This documentation is for OMERO 4.4 and is no longer being updated, to see the documentation for the latest release, refer to http://openmicroscopy.org/site/support/omero/
See also
When first beginning to work with the OMERO server, the omero db, omero config, and omero admin commands will be the first you will need.
Rather than try to provide the functionality of a RDBM tool like psql, the omero db script command helps to generate SQL scripts for building your database. You can then use those scripts from whatever tool is most comfortable for you:
$ bin/omero db script OMERO4 0 secretpassword
Using OMERO4 for version
Using 0 for patch
Using password from commandline
Saving to /omero/OMERO4__0.sql
$ psql omero < OMERO4__0.sql
The omero config command is responsible for reading / writing user-specific profiles stored under etc/grid/config.xml. To get the current profile, use the omero config def command:
$ bin/omero config def
default
You can then examine the current profile keys using omero config get and set key-value pairs using omero config set:
$ bin/omero config get
$ bin/omero config set example "my first value"
$ bin/omero config get
example=my first value
You can use the OMERO_CONFIG environment variable to point at a different profile, e.g.:
$ OMERO_CONFIG=another bin/omero config def
another
$ OMERO_CONFIG=another bin/omero config get
$ OMERO_CONFIG=another bin/omero config set example "my second value"
$ OMERO_CONFIG=another bin/omero config get
example=my second value
The values set via omero config set override those compiled into the server jars. The default values which are set can be seen in etc/omero.properties. To add several values to a configuration, you can pipe them via standard in using omero config load:
$ grep omero.ldap etc/omero.properties | OMERO_CONFIG=ldap bin/omero config load
$ OMERO_CONFIG=ldap bin/omero config get
omero.ldap.attributes=objectClass
omero.ldap.base=ou=example,o=com
omero.ldap.config=false
omero.ldap.groups=
omero.ldap.keyStore=
omero.ldap.keyStorePassword=
omero.ldap.new_user_group=default
omero.ldap.password=
omero.ldap.protocol=
omero.ldap.trustStore=
omero.ldap.trustStorePassword=
omero.ldap.urls=ldap://localhost:389
omero.ldap.username=
omero.ldap.values=person
Each of these values can then be modified to suit your local setup. To remove one of the key-value pairs, pass no second argument:
$ OMERO_CONFIG=ldap bin/omero config set omero.ldap.trustStore
$ OMERO_CONFIG=ldap bin/omero config set omero.ldap.trustStorePassword
$ OMERO_CONFIG=ldap bin/omero config set omero.ldap.keyStore
$ OMERO_CONFIG=ldap bin/omero config set omero.ldap.keyStorePassword
$ OMERO_CONFIG=ldap bin/omero config get
omero.ldap.attributes=objectClass
omero.ldap.base=ou=example,o=com
omero.ldap.config=false
omero.ldap.groups=
omero.ldap.new_user_group=default
omero.ldap.password=
omero.ldap.protocol=
omero.ldap.urls=ldap://localhost:389
omero.ldap.username=
omero.ldap.values=person
If you will be using a particular profile more frequently you can set it as your default using the omero config def command:
$ bin/omero config def ldap
And finally, if you would like to remove a profile, for example to wipe a given password off of a system, use omero config drop:
$ bin/omero config drop
Once your database has been properly configured and your config profile is set to use that database, you are ready to start your server using the omero admin start command:
$ bin/omero admin start
$ bin/omero admin diagnostics
The omero user and omero group commands provide functionalities to add and manage users and groups on your database.
New users can be added to the database using the omero user add command:
$ bin/omero user add -h
During the addition of the new user, you will need to specify the first and last name of the new user and their username as well as the groups the user belongs to. To add John Smith as a member of group 2 identified as jsmith, enter:
$ bin/omero user add jsmith John Smith 2
Additional parameters such as the email address, institution, middle name etc can be passed as optional arguments to the omero user add command.
New groups can be added to the database using the omero group add command:
$ bin/omero group add -h
During the addition of the new group, you need to specify the name of the new group:
$ bin/omero group add newgroup
The permissions of the group are set to private by default. Alternatively you can specify the permissions using --perms or --type optional arguments:
$ bin/omero group add read-only-1 --perms='rwr---'
$ bin/omero group add read-annotate-1 --type=read-annotate
See also
Lists of users/groups on the OMERO server can be queried using the omero user list and omero group list commands:
$ bin/omero user list
$ bin/omero group list
Users can be added to existing groups using the omero user joingroup or omero group adduser commands. Similarly, users can be removed from existing groups using the omero user leavegroup or omero group removeuser commands:
# Add jsmith to group read-annotate-1
$ bin/omero group adduser jsmith --name=read-annotate-1
# Remove jsmith from group read-annotate-1
$ bin/omero group removeuser jsmith --name=read-annotate-1
# Add jsmith to group read-only-1
$ bin/omero user joingroup read-only-1 --name=jsmith
# Remove jsmith from group read-only-1
$ bin/omero user leavegroup read-only-1 --name=jsmith
By passing the --as-owner option, these commands can also be used to manage group owners
# Add jsmith to the owner list of group read-annotate-1
$ bin/omero group adduser jsmith --name=read-annotate-1 --as-owner
# Remove jsmith from the owner list of group read-annotate-1
$ bin/omero user leavegroup read-annotate-1 --name=jsmith --as-owner
To create a copy of a group, you must first create a new group using the omero group add command:
$ bin/omero group add read-only-2 --perms='rwr---'
Then you can use the omero group copyusers command to copy all group members from one group to another:
$ bin/omero group copyusers read-only-1 read-only-2
To copy the group owners, use the same command with the --as-owner optional argument:
$ bin/omero group copyusers read-only-1 read-only-2 --as-owner