OMERO.web installation

OMERO.web is a Python client of the OMERO platform that provides a web-based UI and JSON API. This section provides guidance on how to install and set up OMERO.web on any of the supported UNIX and UNIX-like platforms. Specific walkthroughs are provided for several systems, with detailed step-by-step instructions. OMERO.web can be either installed separately from the OMERO.server or installed with the OMERO.server. Deploying separately is recommended as they perform best under different circumstances and require a different set of dependencies.

OMERO.web can be deployed with:

If you need help configuring your firewall rules, see Server security and firewalls for more details.

If you have installed NGINX, OMERO can automatically generate a configuration file for your webserver. The location of the file will depend on your system, please refer to your webserver’s manual. See Customizing your OMERO.web installation for additional customization options.

Depending upon which platform you are using, you may find a more specific walkthrough listed below.

See also

OMERO.web installation separately from OMERO.server on CentOS 7 and IcePy 3.6
Instructions for installing separately OMERO.web from scratch on CentOS 7 with Ice 3.6.
OMERO.web installation separately from OMERO.server on Ubuntu 16.04 and IcePy 3.6
Instructions for installing separately OMERO.web from scratch on Ubuntu 16.04 with Ice 3.6.
OMERO.web installation separately from OMERO.server on Debian 9 and IcePy 3.6
Instructions for installing separately OMERO.web from scratch on Debian 9 with Ice 3.6.
OMERO.web installation with OMERO.server on CentOS 7 and IcePy 3.6
Instructions for installing OMERO.web with OMERO.server on CentOS 7 with Ice 3.6.
OMERO.web installation with OMERO.server on Ubuntu 16.04 and IcePy 3.6
Instructions for installing OMERO.web with OMERO.server on Ubuntu 16.04 with Ice 3.6.
OMERO.web installation with OMERO.server on Debian 9 and IcePy 3.6
Instructions for installing OMERO.web with OMERO.server on Debian 9 with Ice 3.6.
OMERO.web installation on Mac OS X and IcePy 3.6
Instructions for installing OMERO.web from scratch on on Mac OS X with Homebrew. It is aimed at developers since typically MacOS X is not suited for serious deployment.

Note

Support for Apache deployment has been dropped in 5.3.0.

If your organization’s policies only allow Apache to be used as the external-facing web-server you should configure Apache to proxy connections to an NGINX instance running on your OMERO server i.e. use Apache as a reverse proxy. For more details see Apache mod_proxy documentation.

This guide uses the example of deploying OMERO.web separately from OMERO.server with NGINX and Gunicorn. If you opt to install OMERO.web with the OMERO.server, change OMERO.py to OMERO.server in the commands below.

Prerequisites

  • Python 2.7
    • virtualenv (optional) tool to create isolated Python environments
    • PyPI a package management system used to install and manage software packages written in Python. PyPI is already installed if you are using Python 2 >=2.7.9
    • ZeroC IcePy 3.6
    • Django (1.8) [1]
    • Pillow [2]
    • NumPy >=1.9
    • Matplotlib
  • A WSGI-capable webserver such as NGINX and Gunicorn
[1]The currently supported version of the django module used by OMERO.web (1.8) requires Python 2.7. The older version (1.6) will work with Python 2.6 but lacks security support, and is consequently not recommended for production use. Python 2.7 and Django 1.8 are required for security support.
[2]Make sure to have libjpeg installed when building Pillow. We currently do not support version 3.0+.

If possible, install the following packages:

System Package
BSD Ports lang/python27 graphics/py-pillow math/py-matplotlib math/py-numpy www/nginx
Debian python2.7 python-pil python-matplotlib python-numpy nginx
Homebrew python pillow numpy matplotlib nginx
RedHat python nginx

Note

CentOS 6 users should read OMERO.server installation on CentOS 6 with Python 2.7 and follow the instructions there to install Python and the required modules.

Gunicorn configuration

Additional settings can be configured by changing the following properties:

NGINX configuration

OMERO can automatically generate a configuration file for your web server. The location of the file will depend on your system, please refer to your webserver’s manual. See Customizing your OMERO.web installation for additional customization options.

To create a site configuration file for inclusion in a system-wide NGINX configuration redirect the output of the following command into a file:

$ OMERO.py/bin/omero web config nginx
upstream omeroweb {
    server 127.0.0.1:4080 fail_timeout=0;
}

server {
    listen 80;
    server_name $hostname;

    sendfile on;
    client_max_body_size 0;

    # maintenance page serve from here
    location @maintenance {
        root /home/omero/OMERO.py/etc/templates/error;
        try_files $uri /maintainance.html =502;
    }

    # weblitz django apps serve media from here
    location /static {
        alias /home/omero/OMERO.py/lib/python/omeroweb/static;
    }

    location @proxy_to_app {
        proxy_set_header X-Forwarded-Proto $scheme;
        proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
        proxy_set_header Host $http_host;
        proxy_redirect off;
        proxy_buffering off;

        proxy_pass http://omeroweb;
    }

    location / {

        error_page 502 @maintenance;
        # checks for static file, if not found proxy to app
        try_files $uri @proxy_to_app;
    }

