Bug: 6x4y1z1t1c8b-swatch-tagged.ome not importing correctly

[cxallan]

When 6x4y1z1t1c8b-swatch-tagged.ome is imported from Andrew's new fixed samples, the tag set is missing. It doesn't seem to be linked correctly during the import phase.

In order to work on this ticket PR #307 needs to be merged first:

• ​https://github.com/openmicroscopy/openmicroscopy/pull/307

[jmoore]

Andrew/Roger?: Can any progress be made on this now that PR307 is in?

[mlinkert]

I just tested importing this file with merge-green build 164, and can see two tags ("SampleTagA" and "SampleTagB") attached to the resulting image. I guess that means this ticket can be closed?

The fixes for #9548 and/or #9549 might have something to do with this.

[ajpatterson]

The tags import fine with the 307 fix, this ticket is for the tagset that does not appear. Probably needs passed to Melissa or Jean-Marie.

[mlinkert]

The tag set doesn't appear because it isn't linked to the Image. Adding '<SA:AnnotationRef ID="Annotation:3"/>' under the Image element in this file should solve the problem.

[mlinkert]

Two PRs open:

​https://github.com/openmicroscopy/openmicroscopy/pull/350

​https://github.com/openmicroscopy/openmicroscopy/pull/351

and corresponding commits in bioformats.git:

​https://github.com/melissalinkert/bioformats/commit/f49d0e5fe6cf7f1c941f448a85c10cad0060496e
​https://github.com/melissalinkert/bioformats/commit/28ea8a2b4e2b537e1fdf6343579e81cd5373c6b5

There are now two problems. The first is that the file needs to updated to link to Annotation:3 alone, as discussed with Andrew in devteam.

The second problem is that with a locally fixed file, Insight only shows the tag set and not the tags linked to the tag set.
Peeking in the database suggests that everything is linked up correctly behind the scenes (in my case, the image ID is 551):

omero=> select child from imageannotationlink where parent=551;
 child 
-------
   551
   554
(2 rows)

omero=> select discriminator,id,textvalue from annotation where id=551;
  discriminator   | id  |  textvalue   
------------------+-----+--------------
 /basic/text/tag/ | 551 | SampleTagset
(1 row)

omero=> select child,parent from annotationannotationlink where parent=551;
 child | parent 
-------+--------
   552 |    551
   553 |    551
(2 rows)

omero=> select discriminator,id,textvalue from annotation where id=552;
  discriminator   | id  | textvalue  
------------------+-----+------------
 /basic/text/tag/ | 552 | SampleTagB
(1 row)

omero=> select discriminator,id,textvalue from annotation where id=553;
  discriminator   | id  | textvalue  
------------------+-----+------------
 /basic/text/tag/ | 553 | SampleTagA
(1 row)

...it's just not exposed in the UI. I don't really care how this is handled - the important thing is that everything should now be imported and stored correctly.

[ajpatterson]

Two PRs added:

For develop - ​https://github.com/openmicroscopy/openmicroscopy/pull/352

For schema-2012-06 - ​https://github.com/openmicroscopy/openmicroscopy/pull/272

[Andrew J Patterson <workonly@…>]

(In [43a2795e7142a8b5692d7083596a93843c522eea/ome.git] on branch develop) Fixing linking of tagset to Image, see #9541

[Josh Moore <josh@…>]

(In [31f936814f344379f70d19b4ea57e5989a23552d/ome.git] on branch develop) Merge pull request #352 from qidane/develop-9541-fix

Fixing linking of tagset to Image, see #9541

[jmoore]

Closing. Andrew this should have been closed when you opened the PR.

[Melissa Linkert <melissa@…>]

(In [920904bc0a190cd6cac5792883046b1a55a7788a/ome.git] on branch develop) Add reference handler for Annotation -> Annotation

See #9541.