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 <viewforum.php?f=11>` 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 <system-requirements>` with
:doc:`correct versions <version-requirements>` 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
<http://www.openmicroscopy.org/site/support/omero5.0/sysadmins/server-upgrade.html>`_
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
^^^^^^^^^^^^^^^^^^^^^^^

If you generated configuration stanzas using :omerocmd:`web config` which
enable 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. See also the :doc:`unix/install-web` page.

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.

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
<back-up-the-db>` 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 <restore-the-db>`. 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. The example below assumes you are upgrading from a
|previousversion| 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)


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
`<https://github.com/ome/scripts>`_.

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 generated web-server configurations for Nginx and Apache have been
revised in OMERO 5.1. It is highly recommended that you :ref:`regenerate your
configuration <fastcgi_configuration>`, 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`.


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.