[ome-users] In-place import from CIFS share fails with permission error
Brian Dunnette
dunn0172 at umn.edu
Wed Jan 17 20:47:28 GMT 2018
Simon-
1. I've uploaded the relevant portion of Blitz-0.log (for 1/10-1/12) via
the QA site - hope this is of some help!
2. Yes, this seems to work fine - no error messages when cat-ing the SVS
file as the omero user.
3. I've set the mount permissions to read-only as you suggested - it seems
to read the file data, but still ends with the "cannot flush" error:
[inplace_user at nunstudy-omero ~]$ ls -la
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/
> total 15180800
> dr-xr-xr-x 2 omero inplace_user 0 Jan 10 11:16 .
> dr-xr-xr-x 2 omero inplace_user 0 Sep 14 2015 ..
> -r--r--r-- 1 omero inplace_user 342957409 Feb 17 2009 561.svs
>
> [inplace_user at nunstudy-omero ~]$ omero import -- --transfer=ln_s
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> ...
> 14:42:40.573 [main] DEBUG ome.formats.importer.ImportLibrary - Main file:
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> 14:42:40.574 [main] DEBUG ome.formats.importer.ImportLibrary - Used files
> before:
> 14:42:40.574 [main] DEBUG ome.formats.importer.ImportLibrary -
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> 14:42:40.577 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILESET_UPLOAD_PREPARATION
> 14:42:40.604 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized
> current operating system as being Linux
> 14:42:40.974 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILESET_UPLOAD_START
> 14:42:40.995 [main] INFO o.f.i.transfers.SymlinkFileTransfer -
> Transferring /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...
> 14:42:41.079 [main] INFO o.f.i.cli.LoggingImportMonitor -
> FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> 14:42:53.904 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
> FILE_UPLOAD_BYTES uploaded: 342957409 of: 342957409 bytes (ETA: 0' 0")
> 14:42:53.943 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION:
> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> 14:42:53.944 [main] ERROR o.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]
> 14:42:53.949 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
> FILE_UPLOAD_ERROR
> 14:42:53.949 [main] ERROR ome.formats.importer.ImportLibrary - Error on
> import: cannot flush
> /omero/ManagedRepository/dunn0172_102/2018-01/17/14-42-40.678/561.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]
> 14:42:53.949 [main] INFO ome.formats.importer.ImportLibrary - Exiting on
> error
>
Thanks,
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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On Wed, Jan 17, 2018 at 8:30 AM, Simon Li <spli at dundee.ac.uk> wrote:
> Hi Brian
>
> I've had a discussion with the rest of the team and came up with the
> following. Could you please:
>
> 1. Send us your server Blitz-0.log corresponding to the failed import,
> either copy the relevant lines or upload the whole file to
> https://www.openmicroscopy.org/qa2/qa/upload/
> This would be useful even if you've managed to get it working in the
> meantime, as we may be able to improve the error message seen on the client
> side.
>
> 2. Verify the omero operating system user can read the svs file on the
> CIFS mount, e.g. sudo -u omero cat /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
> > /dev/null
> If this fails it suggests the CIFS mount options are incorrect, or the
> file permissions on the remote filesystem are blocking access.
>
> 3. Change your CIFS mount options to read-only (
> dir_mode=0555,file_mode=0444) instead of 0777. CIFS allows you to mount
> files with a mode that does not match the mode on the remote filesystem so
> the system may think it has more privileges than are possible. This
> shouldn't matter, but we'd like to rule out a problem where OMERO thinks it
> has write access to a file even though it doesn't need it.
>
> Many thanks
>
> Simon
>
> On 16 January 2018 at 21:50, Brian Dunnette <dunn0172 at umn.edu> wrote:
>
>> Simon-
>>
>> An in-place (symlink) import of the same file from local disk works as
>> expected:
>>
>> [inplace_user at nunstudy-omero ~]$ omero import -- --transfer=ln_s
>>> /tmp/571.svs
>>> Using session 452a4118-5a9e-4fce-9cb6-23fc52509d30 (dunn0172 at localhost:4064).
