OMERO.server upgrade

The OME team is committed to providing frequent, project-wide upgrades both with bug fixes and new functionality. We try to make the schedule for these releases as public as possible. You may want to take a look at the Trello boards for exactly what will go into a release.

See the full details of OMERO 5.4.9 features in the OMERO version history.

This guide aims to be as definitive as possible so please do not be put off by the level of detail; upgrading should be a straightforward process.

Warning

If you are upgrading from a version prior to OMERO 5.3 then you must also study the upgrade instructions for those prior versions because they may describe important steps that these instructions assume to already have been done by OMERO 5.3 users. Before proceeding with these instructions you may first need to read the instructions for upgrading to OMERO 5.3 because some extra steps may be required beyond simply running the SQL upgrade scripts described below.

If you are upgrading from 5.2 on Windows and need to migrate to Linux, there is a guide in the OMERO 5.3 documentation.

Upgrade checklist

Check prerequisities

Before starting the upgrade, please ensure that you have reviewed and satisfied all the system requirements with correct versions for installation. In particular, ensure that you are running a suitable version of PostgreSQL to enable successful upgrading of the database, otherwise the upgrade script aborts with a message saying that your database server version is less than the OMERO prerequisite.

Corrupted pyramids

A bug introduced in OMERO 5.2.0 meant that corrupted pyramids were generated for large TIFF files with little endian encoding. This bug was fixed in OMERO 5.4.4 and corrupted pyramids need to be deleted to allow new ones to be generated:

bin/omero admin removepyramids --endian=little

We recommend you run the command with --dry-run first to list the pyramids that will be deleted. If there are a large number of pyramids, you may need to run the command more than once since you cannot remove more than 500 pyramids in one call. For large installations, to avoid any timeout issue it is recommended to run the command with --wait=xxx where xxx is for example 5000 seconds. You can also specify a cut-off date (e.g. the date you upgraded to 5.2) so the command has fewer files to process; use -h for details of the additional arguments possible.

Attempting to remove pyramids imported before OMERO 5.0 (pre-FS) will result in messages like Failed to remove for image 20: pyramid-requires-fileset being printed out. You can safely ignore those messages. The pyramids are not corrupted.

File limits

You may wish to review the open file limits. Please consult the Too many open file descriptors section for further details.

Password usage

The passwords and logins used here are examples. Please consult the Which user account and password do I use where? section for explanation. In particular, be sure to replace the values of db_user and omero_database with the actual database user and database name for your installation.

Memoization files invalidation

All cached Bio-Formats memoization files created at import time will be invalidated by the server upgrade. This means the very first loading of each image after upgrade will be slower. After re-initialization, a new memoization file will be automatically generated and OMERO will be able to load images in a performant manner again.

These files are stored under BioFormatsCache in the OMERO data directory, e.g. /OMERO/BioFormatsCache. You may see error messages in your log files when an old memoization file is found; to avoid these messages delete everything under this directory before starting the upgraded server.

Troubleshooting

If you encounter errors during an OMERO upgrade, database upgrade, etc., you should retain as much log information as possible and notify the OMERO.server team via the mailing lists available on the support page.

Upgrade check

All OMERO products check themselves with the OmeroRegistry for update notifications on startup. If you wish to disable this functionality you should do so now as outlined on the OMERO upgrade checks page.

Upgrade steps

For all users, the basic workflow for upgrading your OMERO.server is listed below. Please refer to each section for additional details.

Check ahead for upgrade issues

There is a precheck SQL script provided that performs various database checks to verify readiness for upgrade. The precheck script works even with the OMERO server running so it may be used before downtime for the actual upgrade is scheduled. Issues that the script reports will need to be resolved before the upgrade may proceed. The precheck script will not make any changes to the database: it merely performs various precautionary checks also done by the actual upgrade script.

$ cd OMERO.server
$ psql -h localhost -U db_user omero_database < sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql
Password for user db_user:
...
...
                           status
---------------------------------------------------------------------
                                                                    +
                                                                    +
                                                                    +
YOUR DATABASE IS READY FOR UPGRADE TO VERSION OMERO5.4__0           +
                                                                    +
                                                                    +

(1 row)

Warning

The sql/psql/OMERO5.4__0/OMERO5.3__1-precheck.sql script referenced by the above psql command assumes a planned upgrade from OMERO 5.3.4. If you are instead currently running OMERO 5.3.3 or an earlier 5.3.x version then you perform the precheck by using the above command with sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql. That script verifies that the database contains no trace of 2017-SV5-filename-2 having been exploited; this vulnerability was fixed in OMERO 5.3.4.

Perform a database backup

The first thing to do before any upgrade activity is to backup your database.

$ pg_dump -h localhost -U db_user -Fc -f before_upgrade.db.dump omero_database

Copy new binaries

Before copying the new binaries, stop the existing server:

$ cd OMERO.server
$ bin/omero web stop
$ bin/omero admin stop

Your OMERO configuration is stored using config.xml in the etc/grid directory under your OMERO.server directory. Assuming you have not made any file changes within your OMERO.server distribution directory, you are safe to follow the following upgrade procedure:

$ cd ..
$ mv OMERO.server OMERO.server-old
$ unzip OMERO.server-5.4.9-ice3x-byy.zip
$ ln -s OMERO.server-5.4.9-ice3x-byy OMERO.server
$ cp OMERO.server-old/etc/grid/config.xml OMERO.server/etc/grid

Note

ice3x and byy need to be replaced by the appropriate Ice version and build number of OMERO.server.

