ATLAS: Task Management System

ATLAS (Adaptive Task & Logic Automation System) is a project, knowledge, and task management system for LLM Agents.

Built on a three-tier architecture:

                  +------------------------------------------+
                  |                PROJECT                   |
                  |------------------------------------------|
                  | id: string                               |
                  | name: string                             |
                  | description: string                      |
                  | status: string                           |
                  | urls?: Array<{title: string, url: string}>|
                  | completionRequirements: string           |
                  | outputFormat: string                     |
                  | taskType: string                         |
                  | createdAt: string                        |
                  | updatedAt: string                        |
                  +----------------+-------------------------+
                            |                    |
                            |                    |
                            v                    v
+----------------------------------+ +----------------------------------+
|               TASK               | |            KNOWLEDGE             |
|----------------------------------| |----------------------------------|
| id: string                       | | id: string                       |
| projectId: string                | | projectId: string                |
| title: string                    | | text: string                     |
| description: string              | | tags?: string[]                  |
| priority: string                 | | domain: string                   |
| status: string                   | | citations?: string[]             |
| assignedTo?: string              | | createdAt: string                |
| urls?: Array<{title: string,     | |                                  |
|   url: string}>                  | | updatedAt: string                |
| tags?: string[]                  | |                                  |
| completionRequirements: string   | |                                  |
| outputFormat: string             | |                                  |
| taskType: string                 | |                                  |
| createdAt: string                | |                                  |
| updatedAt: string                | |                                  |
+----------------------------------+ +----------------------------------+

Implemented as a Model Context Protocol (MCP) server, ATLAS allows LLM agents to interact with project management database, enabling managing projects, tasks, and knowledge items.

Important Version Note: Version 1.5.4 is the last version that uses SQLite as the database. Version 2.0 and onwards has been completely rewritten to use Neo4j, which requires either:

• Self-hosting using Docker (docker-compose included in repository)
• Using Neo4j AuraDB cloud service: https://neo4j.com/product/auradb/

Version 2.5.0 introduces a new 3-node system (Projects, Tasks, Knowledge) that replaces the previous structure.

Table of Contents

• Overview
• Features
• Installation
• Configuration
• Project Structure
• Tools
• Resources
• Database Backup and Restore
• Examples
• Contributing
• License

Overview

ATLAS implements the Model Context Protocol (MCP), enabling standardized communication between LLMs and external systems through:

• Clients: Claude Desktop, IDEs, and other MCP-compatible clients
• Servers: Tools and resources for project, task, and knowledge management
• LLM Agents: AI models that leverage the server's management capabilities

System Integration

The Atlas Platform integrates these components into a cohesive system:

• Project-Task Relationship: Projects contain tasks that represent actionable steps needed to achieve project goals. Tasks inherit context from their parent project while providing granular tracking of individual work items.
• Knowledge Integration: Both projects and tasks can be enriched with knowledge items, providing team members with necessary information and context.
• Dependency Management: Both projects and tasks support dependency relationships, allowing for complex workflows with prerequisites and sequential execution requirements.
• Unified Search: The platform provides cross-entity search capabilities, allowing users to find relevant projects, tasks, or knowledge based on various criteria.

Features

Project Management

• Comprehensive Tracking: Manage project metadata, statuses, and rich content (notes, links, etc.) with built-in support for bulk operations.
• Dependency & Relationship Handling: Automatically validate and track inter-project dependencies.

Task Management

• Task Lifecycle Management: Create, track, and update tasks through their entire lifecycle.
• Prioritization & Categorization: Assign priority levels and categorize tasks with tags for better organization.
• Dependency Tracking: Establish task dependencies to create structured workflows.

Knowledge Management

• Structured Knowledge Repository: Maintain a searchable repository of project-related information.
• Domain Categorization: Organize knowledge by domain and tags for easy retrieval.
• Citation Support: Track sources and references for knowledge items.

Graph Database Integration

• Native Relationship Management: Leverage Neo4j's ACID-compliant transactions and optimized queries for robust data integrity.
• Advanced Search & Scalability: Perform property-based searches with fuzzy matching and wildcards while maintaining high performance.

Unified Search

• Cross-Entity Search: Find relevant projects, tasks, or knowledge based on content, metadata, or relationships.
• Flexible Query Options: Support for case-insensitive, fuzzy, and advanced filtering options.