>>> Id le timeout: 10 min. Current
>>> group: Nun Study
>>> 15:42:05.592 [main] INFO ome.formats.importer.ImportConfig - OMERO
>>> Version: 5.3 .5-ice36-b73
>>> 15:42:05.615 [main] INFO ome.formats.importer.ImportConfig -
>>> Bioformats version : 5.5.3
>>> revision: 7bed1b04d071667d7b8a2e8c5d42f05fbfc07ecc date: 5 July 2017
>>> 15:42:05.687 [main] INFO o.f.importer.cli.CommandLineImporter -
>>> Setting transfe r to ln_s
>>> 15:42:05.689 [main] DEBUG o.f.i.transfers.AbstractFileTransfer -
>>> Loading file tr ansfer class ln_s
>>> 15:42:05.693 [main] INFO o.f.importer.cli.CommandLineImporter - Log
>>> levels -- B io-Formats: null
>>> OMERO.importer: null
>>> 15:42:05.844 [main] DEBUG ome.formats.importer.ImportConfig - Loaded
>>> savedDirect ory from
>>> ome.formats.importer.util.IniFileLoader at 27c20538
>>> 15:42:05.844 [main] DEBUG ome.formats.importer.ImportConfig - Loaded
>>> savedDirect ory from default
>>> 15:42:05.866 [main] DEBUG loci.formats.ClassList - Could not find
>>> loci.formats.i n.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>(CommandL
>>> ineImport er.java:141)
>>> [blitz.jar:na]
>>> at ome.formats.importer.cli.CommandLineImporter.main(CommandLin
>>> eImporter .java:955) [blitz.jar:na]
>>> 15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUtil - processor
>>> is INTEL_6 4 os.arch is amd64
>>> 15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUtil -
>>> architecture is LINU X_64 os.name
>>> is linux
>>> 15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUtil -
>>> architecture is LINU X_64 os.name
>>> is linux
>>> 15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUtil - platform
>>> specific pa th is
>>> META-INF/lib/linux_64/
>>> 15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExtractor -
>>> mappedLib is li bturbojpeg.so
>>> 15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExtractor - URL is
>>> jar:file
>>> :/home/omero/OMERO.server-5.3.5-ice36-b73/lib/client/turbojp
>>> eg.jar!/META-INF/lib
>>> /linux_64/libturbojpeg.so
>>> 15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExtractor - URL
>>> path is fil
>>> e:/home/omero/OMERO.server-5.3.5-ice36-b73/lib/client/turboj
>>> peg.jar!/META-INF/li
>>> b/linux_64/libturbojpeg.so
>>> 15:42:06.219 [main] DEBUG o.scijava.nativelib.BaseJniExtractor -
>>> Extracting 'jar
>>> :file:/home/omero/OMERO.server-5.3.5-ice36-b73/lib/client/
>>> turbojpeg.jar!/META-IN
>>> F/lib/linux_64/libturbojpeg.so' to '/tmp/libturbojpeg896184319828
>>> 3737496.so'
>>> 15:42:06.242 [main] INFO o.formats.importer.ImportCandidates - Depth:
>>> 4 Metadat a Level: MINIMUM
>>> 15:42:06.244 [main] DEBUG o.formats.importer.cli.ErrorHandler -
>>> SCANNING: Depth: 0 Num: 1 Tot:
>>> n/a File: /tmp/571.svs
>>> 15:42:06.245 [main] DEBUG loci.common.Location - Location.mapFile:
>>> embedded-stre am.raw -> null
>>> 15:42:06.246 [main] DEBUG loci.common.Location - Location.mapFile:
>>> embedded-stre am.raw -> null
>>> 15:42:06.248 [main] DEBUG loci.formats.Memoizer - skipping memo: no
>>> directory gi ven
>>> 15:42:06.256 [main] DEBUG loci.common.NIOByteBufferProvider - Using
>>> mapped byte buffer? false
>>> 15:42:06.334 [main] INFO loci.formats.ImageReader - SVSReader
>>> initializing /tmp /571.svs
>>> 15:42:06.334 [main] DEBUG loci.formats.FormatHandler - SVSReader
>>> initializing /t mp/571.svs
>>> 15:42:06.334 [main] DEBUG loci.formats.FormatHandler -
>>> loci.formats.in.SVSReader
>>> .initFile(/tmp/571.svs)
>>> 15:42:06.336 [main] INFO loci.formats.in.MinimalTiffReader - Reading
>>> IFDs
>>> 15:42:06.340 [main] INFO loci.formats.in.MinimalTiffReader -
>>> Populating metadat a
>>> 15:42:06.425 [main] DEBUG loci.formats.in.MinimalTiffReader - Found IFD
>>> with JPE G 2000 compression
>>> 15:42:06.427 [main] INFO l.formats.in.JPEG2000MetadataParser - Unknown
>>> JPEG 200 0 box 0x2f00 at 16
>>> 15:42:06.428 [main] INFO l.formats.in.JPEG2000MetadataParser - File is
>>> a raw co destream not a JP2.
