OMERO.web installation on Ubuntu 22.04 and IcePy 3.6

Please first read OMERO.server installation on Ubuntu 22.04.

This is an example walkthrough for installing OMERO.web in a virtual environment using a dedicated system user. Installing OMERO.web in a virtual environment is the preferred way. For convenience in this walkthrough, we will use the omero-web system user and define the main OMERO.web configuration options as environment variables. Since 5.6, a new OMERODIR variable is used, you should first unset OMERO_HOME (if set) before beginning the installation process. By default, Python 3.10 is installed.

The following steps are run as root.

If required, first create a local system user omero-web and create directory:

useradd -m omero-web

mkdir -p /opt/omero/web/omero-web/etc/grid
chown -R omero-web /opt/omero/web/omero-web

Installing prerequisites

The following steps are run as root.

Install dependencies:

apt-get update

apt-get -y install unzip
apt-get -y install python3
apt-get -y install python3-venv

apt-get -y install nginx

Optional: if you wish to use the Redis cache, install Redis:

apt-get -y install redis-server

service redis-server start

Creating a virtual environment

The following steps are run as root.

Create the virtual environment. This is the recommended way to install OMERO.web:

python3 -mvenv /opt/omero/web/venv3

Install ZeroC IcePy 3.6:

/opt/omero/web/venv3/bin/pip install https://github.com/glencoesoftware/zeroc-ice-py-ubuntu2204-x86_64/releases/download/20221004/zeroc_ice-3.6.5-cp310-cp310-linux_x86_64.whl

Upgrade pip and install OMERO.web:

/opt/omero/web/venv3/bin/pip install --upgrade pip
/opt/omero/web/venv3/bin/pip install omero-web

Installing OMERO.web apps

A number of apps are available to add functionality to OMERO.web, such as OMERO.figure and OMERO.iviewer. See the main website for a list of released apps. These apps are optional and can be installed, as the root user, via pip to your OMERO.web virtual environment and configured as the omero-web system user, at any time.

Configuring OMERO.web

The following steps are run as the omero-web system user.

For convenience the main OMERO.web configuration options have been defined as environment variables. You can either use your own values, or alternatively use the following ones:

export WEBSESSION=True
export OMERODIR=/opt/omero/web/omero-web

Configure OMERO.web and create the NGINX OMERO configuration file to be included in a system-wide NGINX configuration by redirecting the output of the command omero web config nginx below into a file. If an attempt is made to access OMERO.web whilst it is not running, the generated NGINX configuration file will automatically display a maintenance page:

export PATH=/opt/omero/web/venv3/bin:$PATH


omero web config nginx --http "${WEBPORT}" --servername "${WEBSERVER_NAME}" > /opt/omero/web/omero-web/nginx.conf.tmp

OMERO.web offers a number of configuration options. The configuration changes will not be applied until Gunicorn is restarted using omero web restart. The Gunicorn workers are managed separately from other OMERO processes. You can check their status or stop them using omero web status or omero web stop.

• Session engine:

• OMERO.web offers alternative session backends to automatically delete stale data using the cache session store backend, see Django cached session documentation for more details.

• Redis requires django-redis in order to be used with OMERO.web. We assume that Redis has already been installed. To configure the cache, run:

  omero config set omero.web.caches '{"default": {"BACKEND": "django_redis.cache.
  RedisCache", "LOCATION": "redis://127.0.0.1:6379/0"}}'
  

• After installing all the cache prerequisites set the following:

  omero config set omero.web.session_engine django.contrib.sessions.backends.cache
  

• Use a prefix:

  By default OMERO.web expects to be run from the root URL of the webserver. This can be changed by setting omero.web.prefix and omero.web.static_url. For example, to make OMERO.web appear at http://example.org/omero/:

  omero config set omero.web.prefix '/omero'
  omero config set omero.web.static_url '/omero/static/'
  

  and regenerate your webserver configuration.

All configuration options can be found on various sections of Web developers documentation. For the full list, refer to Web properties.

The most popular configuration options include:

• Debug mode, see omero.web.debug.

• Customizing OMERO clients e.g. to add your own logo to the login page (omero.web.login_logo) or use an index page as an alternative landing page for users (omero.web.index_template). See OMERO.web UI customization for further information.

• Enabling a public user see Publishing data using OMERO.web.

