Warning: Can't synchronize with repository "(default)" (/home/git/ome.git does not appear to be a Git repository.). Look in the Trac log for more information.
Notice: In order to edit this ticket you need to be either: a Product Owner, The owner or the reporter of the ticket, or, in case of a Task not yet assigned, a team_member"

Task #5425 (closed)

Opened 13 years ago

Closed 13 years ago

BUG: --debug ALL from CLI leads to error

Reported by: omero-qa Owned by: jamoore
Priority: minor Milestone: OMERO-Beta4.3
Component: Import Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: 0.0d
Sprint: 2011-06-02 (13)

Description

​http://qa.openmicroscopy.org.uk/qa/feedback/3748/

Comment: Sent from CLI

java.io.FileNotFoundException: /opt/omero/OMERO.server-Beta-4.2.3-DEV-cf8a386a/ALL (No such file or directory)
	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.formats.ImageReader.getReader(ImageReader.java:148)
	at loci.formats.ImageReader.setId(ImageReader.java:650)
	at loci.formats.ReaderWrapper.setId(ReaderWrapper.java:480)
	at loci.formats.ChannelFiller.setId(ChannelFiller.java:244)
	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.ImportCandidates.singleFile(ImportCandidates.java:406)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:573)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:370)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:228)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:179)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:74)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:365)

Change History (6)

comment:1 Changed 13 years ago by jmoore

  • Cc HMS-support@… removed
  • Component changed from from QA to Import
  • Milestone changed from Unscheduled to OMERO-Beta4.3

comment:2 Changed 13 years ago by jmoore

The "--debug" argument without the equal sign ("--debug=ALL") is be interpreted as part of the bin/omero (i.e. Python) command line, rather than as part of the arguments for the Java process. All that's left is the "ALL"

~/git/dist $ bin/omero import --debug ALL
...
2011-05-20 20:51:54,001 311        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler  - SCANNING: Depth:0 Num:    1 Tot:  n/a File: ALL
java.io.FileNotFoundException: /Users/moore/GlencoeSoftware.git/git/omero.git/dist/ALL (No such file or directory)
	at java.io.RandomAccessFile.open(Native Method)
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
...
2011-05-20 20:51:54,011 321        [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - FILE_EXCEPTION: /Users/moore/GlencoeSoftware.git/git/omero.git/dist/ALL
java.io.FileNotFoundException: /Users/moore/GlencoeSoftware.git/git/omero.git/dist/ALL (No such file or directory)
	at java.io.RandomAccessFile.open(Native Method)
	at java.io.RandomAccessFile.<init>(RandomAccessFile.java:212)
	at loci.common.NIOFileHandle.<init>(NIOFileHandle.java:100)
...
2011-05-20 20:51:54,013 323        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler  - SCANNING: Depth:0 Num:    1 Tot:    1 File: ALL
2011-05-20 20:51:54,014 324        [      main] INFO      ome.formats.importer.ImportCandidates  - 1 file(s) parsed into 0 group(s) with 1 call(s) to setId in 8ms. (15ms total) [0 unknowns]
2011-05-20 20:51:54,086 396        [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Attempting initial SSL connection to gretzky.openmicroscopy.org.uk:4064
2011-05-20 20:51:55,457 1767       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Insecure connection requested, falling back
No imports due to errors!
2011-05-20 20:52:00,524 6834       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - closing client session.
2011-05-20 20:52:00,590 6900       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - client closed.
2011-05-20 20:52:00,590 6900       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - Logout called, shutting keep alive down.
2011-05-20 20:52:00,591 6901       [      main] DEBUG      ome.formats.OMEROMetadataStoreClient  - keepalive shut down.
  • The FileNotFoundException may should be handled better (above all, it should not illicit user feedback).
  • The command line should "To the Right Thing".

comment:3 Changed 13 years ago by jmoore

Making the command line do the right thing is difficult, since it would require making the argument to "--debug" non-optional. Instead, the handling of the FileNotFoundException can be improved (see below). If the exception is too distracting, special handling can be added.

