Maintenance, Backup and Restore

Maintenance tasks for OMERO

Cleaning up your binary repository

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="omero"
BINARY_REPOSITORY="/OMERO"
OMERO_HOME=/home/omero/OMERO-CURRENT
$OMERO_HOME/bin/omero -s localhost -u $USERNAME -w $PASSWORD admin cleanse $BINARY_REPOSITORY

Managing OMERO.server log files

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.

OMERO.server log file location

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/"/>
...

Backing Up OMERO

Understanding backup sources

OMERO.server has three main backup sources:

PostgreSQL database (assumed to be omero)
OMERO.server binary data store (assumed to be /OMERO)
OMERO.server configuration
In 4.2.0, the lib/scripts directory should also be backed up, but restoring it may pose issues. This will be corrected in a patch release. See Software Limitations

(1) and (2) should be backed up regularly and (3) really only needs backing up before you make changes. You can ensure it is kept safe copying it into /OMERO/backup:

$ 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.

Backing up your PostgreSQL database

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:

#!sh
#!/bin/bash

DATE=`date '+%Y-%m-%d_%H:%M:%S-%Z'`
OUTPUT_DIRECTORY=/OMERO/backup/database
DATABASE="omero"
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"

Other database backup configurations are outside the scope of this document but can be researched on the PostgreSQL website here (Chapter 23. Backup and Restore).

Backing up your binary data store

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 here.

Restoring OMERO

There are three main steps to OMERO.server restoration in the event of a system failure:

OMERO.server etc configuration
PostgreSQL database (assumed to be omero)
OMERO.server binary data store (assumed to be /OMERO)

NOTE: It is important that restoration steps are done in this order unless you are absolutely sure what you are doing.

Restoring your configuration

Once you have retrieved an OMERO.server package from the download 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.

Restoring your PostgreSQL database

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 install. 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 omero.2010-06-05_16:27:29-GMT.pg_dump

Restoring your OMERO.server binary data store

All that remains once you have restored your Java preferences and PostgreSQL database is to restore your /OMERO binary data store backup.

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