Bug: OMETiffReader handling of missing MetadataFiles with BinaryFile is suboptimal

[omero-qa]

​https://www.openmicroscopy.org/qa2/qa2/qa/feedback/11166/

java.lang.IndexOutOfBoundsException: Index: 0, Size: 0
	at java.util.ArrayList.rangeCheck(Unknown Source)
	at java.util.ArrayList.get(Unknown Source)
	at loci.formats.FormatReader.getImageCount(FormatReader.java:684)
	at loci.formats.in.OMETiffReader.initFile(OMETiffReader.java:951)
	at loci.formats.FormatReader.setId(FormatReader.java:1426)
	at loci.formats.ImageReader.setId(ImageReader.java:835)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:223)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:289)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at loci.formats.Memoizer.setId(Memoizer.java:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:651)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:414)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:570)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at org.openmicroscopy.shoola.env.data.OMEROGateway.getImportCandidates(OMEROGateway.java:6772)
	at org.openmicroscopy.shoola.env.data.OmeroImageServiceImpl.importFile(OmeroImageServiceImpl.java:1033)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.importFile(ImagesImporter.java:79)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter.access$000(ImagesImporter.java:55)
	at org.openmicroscopy.shoola.env.data.views.calls.ImagesImporter$1.doCall(ImagesImporter.java:104)
	at org.openmicroscopy.shoola.env.data.views.BatchCall.doStep(BatchCall.java:144)
	at org.openmicroscopy.shoola.util.concur.tasks.CompositeTask.doStep(CompositeTask.java:226)
	at org.openmicroscopy.shoola.env.data.views.CompositeBatchCall.doStep(CompositeBatchCall.java:126)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.exec(ExecCommand.java:165)
	at org.openmicroscopy.shoola.util.concur.tasks.ExecCommand.run(ExecCommand.java:276)
	at org.openmicroscopy.shoola.util.concur.tasks.AsyncProcessor$Runner.run(AsyncProcessor.java:91)
	at java.lang.Thread.run(Unknown Source)

The metadata for movie\ 1_2_MMStack_Pos16.ome.tif is:

<?xml version="1.0" encoding="UTF-8" standalone="no"?>
<OME xmlns="http://www.openmicroscopy.org/Schemas/OME/2012-06" xmlns:xsi="
http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://www.
openmicroscopy.org/Schemas/OME/2012-06 http://www.openmicroscopy.org/Schem
as/OME/2012-06/ome.xsd"><BinaryOnly MetadataFile="movie 1_2_MMStack_Pos1.o
me.tif" UUID="urn:uuid:c4757004-22a9-4075-889f-0d7c2b32fc55"/></OME>

Since movie 1_2_MMStack_Pos1.ome.tif is missing, the metadata can't be loaded and hence there are no series in the core metadata (which is why the exception is thrown). However, we should have errored out before this point was reached, when we failed to load the missing MetadataFile?.

[mlinkert]

This may no longer be an issue given recent changes to Micro-manager OME-TIFF handling. Bumping up to 5.2.0 for verification; feel free to push back to unscheduled if a fix is still needed and not practical in the 5.2.0 timeline.

[sbesson]

Cannot reproduce with OMERO 5.2.2. Closing as Micro-Manager/OME-TIFF improvements in 5.1.x should have fixed it.