Task #4195 (closed)
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.
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
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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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.