Updates and Maintenance

# Check installed MADSci version
madsci version

# Check all installed package versions
pip list | grep madsci

# Back up all databases
madsci-postgres-backup create \
  --db-url postgresql://postgres:postgres@localhost:5432/resources \
  --backup-dir ./backups/pre-upgrade

for db in events experiments data workcell locations; do
  madsci-mongodb-backup create \
    --mongo-url mongodb://localhost:27017 \
    --database $db \
    --backup-dir ./backups/pre-upgrade/mongodb
done

# Stop all services
docker compose down

# If using git (development install)
git pull origin main
pdm install -G:all

# If using pip (released packages)
pip install --upgrade madsci_common madsci_client madsci_node_module \
  madsci_squid madsci_event_manager madsci_experiment_manager \
  madsci_resource_manager madsci_data_manager madsci_workcell_manager \
  madsci_location_manager madsci_experiment_application

# Rebuild all images
docker compose build

# Or rebuild specific services
docker compose build workcell_manager event_manager

# PostgreSQL migrations (Resource Manager)
python -m madsci.resource_manager.migration_tool \
  --db-url postgresql://postgres:postgres@localhost:5432/resources

# MongoDB migrations (per manager, if needed)
# Check release notes for specific migration commands

# Start all services
docker compose up -d

# Verify health
madsci status

# Check for migration warnings
madsci logs --level WARNING --tail 50

# Run diagnostics
madsci doctor

# Test a simple workflow
# (Use your lab's standard smoke test)

# Check current migration status
python -m madsci.resource_manager.migration_tool --status \
  --db-url postgresql://postgres:postgres@localhost:5432/resources

# Run pending migrations
python -m madsci.resource_manager.migration_tool \
  --db-url postgresql://postgres:postgres@localhost:5432/resources

# Scan for files needing migration
madsci migrate scan

# Preview migration
madsci migrate convert --dry-run

# Apply migration
madsci migrate convert --apply

# Verify
madsci migrate status

# After confirming everything works, clean up
madsci migrate finalize

# Environment variable for Event Manager
EVENT_RETENTION_DAYS=90
EVENT_ARCHIVE_ENABLED=true
EVENT_ARCHIVE_DIR=/data/event_archives

# Check database sizes
docker compose exec mongodb mongosh --eval "
  db.adminCommand('listDatabases').databases.forEach(function(d) {
    print(d.name + ': ' + (d.sizeOnDisk / 1024 / 1024).toFixed(2) + ' MB');
  });
"

# Compact a collection (reclaim disk space)
docker compose exec mongodb mongosh events --eval "
  db.runCommand({compact: 'events'})
"

# Check database size
docker compose exec postgres psql -U postgres -c "
  SELECT pg_database.datname,
         pg_size_pretty(pg_database_size(pg_database.datname))
  FROM pg_database
  ORDER BY pg_database_size(pg_database.datname) DESC;
"

# Run vacuum (reclaim space, update statistics)
docker compose exec postgres psql -U postgres -d resources -c "VACUUM ANALYZE;"

# Remove unused images
docker image prune

# Remove unused volumes (careful - don't remove data volumes!)
docker volume prune --filter "label!=keep"

# Remove build cache
docker builder prune

# Full cleanup (stopped containers, unused images, unused networks)
docker system prune

# Check overall disk usage
df -h

# Check Docker disk usage
docker system df

# Find large log files
find /var/lib/docker/containers -name "*.log" -size +100M

# Truncate a large container log (if needed)
truncate -s 0 /var/lib/docker/containers/<container_id>/<container_id>-json.log

docker compose down

# If using git
git checkout <previous_version_tag>
pdm install -G:all

# If using pip
pip install madsci_common==<previous_version> ...

# Restore PostgreSQL
madsci-postgres-backup restore \
  --db-url postgresql://postgres:postgres@localhost:5432/resources \
  --backup-path ./backups/pre-upgrade/resources_backup.sql

# Restore MongoDB
for db in events experiments data workcell locations; do
  madsci-mongodb-backup restore \
    --mongo-url mongodb://localhost:27017 \
    --database $db \
    --backup-path ./backups/pre-upgrade/mongodb/${db}_backup.bson
done

docker compose build
docker compose up -d
madsci status