DrSedman

A geoscience document analysis system that uses Google's Gemini API to extract structured information from scientific papers, focusing on geomorphology and sedimentology. Based on vegaluisjose/mlx-rag, extended with Gemini API for PDF processing, DuckDB for embeddings and enhanced visualization.

DrSedman

Features

• PDF Processing with Gemini API
  • Structured information extraction
  • Automatic metadata parsing
  • Research findings identification
  • Relationship mapping
• Beautiful Output Formats
  • Rich console display
  • HTML export with styling
  • Structured JSON storage
• Vector Database Integration
  • MLX embeddings
  • DuckDB storage
  • Similarity search
• Interactive Chat Interface
  • Context-aware responses
  • Research paper integration
  • Geoscience expertise

Installation

1. Clone the repository:

git clone https://github.com/jameshgrn/drsedman.git
cd drsedman

2. Set up Python environment:

pyenv install 3.10.14
pyenv local 3.10.14
python -m venv .venv
source .venv/bin/activate

3. Install dependencies:

poetry install

4. Set up credentials:

cp config/gemini_credentials_example.json config/gemini_credentials.json
# Edit config/gemini_credentials.json with your API key

Usage

Process PDFs

# Process all PDFs in a directory
./scripts/run_gemini_processing.zsh data/pdfs gemini_output

# Retry failed processing
./scripts/run_gemini_processing.zsh data/pdfs gemini_output --retry-failed

View Results

# View a random processed file
./scripts/view_gemini.sh

# View a specific file
./scripts/view_gemini.sh --file gemini_output/paper_gemini.jsonl

# Save as HTML
./scripts/view_gemini.sh --save-html

Create Embeddings

# Create vector embeddings from processed PDFs
./scripts/process_and_embed.zsh

Chat Interface

./scripts/chat.zsh

Development

# Run tests
make test

# Run linter
make lint

# Format code
make format

# Type checking
make mypy

# Run coverage
make coverage

Architecture

See architecture.md for detailed system design.

Contributing

See CONTRIBUTING.md for development guidelines.

Current Database Stats

The system has processed approximately 750 academic papers in geoscience, extracting:

• 6,465 research findings
• 2,849 methodology entries
• 2,672 identified relationships

License

Copyright 2024 James Hooker Gearon

Licensed under the Apache License, Version 2.0. See LICENSE for details.

Acknowledgments

This project is based on vegaluisjose/mlx-rag, with significant extensions for geoscience document analysis including Gemini API integration, structured information extraction, and enhanced visualization capabilities.