OMERO cheat sheet

omero-cheat-sheet.md

Update root password

omero db password
Please enter password for OMERO root user: 
Please re-enter password for OMERO root user: 
UPDATE password SET hash = 'ibTzrADXfsKFfNwBdQsa+g==' WHERE experimenter_id  = 0;

Check password hash

psql -h localhost omdbprim -U omdbusr1 -c " select * from password"
Password for user omdbusr1: 
experimenter_id |           hash           | changed 
-----------------+--------------------------+---------
               0 | kO7cztnXqU33M8Hk5kr6DQ== | 
               1 |                          |

Update password hash

psql -h localhost omdbprim -U omdbusr1 -c "UPDATE password SET hash = 'ibTzrADXfsKFfNwBdQsa+g==' WHERE experimenter_id  = 0;"

Error messages

• ImportError: No module named pipeline

• Check dependencies
• pip install --upgrade -r share/web/requirements-py27-all.txt

Turn off IPv6

OMERO.server/bin/omero config set Ice.IPv6 0

Generate nginx config file

OMERO.py/bin/omero web config nginx

• Web deployment documentation

Upgrade Instructions 5.2 --> 5.4

#send the database
root@old-omero:~# pg_dump -h localhost -U databaseuser -Fc -f omero.postgresql.before_upgrade.db.dump databasename
root@old-omero:~# rsync -azv omero.postgresql.before_upgrade.db.dump omero-server-address:~

# sync the binary data store, the path is different on the new installation
root@old-omero:/BMC-OMERO# rsync -avz ./ root@omero-server-address:/OMERO/

# I could have used the same database, but I create a new empty one on omero
root@omero:~# export OMERO_DB_USER="databaseuser" 
root@omero:~# export OMERO_DB_NAME=databasename
root@omero:~# su - postgres -c "createdb -E UTF8 -O '$OMERO_DB_USER' '$OMERO_DB_NAME'"

# didn't know how to import data to postgresql as root at this point, so switched to user postgres
root@omero:~# cp omero.postgresql.before_upgrade.db.dump /var/lib/postgresql/.
root@omero:~# su - postgres
postgres@omero:~$ pg_restore -Fc -d databasename omero.postgresql.before_upgrade.db.dump

# changed settings
omero@omero:~$ OMERO.server/bin/omero config edit

# Edit your preferences below. Comments are ignored
omero.config.version=5.1.0
omero.data.dir=/OMERO
omero.db.name=databasename
omero.db.pass=databasepassword
omero.db.user=databaseuser
omero.web.application_server=wsgi-tcp

# save and exit

# pre check for 5.3, went well
omero@omero:~$ psql -h localhost -U databaseuser databasename < OMERO.server/sql/psql/OMERO5.3__0/OMERO5.2__0-precheck.sql
# upgrade to 5.3
omero@omero:~$ psql -h localhost -U databaseuser databasename < OMERO.server/sql/psql/OMERO5.3__0/OMERO5.2__0.sql 

# pre check for 5.4, went well
omero@omero:~$ psql -h localhost -U databaseuser databasename < OMERO.server/sql/psql/OMERO5.4__0/OMERO5.3__0-precheck.sql

# upgrade to 5.4
omero@omero:~$ psql -h localhost -U databaseuser databasename < OMERO.server/sql/psql/OMERO5.4__0/OMERO5.3__0.sql 

# check that all files under /OMERO is owned by user omero, should give no output, which it didn't:
root@omero:/OMERO# find . \! -user omero -print

# then starts the omero and omero-web services

Important links

• OMERO user / group admin
• OMERO system requirements
• OMERO downloads