Backup and Restore

Important

The backup and restore scripts and flows included here are examples for inspiration. They are not recommendations and should be reviewed, tested, and adapted to your environment and policies.

NL-BIOMERO Backup & Restore Scripts

One-command backup and restore for NL-BIOMERO PostgreSQL databases, OMERO server data/config, and Metabase dashboards.

Important: The scripts and approaches described here are examples for inspiration, not prescriptive recommendations. Always review, test, and adapt to your specific environment, security policies, and operational requirements.

Key Features

  • Synchronized backups: All components use a single timestamp for consistency.

  • Flexible targets: Backup/restore to Docker volumes or local folders.

  • Cross-platform: Bash (Linux/macOS, Docker/Podman) and PowerShell (Windows).

  • Zero configuration: Reads from .env, auto-detects containers.

  • Production ready: Error handling, validation, cleanup.

  • Config hierarchy: OMERO config can be restored/overridden in multiple ways.

  • Metabase/OMERO folder backup: Can backup OMERO or Metabase directly from a host folder (no container needed).

Quick Start

Common Options

  • --skip-database / -skipDatabase: Skip both OMERO and BIOMERO DB backup.

  • --skip-server / -skipServer: Skip OMERO server backup.

  • --skip-metabase / -skipMetabase: Skip Metabase backup.

  • --skip-server-data / -skipServerData: Only backup OMERO config (no data tar).

  • --skip-server-config / -skipServerConfig: Only backup OMERO data (no config export).

  • --output-directory <dir> / -outputDirectory <dir>: Custom backup location.

  • --omero-folder <path> / -omeroFolder <path>: Backup OMERO data directly from a host folder (no container needed).

  • --metabase-folder <path> / -metabaseFolder <path>: Backup Metabase directly from a host folder.

Typical Backup Workflow

# 1. Stop user-facing containers (optional for consistency)
docker-compose stop omeroweb metabase biomero-importer

# 2. Run master backup
./backup_and_restore/backup/backup_master.sh

# 3. Restart services
docker-compose up -d

Typical Restore Workflow

# 1. Stop all services
docker-compose down

# 2. Restore databases
./backup_and_restore/restore/restore_db.sh

# 3. Restore OMERO server data/config
./backup_and_restore/restore/restore_server.sh

# 4. Restore Metabase dashboards
./backup_and_restore/restore/restore_metabase.sh

# 5. Update docker-compose.yml to use restored volumes/folders
# 6. Start all services
docker-compose up -d

Individual Script Usage

Database Backup

./backup_and_restore/backup/backup_db.sh

  • Backs up OMERO and BIOMERO DBs from containers.

  • Output: omero.{timestamp}.pg_dump, biomero.{timestamp}.pg_dump

Server Backup

./backup_and_restore/backup/backup_server.sh

  • Backs up OMERO server data/config from container or host folder.

  • Output: omero-server.{timestamp}.tar.gz

  • Use --omero-folder <path> to backup from a host folder (no container needed).

Metabase Backup

./backup_and_restore/backup/backup_metabase.sh

  • Backs up Metabase folder (H2 DB, configs, plugins).

  • Output: metabase.{timestamp}.tar.gz

  • Use --metabase-folder <path> to specify a custom folder.

Restore Scripts

  • restore/restore_db.sh / restore/restore_db.ps1: Restore OMERO/BIOMERO DBs to containers or local folders.

  • restore/restore_server.sh / restore/restore_server.ps1: Restore OMERO server data/config to volume or folder.

  • restore/restore_metabase.sh / restore/restore_metabase.ps1: Restore Metabase dashboards/configs to folder.

OMERO Configuration Hierarchy

  1. Backup config: /OMERO/backup/omero.config (restored automatically)

  2. Custom config files: /opt/omero/server/config/*.omero (mount in docker-compose)

  3. Environment variables: CONFIG_omero_* (override everything)

Example: Backup OMERO from Host Folder

./backup_and_restore/backup/backup_server.sh --omero-folder "/srv/omero"

Example: Backup Metabase from Host Folder

./backup_and_restore/backup/backup_metabase.sh --metabase-folder "/srv/metabase"

Requirements

  • Linux/macOS: Docker or Podman, Bash 4+

  • Windows: Docker Desktop, PowerShell 5.1+

  • For backup: Running NL-BIOMERO containers (unless using folder mode)

  • For restore: Internet access to pull images

Troubleshooting

  • Container not found: Check docker ps or podman ps

  • Permission denied: Ensure backup location is writable

  • Small backup file: Check container names and credentials

  • Restore failed: Check logs with docker logs <container>

  • Config not loading: Check /OMERO/backup/omero.config exists in restored volume/folder

Help

All scripts support --help or -help for usage and options.

For more details, see comments in each script or contact the NL-BIOMERO team.