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:
$ bin/omero admin cleanse /OMERO
Note that only items not listed in the relational database (i.e. previously failed deletes) and now empty directories will be cleaned up by this script.
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_database
) - OMERO.server
binary data store
(assumed to be
/OMERO
) - OMERO.server configuration
Warning
You must back up (1) and (2) regularly.
Regular 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:
$ bin/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 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.
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.
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 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.
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 9.4 Interactive Manual
- Chapter 24: Backup and Restore
- rdiff-backup documentation
- Online documentation of rdiff-backup project