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
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)
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"