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 roadmap for exactly what will go into a release. We always inform our mailing lists of the development status.
See the full details of OMERO 5.0.5 features in the Announcements forum.
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.
Before starting the upgrade, please ensure that you have obtained all the prerequisites for installation, documented for Unix and Windows. In particular, ensure that you are running a suitable version of PostgreSQL to enable successful upgrading of the database.
You may wish to review the open file limits. Please consult the Too many open file descriptors section for further details.
With 5.0.0, the default JDBC password provider has been modified to add password salting support. This implies that once a server has been upgraded and deployed, if passwords are modified, you will not be able to easily revert to a configuration without salting. To keep using the legacy password provider without salting support, you will need to configure omero.security.password_provider to use the legacy chainedPasswordProviderNoSalt as described in the Legacy password providers section.
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.
All OMERO databases created prior to 5.0.1 were susceptible to a Lucene bug which could “hide” some search entries. For example, an image might show up in queries based on its name, but searching for a tag or similar might show nothing.
If you have experienced any issues with search in the past, you should strongly consider reindexing your full text index, the process for which has been significantly stream-lined. See Re-indexing for more information.
OMERO.web plugins are very closely integrated into the webclient. For this reason, it is possible that an update of OMERO will cause issues with an older version of a plugin. It is best when updating the server to also install any available plugin updates according to their own documentation.
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 community page.
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.
For all users, the basic workflow for upgrading your OMERO.server is listed below. Please refer to each section for additional details.
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
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-5.0.5-ice3x-byy.zip $ ln -s OMERO.server-5.0.5-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.
Warning
This section only concerns users upgrading from a 4.4 or earlier server. If upgrading from a 5.0 server, you do not need to upgrade the database.
You must use the same username and password you have defined during OMERO.server installation. The 5.0 upgrade script should execute in a short time. The example below assumes you are upgrading from a 4.4 server.
$ cd OMERO.server
$ psql -h localhost -U db_user omero_database < sql/psql/OMERO5.0__0/OMERO4.4__0.sql
Password for user db_user:
...
...
status
---------------------------------------------------------------------
+
+
+
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO 5.0__0+
+
+
(1 row)
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 'REINDEX DATABASE "omero_database" FORCE;' $ psql -h localhost -U db_user omero_database -c 'VACUUM FULL VERBOSE ANALYZE;'
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 Installing new scripts. If you require help, please contact the OME developers.
If you changed the directory name where the 5.0.5 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.
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.
Since OMERO 5.0.0, Pillow is used as the default imaging library for Python instead of PIL. Refer to the installation page of Pillow documentation to install Pillow on your system.
Warning
As mentioned in the Pillow installation section, if you installed PIL, you will need to remove it first before installing Pillow.
In order to ease deployment and avoid errors for IIS (Windows production deployment) and Apache (notably CentOS/RHEL6) OMERO.web now defaults to being “mounted on /omero”. The new OMERO.web web server stanzas have redirects in them with the notable exception of IIS. Depending on your web server configuration you may need to visit your OMERO.web instance at
http://example.com/omero/
As a result of this your web server configuration stanza generated by the previous version of bin/omero web config has to be replaced with the new version. To generate the relevant configuration, please run bin/omero web config <webserver>, update and restart your web 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 bin/omero admin diagnostics to ome-users@lists.openmicroscopy.org.uk.
Start OMERO.web with the following command:
$ bin/omero web start
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 -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
See also