OMERO Commandline Interface

Overview

The  python-based commandline interface provides system-adminstration and deployment tools. (User-level functionality is planned for future releases.)

You can investigate the various commands available using the -h or --help option:

cd omero
bin/omero -h
usage: bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-s SERVER] [-p PORT]
                 [-g GROUP] [-u USER] [-w PASSWORD] [-k KEY]
                 <subcommand> ...

Command-line tool for local and remote interactions with OMERO.

Optional Arguments:
  In addition to any higher level options

  -h, --help                    show this help message and exit
  -v, --version
  -d DEBUG, --debug DEBUG       Use 'help debug' for more information
  --path PATH                   Add file or directory to plugin list. Supports globs.
  -s SERVER, --server SERVER
  -p PORT, --port PORT
  -g GROUP, --group GROUP
  -u USER, --user USER
  -w PASSWORD, --password PASSWORD
  -k KEY, --key KEY             UUID of an active session

Subcommands:
  Use bin/omero <subcommand> -h for more information.

  <subcommand>
    admin                       Administrative tools including starting/stopping OMERO.
    config                      Commands for server configuration.
    db                          Database tools for creating scripts, setting passwords, etc.
    delete                      Delete OMERO data.
    download                    Download the given file id to the given filename
    export                      Support for exporting data in XML and TIFF formats
    group                       Group administration methods
    help                        Syntax help for all commands
    hql                         Executes an HQL statement with the given parameters.
    import                      Run the Java-based command-line importer
    load                        Load file as if it were sent on standard in.
    node                        Control icegridnode.
    perf                        Run perf_test files
    quit                        Quit application
    script                      Support for launching, uploading and otherwise managing OMERO.scripts
    server                      Start commands for server components
    sessions                    Control and create user sessions
    shell                       Starts an IPython interpreter session
    testengine                  Run the Importer TestEngine suite (devs-only)
    upload                      Upload local files to the OMERO server
    user                        Support for adding and managing users
    version                     Version number
    web                         omero web settings
    login                       Shortcut for 'sessions login'
    logout                      Shortcut for 'sessions logout'

Again, we can use -h repeatedly to get more details on each of these sub-commands:

bin/omero admin -h
bin/omero admin start -h 

NB: The 'help' command can be used to get info on other commands or options.

bin/omero help
bin/omero help debug       # debug is an option
bin/omero help admin       # same as bin/omero admin -h

System Administration Commands

When first beginning to work with the OMERO server, the db, config, and admin commands will be the first you will need.

db

Rather than try to provide the functionality of a RDBM tool like psql, the db 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

config

The config command is responsible for reading / writing user-specific profiles. These are stored in platform-specific, protected locations such as the registry on Windows, ~/.java/.userPrefs on Linux, or ~/Library/Preferences on Mac OS X.

$ bin/omero config def
default

$ bin/omero config get

$ bin/omero config set example "my first value"

$ bin/omero config get
example=my first value

$ 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 config 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:

$ 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 on 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:

$ bin/omero config def ldap

And finally, if you would like to remove a profile, say to wipe a given password off of a system, use "drop":

$ bin/omero config drop

admin

Once your database has been properly configured and your config profile is set to use that database, you're ready to start your server.

$ bin/omero admin start

User commands

"import" is probably the first user command many will want to use. Running the command without any arguments will produce a help listing:

$ bin/omero import
/Users/josh/omero/log
Usage: importer-cli [OPTION]... [FILE]
Import single files into an OMERO instance.

Mandatory arguments:
  -s    OMERO server hostname
  -u    OMERO experimenter name (username)
  -w    OMERO experimenter password
  -k    OMERO session key (can be used in place of -u and -w)

Optional arguments:
  -d    OMERO dataset Id to import image into
  -n    Image name to use
  -p    OMERO server port [defaults to 4063]
  -h    Display this help and exit

ex. importer-cli -s localhost -u bart -w simpson -d 50 foo.tiff

Report bugs to <ome-users@openmicroscopy.org.uk>

So, to upload a file image.tiff, use:

$ bin/omero import -s localhost -u josh -w secret image.tiff

In future versions, session handling will be provided.

Extensions

Plugins can be written and put in the lib/python/omero/plugins directory. On execution, all plugins are registered with the OmeroCli.

For other extensions to OMERO, see ExtendingOmero.

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See also: OmeroCliDesign