>>> 15:42:06.447 [main] DEBUG loci.common.services.ServiceFactory - Loaded
>>> propertie s from:
>>> services.properties
>>> 15:42:06.448 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.POIService and implementation class
>>> loci.formats
>>> .services.POIServiceImpl
>>> 15:42:06.448 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.MDBService and implementation class
>>> loci.formats
>>> .services.MDBServiceImpl
>>> 15:42:06.448 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.JPEGTurboService and implementation class
>>> loci.f
>>> ormats.services.JPEGTurboServiceImpl
>>> 15:42:06.449 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.JAIIIOService and implementation class
>>> loci.form
>>> ats.services.JAIIIOServiceImpl
>>> 15:42:06.450 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.WlzService and implementation class
>>> loci.formats
>>> .services.WlzServiceImpl
>>> 15:42:06.451 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.JHDFService and implementation class
>>> loci.format
>>> s.services.JHDFServiceImpl
>>> 15:42:06.451 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.NetCDFService and implementation class
>>> loci.form
>>> ats.services.NetCDFServiceImpl
>>> 15:42:06.452 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.EXIFService and implementation class
>>> loci.format
>>> s.services.EXIFServiceImpl
>>> 15:42:06.452 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.MetakitService and implementation class
>>> loci.for
>>> mats.services.MetakitServiceImpl
>>> 15:42:06.453 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.LuraWaveService and implementation class loci.fo
>>> rmats.services.LuraWaveServiceImpl
>>> 15:42:06.454 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.OMEXMLService and implementation class
>>> loci.form
>>> ats.services.OMEXMLServiceImpl
>>> 15:42:06.455 [main] DEBUG loci.common.services.ServiceFactory - Added
>>> interface interface
>>> loci.formats.services.JPEGXRService and implementation class
>>> loci.form
>>> ats.services.JPEGXRServiceImpl
>>> 15:42:06.493 [main] INFO loci.formats.in.BaseTiffReader - Populating
>>> OME metada ta
>>> 15:42:06.496 [main] DEBUG loci.formats.Memoizer - start[1516138926248]
>>> time[247]
>>> tag[loci.formats.Memoizer.setId]
>>> 15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile:
>>> embedded-stre am.raw -> null
>>> 15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile:
>>> embedded-stre am.raw -> null
>>> 15:42:06.510 [main] DEBUG o.formats.importer.cli.ErrorHandler -
>>> SCANNING: Depth: 0 Num: 1
>>> Tot: 1 File: /tmp/571.svs
>>> 15:42:06.511 [main] INFO o.formats.importer.ImportCandidates - 1
>>> file(s) parsed into 1 group(s)
>>> with 1 call(s) to setId in 265ms. (269ms total) [0 unknowns]
>>> 15:42:06.698 [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=a
>>> md64;os.version=3.10.0-693.5.2.el7.x86_64;java.runtime.versi
>>> on=1.8.0_151-b12;jav
>>> a.vm.vendor=Oracle+Corporation "Connection refused (Connection refused)"
>>> 15:42:06.773 [main] INFO ome.formats.OMEROMetadataStoreClient -
>>> Attempting init ial SSL connection
>>> to localhost:4064
>>> 15:42:07.295 [main] INFO ome.formats.OMEROMetadataStoreClient -
>>> Insecure connec tion requested,
>>> falling back
>>> 15:42:07.351 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>> closing client session.
>>> 15:42:07.360 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client
>>> closed.
