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Task #12643 (closed)

Opened 5 years ago

Closed 5 years ago

VSI - java.lang.IndexOutOfBoundsException

Reported by: ejrozbicki Owned by:
Priority: minor Milestone: Unscheduled
Component: General Version: 5.0.6
Keywords: n.a. Cc: filipe.devadder@…; melissa@…
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

Exception details:

2014-11-18 05:30:23,239 340 [ main] INFO ome.formats.importer.ImportConfig? - OMERO Version: 5.0.5.152-gs-ice34
2014-11-18 05:30:23,252 353 [ main] INFO ome.formats.importer.ImportConfig? - Bioformats version: 5.0.5.152-gs-ice34 revision: a43215d date: 18 November 2014
2014-11-18 05:30:23,260 361 [ main] INFO formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-11-18 05:30:23,553 654 [ main] INFO ome.formats.importer.ImportCandidates? - Depth: 4 Metadata Level: MINIMUM
2014-11-18 05:30:23,578 679 [ main] ERROR ome.formats.importer.cli.ErrorHandler? - FILE_EXCEPTION: /home/emil/VSI/Si5-1~A.vsi
java.lang.IndexOutOfBoundsException?: Index: 0, Size: 0

at java.util.ArrayList?.rangeCheck(ArrayList?.java:604) ~[na:1.7.0_25]
at java.util.ArrayList?.get(ArrayList?.java:382) ~[na:1.7.0_25]
at loci.formats.in.CellSensReader?.initFile(CellSensReader?.java:649) ~[formats-gpl.jar:na]
at loci.formats.FormatReader?.setId(FormatReader?.java:1317) ~[formats-api.jar:na]
at loci.formats.ImageReader?.setId(ImageReader?.java:753) ~[formats-api.jar:na]
at loci.formats.ReaderWrapper?.setId(ReaderWrapper?.java:569) ~[formats-api.jar:na]
at loci.formats.ChannelFiller?.setId(ChannelFiller?.java:259) ~[formats-bsd.jar:na]
at loci.formats.ReaderWrapper?.setId(ReaderWrapper?.java:569) ~[formats-api.jar:na]
at loci.formats.ChannelSeparator?.setId(ChannelSeparator?.java:270) ~[formats-bsd.jar:na]
at loci.formats.ReaderWrapper?.setId(ReaderWrapper?.java:569) ~[formats-api.jar:na]
at loci.formats.Memoizer.setId(Memoizer.java:509) ~[formats-bsd.jar:na]
at loci.formats.ReaderWrapper?.setId(ReaderWrapper?.java:569) ~[formats-api.jar:na]
at ome.formats.importer.ImportCandidates?.singleFile(ImportCandidates?.java:414) ~[blitz.jar:na]
at ome.formats.importer.ImportCandidates?.handleFile(ImportCandidates?.java:596) ~[blitz.jar:na]
at ome.formats.importer.ImportCandidates?.execute(ImportCandidates?.java:371) ~[blitz.jar:na]
at ome.formats.importer.ImportCandidates?.<init>(ImportCandidates?.java:229) ~[blitz.jar:na]
at ome.formats.importer.ImportCandidates?.<init>(ImportCandidates?.java:180) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:109) ~[blitz.jar:na]
at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:729) ~[blitz.jar:na]

2014-11-18 05:30:23,579 680 [ main] INFO ome.formats.importer.ImportCandidates? - 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 19ms. (26ms total) [0 unknowns]
2014-11-18 05:30:24,368 1469 [ main] WARN ome.system.UpgradeCheck - UPGRADE AVAILABLE:Please upgrade to 5.0.6 See http://trac.openmicroscopy.org.uk/omero for the latest version
2014-11-18 05:30:24,464 1565 [ main] INFO ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2014-11-18 05:30:25,086 2187 [ main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.0.5
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.0.5.152-gs-ice34
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1.7.0_25
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2014-11-18 05:30:25,560 2661 [ main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 2.6.32-358.el6.x86_64
No imports due to errors!

Change History (2)

comment:1 Changed 5 years ago by jamoore

  • Type changed from Bug to Task

comment:2 Changed 5 years ago by mlinkert

  • Component set to General
  • Milestone set to Unscheduled
  • Resolution set to invalid
  • Status changed from new to closed
  • Version set to 5.0.6

See #12483. The dataset in question is not an Olympus/CellSens? .vsi dataset, and so is not currently supported.

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