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Task #4195 (closed)

Opened 13 years ago

Closed 13 years ago

Last modified 13 years ago

BUG: Import - too many files

Reported by: wmoore Owned by: cxallan
Priority: major Milestone: OMERO-Beta4.3
Component: Import Version: n.a.
Keywords: n.a. Cc: mlinkert
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-02-10 (5)

Description

From forum - Command line importer with large number of files.

​https://www.openmicroscopy.org.uk/community/viewtopic.php?f=4&t=607&sid=6b89fe355a2d882484a3d14097115035

java.io.FileNotFoundException: /home/helmerj/rails/metaxpress/transfer-script/out0500/20100825 rbilly_C13_w376F74D57-F0AE-4C0F-A273-A573DC6A1237.ome.tif (Too many open files)
   at java.io.RandomAccessFile.open(Native Method)
   at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
   at loci.common.Location.getHandle(Location.java:196)
   at loci.common.Location.getHandle(Location.java:167)
   at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:71)
   at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:206)
   at loci.formats.FormatReader.openBytes(FormatReader.java:739)
   at loci.formats.ImageReader.openBytes(ImageReader.java:370)
   at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:262)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:245)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:245)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:483)
   at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:223)
   at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:128)
   at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:366)
2011-01-31 11:44:20,272 657081     [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - FILE_EXCEPTION: /home/helmerj/rails/metaxpress/transfer-script/out0500/20100825 rbilly_C13_w376F74D57-F0AE-4C0F-A273-A573DC6A1237.ome.tif
java.io.FileNotFoundException: /home/helmerj/rails/metaxpress/transfer-script/out0500/20100825 rbilly_C13_w376F74D57-F0AE-4C0F-A273-A573DC6A1237.ome.tif (Too many open files)
   at java.io.RandomAccessFile.open(Native Method)
   at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:111)
   at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:119)
   at loci.common.Location.getHandle(Location.java:196)
   at loci.common.Location.getHandle(Location.java:167)
   at loci.common.RandomAccessInputStream.<init>(RandomAccessInputStream.java:71)
   at loci.formats.in.OMETiffReader.openBytes(OMETiffReader.java:206)
   at loci.formats.FormatReader.openBytes(FormatReader.java:739)
   at loci.formats.ImageReader.openBytes(ImageReader.java:370)
   at loci.formats.ChannelFiller.getLookupTableComponentCount(ChannelFiller.java:262)
   at loci.formats.ChannelFiller.setId(ChannelFiller.java:245)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
   at loci.formats.ChannelSeparator.setId(ChannelSeparator.java:238)
   at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
   at ome.formats.importer.ImportLibrary.open(ImportLibrary.java:245)
   at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:483)
   at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:223)
   at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:128)
   at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:366)
2011-01-31 11:44:20,276 657085     [      main] INFO         ome.formats.importer.ImportLibrary  - Exiting on error

Change History (4)

comment:1 Changed 13 years ago by cxallan

  • Status changed from new to accepted

comment:2 Changed 13 years ago by cxallan

  • Status changed from accepted to new

comment:3 Changed 13 years ago by cxallan

  • Resolution set to fixed
  • Status changed from new to closed

In [64c063948b79967e6cfd585106fb63036d49a41c/bioformats.git] fixed the problem in master (along with adding some additional sanity checks) and in [e3e0985f6e61aaa15c287cb1cd152bcb130b3f83/bioformats.git] merged the fix into the 4_2 branch.

comment:4 Changed 13 years ago by Chris Allan <callan@…>

  • Remaining Time set to 0

(In [64c063948b79967e6cfd585106fb63036d49a41c/bioformats.git]) Merged branch 'ticket4195' (Fixes #4195)

  • ticket4195: Ensure that on OMETiffReaderclose() readers for each plane are closed. try/finally for TIFF reader closure safety. try/finally for stream closure safety.
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