[ome-users] In-place import from CIFS share fails with permission error
Brian Dunnette
dunn0172 at umn.edu
Wed Jan 10 17:38:26 GMT 2018
Greetings-
We're attempting to do an in-place import of SVS files from a CIFS share
into our new OMERO 5.3.5 install, and followed the in-place import guide
(set up the inplace_user user & group, gave them ownership of the
ManagedRepository, verified that inplace_user can create a directory in
ManagedRepository and the omero system user can delete it).
However, when trying to import as inplace_user, I get the following
permissions error:
[inplace_user at nunstudy-omero ~]$ cd /mnt/ahc-ns/Pathology/NunStudy/NS-1137/
>
> [inplace_user at nunstudy-omero NS-1137]$ omero import -- --transfer=ln_s
> 561.svs
>
> Previous session expired for dunn0172admin on localhost:4064
>
> Server: [localhost:4064]
>
> Username: [dunn0172admin]
>
> Password:
>
> Created session b9d154f4-0db3-4d23-9cfc-3591f3915049
> (dunn0172admin at localhost:4064). Idle timeout: 10 min. Current group: Nun
> Study
>
> 11:15:04.547 [main] INFO ome.formats.importer.ImportConfig - OMERO
> Version: 5.3.5-ice36-b73
>
> 11:15:04.567 [main] INFO ome.formats.importer.ImportConfig - Bioformats
> version: 5.5.3 revision: 7bed1b04d071667d7b8a2e8c5d42f05fbfc07ecc date: 5
> July 2017
>
> 11:15:04.630 [main] INFO o.f.importer.cli.CommandLineImporter - Setting
> transfer to ln_s
>
> 11:15:04.631 [main] DEBUG o.f.i.transfers.AbstractFileTransfer - Loading
> file transfer class ln_s
>
> 11:15:04.635 [main] INFO o.f.importer.cli.CommandLineImporter - Log
> levels -- Bio-Formats: null OMERO.importer: null
>
> 11:15:04.778 [main] DEBUG ome.formats.importer.ImportConfig - Loaded
> savedDirectory from ome.formats.importer.util.IniFileLoader at 27c20538
>
> 11:15:04.779 [main] DEBUG ome.formats.importer.ImportConfig - Loaded
> savedDirectory from default
>
> 11:15:04.816 [main] DEBUG loci.formats.ClassList - Could not find
> loci.formats.in.SlideBook6Reader
>
> java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader
>
> at java.net.URLClassLoader.findClass(URLClassLoader.java:381)
> ~[na:1.8.0_151]
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:424)
> ~[na:1.8.0_151]
>
> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335)
> ~[na:1.8.0_151]
>
> at java.lang.ClassLoader.loadClass(ClassLoader.java:357)
> ~[na:1.8.0_151]
>
> at java.lang.Class.forName0(Native Method) ~[na:1.8.0_151]
>
> at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_151]
>
> at loci.formats.ClassList.parseLine(ClassList.java:196)
> [formats-api.jar:5.5.3]
>
> at loci.formats.ClassList.parseFile(ClassList.java:258)
> [formats-api.jar:5.5.3]
>
> at loci.formats.ClassList.<init>(ClassList.java:138)
> [formats-api.jar:5.5.3]
>
> at loci.formats.ClassList.<init>(ClassList.java:122)
> [formats-api.jar:5.5.3]
>
> at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:79)
> [formats-api.jar:5.5.3]
>
> at ome.formats.importer.OMEROWrapper.createReader(OMEROWrapper.java:131)
> [blitz.jar:na]
