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

[Damir Sudar]

Thanks Josh, that did the job. Now running 5.1 on my test server and 
everything appears to work great.
Cheers,
- Damir

On 4/2/2015 12:52 PM, Josh Moore wrote:
> 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
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-- 
Damir Sudar - Staff Scientist
Lawrence Berkeley Laboratory / Life Sciences Division
One Cyclotron Road, MS 977, Berkeley, CA 94720, USA
T: 510/486-5346 - F: 510/486-5586 - E: DSudar at lbl.gov
WWW: http://www.lbl.gov/lifesciences/labs/sudar_lab.html