}

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:

$ OMERO.py/bin/omero web config nginx-location > /home/omero/omero-web-location.include

location @maintenance {
    root /home/omero/OMERO.py/etc/templates/error;
    try_files $uri /maintainance.html =502;
}

location /static {
    alias /home/omero/OMERO.py/lib/python/omeroweb/static;
}

location @proxy_to_app {
    proxy_set_header X-Forwarded-Proto $scheme;
    proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;
    proxy_set_header Host $http_host;
    proxy_redirect off;
    proxy_buffering off;

    proxy_pass http://127.0.0.1:4080;
}

location / {

    error_page 502 @maintenance;
    # checks for static file, if not found proxy to app
    try_files $uri @proxy_to_app;
}

and include this in your own manually created NGINX file, such as /etc/nginx/conf.d/omero-web.conf.

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

Start the Gunicorn worker processes listening by default on 127.0.0.1:4080:

$ OMERO.py/bin/omero web start
... static files copied to '/home/omero/OMERO.py/lib/python/omeroweb/static'.
Starting OMERO.web... [OK]

The Gunicorn workers are managed separately from other OMERO.server processes. You can check their status or stop them using the following commands:

$ OMERO.py/bin/omero web status
OMERO.web status... [RUNNING] (PID 59217)
$ OMERO.py/bin/omero web stop
Stopping OMERO.web... [OK]
Django WSGI workers (PID 59217) killed.

Download limitations

In order to offer users the ability to download data from OMERO.web you have to deploy using EXPERIMENTAL: 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.

Benchmark

We run example benchmarks on rendering thumbnails and 512x512 pixels planes for 100 concurrent users making 5000 requests in total:

$ ab -n 5000 -c 100 https://server.openmicroscopy.org/omero/webclient/render_thumbnail/1234/
This is ApacheBench, Version 2.3 <$Revision: 1706008 $>
Copyright 1996 Adam Twiss, Zeus Technology Ltd, http://www.zeustech.net/
Licensed to The Apache Software Foundation, http://www.apache.org/

Benchmarking server.openmicroscopy.org (be patient)
Completed 100 requests
Completed 200 requests
Completed 300 requests
Completed 400 requests
Completed 500 requests
Finished 500 requests


Server Software:        nginx/1.11.10
Server Hostname:        server.openmicroscopy.org
Server Port:            80

Document Path:          /omero/webclient/render_thumbnail/1234/
Document Length:        4405 bytes

Concurrency Level:      20
Time taken for tests:   17.904 seconds
Complete requests:      500
Failed requests:        0
Total transferred:      2271500 bytes
HTML transferred:       2202500 bytes
Requests per second:    27.93 [#/sec] (mean)
Time per request:       716.144 [ms] (mean)
Time per request:       35.807 [ms] (mean, across all concurrent requests)
Transfer rate:          123.90 [Kbytes/sec] received

Connection Times (ms)
              min  mean[+/-sd] median   max
Connect:       45   49   4.3     48      83
Processing:   245  650 113.4    620    1167
Waiting:      244  649 113.4    620    1167
Total:        294  699 113.0    670    1214

Percentage of the requests served within a certain time (ms)
  50%    670
  66%    698
  75%    737
  80%    754
  90%    814
  95%    951
  98%   1070
  99%   1080
 100%   1214 (longest request)

Troubleshooting

In order to identify why OMERO.web is not available run:

$ OMERO.py/bin/omero web status

Then consult NGINX error.log and OMERO.py/var/log/OMEROweb.log

Check OMERO.web issues for more details.

Debugging

To run the WSGI server in debug mode, enable Gunicorn logging using omero.web.wsgi_args:

$ OMERO.py/bin/omero config set omero.web.wsgi_args -- "--log-level=DEBUG --error-logfile=/home/omero/OMERO.py/var/log/error.log".

EXPERIMENTAL: Gunicorn advanced configuration

Note

The following configuration options marked as EXPERIMENTAL have yet to be extensively tested in a production environment, use at your own risk.

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; read more about Download limitations above.

See Gunicorn design for more details.

EXPERIMENTAL: Sync workers

  • Install futures

    $ pip install futures
    

Additional settings can be configured by changing the following properties:

  • The number of worker threads for handling requests, see Gunicorn threads

    $ OMERO.py/bin/omero config set omero.web.wsgi_worker_class
    $ OMERO.py/bin/omero config set omero.web.wsgi_threads $(2-4 x NUM_CORES)
    

EXPERIMENTAL: Async workers

Additional settings can be configured by changing the following properties:

  • The maximum number of simultaneous clients, see Gunicorn worker-connections

    $ OMERO.py/bin/omero config set omero.web.wsgi_worker_class gevent
    $ OMERO.py/bin/omero config set omero.web.wsgi_worker_connections 1000
    $ OMERO.py/bin/omero config set omero.web.application_server.max_requests 0