>
> at ome.formats.importer.OMEROWrapper.<init>(OMEROWrapper.java:93)
> [blitz.jar:na]
>
> at ome.formats.importer.OMEROWrapper.<init>(OMEROWrapper.java:89)
> [blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImporter.java:141)
> [blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:955)
> [blitz.jar:na]
>
> 11:15:05.148 [main] DEBUG o.s.nativelib.NativeLibraryUtil - processor is
> INTEL_64 os.arch is amd64
>
> 11:15:05.148 [main] DEBUG o.s.nativelib.NativeLibraryUtil - architecture
> is LINUX_64 os.name is linux
>
> 11:15:05.157 [main] DEBUG o.s.nativelib.NativeLibraryUtil - architecture
> is LINUX_64 os.name is linux
>
> 11:15:05.157 [main] DEBUG o.s.nativelib.NativeLibraryUtil - platform
> specific path is META-INF/lib/linux_64/
>
> 11:15:05.157 [main] DEBUG o.scijava.nativelib.BaseJniExtractor -
> mappedLib is libturbojpeg.so
>
> 11:15:05.157 [main] DEBUG o.scijava.nativelib.BaseJniExtractor - URL is
> jar:file:/home/omero/OMERO.server-5.3.5-ice36-b73/lib/
> client/turbojpeg.jar!/META-INF/lib/linux_64/libturbojpeg.so
>
> 11:15:05.157 [main] DEBUG o.scijava.nativelib.BaseJniExtractor - URL path
> is file:/home/omero/OMERO.server-5.3.5-ice36-b73/lib/client/
> turbojpeg.jar!/META-INF/lib/linux_64/libturbojpeg.so
>
> 11:15:05.160 [main] DEBUG o.scijava.nativelib.BaseJniExtractor -
> Extracting 'jar:file:/home/omero/OMERO.server-5.3.5-ice36-b73/lib/
> client/turbojpeg.jar!/META-INF/lib/linux_64/libturbojpeg.so' to '/tmp/
> libturbojpeg3509993838924317593.so'
>
> 11:15:05.190 [main] INFO o.formats.importer.ImportCandidates - Depth: 4
> Metadata Level: MINIMUM
>
> 11:15:05.198 [main] DEBUG o.formats.importer.cli.ErrorHandler - SCANNING:
> Depth:0 Num: 1 Tot: n/a File: 561.svs
>
> 11:15:05.199 [main] DEBUG loci.common.Location - Location.mapFile:
> embedded-stream.raw -> null
>
> 11:15:05.200 [main] DEBUG loci.common.Location - Location.mapFile:
> embedded-stream.raw -> null
>
> 11:15:05.208 [main] DEBUG loci.formats.Memoizer - skipping memo: no
> directory given
>
> 11:15:05.220 [main] DEBUG loci.common.NIOByteBufferProvider - Using
> mapped byte buffer? false
>
> 11:15:12.777 [main] INFO loci.formats.ImageReader - SVSReader
> initializing /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:12.778 [main] DEBUG loci.formats.FormatHandler - SVSReader
> initializing /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:12.778 [main] DEBUG loci.formats.FormatHandler -
> loci.formats.in.SVSReader.initFile(/mnt/ahc-ns/Pathology/NunStudy/NS-1137/
> 561.svs)
>
> 11:15:12.785 [main] INFO loci.formats.in.MinimalTiffReader - Reading IFDs
>
> 11:15:12.837 [main] INFO loci.formats.in.MinimalTiffReader - Populating
> metadata
>
> 11:15:12.929 [main] DEBUG loci.formats.in.MinimalTiffReader - Found IFD
> with JPEG 2000 compression
>
> 11:15:12.932 [main] INFO l.formats.in.JPEG2000MetadataParser - Unknown
> JPEG 2000 box 0x2f00 at 16
>
> 11:15:12.932 [main] INFO l.formats.in.JPEG2000MetadataParser - File is a
> raw codestream not a JP2.
