Omero Commandline Interface, the "OmeroShell"
The OMERO system comes with a Python script, bin/omero which is used for commandline interaction, scripting, and OmeroGrid management.
Command Reference
General notes:
- bin/omero will find its installation. Therefore, to install OMERO it is only necessary to unpack the bundle, and put bin/omero somewhere on your path.
- Any command can be produced by symlinking bin/omero to a file of the form "omero-command-arg1-arg2". This is useful under /etc/rc.d to have a startup script.
- All commands respond to "help".
| omero | com[mand] | other args [optional] <choice1|choice2|choice3> | Description |
| [4] | admin | Drops user into an admin console. | |
| [1] [2] | admin | check | Performs checks on the OMERO server. Included are: database version, permissions on configuration (to prototect passwords), minimal check of filesystems. Executed before starting the server to detect possible issues. |
| admin | deploy [target1 [target2 [...]]] | Configures the grid according to the application descriptor and the configuration files under etc. Each optional target activates an optional section of the application descriptor. See OmeroGrid for more information. |
|
| admin | |||
| [6] | admin | unlock-lucene | At times, the Lucene full text index can become locked due to concurrent access. This removes the lock. |
| [1] [4] | admin | adduser username firstname lastname | Add a user to the OMERO system. |
| [1] [4] | admin | addgroup name | |
| [8] | config | Frontend for OmeroConfig. If Java is present, uses the prefs.java class to define preferences for your user. If Java is not present, a config file will be created in your home directory. Multiple "profiles" can be defined at one time. The active profile is chosen either by the OMERO_CONFIG environment variable, or by the "default" setting in your current preferences. The default default is default. |
|
| [3] | load | [/path/to/file] | Loads a file of OmeroCli commands or from stdin if the path is missing. |
| [4] | login | Sets the username and password that will be used to connect to the server. Before admin activities, this can be used for "sudo" like functionality. | |
| [8] | nodename | [nodename] <start|stop|status|restart|>* | nodename defaults to the host name as defined by "uname -n | perl -pe 's/^(.*)[.].*$/$1/'" unless OMERO_NODE is defined. |
| q[uit] | |||
| search | SomeType "your google" -style +query name:here Image name:mitosis* | The search will return a list of objects with minimal information. | |
| start | |||
| status | |||
| [3] [4] | submit | [/path/to/file] | Submit a file of OmeroCli commands to OmeroGrid for execution, or from stdin if the file is missing, or drop the user into a submission shell if stdin is missing. |
| q[uit] | |||
| ? h[elp] |
[1] (1, 2, 3) Requires OMERO admin access
[2] Requires Postgres access
[3] (1, 2) Reads from stdin
[4] (1, 2, 3, 4, 5) Provides a command prompt when inputs are missing.
[6] Should only be executed with the server stopped.
[8] (1, 2) Uses environment variables. See description.
[9] Unimplemented.
