LIF ArrayIndexOutOfBoundsException

[jburel]

java.lang.ArrayIndexOutOfBoundsException: 26
	at loci.formats.in.LIFReader.initFile(LIFReader.java:587)
	at loci.formats.FormatReader.setId(FormatReader.java:1480)
	at loci.formats.ImageReader.setId(ImageReader.java:864)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:258)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:317)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at loci.formats.Memoizer.setId(Memoizer.java:698)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:692)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:384)
	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:5756)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1104)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:103)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:49)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:126)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Thread.java:750)

https://qa.openmicroscopy.org/qa/feedback/91858/
https://qa.openmicroscopy.org/qa/feedback/91860/

[sbesson]

The stack trace looks related to #3873 which was fixed in Bio-Formats 8.0.0.

Which Bio-Formats version was used? Can one of the samples be shared publicly and uploaded to Zenodo?

[jburel]

5.6.14 was used which was released with support for Bio-Formats 8.0.1
File has been submitted via QA. i will ask if it can be uploaded to Zenodo

[sbesson]

Was the image imported via OMERO.insight? If so, what is the version of the application since the setId failure might have been occurring client-side rather than server-side? We don't have the full stack trace on the GitHub issue

[dominikl]

Here's another one: QA 91863

I just tested with Insight 5.8.6. And indeed it's pretty behind regarding blitz and bioformats versions!

2025-09-15 11:30:00,879 INFO  [       ome.formats.importer.ImportConfig] ( Thread-11) OMERO.blitz Version: 5.7.4 
2025-09-15 11:30:00,881 INFO  [       ome.formats.importer.ImportConfig] ( Thread-11) Bioformats version: 7.3.1 revision: 41e12f630ad7349caa0293cba23948c17d22732b date: 11 July 2024 

But how do the dependency versions actually trickle through the build? Would be it be enough to bump the omero-java-gateway to the latest version?

[sbesson]

Would be it be enough to bump the omero-java-gateway to the latest version?

I agree this should be the next action as mentioned in ome/omero-insight#461 (review) (which aims to fix other issues with the build)