• Views
  • Iteration Report
  • My Iteration Report
  •  
OMERO.server
  • Login
  • Help/Guide
  • About Trac
  • Preferences
  • Wiki
  • Timeline
  • Roadmap
  • Browse Source
  • View Tickets
  • Search

Context Navigation

  • Start Page
  • Index
  • History
  • Last Change

OMERO.server Upgrade Instructions

3.0-Beta2 to 3.0-Beta2.2

Upgrading from milestone:3.0-Beta2 to milestone:3.0-Beta2.2 is fairly simple and only really entails the following:

  • Copy the etc/local.properties file from your existing 3.0-Beta2 installation directory to your new 3.0-Beta2.2 installation directory and re-deploy the OMERO.server EAR. This is similar to performing a Reconfiguration in the OmeroInstall documentation. 
    $ cp ~/omero-3.0-Beta2/omero/etc/local.properties ~/omero-3.0-Beta2.2/omero/etc/local.properties
$ cd ~/omero-3.0-Beta2.2/omero
$ export JBOSS_HOME=~/omero-3.0-Beta2.2/jboss-4.2.1.GA
$ java omero update deploy
  • Perform a database backup 
    pg_dump -h <database_host> -U <db_username> -Fc -f <dump_filename> <db_name>

ex. pg_dump -h localhost -U omero -Fc -f before_upgrade.db.dump omero3
  • Update your database from OMERO3__4 to OMERO3__5.

NOTE: You must use the same username and password you have defined in your etc/local.properties file in the hibernate.connection.username and hibernate.connection.password properties. This will also be the same as the database user you created as outlined in the Pre-Installation phase of the OmeroInstall documentation. 

$ cd ~/omero-3.0-Beta2.2/omero
$ psql -h localhost -U omero omero3 < sql/psql/OMERO3__4__OMERO3__5.sql
Password for user omero:
BEGIN
INSERT 0 1
ALTER TABLE
UPDATE 1
COMMIT

You have now successfully updated from milestone:3.0-Beta2 to milestone:3.0-Beta2.2 and can restart your OMERO.server instance as follows: 

$ export JBOSS_HOME=~/omero-3.0-Beta2.2/jboss-4.2.1.GA
$ $JBOSS_HOME/bin/run.sh

(To start OMERO.server in the background: $JBOSS_HOME/bin/run.sh > /dev/null 2>&1)

3.0-Beta2.2 to 3.0-Beta2.3

Upgrading from milestone:3.0-Beta2.2 to milestone:3.0-Beta2.3 is fairly simple and only really entails the following:

  • Copy the etc/local.properties file from your existing 3.0-Beta2.2 installation directory to your new 3.0-Beta2.3 installation directory and re-deploy the OMERO.server EAR. This is similar to performing a Reconfiguration in the OmeroInstall documentation. 
    $ cp ~/omero-3.0-Beta2.2/omero/etc/local.properties ~/omero-3.0-Beta2.3/omero/etc/local/properties
$ cd ~/omero-3.0-Beta2.3/omero
$ export JBOSS_HOME=~/omero-3.0-Beta2.3/jboss-4.2.1.GA
$ java omero update deploy
  • Perform a database backup 
    pg_dump -h <database_host> -U <db_username> -Fc -f <dump_filename> <db_name>

ex. pg_dump -h localhost -U omero -Fc -f before_upgrade.db.dump omero3

NOTE: If you are upgrading from 3.0-Beta2.0 directly to 3.0-Beta2.3 you should perform the Update your database... step from the 3.0-Beta2.0 to 3.0-Beta2.2 documentation above before starting your server.

You have now successfully updated from milestone:3.0-Beta2.2 to milestone:3.0-Beta2.3 and can restart your OMERO.server instance as follows: 

$ export JBOSS_HOME=~/omero-3.0-Beta2.3/jboss-4.2.1.GA
$ $JBOSS_HOME/bin/run.sh

(To start OMERO.server in the background: $JBOSS_HOME/bin/run.sh > /dev/null 2>&1)

3.0-Beta2.3 to Beta3.0

Upgrading from milestone:3.0-Beta2.3 to milestone:3.0-Beta3 is a large upgrade requiring significant time for larger databases:

  1. Copy the etc/local.properties file from your existing 3.0-Beta2.3 installation directory to your new Beta3.0 installation directory and re-deploy the OMERO.server EAR. This is similar to performing a Reconfiguration in the OmeroInstall documentation. 
    $ cp ~/omero-3.0-Beta2.3/omero/etc/local.properties ~/omero-Beta3.0/omero/etc/local.properties
$ cd ~/omero-Beta3.0/omero
$ export JBOSS_HOME=~/omero-Beta3.0/jboss-4.2.1.GA
$ java omero deploy
  2. Perform a database backup 
    pg_dump -h <database_host> -U <db_username> -Fc -f <dump_filename> <db_name>

ex. pg_dump -h localhost -U omero -Fc -f before_upgrade.db.dump omero3
  3. Add the PL/pgSQL language to your database: 
    $ sudo -u postgres createlang plpgsql omero3
  4. Update your database from OMERO3__5 to OMERO3A__4.

NOTE: You must use the same username and password you have defined in your etc/local.properties file in the hibernate.connection.username and hibernate.connection.password properties. This will also be the same as the database user you created as outlined in the Pre-Installation phase of the OmeroInstall documentation.

NOTE: This upgrade can take significant time on large databases (up to 2 or 3 hours) please be patient and ensure you have performed a database backup as above. 

$ cd ~/omero-Beta3.0/omero
$ psql -h localhost -U omero omero3 < sql/psql/OMERO3A__4/OMERO3__5.sql
Password for user omero:
...
...
  1. Update your database from OMERO3A__4 to OMERO3A__5. 
    $ cd ~/omero-Beta3.0/omero
$ psql -h localhost -U omero omero3 < sql/psql/OMERO3A__5/OMERO3A__4.sql
Password for user omero:
...
...
  2. Decide whether or not you wish to preserve Category Group and Category metadata

As of milestone:3.0-Beta3 OMERO no longer provides views for Category Group or Category entities and has replaced this functionality with StructuredAnnotations. As a migration path, you may now wish to make your Category Group and Category entities into Projects and Datasets: 

$ cd ~/omero-Beta3.0/omero
$ psql -h localhost -U omero omero3 < sql/psql/OMERO3A__5/CGCtoPDI.sql
Password for user omero:
...
...

You have now successfully updated from milestone:3.0-Beta2.3 to milestone:3.0-Beta3 and can restart your OMERO.server instance as follows: 

$ export JBOSS_HOME=~/omero-Beta3.0/jboss-4.2.1.GA
$ $JBOSS_HOME/bin/run.sh

(To start OMERO.server in the background: $JBOSS_HOME/bin/run.sh > /dev/null 2>&1)

Update Notification

As of milestone:3.0-Beta2.3, your OMERO.server installation will check for updates each time it is started from the Open Microscopy Environment update server. If you wish to disable this functionality you should do so now as outlined on the UpgradeCheck page.

Troubleshooting

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 OmeroCommunity page. More experienced users may wish to examine the DbUpgrade page for technical information about OMERO.server database upgrades and how to troubleshoot errors themselves.

See also: OmeroInstall, OmeroTroubleshooting, DbUpgrade, UpgradeCheck

Download in other formats:

  • Plain Text
Trac Powered

Powered by Trac 0.11
By Edgewall Software.

Visit the Trac open source project at
http://trac.edgewall.org/