Configuring Gunicorn

The following steps are run as the omero-web system user.

Additional settings can be configured by changing the properties below. Before changing the properties, run export PATH=/opt/omero/web/venv3/bin:$PATH:

• omero.web.wsgi_workers to (2 x NUM_CORES) + 1

  Note

  Do not scale the number of workers to the number of clients you expect to have. OMERO.web should only need 4-12 worker processes to handle many requests per second.

• omero.web.wsgi_args Additional arguments. For more details check Gunicorn Documentation. For example to enable debugging, run the following command:

  omero config set omero.web.wsgi_args -- "--log-level=DEBUG --error-logfile=/opt/omero/web/omero-web/var/log/error.log"
  

Setting up CORS

The following steps are run as root.

Cross Origin Resource Sharing allows web applications hosted at other origins to access resources from your OMERO.web installation. This can be achieved using the django-cors-headers app with additional configuration of OMERO.web. See the django-cors-headers page for more details on the settings.

Since OMERO.web 5.14.0, the package django-cors-headers is installed by default.

The following steps are run as the omero-web system user.

Configure CORS. An index is used to specify the ordering of middleware classes. It is important to add the CorsMiddleware as the first class and CorsPostCsrfMiddleware as the last. You can specify allowed origins in a whitelist, or allow all, for example:

omero config append omero.web.middleware '{"index": 0.5, "class": "corsheaders.middleware.CorsMiddleware"}'
omero config append omero.web.middleware '{"index": 10, "class": "corsheaders.middleware.CorsPostCsrfMiddleware"}'
omero config set omero.web.cors_origin_whitelist '["https://hostname.example.com"]'
# or to allow all
omero config set omero.web.cors_origin_allow_all True

Configuring NGINX

The following steps are run as root.

Copy the generated configuration file into the NGINX configuration directory, disable the default configuration and start NGINX:

sed -i.bak -re 's/( default_server.*)/; #\1/' /etc/nginx/nginx.conf
rm /etc/nginx/sites-enabled/default
cp /opt/omero/web/omero-web/nginx.conf.tmp /etc/nginx/conf.d/omeroweb.conf

service nginx start

For production servers you may need to add additional directives to the configuration file, for example to enable HTTPS. As an alternative to manually modifying the generated file you can generate a minimal configuration and include this in your own manually created NGINX file, such as /etc/nginx/conf.d/omero-web.conf:

omero web config nginx-location > /opt/omero/web/omero-web/omero-web-location.include

This requires more initial work but in the future you can automatically regenerate your OMERO.web configuration and your additional configuration settings will still apply.

Note

If you need help configuring your firewall rules, see the Server security and firewalls page.

Running OMERO.web

Since OMERO.web 5.16.0, the package whitenoise is installed by default.

Optional: Install Django Redis:

/opt/omero/web/venv3/bin/pip install 'django-redis==5.0.0'

The following steps are run as the omero-web system user.

Optional: Configure the cache:

omero config set omero.web.caches '{"default": {"BACKEND": "django_redis.cache.RedisCache","LOCATION": "redis://127.0.0.1:6379/0"}}'
omero config set omero.web.session_engine 'django.contrib.sessions.backends.cache'

Configure WhiteNoise and start OMERO.web manually to test the installation:

omero config append -- omero.web.middleware '{"index": 0, "class": "whitenoise.middleware.WhiteNoiseMiddleware"}'

omero web start

# Test installation e.g. curl -sL localhost:4080

omero web stop

Automatically running OMERO.web

The following steps are run as root.

Should you wish to run OMERO.web automatically, a init.d file could be created. See below an example file omero-web-init.d:

#!/bin/bash
#
# /etc/init.d/omero-web
# Subsystem file for "omero" web
#
### BEGIN INIT INFO
# Provides:             omero-web
# Required-Start:       $local_fs $remote_fs $network $time omero
# Required-Stop:        $local_fs $remote_fs $network $time omero
# Default-Start:        2 3 4 5
# Default-Stop:         0 1 6
# Short-Description:    OMERO.web
### END INIT INFO
#
### Redhat
# chkconfig: - 98 02
# description: init file for OMERO.web
###

