OMERO.server and PostgreSQL

In order to be installed, OMERO.server requires a running PostgreSQL instance that is configured to accept connections over TCP. This section explains how to ensure that you have the correct PostgreSQL version and that it is installed and configured correctly.

Ensuring you have a valid PostgreSQL version

For OMERO 5.6, PostgreSQL version 14 or later is recommended. Make sure you are using a supported version.

You can check which version of PostgreSQL you have installed with any of the following commands:

$ createuser -V
createuser (PostgreSQL) 9.4.1
$ psql -V
psql (PostgreSQL) 9.4.1
$ createdb -V
createdb (PostgreSQL) 9.4.1

If your existing PostgreSQL installation is an earlier version, it is recommended that you upgrade to a more up-to-date version. Before upgrading, stop the OMERO server and then perform a full dump of the database using pg_dump. See the OMERO.server backup and restore section for further details.

If using a Linux distribution-provided PostgreSQL server, upgrading to a newer version of the distribution will usually make a newer version of PostgreSQL available. If the database was not migrated to the new version automatically, restore your backup after installing, configuring and starting the new version of the database server. If a PostgreSQL server was not provided by your system, EnterpriseDB provide an installer.

Checking PostgreSQL port listening status

You can check if PostgreSQL is listening on the default port (TCP/5432) by running the following command:

$ netstat -an | egrep '5432.*LISTEN'
tcp        0      0 0.0.0.0:5432            0.0.0.0:*               LISTEN
tcp        0      0 :::5432                 :::*                    LISTEN

Note

The exact output of this command will vary. The important thing to recognize is whether or not a process is listening on TCP/5432.

If you cannot find a process listening on TCP/5432 you will need to find your postgresql.conf file and enable PostgreSQL’s TCP listening mode. The exact location of the postgresql.conf file varies between installations.

It may be helpful to locate it using the package manager (rpm or dpkg) or by utilizing the find command. Usually, the PostgreSQL data directory (which houses the postgresql.conf file, is located under /var or /usr:

$ sudo find /etc -name 'postgresql.conf'
$ sudo find /usr -name 'postgresql.conf'
$ sudo find /var -name 'postgresql.conf'
/var/lib/postgresql/data/postgresql.conf

Note

The PostgreSQL data directory is usually only readable by the user postgres so you will likely have to be root in order to find it.

Once you have found the location of the postgresql.conf file on your particular installation, you will need to enable TCP listening. The area of the configuration file you are concerned about should look similar to this:

#listen_addresses = 'localhost'         # what IP address(es) to listen on;
                                    # comma-separated list of addresses;
                                    # defaults to 'localhost', '*' = all
#port = 5432
max_connections = 100
# note: increasing max_connections costs ~400 bytes of shared memory per
# connection slot, plus lock space (see max_locks_per_transaction).  You
# might also need to raise shared_buffers to support more connections.
#superuser_reserved_connections = 2
#unix_socket_directory = *
#unix_socket_group = *
#unix_socket_permissions = 0777         # octal
#bonjour_name = *                      # defaults to the computer name

PostgreSQL HBA (host based authentication)

OMERO.server must have permission to connect to the database that has been created in your PostgreSQL instance. This is configured in the host based authentication file, pg_hba.conf. Check the configuration by examining the contents of pg_hba.conf. It’s important that at least one line allows connections from the loopback address (127.0.0.1) as follows:

# TYPE  DATABASE    USER        CIDR-ADDRESS          METHOD
# IPv4 local connections:
host    all         all         127.0.0.1/32          md5
# IPv6 local connections:
host    all         all         ::1/128               md5

Note

The other lines that are in your pg_hba.conf are important either for PostgreSQL internal commands to work or for existing applications you may have. Do not delete them.

Completing configuration

After making any configuration changes to postgresql.conf or pg_hba.conf, reload the server for the changes to take effect.

$ sudo service postgresql reload