Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #13107 (closed)

Opened 5 years ago

Closed 5 years ago

Bug: OME-TIFF reader

Reported by: jburel Owned by: sbesson
Priority: major Milestone: B-F-5.2.0
Component: Bio-Formats Version: OMERO-5.2.0
Keywords: OMETiffReader, our-fault Cc: pognonec@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

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)

Change History (6)

comment:1 Changed 5 years ago by jburel

Import candidates step leads to exception

comment:2 Changed 5 years ago by mlinkert

  • Milestone changed from B-F-5.1.7 to B-F-5.2.0

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

comment:3 Changed 5 years ago by mlinkert

  • Keywords OMETiffReader our-fault added
  • Owner mlinkert deleted

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.

comment:4 Changed 5 years ago by 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.

comment:5 Changed 5 years ago by sbesson

  • Owner set to sbesson

comment:6 Changed 5 years ago by sbesson

  • Resolution set to fixed
  • Status changed from new to closed
Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.138871 sec.)

We're Hiring!