>>> 15:42:07.605 [main] INFO ome.formats.OMEROMetadataStoreClient -
>>> Server: 5.3.5
>>> 15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient -
>>> Client: 5.3.5-i ce36-b73
>>> 15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - Java
>>> Version: 1 .8.0_151
>>> 15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS
>>> Name: Linux
>>> 15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS
>>> Arch: amd64
>>> 15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS
>>> Version: 3.1 0.0-693.5.2.el7.x86_64
>>> 15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary - Main
>>> file: /tmp/5 71.svs
>>> 15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary - Used
>>> files before :
>>> 15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary -
>>> /tmp/571.svs
>>> 15:42:07.708 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> FILESET_UPLOAD_PREPAR ATION
>>> 15:42:07.735 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized
>>> current op erating system as being
>>> Linux
>>> 15:42:08.068 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> FILESET_UPLOAD_START
>>> 15:42:08.077 [main] INFO o.f.i.transfers.SymlinkFileTransfer -
>>> Transferring /tm p/571.svs...
>>> 15:42:08.156 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> FILE_UPLOAD_STARTED: /tmp/571.svs
>>> 15:42:10.456 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>> FILE_UPLOAD_BYTES upl oaded:
>>> 313025695 of: 313025695 bytes (ETA: 0' 0")
>>> 15:42:12.967 [main] DEBUG o.f.importer.transfers.TransferState -
>>> dunn0172_102/20
>>> 18-01/16/15-42-07.816//571.svs id=4295
>>> 15:42:12.967 [main] DEBUG o.f.importer.transfers.TransferState -
>>> checksums: clie
>>> nt=e42776463f16e21dc0c56e232b14b7f89be0053b,server=e42776463
>>> f16e21dc0c56e232b14b 7f89be0053b
>>> 15:42:12.967 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> FILE_UPLOAD_COMPLETE: /tmp/571.svs
>>> 15:42:15.511 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> FILESET_UPLOAD_END
>>> 15:42:15.736 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>> IMPORT_STARTED Logfil e: 4294
>>> 15:42:16.307 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - ME
>>> TADATA_IMPORTED Step: 1 of 5 Logfile: 4294
>>> 15:42:17.411 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - PI
>>> XELDATA_PROCESSED Step: 2 of 5 Logfile: 4294
>>> 15:42:18.501 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - TH
>>> UMBNAILS_GENERATED Step: 3 of 5 Logfile: 4294
>>> 15:42:18.529 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - ME
>>> TADATA_PROCESSED Step: 4 of 5 Logfile: 4294
>>> 15:42:18.548 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - OB
>>> JECTS_RETURNED Step: 5 of 5 Logfile: 4294
>>> 15:42:18.751 [Ice.ThreadPool.Client-1] INFO
>>> o.f.i.cli.LoggingImportMonitor - IM
>>> PORT_DONE Imported file: /tmp/571.svs
>>> Image:151,152,153
>>> Other imported objects:
>>> Fileset:303
>>> 15:42:18.754 [Ice.ThreadPool.Client-1] INFO
>>> o.formats.importer.cli.ErrorHandler
>>> - Number of errors: 0
>>>
>>> ==> Summary
>>> 1 file uploaded, 1 fileset created, 3 images imported, 0 errors in
>>> 0:00:11.056
>>> 15:42:18.793 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>> closing client session.
>>> 15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client
>>> closed.
>>> 15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient - Logout
>>> called, shutting keep alive down.
>>> 15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>> keepalive shut down.
>>>
>>> [inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0
>>> 172_102/2018-01/16/15-42-07.816
>>> total 0
>>> drwxrwsr-x 2 omero inplace_user 21 Jan 16 15:42 .
>>> drwxrwsr-x 4 omero inplace_user 70 Jan 16 15:42 ..
>>> lrwxrwxrwx 1 inplace_user inplace_user 12 Jan 16 15:42 571.svs ->
>>> /tmp/571.svs
>>>
>>>
>> Maybe a problem with the permissions on (or otherwise reading from) the
>> external fileshare?
>>
>> [inplace_user at nunstudy-omero ~]$ ls -la /mnt/ahc-ns/Pathology/NunStudy
>>> /NS-1137/
>>> total 15180800
>>> drwxrwxrwx 2 omero inplace_user 0 Jan 10 11:16 .