>
> 11:15:12.973 [main] DEBUG loci.common.services.ServiceFactory - Loaded
> properties from: services.properties
>
> 11:15:12.974 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.POIService and implementation
> class loci.formats.services.POIServiceImpl
>
> 11:15:12.975 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.MDBService and implementation
> class loci.formats.services.MDBServiceImpl
>
> 11:15:12.975 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.JPEGTurboService and
> implementation class loci.formats.services.JPEGTurboServiceImpl
>
> 11:15:12.976 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.JAIIIOService and
> implementation class loci.formats.services.JAIIIOServiceImpl
>
> 11:15:12.977 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.WlzService and implementation
> class loci.formats.services.WlzServiceImpl
>
> 11:15:12.977 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.JHDFService and implementation
> class loci.formats.services.JHDFServiceImpl
>
> 11:15:12.978 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.NetCDFService and
> implementation class loci.formats.services.NetCDFServiceImpl
>
> 11:15:12.979 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.EXIFService and implementation
> class loci.formats.services.EXIFServiceImpl
>
> 11:15:12.979 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.MetakitService and
> implementation class loci.formats.services.MetakitServiceImpl
>
> 11:15:12.980 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.LuraWaveService and
> implementation class loci.formats.services.LuraWaveServiceImpl
>
> 11:15:12.983 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.OMEXMLService and
> implementation class loci.formats.services.OMEXMLServiceImpl
>
> 11:15:12.984 [main] DEBUG loci.common.services.ServiceFactory - Added
> interface interface loci.formats.services.JPEGXRService and
> implementation class loci.formats.services.JPEGXRServiceImpl
>
> 11:15:13.012 [main] INFO loci.formats.in.BaseTiffReader - Populating OME
> metadata
>
> 11:15:13.014 [main] DEBUG loci.formats.Memoizer - start[1515604505207]
> time[7807] tag[loci.formats.Memoizer.setId]
>
> 11:15:13.081 [main] DEBUG loci.common.Location - Location.mapFile:
> embedded-stream.raw -> null
>
> 11:15:13.082 [main] DEBUG loci.common.Location - Location.mapFile:
> embedded-stream.raw -> null
>
> 11:15:13.087 [main] DEBUG o.formats.importer.cli.ErrorHandler - SCANNING:
> Depth:0 Num: 1 Tot: 1 File: 561.svs
>
> 11:15:13.094 [main] INFO o.formats.importer.ImportCandidates - 1 file(s)
> parsed into 1 group(s) with 1 call(s) to setId in 7883ms. (7903ms total) [0
> unknowns]
>
> 11:15:13.255 [main] ERROR ome.system.UpgradeCheck - Error reading from
> url: http://upgrade.openmicroscopy.org.uk?version=5.3.5-ice36-
> b73;os.name=Linux;os.arch=amd64;os.version=3.10.0-693.5.
> 2.el7.x86_64;java.runtime.version=1.8.0_151-b12;java.vm.
> vendor=Oracle+Corporation "Connection refused (Connection refused)"
>
> 11:15:13.369 [main] INFO ome.formats.OMEROMetadataStoreClient -
> Attempting initial SSL connection to localhost:4064
>
> 11:15:13.901 [main] INFO ome.formats.OMEROMetadataStoreClient - Insecure
> connection requested, falling back
>
> 11:15:13.981 [main] DEBUG ome.formats.OMEROMetadataStoreClient - closing
> client session.
>
> 11:15:13.992 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client
> closed.
>
> 11:15:14.635 [main] INFO ome.formats.OMEROMetadataStoreClient - Server:
> 5.3.5
>
> 11:15:14.636 [main] INFO ome.formats.OMEROMetadataStoreClient - Client:
> 5.3.5-ice36-b73
>
> 11:15:14.636 [main] INFO ome.formats.OMEROMetadataStoreClient - Java
> Version: 1.8.0_151
>
> 11:15:14.636 [main] INFO ome.formats.OMEROMetadataStoreClient - OS Name:
> Linux
>
> 11:15:14.636 [main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch:
> amd64
>
> 11:15:14.636 [main] INFO ome.formats.OMEROMetadataStoreClient - OS
> Version: 3.10.0-693.5.2.el7.x86_64
>
> 11:15:14.776 [main] DEBUG ome.formats.importer.ImportLibrary - Main file:
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:14.777 [main] DEBUG ome.formats.importer.ImportLibrary - Used files
> before:
>
> 11:15:14.777 [main] DEBUG ome.formats.importer.ImportLibrary -
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:14.780 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILESET_UPLOAD_PREPARATION
>
> 11:15:14.806 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized
> current operating system as being Linux
>
> 11:15:15.480 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILESET_UPLOAD_START
>
> 11:15:15.507 [main] INFO o.f.i.transfers.SymlinkFileTransfer -
> Transferring /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...
>
> 11:15:15.718 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:15.797 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION:
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 11:15:15.798 [main] ERROR o.formats.importer.cli.ErrorHandler -
> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> java.lang.RuntimeException:
>
> ---------------------------------------------------
>
> Check failed: /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-15-14.918/561.svs
> cannot be modified locally!
>
> You likely do not have access to the ManagedRepository for in-place import.
>
> Aborting...
>
> ---------------------------------------------------
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> failLocationCheck(AbstractExecFileTransfer.java:150) ~[blitz.jar:na]
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> checkLocation(AbstractExecFileTransfer.java:132) ~[blitz.jar:na]
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> transfer(AbstractExecFileTransfer.java:63) ~[blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437)
> [blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511)
> [blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
> [blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289)
> [blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958)
> [blitz.jar:na]
>
> 11:15:15.799 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
> FILE_UPLOAD_ERROR
>
> 11:15:15.799 [main] ERROR ome.formats.importer.ImportLibrary - Error on
> import
>
> java.lang.RuntimeException:
>
> ---------------------------------------------------
>
> Check failed: /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-15-14.918/561.svs
> cannot be modified locally!
