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Task #12530 (new)

Opened 10 years ago

Last modified 10 years ago

Bug: in 5.1 in-place ln_s dies with "Permission denied" on file — at Initial Version

Reported by: mtbcarroll Owned by: jamoore
Priority: critical Milestone: 5.1.0-m1
Component: Import Version: n.a.
Keywords: n.a. Cc:
Resources: n.a. Referenced By: n.a.
References: n.a. Remaining Time: n.a.
Sprint: n.a.

Description

With 5.0 latest (remotes/origin/dev_5_0),

$ omero import -- --transfer=ln_s test_images_good/peg/2kx2k.jpg
Previously logged in to localhost:4064 as root
Server: [localhost]
Username: [root]user-2
Password:
Created session 6ad13c4f-92ca-4fcf-a78a-dd4c7ed14d6b (user-2@localhost:4064). Idle timeout: 10.0 min. Current group: private-1
2014-08-20 09:10:48,830 179        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.0.4-ice34-SNAPSHOT
2014-08-20 09:10:48,843 192        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.0.4-ice34-SNAPSHOT revision: 5f987c0 date: 20 August 2014
2014-08-20 09:10:48,847 196        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2014-08-20 09:10:48,850 199        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-08-20 09:10:49,043 392        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-08-20 09:10:49,752 1101       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 704ms. (709ms total) [0 unknowns]
2014-08-20 09:10:49,964 1313       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2014-08-20 09:10:50,405 1754       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.0.4
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.0.4-ice34-SNAPSHOT
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 1.7.0_65
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2014-08-20 09:10:50,992 2341       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.2.0-4-amd64
2014-08-20 09:10:51,092 2441       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-08-20 09:10:52,244 3593       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-08-20 09:10:52,268 3617       [      main] INFO   s.importer.transfers.SymlinkFileTransfer - Transferring /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg...
2014-08-20 09:10:52,373 3722       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg
2014-08-20 09:10:52,489 3838       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg
2014-08-20 09:10:52,681 4030       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_END
2014-08-20 09:10:54,060 5409       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_IMPORTED Step: 1 of 5  Logfile: 24
2014-08-20 09:10:54,661 6010       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - PIXELDATA_PROCESSED Step: 2 of 5  Logfile: 24
2014-08-20 09:10:55,928 7277       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - THUMBNAILS_GENERATED Step: 3 of 5  Logfile: 24
2014-08-20 09:10:55,986 7335       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - METADATA_PROCESSED Step: 4 of 5  Logfile: 24
2014-08-20 09:10:56,027 7376       [l.Client-1] INFO   ormats.importer.cli.LoggingImportMonitor - OBJECTS_RETURNED Step: 5 of 5  Logfile: 24
2014-08-20 09:10:56,189 7538       [l.Client-0] INFO   ormats.importer.cli.LoggingImportMonitor - IMPORT_DONE Imported file: /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg
Imported pixels:
1
Other imported objects:
Fileset:1
Image:1
2014-08-20 09:10:56,189 7538       [l.Client-0] INFO      ome.formats.importer.cli.ErrorHandler - Number of errors: 0

