OMERO Command Line Interface

See also

OMERO Command Line Interface

User documentation on the Command Line Interface

OMERO Command Line Interface

System Administrator documentation for the Command Line Interface

Help for any specific CLI command can be displayed using the -h argument. See Command line help for more information.

Working with objects

The omero obj command allows to create and update OMERO objects. More information can be displayed using bin/omero obj -h.

Object creation

The omero obj new subcommand allows to create new objects:

$ bin/omero obj new Object field=value

where Object is the type of object to create, e.g. Dataset or ProjectDatasetLink and field/value is a valid key/value pair for the type of object. For example, the following command creates a new screen with a name and a description:

$ bin/omero obj new Screen name=Screen001 description="screen description"

Object update

The omero obj update subcommand allows to update existing objects:

$ bin/omero obj update Object:ID field=value

where Object:ID is the type and the ID of object to update, e.g. Image:1 or PlateDatasetLink:10 and field/value is a valid key/value pair to update for the specified object.

For example, the following command updates the existing screen of ID 2 with a name and a description:

$ bin/omero obj update Screen:2 name=Screen001 description="screen description"

Piping output

The output of each omero obj command is formatted as Object:ID so that the CLI commands can be redirected and piped together. For example, the following set of commands creates a dataset and a project and links them together:

$ project=$(bin/omero obj new Dataset name=dataset-1)
$ dataset=$(bin/omero obj new Project name=plate-1)
$ bin/omero obj new ProjectDatasetLink parent=$project child=$dataset

Extensions

Plugins can be written and put in the lib/python/omero/plugins directory. On execution, all plugins in that directory are registered with the CLI. Alternatively, the “–path” argument can be used to point to other plugin files or directories.

Thread-safety

The omero.cli.CLI should be considered thread-unsafe. A single connection object is accessible from all plugins via self.ctx.conn(args), and it is assumed that changes to this object will only take place in the current thread. The CLI instance itself, however, can be passed between multiple threads, as long as only one accesses it sequentially, possibly via locking.

See also

Extending OMERO

Other extensions to OMERO

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 omero help.