Fail on import of a plate

[pwalczysko]

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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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.(ImportCandidates.java:222) at ome.formats.importer.ImportCandidates.(ImportCandidates.java:174) at ome.formats.importer.cli.CommandLineImporter.(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]

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/