OMERO Server

This installs and sets up OMERO.server.

Warning: Only works with Python 3. Check CHANGES.md for more information.

Dependencies

You need to have a PostgreSQL server.

Role Variables

All variables are optional. See defaults/main.yml for the complete list.

OMERO.server version:

• omero_server_release: The version of OMERO, e.g., 5.6.0. The default is present, which will install the latest version if nothing is installed. Use latest for automatic updates when new versions are available.

Database connection settings:

• omero_server_dbhost: Host for the database.
• omero_server_dbuser: Username for the database.
• omero_server_dbname: Name of the database.
• omero_server_dbpassword: Password for the database.
• omero_server_rootpassword: Root password for OMERO, default is omero. This is only used for setting up a new database.

OMERO.server configuration settings:

• omero_server_config_set: A set of key-value pairs used for the initial configuration of OMERO.server, default is empty. Values can be strings or objects (lists, dictionaries) that will be converted to JSON.

System user, group, permissions, and data directory settings: You may need to adjust these for imports:

• omero_server_system_user: OMERO.server system user, default is omero-server.
• omero_server_system_user_manage: Create or update the system user if needed, default is True.
• omero_server_system_uid: User ID for the OMERO system user (default is automatic).
• omero_server_system_umask: UMASK for the system user; this might need changing for imports.
• omero_server_system_managedrepo_group: Group for the ManagedRepository.
• omero_server_datadir_mode: Permissions for OMERO data directories, excluding ManagedRepository.
• omero_server_datadir_managedrepo_mode: Permissions for the OMERO ManagedRepository.
• omero_server_datadir: Directory for OMERO data, default is /OMERO.
• omero_server_datadir_managedrepo: Directory for OMERO ManagedRepository.
• omero_server_selfsigned_certificates: Generate self-signed certificates instead of using anonymous ciphers, default is True. Use if your system doesn't support weak ciphers.

Systemd configuration for OMERO.server:

• omero_server_systemd_setup: Create and start the omero-server systemd service, default is True.
• omero_server_systemd_limit_nofile: Systemd limit for the number of open files (default is to ignore this).
• omero_server_systemd_after: List additional service names for systemd unit file "After" statements. Default is empty.
• omero_server_systemd_requires: List additional service names for systemd unit file "Requires" statements. Default is empty.
• omero_server_systemd_environment: Additional environment variables as a dictionary.

Python virtual environment:

• omero_server_python_addons: List of extra Python packages to install in the virtual environment. You can also install packages directly into /opt/omero/server/venv3.

Backups:

• omero_server_database_backupdir: Directory to backup the OMERO database before upgrading, default is empty (disabled).

Configuring OMERO.server

This role regenerates the OMERO configuration file using the files and helper script in /opt/omero/server/config. Use omero_server_config_set for basic configurations. For complex setups, create configuration files under: /opt/omero/server/config/ with a .omero extension.

Manual changes using (omero config ...) will be lost after a restart of omero-server with systemd. To prevent this, set omero_server_always_reset_config: false. Manual changes will not be kept during an upgrade.

For a proposal to support a conf.d style directory directly in OMERO, see https://github.com/ome/design/issues/70.

Example Playbooks

# Install the latest release, including PostgreSQL on the same server
- hosts: localhost
  roles:
  - role: ome.postgresql
    postgresql_version: "13"
    postgresql_databases:
      - name: omero
        owner: omero
    postgresql_users:
      - user: omero
        password: omero
        databases: [omero]
  - role: ome.omero_server


# Install or upgrade to a specific version, with an external database
- hosts: localhost
  roles:
  - role: ome.omero_server
    omero_server_release: 5.6.0
    omero_server_dbhost: postgres.example.org
    omero_server_dbuser: db_user
    omero_server_dbname: db_name
    omero_server_dbpassword: db_password
    # Version needed for the psql client
    postgresql_version: "13"

Author Information

Contact: ome-devel@lists.openmicroscopy.org.uk