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 roadmap_ for exactly what will go into a release. We always inform our :community_plone:`mailing lists <>` of the development status. See the full details of OMERO |release| features in the :forum:`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. Upgrade check list ------------------ .. contents:: :local: :depth: 1 Check prerequisities ^^^^^^^^^^^^^^^^^^^^ Before starting the upgrade, please ensure that you have reviewed and satisfied all the :doc:`system requirements ` with :doc:`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. If you are upgrading from a version earlier than OMERO 5.0 then first review the `5.0 upgrade notes `_ regarding previous changes in OMERO. File limits ^^^^^^^^^^^ You may wish to review the open file limits. Please consult the :ref:`limitations-openfiles` section for further details. Password usage ^^^^^^^^^^^^^^ The passwords and logins used here are examples. Please consult the :ref:`troubleshooting-password` 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. OMERO.web configuration ^^^^^^^^^^^^^^^^^^^^^^^ Check :ref:`unix_omero_web_deployment` or :ref:`windows_omero_web_deployment`, what is the most recent OMERO.web deployment for the platform. If you generated configuration stanzas using :omerocmd:`web config` which enables OMERO.web via Apache or Nginx, they may include hard-coded links to your previous version of OMERO. We recommend using a future-proof symlink if possible, so that these stanzas do not need updating with each OMERO server upgrade. Web plugin updates ^^^^^^^^^^^^^^^^^^ 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. 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 :file:`BioFormatsCache` in the OMERO data directory, e.g. :file:`/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 :community_plone:`community <>` 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 :doc:`UpgradeCheck` 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. .. contents:: :local: :depth: 1 .. _back-up-the-db: Perform a database backup ^^^^^^^^^^^^^^^^^^^^^^^^^ The first thing to do before **any** upgrade activity is to backup your database. .. parsed-literal:: $ 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 :file:`config.xml` in the :file:`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: .. parsed-literal:: $ cd .. $ mv OMERO.server OMERO.server-old $ unzip OMERO.server-|release|-ice3x-byy.zip $ ln -s OMERO.server-|release|-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 ^^^^^^^^^^^^^^^^^^^^^ .. only:: point_release .. warning:: This section only concerns users upgrading from a |previousversion| or earlier server. If upgrading from a |version| server, you do not need to upgrade the database. Ensure Unicode character encoding """"""""""""""""""""""""""""""""" OMERO 5.1 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 :command:`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 :command:`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 :command:`pg_upgradecluster` command available then its :option:`--locale` option can effect the change in encoding. Otherwise, create a Unicode-encoded dump of your database: dump it :ref:`as before ` but to a different dump file and with an additional :option:`-E UTF8` option. Then, create a Unicode-encoded database for OMERO and restore that dump into it with :command:`pg_restore`, similarly to :ref:`effecting a rollback `. If required to achieve this, the :option:`-E UTF8` option is accepted by both :command:`initdb` and :command:`createdb`. Run the upgrade script """""""""""""""""""""" You **must** use the same username and password you have defined during :doc:`unix/server-installation`. The |version| upgrade script should execute in a short time. .. parsed-literal:: $ cd OMERO.server $ psql -h localhost -U **db_user** **omero_database** < sql/psql/|current_dbver|/|previous_dbver|.sql Password for user **db_user**: ... ... status --------------------------------------------------------------------- + + + YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION |current_dbver| + + + (1 row) .. 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 :forum:`this forum thread ` for more information. 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. .. parsed-literal:: $ 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;' .. _upgrademergescript: 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 ``_. For further information on managing your scripts, refer to :doc:`installing-scripts`. If you require help, please contact the OME developers. Update your configuration ^^^^^^^^^^^^^^^^^^^^^^^^^ Environment variables """"""""""""""""""""" If you changed the directory name where the |release| 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 :file:`etc/grid/config.xml`, but you can check the current settings by running :omerocmd:`admin jvmcfg`. See :ref:`jvm_memory_settings` for more information. OMERO.web server configuration """""""""""""""""""""""""""""" The FastCGI support was removed in OMERO 5.2 and OMERO.web can be deployed using WSGI (see, :ref:`unix_omero_web_deployment` for more details). If you already deployed OMERO.web using WSGI it is highly recommended that you regenerate your config files, remembering to merge in any of your own modifications if necessary. See :doc:`/sysadmins/whatsnew` for details of changes. If necessary ensure you have set up a regular task to clear out any stale OMERO.web session files as described in :ref:`unix_omero_web_maintenance` or :ref:`windows_omero_web_maintenance`. Restart your server ^^^^^^^^^^^^^^^^^^^ - Following a successful database upgrade, you can start the server. .. parsed-literal:: $ cd OMERO.server $ bin/omero admin start - If anything goes wrong, please send the output of :omerocmd:`admin diagnostics` to ome-users@lists.openmicroscopy.org.uk. - Start OMERO.web with the following command: :: $ bin/omero web start .. _restore-the-db: 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, .. parsed-literal:: $ 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 .. seealso:: :legacy_plone:`Legacy <>` Legacy part of the OME website containing upgrade instructions for previous versions of the OMERO server.