RETVAL=0
prog=omero-web

# Read configuration variable file if it is present
[ -r /etc/default/$prog ] && . /etc/default/$prog

OMERO_USER=${OMERO_USER:-omero-web}
OMERO=/opt/omero/web/venv3/bin/omero
OMERODIR=/opt/omero/web/omero-web
VENVDIR=${VENVDIR:-/opt/omero/web/venv3}

start() {
    echo -n $"Starting $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web start" &> /dev/null && echo -n ' OMERO.web'
    sleep 5
    RETVAL=$?
    [ "$RETVAL" = 0 ]
        echo
}

stop() {
    echo -n $"Stopping $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web stop" &> /dev/null && echo -n ' OMERO.web'
    RETVAL=$?
    [ "$RETVAL" = 0 ]
        echo
}

status() {
    echo -n $"Status $prog:"
    su - ${OMERO_USER} -c ". ${VENVDIR}/bin/activate;OMERODIR=${OMERODIR} ${OMERO} web status"
    RETVAL=$?
}

case "$1" in
    start)
        start
        ;;
    stop)
        stop
        ;;
    restart)
        stop
        start
        ;;
    status)
        status
        ;;
    *)
        echo $"Usage: $0 {start|stop|restart|status}"
        RETVAL=1
esac
exit $RETVAL

Copy the init.d file, then configure the service:

cp omero-web-init.d /etc/init.d/omero-web
chmod a+x /etc/init.d/omero-web

update-rc.d -f omero-web remove
update-rc.d -f omero-web defaults 98 02

Start up services:

service redis-server start

cron
service nginx start
service omero-web restart

Maintaining OMERO.web

The following steps are run as the omero-web system user.

You can manage the sessions using the following configuration options and commands:

• Session cookies omero.web.session_expire_at_browser_close:

  • A boolean that determines whether to expire the session when the user closes their browser. See Django Browser-length sessions vs. persistent sessions documentation for more details. The default value is True:

    omero config set omero.web.session_expire_at_browser_close "True"
    

  • The age of session cookies, in seconds. The default value is 86400:

    omero config set omero.web.session_cookie_age 86400
    

• Clear session:

  Each session for a logged-in user in OMERO.web is kept in the session store. Stale sessions can cause the store to grow with time. OMERO.web uses by default the OS file system as the session store backend and does not automatically purge stale sessions, see Django file-based session documentation for more details. It is therefore the responsibility of the OMERO administrator to purge the session cache using the provided management command:

  omero web clearsessions
  

  It is recommended to call this command on a regular basis, for example as a daily cron job, see Django clearing the session store documentation for more information.

Troubleshooting

The following steps are run as the omero-web system user.

In order to identify why OMERO.web is not available run omero web status. Then consult NGINX error.log and /opt/omero/web/omero-web/var/log/OMEROweb.log.

Configuring Gunicorn advanced options

OMERO.web deployment can be configured with sync and async workers. Sync workers are faster and recommended for a data repository with Download restrictions. If you wish to offer users the ability to download data then you have to use async workers. OMERO.web is able to handle multiple clients on a single worker thread switching context as necessary while streaming binary data from OMERO.server. Depending on the traffic and scale of the repository you should configure connections and speed limits on your server to avoid blocking resources. We recommend you run benchmark and performance tests. It is also possible to apply Download restrictions and offer alternative access to binary data.

Note

Handling streaming request/responses requires proxy buffering to be turned off. For more details refer to Gunicorn deployment and NGINX configuration.

Note

omero.web.application_server.max_requests should be set to 0

See Gunicorn design for more details.

Experimental: Sync workers

The following steps are run as root.

Install https://pypi.org/project/futures:

/opt/omero/web/venv3/bin/pip install futures

The following steps are run as the omero-web system user.

To find out more about the number of worker threads for handling requests, see Gunicorn threads. Additional settings can be configured by changing the following properties:

omero config set omero.web.wsgi_worker_class
omero config set omero.web.wsgi_threads $(2-4 x NUM_CORES)

Experimental: Async workers

The following steps are run as root.

Install Gevent >= 0.13:

/opt/omero/web/venv3/bin/pip install 'gevent>=0.13'

The following steps are run as the omero-web system user.

To find out more about the maximum number of simultaneous clients, see Gunicorn worker-connections. Additional settings can be configured by changing the following properties:

omero config set omero.web.wsgi_worker_class gevent
omero config set omero.web.wsgi_worker_connections 1000
omero config set omero.web.application_server.max_requests 0