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Bump Bio-Formats to 5.2.3 #4879

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merged 1 commit into from
Oct 6, 2016
Merged

Bump Bio-Formats to 5.2.3 #4879

merged 1 commit into from
Oct 6, 2016

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sbesson
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@sbesson sbesson commented Oct 5, 2016

What this PR does

This PR bumps the Bio-Formats dependency to use the latest patch release 5.2.3

Testing this PR

Apart from testing that all the CI jobs are green with this PR included, the following optional checks could be performed:

  • bin/omero import -f test.fake should allow to check the bundled version of Bio-Formats
  • as Bio-Formats 5.2.3 includes the minor schema update, images with new AcquisitionMode should now import and populate the value in the DB - see add enumeration values for acquisition mode #4820 for examples

@mtbc
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mtbc commented Oct 6, 2016

2016-10-06 10:20:36,758 254        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.2.3 revision: d7d2c4f6021c36a31a536fc36a3c950973eab1c0 date: 4 October 2016
$ omero hql "SELECT pixels.image.name, logicalChannel.mode.value FROM Channel"
Using session 241c1d78-c1f0-4026-9d39-5fb9ceaa2647 (user-2@localhost:4064). Idle timeout: 10 min. Current group: private-1
 # | Col1                      | Col2                            
---+---------------------------+---------------------------------
 0 | Captured 1.jp2            | LaserScanningConfocalMicroscopy 
 1 | Mc_04-Feb-2014_Angle0.czi | SPIM                            
(2 rows)

Good to merge.

@jburel jburel merged commit a9249c0 into ome:develop Oct 6, 2016
@sbesson sbesson deleted the bio-formats-5.2.3 branch October 6, 2016 09:40
@jburel jburel added this to the 5.3.0 milestone Mar 29, 2017
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3 participants