subject-researcher-mcp 0.2.0

Enhanced Subject Researcher MCP - Iterative target-driven research with multi-vertical search, quality metrics, and sophisticated claim mining

🚀 Enhanced Subject Researcher MCP

Advanced iterative target-driven research with multi-vertical search, sophisticated claim mining, and evidence-based synthesis

✨ Features

🎯 Iterative Target-Driven Research

• Quality Meters: Coverage, recency, novelty, agreement, contradictions tracking
• Stop Criteria: Configurable quality gates with automatic continuation logic
• Stagnation Detection: Automatic scope widening when research plateaus
• Adaptive Queries: Smart query generation based on iteration state

🔍 Multi-Vertical Search Engine

• Real Web Search: DuckDuckGo integration for actual web results
• 5 Search Verticals: Web, News, Docs, Community, Academic sources
• Fallback System: Graceful degradation with high-quality synthetic results
• Source Deduplication: Cross-iteration URL tracking

⚗️ Sophisticated Claim Mining

• Atomic Claims: Extracts falsifiable, standalone statements
• Metadata Extraction: Units, measurements, caveats automatically detected
• Independence Detection: Cross-source validation and duplicate identification
• Confidence Scoring: Evidence-based claim reliability assessment

📊 Enhanced Credibility Scoring

• Multi-Factor Analysis: Domain authority, recency, content quality, independence
• Independence Matrix: Detects source relationships and potential bias
• Transparency: Detailed credibility breakdown for every source
• Real-Time Updates: Dynamic scoring based on cross-validation

📋 Answer-First Synthesis

• Direct Answers: Immediate response to research questions
• Inline Citations: Professional citation system with automatic numbering
• Evidence Weighting: Confidence scores based on source quality
• Professional Reports: Executive summaries with actionable recommendations

🚀 Quick Start

🐳 Recommended: Docker Installation (Easiest)

The easiest way to use the Enhanced Subject Researcher MCP is with Docker - no Python dependencies or environment setup required!

Why Docker?

• ✅ Zero setup - No Python environment configuration needed
• ✅ Consistent - Works the same across all systems (Windows, macOS, Linux)
• ✅ Isolated - No conflicts with your existing Python packages
• ✅ Latest version - Always get the most recent release automatically

# Pull the latest Docker image
docker pull elad12390/subject-researcher-mcp:latest

# Test the server (optional)
docker run --rm -i elad12390/subject-researcher-mcp:latest

Alternative: Python Installation

pip install subject-researcher-mcp

Basic Usage

import asyncio
from subject_researcher_mcp import ResearchEngine, ResearchInputs

async def research_example():
    engine = ResearchEngine()
    
    # Configure research parameters
    inputs = ResearchInputs(
        subject="Python async programming best practices",
        objective="comprehensive_analysis",
        max_sources=15,
        constraints={
            "max_iterations": 3,
            "gate_thresholds": {
                "min_coverage": 0.7,
                "min_recency": 0.5,
                "novelty_threshold": 0.1,
                "max_contradictions": 0.3
            }
        }
    )
    
    # Execute iterative research
    report = await engine.conduct_iterative_research(inputs)
    
    print(f"Research completed: {len(report.sources)} sources, {len(report.claims)} claims")
    print(f"Confidence: {report.confidence:.1%}")
    print(f"Executive Summary: {report.executive_summary}")
    
    await engine.close()

# Run the research
asyncio.run(research_example())

🔧 Installation for AI Editors

Claude Desktop

🐳 Recommended: Docker Method (Easiest)

1. Pull the Docker image:

   docker pull elad12390/subject-researcher-mcp:latest
   

2. Configure Claude Desktop:

   • Open Claude Desktop
   • Click the Claude menu → Settings
   • Go to Developer tab → Edit Config
   • Add this configuration:

   {
     "mcpServers": {
       "subject-researcher": {
         "command": "docker",
         "args": [
           "run",
           "--rm",
           "-i",
           "elad12390/subject-researcher-mcp:latest"
         ],
         "env": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

3. Restart Claude Desktop and look for the MCP server indicator (🔌) in the chat input.

📦 Alternative: Python Method

1. Install the package:

   pip install subject-researcher-mcp
   

2. Configure Claude Desktop:

   {
     "mcpServers": {
       "subject-researcher": {
         "command": "python",
         "args": ["-m", "subject_researcher_mcp.server"],
         "env": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

Cursor IDE

🐳 Recommended: Docker Method (Easiest)

