Web on production

OMERO.web Install and Configuration

OMERO.web is the web application component of the OMERO platform which allows for the management, visualisation (in a fully multi-dimensional image viewer) and annotation of images from a web browser. It also includes OMERO.webadmin for managing users and groups.

NOTE: OMERO.web configuration has changed SIGNIFICANTLY in OMERO 4.2.1 it is recommended that you review this documentation thoroughly if you are upgrading from OMERO 4.2.0.

OMERO.web ships with OMERO platform and can be started with:

IIS 5.1, 6.0 or 7.0 on Microsoft Windows (since OMERO 4.2.1)
FastCGI using a FastCGI capable web server such as Apache (with mod_fastcgi), nginx or lighttpd (since OMERO 4.2.1)
The built-in Django lightweight development server (for testing only)

You can find more information about FastCGI and where to get modules or packages for your distribution here.

If you need help configuring your firewall rules, see the Security page.

Prerequisites

OMERO 4.3.0 and its prerequisites
Python version from 2.4, 2.5 or 2.6 (due to backwards incompatibilities in Python 3.0, Django does not currently work with Python 3.0; for more information see the Django Installation page).
Python Imaging Library Packages should be available for your distribution from here
Matplot Lib Packages should be available for your distribution from here
A FastCGI capable web server or IIS

Pre-configuration

Configuration options can be set using bin/omero config set:

$ bin/omero config set <parameter> "<value>"

NB: The double quotes are not required by OMERO, they are interpreted by your shell/console and will be useful if you have spaces in the value or if you are using Windows. They should not be saved as part of the value (see below).

To remove a configuration option (to return to default values where mentioned), simply omit the value:

$ bin/omero config set <parameter>

These options will be stored in a file: etc/grid/config.xml which you can read for reference. DO NOT edit this file directly.

You can also review all your settings by using:

$ bin/omero config get

which should return values without quotation marks.

Customising your OMERO.web installation

NOTE: The following sections describe minimum required settings to perform installation. REQUIRED settings should be customised accordingly.

(REQUIRED) Application settings:
- OMERO.web application server. Default: fastcgi-tcp.
```
$ bin/omero config set omero.web.application_server "fastcgi-tcp" / "fastcgi" / "development"
```
- Target bind URL for the OMERO.web install. Default: http://localhost:80/.
```
$ bin/omero config set omero.web.application_host "http://mydomain.com:80/"
```
NOTE: Please ensure you specify the port explicitly as in "http://mydomain.com:80/" rather than "http://mydomain.com/".
Advanced options:
- Server list. Default: [["localhost", 4064, "omero"]].
```
$ bin/omero config set omero.web.server_list '[["prod.a.com", 4064, "prod"], ["dev.a.com", 4064, "dev"]]'
```
- Email server and notification:
  - (REQUIRED) From : address to be used when sending e-mail. Default: 'root@localhost'
```
$ bin/omero config set omero.web.server_email "webmaster@server.com"
```
  - (REQUIRED) Mail server hostname. Default: 'localhost'.
```
$ bin/omero config set omero.web.email_host "email.server.com"
```
  - Mail server login username. Default: '' (Empty string).
```
$ bin/omero config set omero.web.email_host_user "username"
```
  - Mail server login password. Default: '' (Empty string).
```
$ bin/omero config set omero.web.email_host_password "password"
```
  - Mail server port. Default: 25.
```
$ bin/omero config set omero.web.email_host_port 2255
```
  - Enabled or disables TLS when sending e-mail. Default: False.
```
$ bin/omero config set omero.web.email_use_tls "True"
```
  - Subject prefix for sent e-mail. Default: '[Django] '.
```
$ bin/omero config set omero.web.email_subject_prefix "Subject prefix for sent e-mail"
```
- Controlling displayed scripts:
  - Since OMERO 4.3.2 OMERO.web has the ability to dynamically display scripts in the script runner menu just like OMERO.insight. Some scripts were not suitable for display initially and are excluded from the menu. You may wish to control which scripts your users can see in OMERO.web using this configuration option. Default: '["/omero/figure_scripts/Movie_Figure.py", "/omero/figure_scripts/Split_View_Figure.py", "/omero/figure_scripts/Thumbnail_Figure.py", "/omero/figure_scripts/ROI_Split_Figure.py", "/omero/export_scripts/Make_Movie.py"]'
```
$ bin/omero config set omero.web.scripts_to_ignore '[]'
$ bin/omero config set omero.web.scripts_to_ignore '["/omero/my_scripts/really_buggy.py", ... ]'
```
- Open Astex (Volume Viewer) size limits:
  - Since OMERO 4.3.2 OMERO web has included the Open Astex Viewer, which is a Java Applet for viewing volume surfaces. See the Open Astex Viewer introduction. SciPy is used on the web server to down-sample large images for viewing in the web. Since OMERO 4.3.3 it has been possible to limit the size of Images that display the 'Open Astex Viewer' icon, so as to prevent users attempting to open large images (poor scaling performance). The size restrictions are based on maximum number of voxels and maximum & minimum length of X, Y or Z sides. The default values are a balence between functionality and performance, but you may wish to increase the threshold a little to view particular images. NB: These values only affect the size of images that will be scaled by SciPy. If SciPy is not available on the server, no images above 160 x 160 x 160 will be viewable in the Open Astex Viewer.
```
$ bin/omero config set omero.web.open_astex_max_side 500             # default is 400
$ bin/omero config set omero.web.open_astex_min_side 50              # default is 20
$ bin/omero config set omero.web.open_astex_max_voxels 15625000      # default is 27000000 (300 * 300 * 300)
```
- Administrator e-mail notification:
  - Admins list of people who get code error notifications. When debug mode is off and a view raises an exception, Django will e-mail these people with the full exception information. Default: empty.
```
$ bin/omero config set omero.web.admins '[["Dave", "dave@example.com"], ["Bob", "bob@example.com"]]'
```
- Debug mode:
  - A boolean that turns on/off debug mode. Default: False.
```
$ bin/omero config set omero.web.debug "True"
```
- Web caching:
  
