🔧 AUTOMATION TOOLS

Balazs, is this something we need and should use? Is it even realistic to expect lab members to use these tools?

Purpose: Alert before running out of space

Usage:

# Run weekly (automated via cron)
python storage_monitor.py /RDS_Lab_Storage --threshold-warning 80 --threshold-critical 90

Output: - Email alert when >80% full (warning) - Email alert when >90% full (critical) - Weekly report of storage trends

See storage_monitor.py script (provided earlier)

Purpose: Compress old imaging data automatically

Usage:

# Compress all TIFF images older than 90 days
python compress_imaging.py --input /RDS/00_ACTIVE_PROJECTS --days-old 90 --format ome-tiff

Expected results: - 30-50% size reduction - No quality loss - Maintains all metadata - Automatically verifies integrity

Purpose: Check projects follow required structure

Usage:

# Check all active projects weekly
python validate_organization.py /RDS/00_ACTIVE_PROJECTS

Checks: - README.md exists - metadata.yaml exists and valid - File naming conventions followed - Required subdirectories present

Output: - List of non-compliant projects - Specific issues for each project - Email report to Data Steward

Purpose: Verify backup integrity automatically

Usage:

# Verify all checksums in backup directory
python verify_backup.py /backup/external_hdd

Checks: - All files have checksums - Checksums match actual file hashes - No corrupted files in backup

Output: - Number of files verified - List of any errors found - Email report if errors detected