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Fail on import of a plate #43

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pwalczysko opened this issue Nov 1, 2022 · 1 comment
Open

Fail on import of a plate #43

pwalczysko opened this issue Nov 1, 2022 · 1 comment

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@pwalczysko
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Trying to import a plate from https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr - the import into OMERO fails with
Discovered during the ngff viewers testing.

bash-4.2$ cat 2551.err 
2022-10-31 14:55:30,596 207        [      main] INFO          ome.formats.importer.ImportConfig - OMERO.blitz Version: 5.5.13-SNAPSHOT
2022-10-31 14:55:30,613 224        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 6.11.1-SNAPSHOT revision: 46a7da6ff85e45f048e39190169950d624361df1 date: 29 October 2022
2022-10-31 14:55:30,655 266        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting checksum algorithm to File-Size-64
2022-10-31 14:55:30,656 267        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2022-10-31 14:55:30,660 271        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting parallel upload: 10
2022-10-31 14:55:30,660 271        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2022-10-31 14:55:31,112 723        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 10 Metadata Level: MINIMUM
2022-10-31 15:14:53,455 1163066    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/7/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 15:30:13,493 2083104    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/6/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 15:45:58,735 3028346    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/3/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 16:01:19,153 3948764    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/11/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 16:16:53,035 4882646    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/14/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 16:32:23,998 5813609    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/5/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-10-31 16:47:48,786 6738397    [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/3/1/2/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
....
....
2022-11-01 13:00:54,186 79523797   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/1/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 13:16:18,745 80448356   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/13/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 13:31:40,268 81369879   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/0/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 13:47:00,420 82290031   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/9/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 14:02:13,356 83202967   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/12/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 14:17:30,282 84119893   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/15/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 14:32:43,139 85032750   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/10/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 14:47:56,011 85945622   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/1/8/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)
2022-11-01 15:03:22,279 86871890   [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/G/7/3/4/0/7/0/0
java.lang.ClassCastException: java.lang.Long cannot be cast to java.lang.String
	at loci.formats.in.ZarrReader.parsePlate(ZarrReader.java:541)
	at loci.formats.in.ZarrReader.initFile(ZarrReader.java:287)
	at loci.formats.FormatReader.setId(FormatReader.java:1443)
	at loci.formats.ImageReader.setId(ImageReader.java:849)
	at ome.formats.importer.OMEROWrapper$4.setId(OMEROWrapper.java:167)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:234)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:293)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at loci.formats.Memoizer.setId(Memoizer.java:662)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:650)
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:427)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:576)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:387)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:384)
	at org.apache.commons.io.DirectoryWalker.walk(DirectoryWalker.java:355)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:381)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:222)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:174)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:148)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:997)

The import was attempted on merge-ci, the file is there downloaded from S3 using aws under /uod/idr-scratch/petr-test/aws-downloads/2551.zarr/

cc @will-moore @dgault
@will-moore
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Looks like the error is coming from inside this image at G/7 but that seems valid: (assuming this is the same as what was downloaded) https://ome.github.io/ome-ngff-validator/?source=https://uk1s3.embassy.ebi.ac.uk/idr/zarr/v0.4/idr0001A/2551.zarr/G/7/3/

@pwalczysko pwalczysko mentioned this issue Nov 4, 2022
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@will-moore @pwalczysko