Python bindings to the OMERO.blitz server is a software platform that enables access to and use of a wide range of biological data. ezomero is module with convenience functions for writing Python code that interacts with OMERO.


Important Notes

Interactive job
Interactive jobs should be used for debugging, graphics, or applications that cannot be run as batch jobs.

Allocate an interactive session and run the program. Sample session:

[user@biowulf]$ sinteractive
[user@cn3144 ~]$ module load espresso
[+] Loading singularity  4.0.1  on cn3144
[+] Loading omeropy  5.19.3
[user@cn3144 ~]$ omero -h

bash: omeropy: command not found
[denisovga@cn1103 espresso]$ omero -h
WARN: OMERO_HOME usage is ignored in omero-py
usage: /opt/conda/envs/omeropy/bin/omero [-h] [-v] [-d DEBUG] [--path PATH]
                                         [-C] [-s SERVER] [-p PORT] [-g GROUP]
                                         [-u USER] [-w PASSWORD] [-k KEY]
                                         [--sudo ADMINUSER] [-q]

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.

Login arguments:
  Environment variables:

    OMERO_USERDIR     Set the base directory containing the user's files.
                      Default: $HOME/omero
    OMERO_SESSIONDIR  Set the base directory containing local sessions.
                      Default: $OMERO_USERDIR/sessions
    OMERO_TMPDIR      Set the base directory containing temporary files.
                      Default: $OMERO_USERDIR/tmp
    OMERO_PASSWORD    Set the user's password for creating new sessions.
                      Ignored if -w or --password is used.

  Optional session arguments:

  -C, --create                      Create a new session regardless of existing ones
  -s SERVER, --server SERVER        OMERO server hostname
  -p PORT, --port PORT              OMERO server port
  -g GROUP, --group GROUP           OMERO server default group
  -u USER, --user USER              OMERO username
  -w PASSWORD, --password PASSWORD  OMERO password
  -k KEY, --key KEY                 OMERO session key (UUID of an active session)
  --sudo ADMINUSER                  Create session as this admin. Changes meaning of password!
  -q, --quiet                       Quiet mode. Causes most warning and diagnostic messages to be suppressed.

  Use /opt/conda/envs/omeropy/bin/omero  -h for more information.

    admin                           Administrative tools including starting/stopping OMERO.
    chgrp                           Move data between groups
    chown                           Transfer ownership of data between users. Entire graphs of data,
    config                          Commands for server configuration
    db                              Database tools for creating scripts, setting passwords, etc.
    delete                          Delete OMERO data.
    download                        Download a File, Image or Fileset with a specified ID to a target file
    errors                          Display all plugin error codes
    export                          Support for exporting data in XML and TIFF formats
    fs                              Filesystem utilities
    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
    ldap                            Administrative support for managing users' LDAP settings
    load                            Load file as if it were sent on standard in.
    node                            Control icegridnode.
    obj                             Create, Update and Query OMERO objects
    perf                            Run perf_test files
    quit                            Quit application
    script                          Support for launching, uploading and otherwise managing OMERO.scripts
    search                          Search for object ids by string.
    sessions                        Control and create user sessions
    shell                           Starts an IPython interpreter session
    tag                             Manage OMERO user tags.
    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
    login                           Shortcut for 'sessions login'
    logout                          Shortcut for 'sessions logout'

[user@cn3144 ~]$ python-omero 
Python 3.8.18 (default, Sep 11 2023, 13:20:55)
[GCC 11.2.0] :: Anaconda, Inc. on linux
Type "help", "copyright", "credits" or "license" for more information.
>>>  import ezomero 

End the interactive session:
[user@cn3111 ~]$ exit
salloc.exe: Relinquishing job allocation 46116226
[user@biowulf ~]$