OMERO.server backup and restore

Cleaning up your binary repository

As detailed in Binary data, it is possible that some files may be left behind when a delete action is performed. This was mostly an issue on Windows, which is no longer supported for OMERO server, but is still possible on Posix systems. If you think files have been left behind e.g. after a hard-reboot, a script to clean these up is included in the OMERO.server distribution lib/python/omero/util/cleanse.py, which can be used so:

$ omero admin cleanse /OMERO

Note that only items not listed in the relational database (i.e. previously failed deletes) and empty directories will be cleaned up by this script.

Note

If you are cleaning a large repository and the process runs for a long time but does not appear to succeed, you may find that running $ omero sessions keepalive in one shell and then running the cleanse command from another shell allows the process to finish without timing out.

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:

  1. PostgreSQL database (assumed to be omero_database)

  2. OMERO.server binary data store (assumed to be /OMERO)

  3. OMERO.server configuration

Warning

You must back up (1) and (2) frequently.

Frequent backups taken while the server is still running are usually sufficient but you should be aware that they may not be consistent snapshots. The safest course of action is to perform backups during server downtime when possible, especially if you think you may need the backup.

You need to back up (3) only before you make changes. You can copy it into /OMERO/backup to ensure it is kept safe:

$ omero config get > /OMERO/backup/omero.config

Other backup sources

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.

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 available at https://github.com/ome/scripts which provides help for merging your scripts directories.

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:

#!/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 25. Backup and Restore).

Note

Frequent backups of your PostgreSQL database are crucial; you do not want to be in the position of trying to restore your server without one.

Note

Consider OMERO database dumps to be sensitive and be accordingly cautious in allowing access to them. For example, the session.uuid column contains UUIDs with which OMERO clients can attach to existing sessions.

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 frequently 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.

Restoring OMERO

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

  1. OMERO.server etc configuration

  2. PostgreSQL database (assumed to be omero)

  3. 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 downloads page that matches the version you originally had installed, all that is required is to restore your backup preferences by running:

$ 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 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

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.

See also

List of backup software

Wikipedia page listing the backup softwares.

PostgreSQL 10 Interactive Manual

Chapter 25: Backup and Restore

rdiff-backup documentation

Online documentation of rdiff-backup project