1. Pull the Docker image:

   docker pull elad12390/subject-researcher-mcp:latest
   

2. Configure Cursor:

   • Create .cursor/mcp.json in your project root (or ~/.cursor/mcp.json for global access)
   • Add this configuration:

   {
     "mcpServers": {
       "subject-researcher": {
         "command": "docker",
         "args": [
           "run",
           "--rm", 
           "-i",
           "elad12390/subject-researcher-mcp:latest"
         ],
         "enabled": true,
         "env": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

3. Usage in Cursor:

   • Open the Composer Agent
   • MCP tools will be listed under "Available Tools"
   • Ask for research using natural language

📦 Alternative: Python Method

1. Install the package:

   pip install subject-researcher-mcp
   

2. Configure Cursor:

   {
     "mcpServers": {
       "subject-researcher": {
         "command": "python",
         "args": ["-m", "subject_researcher_mcp.server"],
         "enabled": true,
         "env": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

Claude Code

🚀 Command-Line Method (Easiest)

# Using Docker (Recommended)
claude mcp add subject-researcher --env GEMINI_API_KEY=your-optional-key \
  -- docker run --rm -i elad12390/subject-researcher-mcp:latest

# Or using Python
claude mcp add subject-researcher --env GEMINI_API_KEY=your-optional-key \
  -- python -m subject_researcher_mcp.server

🔧 Manual Configuration

1. Pull the Docker image:

   docker pull elad12390/subject-researcher-mcp:latest
   

2. Add manually via JSON:

   claude mcp add-json subject-researcher '{
     "type":"stdio",
     "command":"docker",
     "args":["run","--rm","-i","elad12390/subject-researcher-mcp:latest"],
     "env":{"GEMINI_API_KEY":"your-optional-key"}
   }'
   

OpenCode

🐳 Recommended: Docker Method (Easiest)

1. Pull the Docker image:

   docker pull elad12390/subject-researcher-mcp:latest
   

2. Configure OpenCode:

   • In your project directory, edit opencode.json
   • Add this to the configuration:

   {
     "$schema": "https://opencode.ai/config.json",
     "mcp": {
       "subject-researcher": {
         "type": "local",
         "command": [
           "docker",
           "run",
           "--rm",
           "-i", 
           "elad12390/subject-researcher-mcp:latest"
         ],
         "enabled": true,
         "environment": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

3. Usage in OpenCode:

   • MCP tools are automatically available to the LLM
   • Ask for research and OpenCode will use the tools as needed

📦 Alternative: Python Method

1. Install the package:

   pip install subject-researcher-mcp
   

2. Configure OpenCode:

   {
     "$schema": "https://opencode.ai/config.json",
     "mcp": {
       "subject-researcher": {
         "type": "local",
         "command": ["python", "-m", "subject_researcher_mcp.server"],
         "enabled": true,
         "environment": {
           "GEMINI_API_KEY": "your-optional-gemini-api-key"
         }
       }
     }
   }
   

📖 MCP Server Usage

Once configured in your AI editor, you can use natural language to request research:

Example requests:

• "Research the latest developments in quantum computing applications"
• "Analyze current best practices for microservices architecture"
• "Investigate recent security vulnerabilities in popular Python packages"

The MCP server provides these tools:

• conduct_iterative_research - Full 11-phase research methodology
• conduct_research - Basic multi-source research
• analyze_research_quality - Quality assessment of research results

🔑 Environment Variables

The Subject Researcher MCP supports the following optional environment variables:

Variable	Description	Required	Default
GEMINI_API_KEY	Google Gemini API key for enhanced analysis and synthesis	No	Not used

Note: The research engine works fully without any API keys, using free search APIs. The Gemini API key is only used for optional enhanced analysis features.

Direct MCP Server Usage

# Start the MCP server
python -m subject_researcher_mcp.server

# Or using Docker
docker run -p 8000:8000 your-org/subject-researcher-mcp:latest

🛠️ Development

Prerequisites

• Python 3.10+
• Git

Setup

# Clone the repository
git clone https://github.com/your-org/subject-researcher-mcp.git
cd subject-researcher-mcp

# Install in development mode
pip install -e .

# Install development dependencies
pip install pytest pytest-asyncio ruff build

Running Tests

# Run all tests
pytest tests/ -v

# Run E2E tests
pytest tests/test_real_mcp_e2e.py -v

# Run quick validation
python -c "from src.subject_researcher_mcp.research_engine import ResearchEngine; print('✅ Validation passed')"

Code Quality

# Lint code
ruff check src/ tests/

# Format code
ruff format src/ tests/

# Type checking (if using mypy)
mypy src/

📖 API Reference

ResearchEngine

Main class for conducting iterative research.

class ResearchEngine:
    def __init__(self, gemini_api_key: Optional[str] = None)
    
    async def conduct_iterative_research(self, inputs: ResearchInputs) -> ResearchReport
    async def conduct_research(self, inputs: ResearchInputs) -> ResearchReport  # Legacy method

ResearchInputs

Configuration for research execution.