~/git/dist $ bin/omero import --report X
Using session 74b498a3-8558-4498-84a6-6a25a46153c6 (jmoore@gretzky.openmicroscopy.org.uk:4064). Idle timeout: 10.0 min. Current group: Swedlow Group
['ome.formats.importer.cli.CommandLineImporter', '-s', 'gretzky.openmicroscopy.org.uk', '-p', '4064', '-k', '74b498a3-8558-4498-84a6-6a25a46153c6', '--report', 'X']
2011-05-20 21:58:39,652 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.3.0-DEV
2011-05-20 21:58:39,657 5          [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.3-DEV revision: 330dd7f date: 18 May 2011
2011-05-20 21:58:39,667 15         [      main] INFO   formats.importer.cli.CommandLineImporter  - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2011-05-20 21:58:39,934 282        [      main] INFO      ome.formats.importer.ImportCandidates  - Depth: 4 Metadata Level: MINIMUM
2011-05-20 21:58:39,937 285        [      main] ERROR     ome.formats.importer.cli.ErrorHandler  - UNREADABLE_FILE: /Users/moore/GlencoeSoftware.git/git/omero.git/dist/X
java.io.FileNotFoundException: /Users/moore/GlencoeSoftware.git/git/omero.git/dist/X
	at ome.formats.importer.ImportCandidates.singleFile(ImportCandidates.java:398)
	at ome.formats.importer.ImportCandidates.handleFile(ImportCandidates.java:587)
	at ome.formats.importer.ImportCandidates.execute(ImportCandidates.java:371)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:229)
	at ome.formats.importer.ImportCandidates.<init>(ImportCandidates.java:180)
	at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:74)
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:374)
2011-05-20 21:58:39,938 286        [      main] INFO      ome.formats.importer.ImportCandidates  - 1 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (4ms total) [0 unknowns]
2011-05-20 21:58:40,006 354        [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Attempting initial SSL connection to gretzky.openmicroscopy.org.uk:4064
2011-05-20 21:58:41,319 1667       [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Insecure connection requested, falling back
No imports found

 Usage:  importer-cli [OPTION]... [DIR|FILE]... 
   or:   importer-cli [OPTION]... - 

Import any number of files into an OMERO instance.
If "-" is the only path, a list of files or directories 
is read from standard in. Directories will be searched for 
all valid imports.

Mandatory arguments:
  -s	OMERO server hostname
  -u	OMERO experimenter name (username)
  -w	OMERO experimenter password
  -k	OMERO session key (can be used in place of -u and -w)
  -f	Display the used files (does not require other mandatory arguments)

Optional arguments:
  -c	Continue importing after errors
  -a	Archive the original file on the server
  -l	Use the list of readers rather than the default
  -d	OMERO dataset Id to import image into
  -r	OMERO screen Id to import plate into
  -n	Image name to use
  -x	Image description to use
  -p	OMERO server port [defaults to 4064]
  -h	Display this help and exit

  --no_thumbnails	Do not perform thumbnailing after import
  --plate_name		Plate name to use
  --plate_description	Plate description to use
  --debug[=ALL|DEBUG|ERROR|FATAL|INFO|TRACE|WARN]	Turn debug logging on (optional level)
  --report		Report errors to the OME team
  --upload		Upload broken files with report
  --logs		Upload log file with report
  --email=...		Email for reported errors
 
ex. importer-cli -s localhost -u bart -w simpson -d 50 foo.tiff

Report bugs to <ome-users@lists.openmicroscopy.org.uk>
2011-05-20 21:58:47,977 8325       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "74b498a3-8558-4498-84a6-6a25a46153c6/86:24:41:e3:4bbecced:1300c8cb336:-79e9omero.api.RawFileStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:58:47,980 8328       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "74b498a3-8558-4498-84a6-6a25a46153c6/86:24:41:e3:4bbecced:1300c8cb336:-79e8omero.api.RawPixelsStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:58:47,981 8329       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "74b498a3-8558-4498-84a6-6a25a46153c6/86:24:41:e3:4bbecced:1300c8cb336:-79e7omero.api.ThumbnailStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:58:47,981 8329       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing 74b498a3-8558-4498-84a6-6a25a46153c6/f9f9e74a-74df-4da9-97d8-61bdcf42c7d1omero.api.MetadataStore -t:tcp -h 134.36.65.227 -p 34577
~/git/dist $ vi ../components/tools/OmeroImporter/src/ome/formats/importer/cli/CommandLineImporter.java

comment:4 Changed 13 years ago by jmoore

  • Remaining Time set to 0.25
  • Sprint set to 2011-06-02 (13)

comment:5 Changed 13 years ago by jmoore

  • Status changed from new to accepted

comment:6 Changed 13 years ago by jmoore <josh@…>

  • Remaining Time changed from 0.25 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [3f18063f1d0abc3982367e5308707cb312da8e51/ome.git] on branch develop) Add UNREADABLE_FILE event instead of FileNotFoundException (Fix #5425)

Note: See TracTickets for help on using tickets. You may also have a look at Agilo extensions to the ticket.

1.3.13-PRO © 2008-2011 Agilo Software all rights reserved (this page was served in: 0.67842 sec.)

© 2000-2014 University of Dundee & Open Microscopy Environment. Creative Commons Attribution 3.0 Unported License
OME source code is available under the GNU General public license or through commercial license from Glencoe Software

We're Hiring!