With 5.1 latest (remotes/origin/develop),

$ omero import -- --transfer=ln_s test_images_good/jpeg/2kx2k.jpg
Previously logged in to localhost:4064 as root
Server: [localhost]
Username: [root]user-2
Password:
Created session 91407559-0dc8-4e96-a485-a752dae1964e (user-2@localhost:4064). Idle timeout: 10.0 min. Current group: private-1
2014-08-20 09:02:55,368 187        [      main] INFO          ome.formats.importer.ImportConfig - OMERO Version: 5.1.0-m0.5-ice34-SNAPSHOT
2014-08-20 09:02:55,382 201        [      main] INFO          ome.formats.importer.ImportConfig - Bioformats version: 5.1.0-m0.5-ice34-SNAPSHOT revision: 87fbabc date: 20 August 2014
2014-08-20 09:02:55,386 205        [      main] INFO   formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
2014-08-20 09:02:55,389 208        [      main] INFO   formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats: ERROR OMERO.importer: INFO
2014-08-20 09:02:55,603 422        [      main] INFO      ome.formats.importer.ImportCandidates - Depth: 4 Metadata Level: MINIMUM
2014-08-20 09:02:56,269 1088       [      main] INFO      ome.formats.importer.ImportCandidates - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 656ms. (665ms total) [0 unknowns]
2014-08-20 09:02:57,496 2315       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Attempting initial SSL connection to localhost:4064
2014-08-20 09:02:57,938 2757       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Insecure connection requested, falling back
2014-08-20 09:02:58,596 3415       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Server: 5.1.0
2014-08-20 09:02:58,596 3415       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Client: 5.1.0-m0.5-ice34-SNAPSHOT
2014-08-20 09:02:58,596 3415       [      main] INFO       ome.formats.OMEROMetadataStoreClient - Java Version: 1.7.0_65
2014-08-20 09:02:58,597 3416       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Name: Linux
2014-08-20 09:02:58,597 3416       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Arch: amd64
2014-08-20 09:02:58,597 3416       [      main] INFO       ome.formats.OMEROMetadataStoreClient - OS Version: 3.2.0-4-amd64
2014-08-20 09:02:58,766 3585       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
2014-08-20 09:02:59,661 4480       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
2014-08-20 09:02:59,679 4498       [      main] INFO   s.importer.transfers.SymlinkFileTransfer - Transferring /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg...
2014-08-20 09:02:59,813 4632       [      main] INFO   ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg
2014-08-20 09:03:00,074 4893       [      main] ERROR     ome.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /home/mtbc/ome/data_repo/test_images_good/jpeg/2kx2k.jpg
omero.ResourceError: null
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_65]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_65]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_65]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:526) ~[na:1.7.0_65]
	at java.lang.Class.newInstance(Class.java:374) ~[na:1.7.0_65]
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]
	at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]
	at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183) ~[blitz.jar:na]
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527) ~[blitz.jar:na]
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500) ~[blitz.jar:na]
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113) ~[blitz.jar:na]
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:111) ~[blitz.jar:na]
	at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:81) ~[blitz.jar:na]
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) [blitz.jar:na]
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) [blitz.jar:na]
	at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) [blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:731) [blitz.jar:na]
2014-08-20 09:03:00,079 4898       [      main] ERROR        ome.formats.importer.ImportLibrary - Error on import: /home/mtbc/var/omero/ManagedRepository/user-2_3/2014-08/20/09-02-58.928/2kx2k.jpg (Permission denied)
omero.ResourceError: null
	at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.7.0_65]
	at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:57) ~[na:1.7.0_65]
	at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.7.0_65]
	at java.lang.reflect.Constructor.newInstance(Constructor.java:526) ~[na:1.7.0_65]
	at java.lang.Class.newInstance(Class.java:374) ~[na:1.7.0_65]
	at IceInternal.BasicStream$DynamicUserExceptionFactory.createAndThrow(BasicStream.java:2142) ~[ice.jar:na]
	at IceInternal.BasicStream.throwException(BasicStream.java:1564) ~[ice.jar:na]
	at IceInternal.Outgoing.throwUserException(Outgoing.java:443) ~[ice.jar:na]
	at omero.api._RawFileStoreDelM.save(_RawFileStoreDelM.java:183) ~[blitz.jar:na]
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:527) ~[blitz.jar:na]
	at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:500) ~[blitz.jar:na]
	at ome.formats.importer.transfers.TransferState.save(TransferState.java:113) ~[blitz.jar:na]
	at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:111) ~[blitz.jar:na]
	at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:81) ~[blitz.jar:na]
	at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:414) ~[blitz.jar:na]
	at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:477) ~[blitz.jar:na]
	at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:271) ~[blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:216) [blitz.jar:na]
	at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:731) [blitz.jar:na]
2014-08-20 09:03:00,079 4898       [      main] INFO         ome.formats.importer.ImportLibrary - Exiting on error

Change History (1)

Changed 10 years ago by mtbcarroll

5.1 failed import

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