OMERO.web upgrade

The OME team is committed to providing frequent, project-wide upgrades both with bug fixes and new functionality. We try to make the schedule for these releases as public as possible. You may want to take a look at the Trello boards for exactly what will go into a release.

See the full details of OMERO 5.4.9 features in the OMERO version history.

This guide aims to be as definitive as possible so please do not be put off by the level of detail; upgrading should be a straightforward process.

Upgrade checklist

Check prerequisities

Before starting the upgrade, please ensure that you have reviewed and satisfied all the system requirements with correct versions for installation.

Note that support for Apache deployment has been dropped in 5.3.0.

Configuration

Since OMERO 5.3, OMERO.web can be deployed separately from OMERO.server. This is the recommended installation set-up as they perform best under different circumstances and require a different set of dependencies. Please check Prerequisites for the latest advice on how to deploy OMERO.web.

Warning

If you generated configuration stanzas using omero web config which enables OMERO.web via NGINX, they will include hard-coded links to your previous version of OMERO. Therefore, you should regenerate your config files when upgrading, remembering to merge in any of your own modifications if necessary. You should carry out this step even for minor version upgrades as there may be fixes which require it.

Dependencies

While upgrading the server you should keep OMERO.web dependencies up to date to ensure that security updates are applied:

$ pip install --upgrade -r share/web/requirements-py27-all.txt

Warning

Missing this step can result in OMERO.web failing to start after upgrading.

Since OMERO 5.2, the OMERO.web framework no longer bundles a copy of the Django package, instead manual installation of the Django dependency is required (the command above will do this for you). It is highly recommended to use Django 1.8 (LTS) which requires Python 2.7. For more information see Python on the Version requirements page.

Plugin updates

OMERO.web plugins are very closely integrated into the webclient. For this reason, it is possible that an update of OMERO will cause issues with an older version of a plugin. It is best when updating the server to also install any available plugin updates according to their own documentation.

Since 5.3, all official OMERO.web plugins can be installed from PyPI. You should remove all previously installed plugins and install the latest versions using pip.

Also introduced in 5.3, the Open with configuration allows users to open data in other web applications e.g. open images in a custom viewer or open images in a new figure with OMERO.figure. After installing OMERO.figure (or any other app), run the following command to add it to the Open with options, so that the app is available from the context menu on the webclient tree:

$ bin/omero config append omero.web.open_with '["omero_figure", "new_figure",
  {"supported_objects":["images"], "target": "_blank", "label": "OMERO.figure"}]'

Updating ‘Open with’ config

If you have configured omero.web.open_with prior to OMERO 5.3.3 and also set the default viewer with omero.web.viewer.view, for example as described for OMERO.iviewer then you will find that Open with > Image Viewer also opens the OMERO.iviewer instead of the webgateway viewer.

To fix this, you need to update the Image Viewer option within your omero.web.open_with config.

The best way to do this without changing the ordering of the options is to get the complete current config, edit the Image Viewer option, replacing "webindex" with "webgateway" and then set this as the updated config:

$ bin/omero config get omero.web.open_with
[["Image viewer", "webindex", {"supported_objects": ["image"], "script_url": "we....

# Replace "webindex" with "webgateway" and paste everything back to set, within single quotes

$ bin/omero config set omero.web.open_with '[["Image viewer", "webgateway", {"supported_objects": ["image"], "scr....'

Re-enabling the version checker

If you used the workaround for 2017-SV4-guest-user then you should revert the change to omero.web.check_version configuration property:

$ bin/omero config set omero.web.check_version true

Troubleshooting

If you encounter errors during an OMERO.web upgrade, etc., you should retain as much log information as possible and notify the OMERO.server team via the mailing lists available on the support page.

Update your OMERO.web server configuration

FastCGI support was removed in OMERO 5.2 and OMERO.web can be deployed using WSGI (see Prerequisites for more details). If you have already deployed OMERO.web using WSGI you should regenerate your config files, remembering to merge in any of your own modifications if necessary. Due to changes in OMERO.web, you should carry out this step even for minor version upgrades as there may be fixes which require it.

If necessary ensure you have set up a regular task to clear out any stale OMERO.web session files as described in OMERO.web maintenance.

Migrating from Apache to NGINX

Support for Apache and mod_wsgi deployment was deprecated in OMERO 5.2.6 and dropped in 5.3.0. It is recommended to use a WSGI-capable server such as NGINX and Gunicorn.

See also

OMERO.web migrating from Apache to NGINX

Restart OMERO.web