>>> drwxrwxrwx 2 omero inplace_user 0 Sep 14 2015 ..
>>> -rwxrwxrwx 1 omero inplace_user 313025695 Feb 17 2009 571.svs
>>> -rwxrwxrwx 1 omero inplace_user 302926913 Feb 17 2009 572.svs
>>
>>
>> Thanks again for your help!
>>
>>
>> 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)
>> -----
>> The information transmitted in this e-mail is intended only for the
>> person or entity to which it is addressed and may contain confidential
>> and/or privileged material, including 'protected health information'. If
>> you are not the intended recipient, you are hereby notified that any
>> review, retransmission, dissemination, distribution, or copying of this
>> message is strictly prohibited. If you have received this communication in
>> error, please destroy and delete this message from any computer and contact
>> us immediately by return e-mail.
>>
>> On Mon, Jan 15, 2018 at 7:24 AM, Simon Li <spli at dundee.ac.uk> wrote:
>>
>>> Hi Brian
>>>
>>> Please accept my apologies. As you've figured out I should've said 0022
>>> is the default and 0002 should be in the systemd service.
>>>
>>> The fact that the symlink was created implies the permissions are
>>> correct. To try and track down the problem could you do an in-place import
>>> of a file on your local disk? If the SVS is too large to copy try a small
>>> image (e.g. tiff/png/jpg) instead.
>>>
>>> Simon
>>>
>>>
>>>
>>> On 12 January 2018 at 17:49, Brian Dunnette <dunn0172 at umn.edu> wrote:
>>>
>>>> Simon-
>>>>
>>>> Thanks for the tip - however, when I add "UMask=0022" to the systemd
>>>> file and reload the service, I get the same error:
>>>>
>>>> [Service]
>>>>> UMask=0022
>>>>>
>>>>> [dunn0172 at nunstudy-omero system]$ sudo systemctl daemon-reload &&
>>>>> sudo systemctl reload-or-restart omero-admin
>>>>> [inplace_user at nunstudy-omero ~]$ omero import -- --transfer=ln_s
>>>>> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> ...
>>>>> 11:36:07.268 [main] INFO o.f.i.transfers.SymlinkFileTransfer -
>>>>> Transferring /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...
>>>>> 11:36:07.388 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> 11:36:07.422 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> 11:36:07.422 [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/dunn0
>>>>> 172admin_3/2018-01/12/11-36-06.810/561.svs cannot be modified locally!
>>>>> You likely do not have access to the ManagedRepository for in-place
>>>>> import.
>>>>> Aborting...
>>>>>
>>>>> [inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0
>>>>> 172admin_3/2018-01/12/11-36-06.810/561.svs
>>>>> -rw-r--r-- 1 omero inplace_user 36 Jan 12 11:36
>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/12/11-36-06
>>>>> .810/561.svs
>>>>>
>>>>
>>>> However, when I change the umask to the 0002 mentioned in the
>>>> inplace-import document, it seems to move things along some, creating the
>>>> link and reading data (but still erroring later - maybe because the omero
>>>> system user doesn't own the link?):
>>>>
>>>> [Service]
>>>>> UMask=0002
>>>>>
>>>>> [dunn0172 at nunstudy-omero system]$ sudo systemctl daemon-reload &&
>>>>> sudo systemctl reload-or-restart omero-admin
>>>>>
>>>>> [inplace_user at nunstudy-omero ~]$ omero import -- --transfer=ln_s
>>>>> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> ...
>>>>> 11:42:46.521 [main] INFO o.f.i.transfers.SymlinkFileTransfer -
>>>>> Transferring /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...