Installation

1. Clone the repository:

git clone https://github.com/cyanheads/atlas-mcp-server.git
cd atlas-mcp-server

2. Install dependencies:

npm install

3. Configure Neo4j:

# Start Neo4j using Docker
docker-compose up -d

4. Build the project:

npm run build

Configuration

Environment Variables

Create a .env file based on .env.example:

# Neo4j Configuration
NEO4J_URI=bolt://localhost:7687
NEO4J_USER=neo4j
NEO4J_PASSWORD=password2

# Application Configuration
LOG_LEVEL=info # debug, info, warn, error
NODE_ENV=development # development, production

# Research API Keys
OPENAI_API_KEY=your_openai_api_key
PERPLEXITY_API_KEY=your_perplexity_api_key
XAI_GROK_API_KEY=your_grok_api_key
FIRECRAWL_API_KEY=your_firecrawl_api_key
AGENTSPACE_API_KEY=your_agentspace_api_key
AGENTSPACE_BASE_URL=https://api.agentspace.dev

MCP Client Settings

Add to your MCP client settings:

{
  "mcpServers": {
    "atlas": {
      "command": "node",
      "args": ["/path/to/atlas-mcp-server/dist/index.js"],
      "env": {
        "NEO4J_URI": "bolt://localhost:7687",
        "NEO4J_USER": "neo4j",
        "NEO4J_PASSWORD": "password2",
        "LOG_LEVEL": "info",
        "NODE_ENV": "production"
      }
    }
  }
}

Project Structure

The codebase follows a modular structure:

src/
├── config/          # Configuration management (index.ts)
├── index.ts         # Main server entry point
├── mcp/             # MCP server implementation (server.ts)
│   ├── resources/   # MCP resource handlers (index.ts, types.ts, knowledge/, projects/, tasks/)
│   └── tools/       # MCP tool handlers (individual tool directories)
├── services/        # Core application services
│   └── neo4j/       # Neo4j database services (index.ts, driver.ts, backupRestoreService.ts, etc.)
├── types/           # Shared TypeScript type definitions (errors.ts, mcp.ts, tool.ts)
└── utils/           # Utility functions (logger.ts, errorHandler.ts, etc.)

Note: ID generation logic is primarily located in src/services/neo4j/helpers.ts.

Tools

ATLAS provides a comprehensive suite of tools for project, task, and knowledge management, callable via the Model Context Protocol.

Project Operations

Tool Name	Description	Key Arguments
atlas_project_create	Creates new projects (single/bulk).	mode ('single'/'bulk'), project details (name, description, status, urls, completionRequirements, dependencies, outputFormat, taskType), responseFormat ('formatted'/'json', optional).
atlas_project_list	Lists projects (all/details).	mode ('all'/'details'), id (for details), filters (status, taskType), pagination (page, limit), includes (includeKnowledge, includeTasks), responseFormat ('formatted'/'json', optional).
atlas_project_update	Updates existing projects (single/bulk).	mode ('single'/'bulk'), id, updates object, responseFormat ('formatted'/'json', optional). Bulk mode uses projects array.
atlas_project_delete	Deletes projects (single/bulk).	mode ('single'/'bulk'), id (single) or projectIds array (bulk), responseFormat ('formatted'/'json', optional).

Task Operations

Tool Name	Description	Key Arguments
atlas_task_create	Creates new tasks (single/bulk).	mode ('single'/'bulk'), projectId, task details (title, description, priority, status, assignedTo, tags, completionRequirements, dependencies, outputFormat, taskType), responseFormat ('formatted'/'json', optional).
atlas_task_update	Updates existing tasks (single/bulk).	mode ('single'/'bulk'), id, updates object, responseFormat ('formatted'/'json', optional). Bulk mode uses tasks array.
atlas_task_delete	Deletes tasks (single/bulk).	mode ('single'/'bulk'), id (single) or taskIds array (bulk), responseFormat ('formatted'/'json', optional).
atlas_task_list	Lists tasks for a specific project.	projectId (required), filters (status, assignedTo, priority, tags, taskType), sorting (sortBy, sortDirection), pagination (page, limit), responseFormat ('formatted'/'json', optional).

Knowledge Operations

Tool Name	Description	Key Arguments
atlas_knowledge_add	Adds new knowledge items (single/bulk).	mode ('single'/'bulk'), projectId, knowledge details (text, tags, domain, citations), responseFormat ('formatted'/'json', optional). Bulk mode uses knowledge array.
atlas_knowledge_delete	Deletes knowledge items (single/bulk).	mode ('single'/'bulk'), id (single) or knowledgeIds array (bulk), responseFormat ('formatted'/'json', optional).
atlas_knowledge_list	Lists knowledge items for a specific project.	projectId (required), filters (tags, domain, search), pagination (page, limit), responseFormat ('formatted'/'json', optional).

Search Operations

Tool Name	Description	Key Arguments
atlas_unified_search	Performs unified search across entities.	value (search term), property (optional), filters (entityTypes, taskType), options (caseInsensitive, fuzzy), pagination (page, limit), responseFormat ('formatted'/'json', optional).

