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OMERO Server

Actions Status Ansible Role

Installs and configures OMERO.server.

Warning: Only supports Python 3. See CHANGES.md for details.

Dependencies

A PostgreSQL server is required.

Role Variables

All variables are optional, see defaults/main.yml for the full list

OMERO.server version.

  • omero_server_release: The OMERO release, e.g. 5.6.0. The default is present which will install the latest server if no server is installed, but will not modify an existing server. Use latest to automatically upgrade when a new version is released.

Database connection parameters and initialisation.

  • omero_server_dbhost: Database host
  • omero_server_dbuser: Database user
  • omero_server_dbname: Database name
  • omero_server_dbpassword: Database password
  • omero_server_rootpassword: OMERO root password, default omero. This is only used when initialising a new database.

OMERO.server configuration.

  • omero_server_config_set: A dictionary of config-key: value which will be used for the initial OMERO.server configuration, default empty. value can be a string, or an object (list, dictionary) that will be automatically converted to quoted JSON. Note configuration can also be done pre/post installation using the server/config conf.d style directory.

OMERO system user, group, permissions, and data directory. You may need to change these for in-place imports.

  • omero_server_system_user: OMERO.server system user, default omero-server.
  • omero_server_system_user_manage: Create or update the OMERO.server system user if necessary, default True.
  • omero_server_system_uid: OMERO system user ID (default automatic)
  • omero_server_system_umask: OMERO system user umask, may need to be changed for in-place imports
  • omero_server_system_managedrepo_group: OMERO system group for the ManagedRepository
  • omero_server_datadir_mode: Permissions for OMERO data directories apart from ManagedRepository
  • omero_server_datadir_managedrepo_mode: Permissions for OMERO ManagedRepository
  • omero_server_datadir: OMERO data directory, default /OMERO
  • omero_server_datadir_managedrepo: OMERO ManagedRepository directory
  • omero_server_selfsigned_certificates: Generate self-signed certificates instead of using anonymous ciphers, default True, use this if your system does not support insecure ciphers

OMERO.server systemd configuration.

  • omero_server_systemd_setup: Create and start the omero-server systemd service, default True
  • omero_server_systemd_limit_nofile: Systemd limit for number of open files (default ignore)
  • omero_server_systemd_after: A list of strings with additional service names to appear in systemd unit file "After" statements. Default empty/none.
  • omero_server_systemd_requires: A list of strings with additional service names to appear in systemd unit file "Requires" statements. Default empty/none.
  • omero_server_systemd_environment: Dictionary of additional environment variables.

Python virtualenv

  • omero_server_python_addons: List of additional Python packages to be installed into virtualenv. Alternatively you can install packages into /opt/omero/server/venv3 independently from this role.

Backups

  • omero_server_database_backupdir: Dump the OMERO database to this directory before upgrading, default empty (disabled)

Configuring OMERO.server

This role regenerates the OMERO configuration file using the configuration files and helper script in /opt/omero/server/config. omero_server_config_set can be used for simple configurations, for anything more complex consider creating one or more configuration files under: /opt/omero/server/config/ with the extension .omero.

Manual configuration changes (omero config ...) will be lost following a restart of omero-server with systemd, you can disable this by setting omero_server_always_reset_config: false. Manual configuration changes will never be copied during an upgrade.

See ome/design#70 for a proposal to add support for a conf.d style directory directly into OMERO.

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 particular version, with an external database
- hosts: localhost
  roles:
  - 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 required for the psql client
    postgresql_version: "13"

Author Information

ome-devel@lists.openmicroscopy.org.uk