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Install - Web

OMERO.web Install and Configuration

OMERO.web is the web application component of the OMERO platform which allows for the management, viewing (a fully multi-dimensional image viewer), attachment and association of files to images, datasets, and projects from one or more OMERO.server's. It also includes webadmin for managing users and groups. With one or two commands, OMERO.web can be started with the Django lightweight development Web server bound to port 8000 on 127.0.0.1 when you deploy your OMERO.server instance.

We do not recommend using this server in a production setting. It has not gone through security audits or performance tests. Apache with mod_python is the preferred setup for deploying a Django application on a production server. You can find more information on the Django site here.

Prerequisites

PYTHONPATH

on non-Windows platform: 

$ export PYTHONPATH=$PYTHONPATH:/home/omero/omero_dist/lib/python/
$ echo $PYTHONPATH
/opt/local/share/ice/python:/home/omero/omero_dist/lib/python/:

on Windows platform: 

C:\>set PYTHONPATH=%PYTHONPATH%;C:\OMERO\lib\python
C:\>echo %PYTHONPATH%
C:\Ice-3.3.0\python;C:\omero-Beta4.0.0\lib\python

Configuration for Django Web server (non-production)

On non-Windows* platforms, OMERO.web is configured to be started with a single command

  • Use:

    Start up OMERO.web manually: 

    $ cd /home/omero/omero-dist/
$ bin/omero admin ice
Ice 3.3.0  Copyright 2003-2008 ZeroC, Inc.
>>> server enable Web
>>> server start Web
>>> exit

    Shut down OMERO.web manually: 

    $ cd /home/omero/omero-dist/
$ bin/omero admin ice
Ice 3.3.0  Copyright 2003-2008 ZeroC, Inc.
>>> server disable Web
>>> server stop Web
>>> exit

  • Or have it started automatically:

    If you wish to have the server always on, configure the following in /home/omero/omero_dist/etc/grid/default.xml: 

    <server-instance template="ShellTemplate" id="Web" act="always"/>

  • If you require to configure the out of the box setup to listen for webadmin and webclient connections on different host configure the following:

    Configure the following in /home/omero/omero_dist/etc/grid/templates.xml by adding after --noreload: 

    <server-template id="WebTemplate"> 
  <parameter name="act" default="on-demand"/> 
  <server id="Web" exe="python" activation="${act}" pwd="${OMEROPY_HOME}omeroweb"> 
    <option>manage.py</option> 
    <option>runserver</option> 
    <option>--noreload</option> 
    <option>10.0.0.1:8000</option><!-- your ip & port here -->
    <env>${PYTHONPATH}</env> 
    <adapter name="WebAdapter" register-process="true" endpoints="tcp" server-lifetime="false"/> 
  </server> 
</server-template>

    In your /home/omero/omero_dist/lib/python/omero/plugins/ directory configure the following in server.py: 

    django = ["python","manage.py","runserver","0.0.0.0:8080","--noreload"]+list(args)

    On Windows* platforms, please follow the instruction on OMERO install - windows

Configuration Guide for mod_python (production)

  • If you've enabled the OMERO.web instance that is using the Django lightweight development web server, you will need to shut it down:

    Shut down the OMERO.web manually: 

    $ cd /home/omero/omero_dist/
$ bin/omero admin ice
Ice 3.3.0  Copyright 2003-2008 ZeroC, Inc.
>>> server disable Web
>>> server stop Web

    In your /home/omero/omero_dist/etc/grid/ directory re-configure the Web server in default.xml to be on-demand: 

    <server-instance template="ShellTemplate" id="Web" act="on-demand"/>

  • In your /home/omero/omero_dist/lib/python/omeroweb/ directory configure the following in settings.py:

    • DATABASE_NAME 

      DATABASE_NAME = '/home/omero/webdb/db.sqlite3'

    • LOGDIR 

      # LOGS
# to change the log place, please specify new path for LOGDIR.
# LOGDIR = os.path.join(os.path.dirname(__file__), 'log')
# LOGDIR = os.path.join(os.path.join(os.path.join(os.path.join(os.path.dirname(__file__), '../'), '../'), 'var'), 'log')
LOGDIR = '/home/omero/weblog/'

    • Notification options: EMAIL_NOTIFICATION, EMAIL_SENDER_ADDRESS and EMAIL_SMTP_SERVER 

      # Notification
# Application allows to notify user about new shares
EMAIL_NOTIFICATION = True
EMAIL_SENDER_ADDRESS = 'omero-admin@example.com'
EMAIL_SMTP_SERVER = 'smtp.example.com'
# Optional settings
# EMAIL_SMTP_PORT = 25
# EMAIL_SMTP_USER = 'login'
# EMAIL_SMTP_PASSWORD = 'password'
# EMAIL_SMTP_TLS = True

    • Notification option for sharing: 

      # If web server is running behind a proxy server please set the host. 
# That option is required by share notification sendere.
APPLICATION_HOST='http://www.domain.com:80'

  • Create log and database directories with apache_user:apache_group ownership: 

    mkdir /home/omero/weblog
chown apache_user:apache_group /home/omero/weblog
mkdir /home/omero/webdb
chown apache_user:apache_group /home/omero/webdb

  • Initialize the Django settings database, specifying an OMERO.web superuser username, password and e-mail address: 

    # cd /home/omero/omero_dist/lib/python/omeroweb/
# sudo -u apache_user PYTHONPATH=/home/omero/omero_dist/lib/python/ python manage.py syncdb

Creating table django_admin_log
Creating table auth_permission
Creating table auth_group
Creating table auth_user
Creating table auth_message
Creating table django_content_type
Creating table django_session
Creating table django_site
Creating table webadmin_gateway

You just installed Django's auth system, which means you don't have any superusers defined.
Would you like to create one now? (yes/no): yes 
Username (Leave blank to use 'omero'): omero
E-mail address: omero-admin@example.com
Password: 
Password (again): 
Superuser created successfully.
Installing custom SQL for webadmin.Gateway model
Installing index for admin.LogEntry model
Installing index for auth.Permission model
Installing index for auth.Message model

  • Configure mod_python: 

    <Location "/">
    SetHandler python-program
    PythonHandler django.core.handlers.modpython
    SetEnv DJANGO_SETTINGS_MODULE omeroweb.settings
    PythonDebug On

    (for 4.0.0) PythonPath "['/home/omero/omero_dist/lib', '/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/omeroweb'] + sys.path"

    (as of 4.0.1) PythonPath "['/home/omero/omero_dist/lib/python', '/home/omero/omero_dist/lib/python/omeroweb'] + sys.path"

</Location>

  • Go to the link http://your_host/webclient/ or http://your_host/webadmin/

  • If you wish to modify the predefined list of the OMERO.servers please go to admin panel: http://your_host/admin/webadmin/gateway/. To login, use the user superuser username and password created you created when initializing the Django settings database above.

Once you have deployed and started the server you can use your browser to access the OMERO.webadmin or OMERO.webclient:

  • http://your_host/webadmin

  • http://your_host/webclient

    OMERO.webadmin login

Troubleshooting

My OMERO install doesn't work! What do I do now!?! Examine the Troubleshooting page and if all else fails post a message to our ome-users mailing list discussed on the Community page.

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