.. _server_backup: OMERO.server backup and restore =============================== Cleaning up your binary repository ---------------------------------- As detailed in :ref:`DeleteBinaryData`, 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:: ... ... Backing up OMERO ---------------- Understanding backup sources ^^^^^^^^^^^^^^^^^^^^^^^^^^^^ OMERO.server has three main backup sources: 1. PostgreSQL database (assumed to be ``omero_database``) 2. OMERO.server :doc:`binary data store ` (assumed to be :file:`/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 :file:`etc/grid/(win)default.xml` directly for any reason then you will also need to copy that file to somewhere safe, such as :file:`/OMERO/backup`. The :file:`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 ``_ which provides help for merging your scripts directories. .. _backup-and-restore_postgresql: 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 :file:`/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 :doc:`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 :ref:`backup-and-restore_postgresql` 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:`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 :doc:`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 :doc:`unix/server-installation`. Once you have ensured that the database user and empty database exist, you can restore the :file:`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`` :doc:`binary data store ` backup. .. seealso:: `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