[ome-devel] Release of OMERO & Bio-Formats 5.1.0

[Josh Moore]

On Thu, Apr 2, 2015 at 9:36 PM, Damir Sudar <dsudar at lbl.gov> wrote:
> OME team,
>
> Congrats and thanks all on this great milestone.

Thanks! :)


> One quick question from someone who was somewhat impatient. I had OMERO
> 5.1.0-m4 installed on a test server and loaded some data into that to try
> out some of the new functionality. Now I updated that to the released 5.1.0
> but it refuses to start up probably due to these error messages in
> Blitz-0.log:
>
> ***************************************************************************************
> DB version (OMERO5.1DEV__20) does not match omero.properties (OMERO5.1__1).
> Please apply a db upgrade.
> See
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html
> ***************************************************************************************
>
> The server-upgrade.html instructions address how to upgrade the DB from a
> 5.0.x version but that probably will not work when upgrading from m4, right?

The linked instructions are for the production versions, but the same
process follows for DEV versions as well. You can get from any given
version X to the next version Y by looking for a script under
sql/psql/ named Y/X.sql.

> Anything I can do to upgrade or should I just wipe my DB and create a new
> one?

In this case, you need to apply 2 scripts in order to get to the
current production version 5.1__1:

 * https://github.com/openmicroscopy/openmicroscopy/blob/v5.1.0/sql/psql/OMERO5.1__0/OMERO5.1DEV__20.sql

 * https://github.com/openmicroscopy/openmicroscopy/blob/v5.1.0/sql/psql/OMERO5.1__1/OMERO5.1__0.sql

Then restart the server and you should be good to go.

Cheers,
~Josh.



> Thanks,
> - Damir
>
>
> On 4/2/2015 5:11 AM, Helen Flynn (Staff) wrote:
>
> Dear All,
>
> Today we are releasing OMERO and Bio-Formats 5.1.0. This is a full,
> production-ready release of OME's new software tools. With this release, the
> 5.0.x line enters maintenance mode and while we will continue to support it
> throughout 2015, it will only be updated for major bug fixes and security
> issues. We will not be releasing any further updates to the 4.4.x line.
>
> The 5.1.0 release updates the Data Model to the January 2015 schema (see
> http://www.openmicroscopy.org/site/support/ome-model/schemas/january-2015.html),
> including support for units and new more flexible user-added metadata,
> improves performance for a number of operations and formats, especially
> import times for large datasets such as HCS and SPIM, fixes many bugs, and
> features a substantial code clean-up across the platform and upgrade to
> OMERO.web.
>
> Bio-Formats 5.1.0 includes substantially improved performance with network
> file systems, and initial version of a native C++ implementation with its
> own viewer, improved support for ImageJ, and support for several new file
> formats; CellH5[1], Perkin Elmer Nuance[2], Amnis FlowSight[3], Veeco AFM,
> Zeiss .lms, I2I, plus support for writing Vaa3D data[4].
>
>
> Other features of this release are:
>
> For Bio-Formats:
>
>     Improvements to developer documentation
>     Improved support for opening and saving ROI data with ImageJ and other
> ImageJ improvements/fixes
>     Updated RandomAccessInputStream and RandomAccessOutputStream to read and
> write bits
>     Bug fixes for many file formats
>     Fixes and improvements to bfconvert
>
>
> Full details can be found at
> http://www.openmicroscopy.org/site/support/bio-formats5.1/about/whats-new.html
>
> The software is available at:
> http://downloads.openmicroscopy.org/bio-formats/5.1.0
> and the C++ implementation is available from:
> http://downloads.openmicroscopy.org/bio-formats-cpp/5.1.0/
>
> For OMERO:
>
>      New key-value pairs annotations for adding experimental metadata
>      Improved workflow for rendering settings and parity between the clients
>      Import images to OMERO from ImageJ and save ROIs and overlays from
> ImageJ to OMERO
>      Changing groups and delete operations are now faster
>      Import times are much improved for large datasets
>      OMERO.mail lets admins configure the server to email users
>      Configurable server download policy for controlling the download of
> original files
>      Many developer updates such as removal of deprecated methods, updates
> to OMERO.web and the C++ implementation
>
>
> Further details are available on the What's New pages:
> http://www.openmicroscopy.org/site/support/omero5.1/users/whatsnew.html
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/whatsnew.html
> http://www.openmicroscopy.org/site/support/omero5.1/developers/whatsnew.html
>
> External developers who have not been following the milestone releases
> should also read the 5.1.0-m1 to 5.1.0-m5 version histories on
> http://www.openmicroscopy.org/site/support/omero5.1/users/history.html
>
> The software is available at:
> http://downloads.openmicroscopy.org/omero/5.1.0
>
> Upgrade information is at
> http://www.openmicroscopy.org/site/support/omero5.1/sysadmins/server-upgrade.html.
>
> NOTE: PostgreSQL 9.2 is the new minimum required version. Sysadmins who
> don't currently meet this will need to upgrade to a later version, 9.3+ is
> recommended.
>
> NOTE: Upgrades to OMERO.web break both OMERO.figure (version 1.0.0 and
> earlier) and OMERO.webtagging (version 1.1.0 and earlier). We will be
> releasing updated versions which are compatible with OMERO 5.1 imminently
> but in the meantime, you should not upgrade if you rely on either of these
> optional extensions.
>
>
> Any problems or comments, please use the OME Forums or mailing lists:
>
> http://www.openmicroscopy.org/site/community
>
> Regards,
>
> The OME Team
>
> [1] Thanks to Christophe Sommer
> [2] Thanks to Lee Kamentsky
> [3] Thanks to Lee Kamentsky and Sebastien Simard
> [4] Thanks to Brian Long