Research Operations

Tool Name	Description	Key Arguments
atlas_deep_research	Initiates a structured deep research process by creating a hierarchical plan within the Atlas knowledge base.	projectId (required), researchTopic (required), researchGoal (required), scopeDefinition (optional), subTopics (required array with questions and search queries), researchDomain (optional), initialTags (optional), planNodeId (optional), responseFormat (optional).
openai-deep-research	Perform deep research using OpenAI with web browsing capabilities	query (required), options (optional) with maxResults, includePageContent, browsePage
perplexity-sonar	Perform real-time web search using Perplexity Sonar	query (required), options (optional) with maxResults, recency (day/week/month/year)
grok3	Perform research using Grok-3 with real-time web access	query (required), options (optional) with maxResults, includePageContent, browsePage
firecrawl-deep-research	Perform deep research using Firecrawl with web crawling and content extraction	query (required), options (optional) with maxResults, browsePage, onlyMainContent, includeHtml
agentspace-google-research	Perform Google Deep Research via Agentspace with comprehensive analysis	query (required), options (optional) with maxResults, depth (quick/standard/comprehensive), includeAnalysis, language, region, browsePage

Database Operations

Tool Name	Description	Key Arguments
atlas_database_clean	Destructive: Completely resets the database, removing all projects, tasks, and knowledge.	acknowledgement (must be set to true to confirm), responseFormat ('formatted'/'json', optional).

Resources

ATLAS exposes project, task, and knowledge data through standard MCP resource endpoints.

Direct Resources

Resource Name	Description
atlas://projects	List of all projects in the Atlas platform with pagination support.
atlas://tasks	List of all tasks in the Atlas platform with pagination and filtering support.
atlas://knowledge	List of all knowledge items in the Atlas platform with pagination and filtering support.

Resource Templates

Resource Name	Description
atlas://projects/{projectId}	Retrieves a single project by its unique identifier (projectId).
atlas://tasks/{taskId}	Retrieves a single task by its unique identifier (taskId).
atlas://projects/{projectId}/tasks	Retrieves all tasks belonging to a specific project (projectId).
atlas://knowledge/{knowledgeId}	Retrieves a single knowledge item by its unique identifier (knowledgeId).
atlas://projects/{projectId}/knowledge	Retrieves all knowledge items belonging to a specific project (projectId).

Database Backup and Restore

ATLAS provides functionality to back up and restore the Neo4j database content. The core logic resides in src/services/neo4j/backupRestoreService.ts.

Automatic Backups (Note)

Important: The automatic backup functionality has been removed due to inefficiency. The call to triggerBackgroundBackup in src/services/neo4j/driver.ts is commented out with a note indicating it was removed. Please use the manual backup process described below to protect your data.

Backup Process

• Mechanism: The backup process exports all Project, Task, and Knowledge nodes, along with their relationships, into separate JSON files.
• Output: Each backup creates a timestamped directory (e.g., atlas-backup-YYYYMMDDHHMMSS) within the configured backup path (default: ./atlas-backups/). This directory contains projects.json, tasks.json, knowledge.json, and relationships.json.
• Manual Backup: You can trigger a manual backup using the provided script:

  npm run db:backup

  This command executes scripts/db-backup.ts, which calls the exportDatabase function.

Restore Process

• Mechanism: The restore process first completely clears the existing Neo4j database. Then, it imports nodes and relationships from the JSON files located in the specified backup directory.
• Warning: Restoring from a backup is a destructive operation. It will overwrite all current data in your Neo4j database.
• Manual Restore: To restore the database from a backup directory, use the import script:

  npm run db:import <path_to_backup_directory>

  Replace <path_to_backup_directory> with the actual path to the backup folder (e.g., ./atlas-backups/atlas-backup-20250326120000). This command executes scripts/db-import.ts, which calls the importDatabase function.
• Relationship Handling: The import process attempts to recreate relationships based on the id properties stored within the nodes during export. Ensure your nodes have consistent id properties for relationships to be restored correctly.

Examples

The examples/ directory contains practical examples demonstrating various features of the ATLAS MCP Server.

• Backup Example: Located in examples/backup-example/, this shows the structure and format of the JSON files generated by the npm run db:backup command. See the Examples README for more details.
• Deep Research Example: Located in examples/deep-research-example/, this demonstrates the output and structure generated by the atlas_deep_research tool. It includes a markdown file (covington_community_grant_research.md) summarizing the research plan and a JSON file (full-export.json) containing the raw data exported from the database after the research plan was created. See the Examples README for more details.

Contributing

1. Fork the repository
2. Create a feature branch
3. Commit your changes with a descriptive message
4. Push to the branch
5. Create a Pull Request

For bugs and feature requests, please create an issue.

License

Apache License 2.0

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Built with the Model Context Protocol