Medical GraphRAG Assistant

#!/bin/bash # Download sample MIMIC-CXR DICOM images for testing # Requires PhysioNet credentials set -e SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)" REPO_ROOT="$(dirname "$SCRIPT_DIR")" IMAGES_DIR="$REPO_ROOT/tests/fixtures/sample_medical_images" # Check for physionet credentials if [ -z "$PHYSIONET_USER" ] || [ -z "$PHYSIONET_PASS" ]; then echo "Set PHYSIONET_USER and PHYSIONET_PASS environment variables" echo "Register at https://physionet.org/ and get MIMIC-CXR access" exit 1 fi mkdir -p "$IMAGES_DIR" # Sample image IDs from MIMIC-CXR (known good chest X-rays) # These are example paths - adjust based on actual PhysioNet access SAMPLE_IMAGES=( "p10/p10000032/s50414267/02aa804e-bde0afdd-112c0b34-7bc16630-4e384014.dcm" "p10/p10000032/s53189527/2a2277a9-b0ded155-c0de8eb9-c124d10e-82c5caab.dcm" "p10/p10000764/s57375967/5a570b6f-2ee6d914-cb5135a9-5e5f9ca4-80f0c40d.dcm" ) BASE_URL="https://physionet.org/files/mimic-cxr/2.1.0/files" echo "Downloading sample DICOM images..." cd "$IMAGES_DIR" for img_path in "${SAMPLE_IMAGES[@]}"; do filename=$(basename "$img_path") if [ ! -f "$filename" ]; then echo "Downloading $filename..." wget --user="$PHYSIONET_USER" --password="$PHYSIONET_PASS" \ -q -O "$filename" "$BASE_URL/$img_path" || echo "Failed: $img_path" else echo "Already have $filename" fi done echo "Downloaded $(ls -1 *.dcm 2>/dev/null | wc -l) DICOM files to $IMAGES_DIR" # Also sync from S3 if available if aws s3 ls s3://medical-graphrag-backup/medical-images/ &>/dev/null; then echo "Syncing additional images from S3 backup..." aws s3 sync s3://medical-graphrag-backup/medical-images/ "$IMAGES_DIR/" --exclude "*" --include "*.dcm" fi echo "Done!"