  (WARNING) The web framework supports caching for images, json data and thumbnails. This experimental implementation supports only Unix machines and additional problems may occur. To activate caching, you need to specify a cache location by the following (the necessary directories will be created automatically):
  - Unix:
    
    $ bin/omero config set omero.web.webgateway_cache "/Users/omero/Desktop/omero/var/weblitz_cache"
  - Windows:
    
    $ bin/omero config set omero.web.webgateway_cache "C:omero_distvarweblitz_cache"

Quick Start

Using FastCGI (UNIX)

Once you have installed a FastCGI capable web server, configuration of OMERO.web is quite straight forward.

Choose between FastCGI TCP (recommended) or FastCGI (advanced):

$ bin/omero config set omero.web.application_server "fastcgi" / "fastcgi-tcp"

Set the application host to the URL that you're going to have people connecting to:
```
$ bin/omero config set omero.web.application_host "http://omero.inst.edu:80"
```
NOTE: Please ensure you specify the port explicitly as in "http://omero.inst.edu:80" rather than "http://omero.inst.edu".

Place a stanza in your web server configuration file. Apache and nginx configurations can be automatically generated for you by OMERO.web as follows:

$ bin/omero web config "apache" / "nginx"
$ bin/omero web config apache
###
### Stanza for OMERO.web created 2010-11-08 14:06:57.811802
###
FastCGIExternalServer "/Users/omero/Desktop/omero/var/omero.fcgi" -host 0.0.0.0:4080

<Directory "/Users/omero/Desktop/omero/var">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

<Directory "/Users/omero/Desktop/omero/lib/python/omeroweb/media">
    Options -Indexes FollowSymLinks
    Order allow,deny
    Allow from all
</Directory>

Alias /appmedia /Users/omero/Desktop/omero/lib/python/omeroweb/media
Alias / "/Users/omero/Desktop/omero/var/omero.fcgi/"

Syncing media:
```
$ bin/omero web syncmedia
```

Start the Django FastCGI workers:

$ bin/omero web start
Starting OMERO.web... [OK]

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

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

Using IIS (Windows)

Once you have IIS installed on your system straight forward set of steps is required to get the ISAPI WSGI handler for OMERO.web bound to your IIS deployment.

Ensure that the ISAPI for IIS options are installed
Download and install ISAPI WSGI (we suggest the Windows Installer)
For extended compatibility with multiple IIS versions ISAPI WSGI uses the IIS 5/6 WMI interface to interact with your IIS deployment. If you are using IIS 7 you must enable the IIS 6 WMI backwards compatibility options, an example follows:

IIS 7 configuration options

OMERO.web and ISAPI WSGI are 32-bit applications on Windows at present. If you are attempting to run OMERO.web on a 64-bit version of Windows, you must enable 32-bit compatibility in the Advanced Settings... for the Application Pool assigned to your default Site. You can do this in the IIS Manager as follows:

IIS 7 Application Pool Advanced Settings

Configure OMERO.web bindings for IIS

C:\omero_dist>bin\omero config set omero.web.session_engine "django.contrib.sessions.backends.cache"

C:\omero_dist>bin\omero config set omero.web.cache_backend "file://C:/windows/temp/"

C:\omero_dist>bin\omero web iis

Syncing media:

C:\omero_dist\lib\python>cd C:\omero_dist
C:\omero_dist> bin\omero web syncmedia

Logging in to OMERO.web

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

http://your_host/webadmin
http://your_host/webclient

Using the lightweight development server (UNIX or Windows)

All that is required to use the Django lightweight development server (on UNIX or Windows) is to set the omero.web.application_server configuration option and start the server up:

$ bin/omero config set omero.web.application_server development
$ bin/omero web syncmedia
$ bin/omero web start
Starting OMERO.web... Validating models...
0 errors found

Django version 1.1.1, using settings 'omeroweb.settings'
Development server is running at http://0.0.0.0:4080/
Quit the server with CONTROL-C.

NOTE: This starts the server in the foreground. It is your responsibility to place it in the background, if required, and manage its shutdown.

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 forums or ome-users mailing list or discussed on the Community page.

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