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 |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 ^^^^^^^^^^^^^^^^^^^^^^^ Since OMERO 5.3, OMERO.web can be deployed **separately** from OMERO.server. This is the recommended installation set-up as they perform best under different circumstances and require a different set of dependencies. Please check :ref:`omero_web_deployment` for the latest advice on how to deploy OMERO.web. If you generated configuration stanzas using :omerocmd:`web config` which enables OMERO.web via Nginx, they will include **hard-coded links** to your previous version of OMERO. Therefore, you should regenerate your config files when upgrading, remembering to merge in any of your own modifications if necessary. You should carry out this step even for minor version upgrades as there may be fixes which require it. .. note:: Since OMERO 5.2, the OMERO.web framework no longer bundles a copy of the Django package, instead manual installation of the Django dependency is required. It is highly recommended to use `Django 1.8`_ (LTS) which requires Python 2.7. For more information see :ref:`python-requirements` on the :doc:`/sysadmins/version-requirements` page. Also note that support for Apache deployment has been dropped in 5.3.0. OMERO.web dependencies ^^^^^^^^^^^^^^^^^^^^^^ While upgrading the server you should keep OMERO.web dependencies up to date to ensure that security updates are applied:: $ pip install --upgrade -r share/web/requirements-py27-all.txt .. warning:: Missing this step can result in OMERO.web failing to start after upgrading. OMERO.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. Since 5.3, all official OMERO.web plugins can be installed from :pypi:`Python Package Index <>`. You should remove all previously installed plugins and install the latest versions using `pip `_. Also introduced in 5.3, the ``Open with`` configuration allows users to open data in other web applications e.g. open images in a custom viewer or open images in a new figure with OMERO.figure. After installing OMERO.figure (or any other app), run the following command to add it to the ``Open with`` options, so that the app is available from the context menu on the webclient tree:: $ bin/omero config append omero.web.open_with '["omero_figure", "new_figure", {"supported_objects":["images"], "target": "_blank", "label": "OMERO.figure"}]' Updating 'Open with' config ^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you have configured :property:`omero.web.open_with` prior to OMERO 5.3.3 and also set the default viewer with :property:`omero.web.viewer.view`, for example as described for `OMERO.iviewer `_ then you will find that ``Open with > Image Viewer`` also opens the OMERO.iviewer instead of the ``webgateway`` viewer. To fix this, you need to update the ``Image Viewer`` option within your :property:`omero.web.open_with` config. The best way to do this without changing the ordering of the options is to ``get`` the complete current config, edit the ``Image Viewer`` option, replacing ``"webindex"`` with ``"webgateway"`` and then ``set`` this as the updated config:: $ bin/omero config get omero.web.open_with [["Image viewer", "webindex", {"supported_objects": ["image"], "script_url": "we.... # Replace "webindex" with "webgateway" and paste everything back to set, within single quotes $ bin/omero config set omero.web.open_with '[["Image viewer", "webgateway", {"supported_objects": ["image"], "scr....' 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:`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 :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 Check ahead for upgrade issues ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ If you are upgrading an OMERO 5.2 server, 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. .. parsed-literal:: $ cd OMERO.server $ psql -h localhost -U **db_user** **omero_database** < sql/psql/|current_dbver|/|previous_dbver|-precheck.sql Password for user **db_user**: ... ... status --------------------------------------------------------------------- + + + YOUR DATABASE IS READY FOR UPGRADE TO VERSION |current_dbver| + + + (1 row) .. _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. .. _upgradedb: 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 """"""""""""""""""""""""""""""""" Versions of OMERO from 5.1.0 onwards require 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`. For a large production system you should plan for the fact that the upgrade script may take several hours to run. If you are upgrading an OMERO 5.2 server: .. 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) If you are upgrading an OMERO 5.3 server: .. parsed-literal:: $ cd OMERO.server $ psql -h localhost -U **db_user** **omero_database** < sql/psql/|current_dbver|/OMERO5.3__0.sql Password for user **db_user**: ... ... status --------------------------------------------------------------------- + + + YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION |current_dbver| + + + (1 row) If you are upgrading from a server earlier than |previousversion| then it suffices to 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. .. 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. Delete certain annotations (optional) """"""""""""""""""""""""""""""""""""" For various reasons, production databases may accumulate non-sharable annotations that are orphaned. These are :doc:`structured annotations ` that are 'basic' (`Boolean`, `Timestamp`, `Term`), 'numeric' (`Double`, `Long`), or `Comment`, and that are *not* annotating an object. An illustrative example is that deleting a rating in OMERO.insight 5.2 may have left behind the corresponding `Long` annotation that captured the rating's number of stars. Non-sharable annotations, like comments and ratings, cannot be viewed from OMERO.insight or OMERO.web after they have been orphaned because they are no longer associated with any model object such as an image. The deletion script does *not* delete annotations that have a custom/non-OME namespace (ns) set. .. parsed-literal:: $ cd OMERO.server $ psql -h localhost -U **db_user** **omero_database** < sql/psql/|current_dbver|/delete-ns-orphans.sql This script may be used during some maintenance window subsequent to the actual upgrade as long as it runs on a |current_dbver| database. If at upgrade time you have questions about the script then you may perform further research before :ref:`backing up the database again ` then running the script. There is no requirement to ever use it. 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 'VACUUM FULL VERBOSE ANALYZE;' Reset ROI shape color (optional) """""""""""""""""""""""""""""""" Regions of interest generated using OMERO.insight did not follow the OME model specification. The color of shapes is now handled according to the data model, using RGBA rather than ARGB format. A script is provided to upgrade the color settings of shapes created using OMERO.insight or a different client that saved them in the ARGB format. If you only wish to apply the changes to a subset of ROIs, edit the ``TRUE`` in the script below before running it: .. parsed-literal:: $ psql -h localhost -U **db_user** **omero_database** < sql/psql/|current_dbver|/shape_color_argb_to_rgba.sql If you need to roll back the changes, a reverse script ``reverse_shape_color_argb_to_rgba.sql`` is also available in the same folder. Edit the ``TRUE`` if you wish to roll back the changes to a subset of ROIs. Move annotation from Image to Well (optional) """"""""""""""""""""""""""""""""""""""""""""" Since 5.3, users can annotate Wells in both OMERO.web and OMERO.insight. Previously they could only annotate Images linked to WellSamples. The official script `Move_Annotations.py `_ can be run by users to move annotations from Images to Wells but an administrator can run the script on any user's data. .. _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 environment variables and memory settings ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ 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. Update your OMERO.web server configuration ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ FastCGI support was removed in OMERO 5.2 and OMERO.web can be deployed using WSGI (see :ref:`omero_web_deployment` for more details). If you have already deployed OMERO.web using WSGI you should regenerate your config files, remembering to merge in any of your own modifications if necessary. **Due to the nature of OMERO.web development for the 5.2.x line, you should carry out this step even for minor version upgrades as there may be fixes which require it.** If necessary ensure you have set up a regular task to clear out any stale OMERO.web session files as described in :ref:`omero_web_maintenance`. OMERO.web migrating from Apache to Nginx """""""""""""""""""""""""""""""""""""""" Support for Apache and mod_wsgi deployment was deprecated in OMERO 5.2.6 and dropped in 5.3.0. It is recommended to use :doc:`/sysadmins/unix/install-web/web-deployment`. .. seealso:: :ref:`troubleshooting-omeroweb-migrate-to-nginx` 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