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Task #5426 (closed)

Opened 13 years ago

Closed 13 years ago

Bug: import cli WARNS on service cleanup

Reported by: jamoore 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

Either the OMEROMetadataStoreClient should be cleaned up before the Ice.Communicator or these messages should be DEBUG since there is nothing we can do about them:

~/git/dist $ bin/omero import -- --debug ALL
Using session 795f56a6-ef66-4172-82ed-10939a92163b (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', '795f56a6-ef66-4172-82ed-10939a92163b', '--debug', 'ALL']
2011-05-20 21:36:07,025 0          [      main] INFO          ome.formats.importer.ImportConfig  - OMERO Version: 4.3.0-DEV
2011-05-20 21:36:07,029 4          [      main] INFO          ome.formats.importer.ImportConfig  - Bioformats version: 4.3-DEV revision: 330dd7f date: 18 May 2011
2011-05-20 21:36:07,039 14         [      main] INFO   formats.importer.cli.CommandLineImporter  - Log levels -- Bio-Formats: DEBUG OMERO.importer: DEBUG
2011-05-20 21:36:07,039 14         [      main] DEBUG         ome.formats.importer.ImportConfig  - Loaded savedDirectory from User Preference Node: /ome/formats/importer
2011-05-20 21:36:07,361 336        [      main] INFO      ome.formats.importer.ImportCandidates  - Depth: 4 Metadata Level: MINIMUM
2011-05-20 21:36:07,362 337        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler  - SCANNING: Depth:0 Num:    1 Tot:  n/a File: ALL
2011-05-20 21:36:07,363 338        [      main] DEBUG     ome.formats.importer.cli.ErrorHandler  - SCANNING: Depth:0 Num:    1 Tot:    1 File: ALL
2011-05-20 21:36:07,363 338        [      main] INFO      ome.formats.importer.ImportCandidates  - 1 file(s) parsed into 0 group(s) with 0 call(s) to setId in 0ms. (2ms total) [0 unknowns]
2011-05-20 21:36:07,431 406        [      main] INFO       ome.formats.OMEROMetadataStoreClient  - Attempting initial SSL connection to gretzky.openmicroscopy.org.uk:4064
2011-05-20 21:36:08,881 1856       [      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 21:36:13,932 6907       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "795f56a6-ef66-4172-82ed-10939a92163b/86:24:41:e3:4bbecced:1300c8cb336:-79ffomero.api.RawFileStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:36:13,932 6907       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Ice.CommunicatorDestroyedException
2011-05-20 21:36:13,937 6912       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "795f56a6-ef66-4172-82ed-10939a92163b/86:24:41:e3:4bbecced:1300c8cb336:-79feomero.api.RawPixelsStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:36:13,937 6912       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Ice.CommunicatorDestroyedException
2011-05-20 21:36:13,938 6913       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing "795f56a6-ef66-4172-82ed-10939a92163b/86:24:41:e3:4bbecced:1300c8cb336:-79fdomero.api.ThumbnailStore" -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:36:13,938 6913       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Ice.CommunicatorDestroyedException
2011-05-20 21:36:13,939 6914       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Exception closing 795f56a6-ef66-4172-82ed-10939a92163b/fbff72e0-9885-4343-a8b7-85a2983c705bomero.api.MetadataStore -t:tcp -h 134.36.65.227 -p 34577
2011-05-20 21:36:13,939 6914       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Ice.CommunicatorDestroyedException
2011-05-20 21:36:13,939 6914       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - closing client session.
2011-05-20 21:36:13,939 6914       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - client closed.
2011-05-20 21:36:13,939 6914       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Logout called, shutting keep alive down.
2011-05-20 21:36:13,940 6915       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - keepalive shut down.

Change History (5)

comment:1 Changed 13 years ago by jmoore

  • Owner set to jmoore
  • Remaining Time set to 0.1
  • Sprint set to 2011-06-02 (13)
  • Status changed from new to accepted

Problem stems from the fact that usage() which is called when no imports are found calls System.exit(), at which point first the omero.clients shutdown thread gets to run (closing the connection) and then the CommandLineImporter shutdown thread runs, showing the exceptions.

comment:2 Changed 13 years ago by jmoore <josh@…>

  • Remaining Time changed from 0.1 to 0
  • Resolution set to fixed
  • Status changed from accepted to closed

(In [07edd5dac8bde8d07d5dd7324970591aea4e1674/ome.git] on branch develop) Better cleanup on 'No imports found' from CLI (Fix #5426)

comment:3 Changed 13 years ago by jmoore

  • Remaining Time changed from 0 to 0.25
  • Resolution fixed deleted
  • Status changed from closed to reopened

Similar warning print on Ctrl-C. Reopening.

^C2011-05-23 17:04:13,554 6968       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Communicator already closed; cannot close "12431afc-2b3f-45f2-b8ba-06ec18d6cfdb/86:24:41:e3:-29a44f12:1301cd98d14:-7dd9omero.api.RawFileStore" -t:tcp -h 134.36.65.227 -p 56421
2011-05-23 17:04:13,557 6971       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Communicator already closed; cannot close "12431afc-2b3f-45f2-b8ba-06ec18d6cfdb/86:24:41:e3:-29a44f12:1301cd98d14:-7dd8omero.api.RawPixelsStore" -t:tcp -h 134.36.65.227 -p 56421
2011-05-23 17:04:13,558 6972       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Communicator already closed; cannot close "12431afc-2b3f-45f2-b8ba-06ec18d6cfdb/86:24:41:e3:-29a44f12:1301cd98d14:-7dd7omero.api.ThumbnailStore" -t:tcp -h 134.36.65.227 -p 56421
2011-05-23 17:04:13,559 6973       [ Thread-12] WARN       ome.formats.OMEROMetadataStoreClient  - Communicator already closed; cannot close 12431afc-2b3f-45f2-b8ba-06ec18d6cfdb/8a55e316-c9f9-4067-8e22-44eae83af798omero.api.MetadataStore -t:tcp -h 134.36.65.227 -p 56421
2011-05-23 17:04:13,559 6973       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - closing client session.
2011-05-23 17:04:13,559 6973       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - client closed.
2011-05-23 17:04:13,559 6973       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - Logout called, shutting keep alive down.
2011-05-23 17:04:13,560 6974       [ Thread-12] DEBUG      ome.formats.OMEROMetadataStoreClient  - keepalive shut down.
Cancelled

comment:4 Changed 13 years ago by jmoore

  • Remaining Time changed from 0.25 to 0.1

Handling the WARN statements in the previous comment would most likely require a SignalHandler (or at least a static call to Runtime.addShutdownHook) so that cleanup could happen before the shutdown hook in omero.client. This seems too complicated for the moment. Instead, I'm going to reduce the log of the statements down to DEBUG to not confuse users, and let the SignalHandler that will be added for #5252 take care of calling logout on the OMEROMetadataStoreClient.

comment:5 Changed 13 years ago by jmoore <josh@…>

  • Remaining Time changed from 0.1 to 0
  • Resolution set to fixed
  • Status changed from reopened to closed

(In [57915cc1e8f409a3c62c5361c1ea4c14b3046252/ome.git] on branch develop) Changing DEBUG to WARN on CommunicatorDestroyedException (Fix #5426)

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