Running locally

Prerequisites

• Python 3.8 or higher
• Git

Complete Setup Instructions

1. Clone the repository:

git clone https://github.com/SCAI-BIO/primekg-rag.git
cd primekg-rag

2. Create and activate a Python virtual environment:

# Create virtual environment
python -m venv venv

# Activate virtual environment
# On Windows (Git Bash):
source venv/Scripts/activate
# On Windows (Command Prompt):
venv\Scripts\activate
# On macOS/Linux:
source venv/bin/activate

3. Install dependencies:

pip install -r requirements.txt

4. Set up environment file:

# Create .env file with correct paths
echo "OPENAI_API_KEY=your_key_here" > .env

Replace your_key_here with your actual OpenAI API key

5. Download and set up databases:

cd primekg-rag
python setup_databases.py

This will download ~450MB of data including CSV files and database collections

6. Run the application:

# Make sure you're in the primekg-rag directory
streamlit run app.py

The application will be available at http://localhost:8501

Troubleshooting

Common Issues:

"streamlit: command not found"

• Make sure the virtual environment is activated: source venv/Scripts/activate

"PUBMED_DB_PATH not set in .env file"

• Ensure the .env file is in the root directory (not in primekg-rag/)
• Check that PUBMED_DB_PATH=pubmed_db (not primekg-rag/pubmed_db)

"Collection [pubmed_abstracts] does not exist"

• Run the database setup again: cd primekg-rag && python setup_databases.py
• Verify the .env file has the correct PUBMED_DB_PATH

Missing CSV files warnings

• The setup script should download nodes.csv and best_question_matches.csv automatically
• If missing, re-run: cd primekg-rag && python setup_databases.py

Running via Docker

Prerequisites

• Docker and Docker Compose installed
• Git

Setup Instructions

1. Clone the repository:

git clone https://github.com/SCAI-BIO/primekg-rag.git
cd primekg-rag

2. Set up environment file:

echo "OPENAI_API_KEY=your_key_here" > .env

Replace your_key_here with your actual OpenAI API key

3. Build and run with Docker Compose:

docker-compose up --build

The application will be available at http://localhost:8501

Additional Notes

• Make sure to replace your_key_here with your actual OpenAI API key in the .env file
• The first run may take longer as it downloads and sets up the required databases
• For development, you may want to use the local setup instead of Docker for faster iteration