Upgrade your database

Warning

This section only concerns users upgrading from a 5.3 or earlier server. If upgrading from a 5.4 server, you do not need to upgrade the database.

Ensure Unicode character encoding

OMERO requires a Unicode-encoded database; without it, the upgrade script aborts with a message warning how the OMERO database character encoding must be UTF8. From psql:

# SELECT datname, pg_encoding_to_char(encoding) FROM pg_database;
  datname   | pg_encoding_to_char
------------+---------------------
 template1  | UTF8
 template0  | UTF8
 postgres   | UTF8
 omero      | UTF8
(4 rows)

Alternatively, simply run psql -l and check the output. If your OMERO database is not Unicode-encoded with UTF8 then it must be re-encoded.

If you have the pg_upgradecluster command available then its --locale option can effect the change in encoding. Otherwise, create a Unicode-encoded dump of your database: dump it as before but to a different dump file and with an additional -E UTF8 option. Then, create a Unicode-encoded database for OMERO and restore that dump into it with pg_restore, similarly to effecting a rollback. If required to achieve this, the -E UTF8 option is accepted by both initdb and createdb.

Run the upgrade script

You must use the same username and password you have defined during OMERO.server installation. For a large production system you should plan for the fact that the upgrade script may take several hours to run.

$ cd OMERO.server
$ psql -h localhost -U db_user omero_database < sql/psql/OMERO5.4__0/OMERO5.3__1.sql
Password for user db_user:
...
...
                           status
---------------------------------------------------------------------
                                                                    +
                                                                    +
                                                                    +
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO5.4__0 +
                                                                    +
                                                                    +

(1 row)

If you are upgrading from a server earlier than 5.3 then you must run the earlier upgrade scripts in sequence before the one above. There is no need to download and run the server from an intermediate major release but you must still study the upgrade instructions for earlier versions in case there are additional steps. For example, any optional SQL scripts that affect the database probably run only on the specific version before the next upgrade script.

Note

If you perform the database upgrade using SQL shell, make sure you are connected to the database using db_user before running the script. See this forum thread for more information.

Warning

The sql/psql/OMERO5.4__0/OMERO5.3__1.sql script referenced by the above psql command assumes upgrade from OMERO 5.3.4. If you are instead currently running OMERO 5.3.3 or an earlier 5.3.x version then you upgrade the database directly to OMERO 5.4.0 by using the above command with sql/psql/OMERO5.4__0/OMERO5.3__0.sql.

Remove the guest user password (optional)

If a password was set on the guest user to work around 2017-SV4-guest-user then you will need to remove it to restore the forgotten password reset functionality in OMERO.web:

$ psql -h localhost -U db_user omero_database < sql/psql/OMERO5.4__0/allow-guest-user-without-password.sql

This can be done at any time during the OMERO 5.4 series and is optional if you do not deploy OMERO.web.

Note

The above script assumes that the guest user has an ID of 1 as is typical. Otherwise the script will do nothing until it is adjusted. Please feel free to contact us for assistance with that if required.

Optimize an upgraded database (optional)

After you have run the upgrade script, you may want to optimize your database which can both save disk space and speed up access times.

$ psql -h localhost -U db_user omero_database -c 'VACUUM FULL VERBOSE ANALYZE;'

Merge script changes

If any new official scripts have been added under lib/scripts or if you have modified any of the existing ones, then you will need to backup your modifications. Doing this, however, is not as simple as copying the directory over since the core developers will have also improved these scripts. In order to facilitate saving your work, we have turned the scripts into a Git submodule which can be found at https://github.com/ome/scripts.

For further information on managing your scripts, refer to OMERO.scripts. If you require help, please contact the OME developers.

Update your environment variables and memory settings

Environment variables

If you changed the directory name where the 5.4.9 server code resides, make sure to update any system environment variables. Before restarting the server, make sure your PATH and PYTHONPATH system environment variables are pointing to the new locations.

JVM memory settings

Your memory settings should be copied along with etc/grid/config.xml, but you can check the current settings by running omero admin jvmcfg. See Memory configuration for more information.

Restart your server

• Following a successful database upgrade, you can start the server.

  $ cd OMERO.server
  $ bin/omero admin start
  

• If anything goes wrong, please send the output of omero admin diagnostics to ome-users@lists.openmicroscopy.org.uk.

Restore a database backup

If the upgraded database or the new server version do not work for you, or you otherwise need to rollback to a previous database backup, you may want to restore a database backup. To do so, create a new database,

$ createdb -h localhost -U postgres -E UTF8 -O db_user omero_from_backup

restore the previous archive into this new database,

$ pg_restore -Fc -d omero_from_backup before_upgrade.db.dump

and configure your server to use it.

$ bin/omero config set omero.db.name omero_from_backup