Release of OMERO 5.4.2

[Helen Flynn (Staff)]

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Dear All,

We are pleased to announce the release of OMERO 5.4.2, a bug-fix release.

Improvements include:

  *   added documentation on a complete workflow for publishing data from OMERO.server (see https://docs.openmicroscopy.org/omero/5.4.2/sysadmins/public.html)
  *   added references to the new OMERO pyramid format documentation (within the OME Data Model and File Formats documentation - see https://docs.openmicroscopy.org/latest/ome-model/omero-pyramid/index.html)
  *   faster loading of thumbnails for large Plates after a recent regression
  *   made projecting images belonging to another user only possible for users with the required permissions to save the new images
  *   improved the public user experience for password-less access
  *   updated SwingX library version used by OMERO.insight to stop insight-ij plugin crashing in Fiji
  *   CLI updates:
     *   ``import --target`` into a container without the necessary permissions now fails before file upload starts and more transparently
     *   ``admin mail`` timeout is now configurable via ``--wait``
     *   added ``admin log`` command for inserting statements to the server log

Sysadmin changes include:

  *   added warning about the need to regenerate your NGINX config for every upgrade
  *   fixed documentation bug affecting OMERO-version-specific guidance
  *   improved OMERO.tables startup stability
  *   server performance improvements and reduction in ERROR logging

Developer updates include:

  *   extended Python and Java examples to include Map Annotations and histograms
  *   added methods for updating OMERO.tables
  *   Java Gateway fixes for sessions and rendering
  *   fixed retrieval of Plate thumbnail URLs
  *   improved Editing OMERO.web documentation
  *   improved Slice documentation for API deprecations
  *   added instructions to documentation for OMERO.cli extensions on how to create CLI plugins that are ``pip`` installable (see https://docs.openmicroscopy.org/omero/5.4.2/developers/cli/extending.html)
  *   substantial effort to make third-party repositories easily testable; see https://github.com/openmicroscopy/omero-test-infra for more information

This release also upgrades the version of Bio-Formats that OMERO uses to 5.7.3, see https://docs.openmicroscopy.org/bio-formats/5.7.3/about/whats-new.html.

Upgrade information is on the server upgrade page - https://docs.openmicroscopy.org/omero/5.4.2/sysadmins/server-upgrade.html.

The software is available at https://www.openmicroscopy.org/omero/downloads/

Any problems or comments, please use the OME Forums or mailing lists - https://www.openmicroscopy.org/support/

Regards,

The OME Team


Dr Helen Flynn
OME Technical Writer
Centre for Gene Regulation & Expression
Open Microscopy Environment
University of Dundee
http://openmicroscopy.org<http://openmicroscopy.org/>


The University of Dundee is a registered Scottish Charity, No: SC015096

[Josh Moore]

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On Tue, Jan 23, 2018 at 12:44 PM, Helen Flynn (Staff)
<[hidden email]> wrote:
> Dear All,
>
> We are pleased to announce the release of OMERO 5.4.2, a bug-fix release...

... but less pleased that we must warn you: while upgrading our
production servers to 5.4.2, we have identified a problem afflicting
OMERO.web. Long-running Python processes, like OMERO.web’s gunicorn
workers, can leak file handles. After a period of usage, OMERO.web may
become unresponsive and need to be restarted. We have now identified
the issue and are testing a fix [1].

In the meantime, we recommend that you *do not upgrade to 5.4.2* if
you are using OMERO.web: we will release 5.4.3 early next week.

We unfortunately did not discover the issue during our testing since
the instability only arises after extended uptime. We will review our
testing process accordingly to avoid such problems in the future.

Thanks for your understanding and please accept our apologies.

The OME team

[1] https://github.com/openmicroscopy/openmicroscopy/commit/fe9eda48f96928801dff15a13d37853a188f7288