Medical GraphRAG Assistant

#!/bin/bash # Deploy sample medical images to AWS and ingest them set -e # Exit on error echo "=========================================" echo "Deploy Sample Medical Images to AWS" echo "=========================================" echo "" # Configuration AWS_HOST="ubuntu@3.84.250.46" SSH_KEY="$HOME/.ssh/medical-graphrag-key.pem" PROJECT_DIR="medical-graphrag" SAMPLE_IMAGES_DIR="tests/fixtures/sample_medical_images" # Step 1: Copy sample images directory to AWS echo "Step 1: Copying sample images to AWS..." rsync -avz -e "ssh -i $SSH_KEY" \ --exclude="._*" \ --exclude=".DS_Store" \ "$SAMPLE_IMAGES_DIR/" \ "$AWS_HOST:~/$PROJECT_DIR/$SAMPLE_IMAGES_DIR/" echo "✅ Images copied to AWS" echo "" # Step 2: Run ingestion on AWS echo "Step 2: Ingesting images with NV-CLIP embeddings..." ssh -i "$SSH_KEY" "$AWS_HOST" "cd $PROJECT_DIR && source venv/bin/activate && python ingest_mimic_images.py $SAMPLE_IMAGES_DIR --limit 50" echo "" echo "=========================================" echo "✅ Deployment Complete!" echo "=========================================" echo "" echo "Verification:" echo " ssh -i $SSH_KEY $AWS_HOST" echo " cd $PROJECT_DIR && source venv/bin/activate" echo " python -c \"from src.db.connection import get_connection; conn = get_connection(); cursor = conn.cursor(); cursor.execute('SELECT COUNT(*) FROM VectorSearch.MIMICCXRImages'); print(f'Total images: {cursor.fetchone()[0]}')\"" echo ""