Note
This documentation is for OMERO 5.2. This version is now in maintenance mode and will only be updated in the event of critical bugs or security concerns. OMERO 5.3 is expected in the first quarter of 2017.
The OMERO.server does not remove files from disk until a cleanup task has been run. A script to do this is included in the OMERO.server distribution lib/python/omero/util/cleanse.py which can be used so:
$ bin/omero admin cleanse /OMERO
This can be performed daily using cron with a script such as:
#!sh
#!/bin/bash
USERNAME="root"
PASSWORD="root_password"
BINARY_REPOSITORY="/OMERO"
OMERO_PREFIX=/home/omero/OMERO-CURRENT
$OMERO_PREFIX/bin/omero -s localhost -u $USERNAME -w $PASSWORD admin cleanse $BINARY_REPOSITORY
Warning
If you are running OMERO 5.2.3 or earlier, do not run this script as an operating system user while logged into OMERO as a non-administrative user as this will lead to data loss. Instead, you should always run as an administrative user such as “root”. See this announcement for further details. More recent versions enforce this by making the script and command admin-only.
Your OMERO.server will produce log files that are rotated when they reach 512MB. These directories will look like:
omero_dist $ ls var/log
Blitz-0.log FileServer.log MonitorServer.log Processor-0.log master.out
DropBox.log Indexer-0.log OMEROweb.log master.err
Any files with a .1, .2, .3 etc. suffix may be compressed or deleted.
The log file directory may also be relocated to different storage by modifying the etc/grid/default.xml file:
...
<variable name="OMERO_LOGS" value="var/log/"/>
...
OMERO.server has three main backup sources:
PostgreSQL database (assumed to be omero_database)
OMERO.server binary data store (UNIX/Mac information page or Windows information page; assumed to be /OMERO or C:\OMERO)
OMERO.server configuration
Note
The lib/scripts directory should also be backed up, but restoring it may pose issues if any of your users have added their own “official scripts”. A github repository is now available under https://github.com/ome/scripts which provides help for merging your lib/scripts directories.
You should back up (1) and (2) regularly.
Warning
Although losing your PostgreSQL database is not as catastrophic for OMERO version 5.0 as it is for 4.4, you still do not want to be in the position of trying to recover your server without a backup of this resource.
You need to back up (3) only before you make changes. You can copy it into /OMERO/backup to ensure it is kept safe:
$ bin/omero config get > /OMERO/backup/omero.config
Note
If you have edited etc/grid/(win)default.xml directly for any reason then you will also need to copy that file to somewhere safe, such as /OMERO/backup.
Database backups can be achieved using the PostgreSQL pg_dump command. Here is an example backup script that can be placed in /etc/cron.daily to perform daily database backups:
#!/bin/bash
DATE=`date '+%Y-%m-%d_%H:%M:%S-%Z'`
OUTPUT_DIRECTORY=/OMERO/backup/database
DATABASE="omero_database"
DATABASE_ADMIN="postgres"
mkdir -p $OUTPUT_DIRECTORY
chown -R $DATABASE_ADMIN $OUTPUT_DIRECTORY
su $DATABASE_ADMIN -c "pg_dump -Fc -f $OUTPUT_DIRECTORY/$DATABASE.$DATE.pg_dump $DATABASE"
Other database backup configurations are outside the scope of this document but can be researched on the PostgreSQL website (Chapter 24. Backup and Restore).
Note
Regular backups of your PostgreSQL database are crucial; you do not want to be in the position of trying to restore your server without one.
To simplify backup locations we have, in this document, located all database and configuration backups under /OMERO, your binary data store. The entire contents of /OMERO should be backed up regularly as this will, especially if this document’s conventions are followed, contain all the relevant data to restore your OMERO.server installation in the unlikely event of a system failure, botched upgrade or user malice.
File system backup is often a very personal and controversial topic amongst systems administrators and as such the OMERO project does not make any explicit recommendations about backup software. In the interest of providing a working example we will use open source rdiff-backup project and like Backing up your PostgreSQL database above, provide a backup script which can be placed in /etc/cron.daily to perform daily /OMERO backups:
#!sh
#!/bin/bash
FROM=/OMERO
TO=/mnt/backup_server
rdiff-backup $FROM $TO
rdiff-backup can also be used to backup /OMERO to a remote machine:
#!sh
#!/bin/bash
FROM=/OMERO
TO=backup_server.example.com::/backup/omero
rdiff-backup $FROM $TO
More advanced rdiff-backup configurations are beyond the scope of this document. If you want to know more you are encouraged to read the documentation available on the rdiff-backup website.
There are three main steps to OMERO.server restoration in the event of a system failure:
Note
It is important that restoration steps are done in this order unless you are absolutely sure what you are doing.
Once you have retrieved an OMERO.server package from the downloads page that matches the version you originally had installed, all that is required is to restore your backup preferences by running:
$ bin/omero config load /OMERO/backup/omero.config
You should then follow the Reconfiguration steps of install.
If you have had a PostgreSQL crash and database users are missing from your configuration, you should follow the first two (Create a non-superuser database user and Create a database for OMERO data to reside in) steps of OMERO.server installation. Once you have ensured that the database user and empty database exist, you can restore the pg_dump file as follows:
$ sudo -u postgres pg_restore -Fc -d omero_database omero.2010-06-05_16:27:29-GMT.pg_dump
All that remains once you have restored your Java preferences and PostgreSQL database is to restore your /OMERO binary data store backup.
See also