>
> You likely do not have access to the ManagedRepository for in-place import.
>
> Aborting...
>
> ---------------------------------------------------
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> failLocationCheck(AbstractExecFileTransfer.java:150) ~[blitz.jar:na]
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> checkLocation(AbstractExecFileTransfer.java:132) ~[blitz.jar:na]
>
> at ome.formats.importer.transfers.AbstractExecFileTransfer.
> transfer(AbstractExecFileTransfer.java:63) ~[blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437)
> ~[blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511)
> ~[blitz.jar:na]
>
> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
> ~[blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289)
> [blitz.jar:na]
>
> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958)
> [blitz.jar:na]
>
> 11:15:15.799 [main] INFO ome.formats.importer.ImportLibrary - Exiting on
> error
>
> ==> Summary
>
> 0 files uploaded, 0 filesets created, 0 images imported, 1 error in
> 0:00:01.024
>
> 11:15:15.848 [main] DEBUG ome.formats.OMEROMetadataStoreClient - closing
> client session.
>
> 11:15:15.861 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client
> closed.
>
> 11:15:15.861 [main] DEBUG ome.formats.OMEROMetadataStoreClient - Logout
> called, shutting keep alive down.
>
> 11:15:15.861 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
> keepalive shut down.
>
> !! 01/10/18 11:15:16.037 error: communicator not destroyed during global
> destruction.
>
On a hunch, I tried importing as the omero system user - this seemed to go
a bit further along (20 seconds vs. 1), but resulted in a different error:
[omero at nunstudy-omero NS-1137]$ omero import -- --transfer=ln_s 561.svs
>
> Previous session expired for dunn0172admin on localhost:4064
>
> Server: [localhost:4064]
>
> Username: [dunn0172admin]
>
> Password:
>
> Created session f8b21c70-6cfa-45e8-85e8-1902e965924b
> (dunn0172admin at localhost:4064). Idle timeout: 10 min. Current group: Nun
> Study
>
> 2018-01-10 11:19:51,462 316 [ main] INFO ome.formats.importer.ImportConfig
> - OMERO Version: 5.3.5-ice36-b73
>
> 2018-01-10 11:19:51,480 334 [ main] INFO ome.formats.importer.ImportConfig
> - Bioformats version: 5.5.3 revision:
> 7bed1b04d071667d7b8a2e8c5d42f05fbfc07ecc date: 5 July 2017
>
> 2018-01-10 11:19:51,534 388 [ main] INFO
> formats.importer.cli.CommandLineImporter - Setting transfer to ln_s
>
> 2018-01-10 11:19:51,538 392 [ main] INFO
> formats.importer.cli.CommandLineImporter - Log levels -- Bio-Formats:
> ERROR OMERO.importer: INFO
>
> 2018-01-10 11:19:51,964 818 [ main] INFO ome.formats.importer.ImportCandidates
> - Depth: 4 Metadata Level: MINIMUM
>
> 2018-01-10 11:19:53,038 1892 [ main] INFO ome.formats.importer.ImportCandidates
> - 1 file(s) parsed into 1 group(s) with 1 call(s) to setId in 1048ms.
> (1074ms total) [0 unknowns]
>
> 2018-01-10 11:19:53,189 2043 [ main] ERROR ome.system.UpgradeCheck
> - Error reading from url:
> http://upgrade.openmicroscopy.org.uk?version=5.3.5-ice36-b73;os.name=Linux;os.arch=amd64;os.version=3.10.0-693.5.2.el7.x86_64;java.runtime.version=1.8.0_151-b12;java.vm.vendor=Oracle+Corporation
> "Connection refused (Connection refused)"
>
> 2018-01-10 11:19:53,256 2110 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - Attempting initial SSL connection to localhost:4064
>
> 2018-01-10 11:19:53,755 2609 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - Insecure connection requested, falling back
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - Server: 5.3.5
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - Client: 5.3.5-ice36-b73
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - Java Version: 1.8.0_151
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - OS Name: Linux
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - OS Arch: amd64
>
> 2018-01-10 11:19:54,073 2927 [ main] INFO ome.formats.OMEROMetadataStoreClient
> - OS Version: 3.10.0-693.5.2.el7.x86_64
>
> 2018-01-10 11:19:54,170 3024 [ main] INFO
> ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION
>
> 2018-01-10 11:19:54,602 3456 [ main] INFO
> ormats.importer.cli.LoggingImportMonitor - FILESET_UPLOAD_START
>
> 2018-01-10 11:19:54,623 3477 [ main] INFO
> s.importer.transfers.SymlinkFileTransfer - Transferring
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...
