Bug: Description lost on import if XML

[wmoore]

From ​https://www.openmicroscopy.org/community/viewtopic.php?f=6&t=7442&p=13607

and ​https://www.openmicroscopy.org/community/viewtopic.php?f=5&t=7361

An OME.tiff file that has OME-XML in the Description block currently loses this text when imported.

Sample file attached. When opened with LOCI in ImageJ you see the description (OME-XML) but when imported into OMERO this is lost:

omero=# select name, description from image where id=1317;
             name              | description 
-------------------------------+-------------
 descriptionOmeXml.png.ome.tif | 

[wmoore]

Imported png to OMERO, edited Description with XML and exported OME.TIFF

[wmoore]

Raising the priority since this is a blocker for an external user (and I think it's a regression from OMERO 4.4)

[jamoore]

This is the last un-PR'd blocker for 5.0.1, Melissa. Thoughts on the priority and the timeline?

[mlinkert]

Leaving the priority as-is, but this isn't likely to happen for 5.0.1. All I know so far is that Bio-Formats is parsing out the correct description and passing that through MetadataStore?, but for whatever reason that gets eaten before being stored in the database. Possible causes are the length or something to do with the fact that the description is XML (e.g. unescaped characters).

[jamoore]

Removing Melissa from the owner of this in case someone else can pick it while she focuses on CZI.

[bpindelski]

I shall try and investigate what is happening here.

[bpindelski]

Initial investigation shows, that it doesn't only apply to XML-type descriptions. Any string added to an image gets saved in the DB, but exporting that image as OME-TIFF an re-importing doesn't preserve the description field.

[bpindelski]

Digging deeper, ​https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_0/components/blitz/src/ome/formats/model/PixelsProcessor.java#L195 seems to be the culprit. On dev_4_4 the userSpecifiedDescription manages to stay null. On dev_5_0 and due to the stuff that ​https://github.com/openmicroscopy/openmicroscopy/blob/dev_5_0/components/blitz/src/ome/services/blitz/repo/ManagedImportRequestI.java#L198 does, userSpecifiedDescription becomes an empty, but initialized string and passes the null check, hence overwriting the description field value in the Image object.

[bpindelski]

PR open - ​https://github.com/openmicroscopy/openmicroscopy/pull/2407.

[bpindelski]

Closing. ​PR 2407 merged.

[Josh Moore <josh@…>]

(In [286607c816921df834ef4cdfd28028f930d555fe/ome.git] on branch develop) Merge pull request #2427 from bpindelski/rebased/develop/12056-description

Don't use rstring on null values (fix #12056). (rebased onto develop)