Bug: OME-TIFF reader

[jburel]

​http://qa.openmicroscopy.org.uk/qa/feedback/16917/

I don't know why it is refused... Acquired with MM1.4.23. Associated metadata file also failed. Sent to you just after this one.

java.lang.NullPointerException
	at loci.formats.in.OMETiffReader.close(OMETiffReader.java:367)
	at loci.formats.ImageReader.close(ImageReader.java:581)
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
	at loci.formats.ChannelSeparator.close(ChannelSeparator.java:246)
	at loci.formats.ReaderWrapper.close(ReaderWrapper.java:366)
	at loci.formats.Memoizer.close(Memoizer.java:632)
	at loci.formats.MinMaxCalculator.close(MinMaxCalculator.java:278)
	at ome.formats.importer.OMEROWrapper.close(OMEROWrapper.java:255)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:437)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:566)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:367)
	at ome.formats.importer.ImportCandidates.(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:5989)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1035)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:73)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:48)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:97)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)

[jburel]

Import candidates step leads to exception

[mlinkert]

Won't have time to look at this for 5.1.7.

[mlinkert]

See also ​https://trello.com/c/mVFYhwcJ/87-qa16988-16991. I haven't to date had luck reproducing this problem with just showinf (even with the '-cache' option), so reproducing and testing will likely require a full OMERO import. Fixing the actual NPEs should be straightforward, but I don't know if the NPE is masking other issues so it would be good to check the imported images and metadata very carefully once the NPE is resolved. If there are other non-NPE issues, ​https://trac.openmicroscopy.org/ome/ticket/12740 may be related.

[sbesson]

See also ​https://www.openmicroscopy.org/qa2/qa/feedback/17201/. Looking more closely at the issue, it is possible to reproduce it by taking a multi-file OME-TIFF, deleting one of its constituent TIFF and importing it into OMERO (see ​https://www.openmicroscopy.org/qa2/qa/feedback/17202/ using one of our samples). Bio-Formats command-line tools will (semi-)gracefully fail with a

Exception in thread "main" loci.formats.FormatException: Unmatched UUID: urn:uuid:f4927e53-35eb-45b3-ac16-a9255a58860c

However ImportLibrary.importCandidates will invoke reader.close in a finally statement - see ​https://github.com/openmicroscopy/openmicroscopy/blob/v5.2.3/components/blitz/src/ome/formats/importer/ImportCandidates.java#L437 eating the setId() exception.

As proposed in ticket:13107#comment:3, I think the first step should be to fix the NPE in OMETiffReader.close(). This might lead us to a usability question on the nature of the error message.

[sbesson]

See ​https://github.com/openmicroscopy/bioformats/pull/2438