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server-upgrade.txt
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server-upgrade.txt
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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. Finally, all the 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:`/sysadmins/UpgradeCheck` page.
.. note::
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.
If you encounter errors during a 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.
See the full details of OMERO |release| features in the
:forum:`Announcements <viewforum.php?f=11>` forum.
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
.. warning::
with 5.0.0-beta2, the default JDBC password provider has been modified to
add password salting support. This implies that once a server has been
upgraded and deployed, passwords will be modified, you will not be able
to easily revert to the 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
:ref:`legacy_password_providers` section.
.. warning:: The passwords and logins used here are examples. Please consult
the :ref:`troubleshooting-password` section for explanation. In particular,
make sure to replace the values of **db_user** and **omero_database**
with the actual database user and database name for your installation.
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 ``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:
.. parsed-literal::
$ cd ..
$ mv OMERO.server OMERO.server-old
$ unzip |OMEROserverzip|
$ cp OMERO.server-old/etc/grid/config.xml |OMEROserverzip|/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.
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.
From a |previousversion|.x server
"""""""""""""""""""""""""""""""""
.. parsed-literal::
$ cd |OMEROserverzip|
$ psql -h localhost -U **db_user** **omero_database** < sql/psql/OMERO\ |version|\_\_0/OMERO\ |previousversion|\_\_0.sql
Password for user **db_user**:
...
...
status
---------------------------------------------------------------------
+
+
+
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO |version|\_\_0+
+
+
(1 row)
From a 5.0.0-beta1 server
""""""""""""""""""""""""""
.. parsed-literal::
$ cd |OMEROserverzip|
$ psql -h localhost -U **db_user** **omero_database** < sql/psql/OMERO\ |version|\_\_0/OMERO\ |version|\DEV\_\_6.sql
Password for user **db_user**:
...
...
status
---------------------------------------------------------------------
+
+
+
YOU HAVE SUCCESSFULLY UPGRADED YOUR DATABASE TO VERSION OMERO |version|\_\_0+
+
+
(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
^^^^^^^^^^^^^^^^^^^
If you modified your memory settings, you will need to remodify these settings
for the new server. Refer to the `JVM memory settings` sub-section of the :doc:`installation <unix/server-installation>` section
(:doc:`Windows <windows/server-installation>`) for more information.
Changes to OMERO.web URLs
^^^^^^^^^^^^^^^^^^^^^^^^^
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.
Restart your database
---------------------
- Following a successful database upgrade, you can start the server.
.. parsed-literal::
$ cd |OMEROserverzip|
$ 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
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 -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
.. |OMEROserverzip| replace:: OMERO.server-|release|-ice3x-byy.zip
.. seealso::
:legacy_plone:`Legacy <>`
Legacy part of the OME website containing upgrade instructions for
previous versions of the OMERO server.