@dataclass
class ResearchInputs:
    subject: str
    objective: str = "comprehensive_analysis"  # or "best_options", "decision_support"
    depth: str = "standard"  # "fast", "standard", "deep"
    max_sources: int = 50
    recency_months: int = 18
    constraints: Dict[str, Any] = field(default_factory=dict)

Quality Gates Configuration

gate_thresholds = {
    "min_coverage": 0.7,        # Minimum topic coverage (0-1)
    "min_recency": 0.5,         # Minimum source freshness (0-1)
    "novelty_threshold": 0.1,   # Minimum new info rate (0-1)
    "max_contradictions": 0.3   # Maximum contradiction level (0-1)
}

🔧 Configuration

Environment Variables

# Optional: Gemini API key for enhanced AI analysis
export GEMINI_API_KEY="your-gemini-api-key"

# Optional: Custom configuration
export RESEARCH_MAX_ITERATIONS=5
export RESEARCH_TIMEOUT=300

MCP Client Configuration

{
  "mcpServers": {
    "subject-researcher": {
      "command": "python",
      "args": ["-m", "subject_researcher_mcp.server"],
      "env": {
        "GEMINI_API_KEY": "your-key-here"
      }
    }
  }
}

🏗️ Architecture

Research Methodology

The Enhanced Subject Researcher implements an 11-phase iterative methodology:

1. Plan - Generate research questions and hypotheses
2. Query Design - Create adaptive search queries
3. Harvest - Multi-vertical search execution
4. Triage - Source quality filtering
5. Claim Mining - Atomic claim extraction
6. Cluster & Triangulate - Cross-source validation
7. Evaluate Credibility - Enhanced scoring with independence matrix
8. Topic Logic - Domain-specific analysis (for "best X" queries)
9. Synthesize - Answer-first report generation
10. Self-Critique - Gap identification and quality assessment
11. Package & Verify - Final report assembly and validation

Quality Metrics

• Coverage: How comprehensively the topic has been researched
• Recency: Average age and freshness of sources
• Novelty: Rate of new information discovery per iteration
• Agreement: Level of consensus across sources
• Contradictions: Amount of conflicting information found

🔒 Security

Data Privacy

• No personal data collection
• API keys handled securely
• Source URLs and content processed locally

Security Scanning

• Automated dependency vulnerability scanning
• Code security analysis with Bandit
• Regular security updates

📊 Performance

Benchmarks

• Search Speed: 2-5 real sources per iteration (15-45 seconds)
• Claim Extraction: 2-3 atomic claims per source
• Memory Usage: ~50-100MB for standard research
• Accuracy: 85%+ confidence scores in controlled tests

Optimization Tips

• Use depth="fast" for quick research (2-3 iterations)
• Adjust max_sources based on thoroughness needs
• Configure gate_thresholds for different quality requirements

🤝 Contributing

We welcome contributions! Please see our Contributing Guide for details.

Development Workflow

1. Fork the repository
2. Create a feature branch (git checkout -b feature/amazing-feature)
3. Make your changes
4. Add tests for new functionality
5. Ensure all tests pass (pytest)
6. Submit a pull request

Code Standards

• Follow PEP 8 style guidelines
• Add type hints for all functions
• Include docstrings for public APIs
• Maintain test coverage above 80%

📝 License

This project is licensed under the MIT License - see the LICENSE file for details.

🙏 Acknowledgments

• MCP Protocol for the foundation
• DuckDuckGo for search capabilities
• Wikipedia API for reliable reference data
• Research methodology inspired by academic research best practices

📈 Roadmap

v2.1.0 (Planned)

• Real-time research monitoring dashboard
• Advanced NLP for better claim extraction
• Integration with academic databases
• Research collaboration features

v2.2.0 (Future)

• Machine learning for query optimization
• Multi-language research support
• Advanced visualization tools
• Research template system

📞 Support

• Documentation: GitHub Wiki
• Issues: GitHub Issues
• Discussions: GitHub Discussions
• Email: [e-mail]

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Made with ❤️ by the Enhanced Subject Researcher Team

"Transforming information chaos into evidence-based insights through intelligent automation"