classic scopes, you'll need to update your OAuth app to use granular scopes and re-authenticate to get fresh tokens.

## Supply Chain Security

This project implements comprehensive supply chain security measures:

### Dependency Management
- **Pinned Versions**: All dependencies use exact version pins to prevent unexpected updates
- **Security Scanning**: Automated vulnerability scanning with Safety and pip-audit
- **Dependency Tracking**: Complete dependency documentation in `docs/DEPENDENCIES.md`
- **Regular Updates**: Weekly automated security checks via GitHub Actions

### Security Tools
```bash
# Generate dependency report
python3 scripts/generate_dependency_report.py

# Check for vulnerabilities
pip3 install safety pip-audit
safety check
pip-audit

# Update dependencies safely
python3 scripts/update_dependencies.py
```

### Files
- `requirements.txt` - Pinned production dependencies
- `docs/DEPENDENCIES.md` - Human-readable dependency report
- `docs/dependency-report.json` - Machine-readable dependency data
- `SECURITY.md` - Security policy and vulnerability response
- `.github/workflows/dependency-security.yml` - Automated security checks

## Development

The server is built using:
- **FastMCP**: Modern MCP server framework
- **httpx**: Async HTTP client
- **Pydantic**: Data validation and settings management

## License

MIT License - see LICENSE file for details.