>
> 2018-01-10 11:19:54,758 3612 [ main] INFO
> ormats.importer.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED:
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> 2018-01-10 11:20:14,642 23496 [ main] ERROR ome.formats.importer.cli.ErrorHandler
> - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> omero.ResourceError: null
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method) ~[na:1.8.0_151]
>
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> ~[na:1.8.0_151]
>
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> ~[na:1.8.0_151]
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> ~[na:1.8.0_151]
>
> at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_151]
>
> at
> IceInternal.BasicStream.createUserException(BasicStream.java:2779)
> ~[ice.jar:na]
>
> at IceInternal.BasicStream.access$300(BasicStream.java:14)
> ~[ice.jar:na]
>
> at
> IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298)
> ~[ice.jar:na]
>
> at IceInternal.BasicStream.throwException(BasicStream.java:2291)
> ~[ice.jar:na]
>
> at
> IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
> ~[ice.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.end_save(RawFileStorePrxHelper.java:724)
> ~[blitz.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:611)
> ~[blitz.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:598)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.TransferState.save(TransferState.java:128)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:114)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:70)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437)
> [blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511)
> [blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
> [blitz.jar:na]
>
> at
> ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289)
> [blitz.jar:na]
>
> at
> ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958)
> [blitz.jar:na]
>
> 2018-01-10 11:20:14,648 23502 [ main] ERROR ome.formats.importer.ImportLibrary
> - Error on import: cannot flush
> /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-19-54.269/561.svs:
> java.io.IOException: Permission denied
>
> omero.ResourceError: null
>
> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native
> Method) ~[na:1.8.0_151]
>
> at
> sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
> ~[na:1.8.0_151]
>
> at
> sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45)
> ~[na:1.8.0_151]
>
> at java.lang.reflect.Constructor.newInstance(Constructor.java:423)
> ~[na:1.8.0_151]
>
> at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_151]
>
> at
> IceInternal.BasicStream.createUserException(BasicStream.java:2779)
> ~[ice.jar:na]
>
> at IceInternal.BasicStream.access$300(BasicStream.java:14)
> ~[ice.jar:na]
>
> at
> IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298)
> ~[ice.jar:na]
>
> at IceInternal.BasicStream.throwException(BasicStream.java:2291)
> ~[ice.jar:na]
>
> at
> IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399)
> ~[ice.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.end_save(RawFileStorePrxHelper.java:724)
> ~[blitz.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:611)
> ~[blitz.jar:na]
>
> at
> omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:598)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.TransferState.save(TransferState.java:128)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:114)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:70)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289)
> ~[blitz.jar:na]
>
> at
> ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289)
> [blitz.jar:na]
>
> at
> ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958)
> [blitz.jar:na]
>
> 2018-01-10 11:20:14,648 23502 [ main] INFO ome.formats.importer.ImportLibrary
> - Exiting on error
>
> ==> Summary
>
> 0 files uploaded, 0 filesets created, 0 images imported, 1 error in
> 0:00:20.483
>
> !! 01/10/18 11:20:14.775 error: communicator not destroyed during global
> destruction.
>
>
Any thoughts as to why this is failing, or how/where the permissions should
be corrected?
If it helps any, here are the permissions on the original file and the link
created during import:
> [omero at nunstudy-omero NS-1137]$ ls -ltrad
> /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-22-20.587/561.svs
>
> lrwxrwxrwx 1 omero inplace_user 46 Jan 10 11:22
> /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-22-20.587/561.svs ->
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
[omero at nunstudy-omero NS-1137]$ ls -ltrad
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
> -rwxrwxrwx 1 omero inplace_user 342957409 Feb 17 2009
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>
Thanks much,
Brian Dunnette
Digital Imaging & Info Tech
Lab Medicine and Pathology <http://pathology.umn.edu>
University of Minnesota
dunn0172 at umn.edu
(612) 424-8187 (Mobile)
(612) 624-6176 (Office)
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