>>>>> 11:42:46.778 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> 11:42:59.066 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_UPLOAD_BYTES uploaded: 342957409 of: 342957409 bytes (ETA: 0' 0")
>>>>> 11:42:59.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> 11:42:59.105 [main] ERROR o.formats.importer.cli.ErrorHandler -
>>>>> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>> omero.ResourceError: null
>>>>> at sun.reflect.NativeConstructorA
>>>>> ccessorImpl.newInstance0(Native Method) ~[na:1.8.0_151]
>>>>> at sun.reflect.NativeConstructorA
>>>>> ccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>>> ~[na:1.8.0_151]
>>>>> at sun.reflect.DelegatingConstruc
>>>>> torAccessorImpl.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.create
>>>>> UserException(BasicStream.java:2779) ~[ice.jar:na]
>>>>> at IceInternal.BasicStream.access$300(BasicStream.java:14)
>>>>> ~[ice.jar:na]
>>>>> at IceInternal.BasicStream$Encaps
>>>>> Decoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]
>>>>> at IceInternal.BasicStream.throwE
>>>>> xception(BasicStream.java:2291) ~[ice.jar:na]
>>>>> at IceInternal.OutgoingAsync.thro
>>>>> wUserException(OutgoingAsync.java:399) ~[ice.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.end_save(RawFileStorePrxHelper.java:724) ~[blitz.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.save(RawFileStorePrxHelper.java:611) ~[blitz.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.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.ImportLib
>>>>> rary.uploadFile(ImportLibrary.java:437) [blitz.jar:na]
>>>>> at ome.formats.importer.ImportLib
>>>>> rary.importImage(ImportLibrary.java:511) [blitz.jar:na]
>>>>> at ome.formats.importer.ImportLib
>>>>> rary.importCandidates(ImportLibrary.java:289) [blitz.jar:na]
>>>>> at ome.formats.importer.cli.Comma
>>>>> ndLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]
>>>>> at ome.formats.importer.cli.Comma
>>>>> ndLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]
>>>>> 11:42:59.110 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>>>> FILE_UPLOAD_ERROR
>>>>> 11:42:59.110 [main] ERROR ome.formats.importer.ImportLibrary - Error
>>>>> on import: cannot flush /omero/ManagedRepository/dunn0
>>>>> 172admin_3/2018-01/12/11-42-45.714/561.svs: java.io.IOException:
>>>>> Permission denied
>>>>> omero.ResourceError: null
>>>>> at sun.reflect.NativeConstructorA
>>>>> ccessorImpl.newInstance0(Native Method) ~[na:1.8.0_151]
>>>>> at sun.reflect.NativeConstructorA
>>>>> ccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62)
>>>>> ~[na:1.8.0_151]
>>>>> at sun.reflect.DelegatingConstruc
>>>>> torAccessorImpl.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.create
>>>>> UserException(BasicStream.java:2779) ~[ice.jar:na]
>>>>> at IceInternal.BasicStream.access$300(BasicStream.java:14)
>>>>> ~[ice.jar:na]
>>>>> at IceInternal.BasicStream$Encaps
>>>>> Decoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]
>>>>> at IceInternal.BasicStream.throwE
>>>>> xception(BasicStream.java:2291) ~[ice.jar:na]
>>>>> at IceInternal.OutgoingAsync.thro
>>>>> wUserException(OutgoingAsync.java:399) ~[ice.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.end_save(RawFileStorePrxHelper.java:724) ~[blitz.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.save(RawFileStorePrxHelper.java:611) ~[blitz.jar:na]
>>>>> at omero.api.RawFileStorePrxHelpe
>>>>> r.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.ImportLib
>>>>> rary.uploadFile(ImportLibrary.java:437) ~[blitz.jar:na]
>>>>> at ome.formats.importer.ImportLib
>>>>> rary.importImage(ImportLibrary.java:511) ~[blitz.jar:na]
>>>>> at ome.formats.importer.ImportLib
>>>>> rary.importCandidates(ImportLibrary.java:289) ~[blitz.jar:na]
>>>>> at ome.formats.importer.cli.Comma
>>>>> ndLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]
>>>>> at ome.formats.importer.cli.Comma
>>>>> ndLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]
>>>>> 11:42:59.110 [main] INFO ome.formats.importer.ImportLibrary -
>>>>> Exiting on error
>>>>>
>>>>> ==> Summary
>>>>> 0 files uploaded, 0 filesets created, 0 images imported, 1 error in
>>>>> 0:00:13.564
>>>>> 11:42:59.166 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>>>> closing client session.
>>>>> 11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>>>> client closed.
>>>>> 11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>>>> Logout called, shutting keep alive down.
>>>>> 11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStoreClient -
>>>>> keepalive shut down.
>>>>> !! 01/12/18 11:42:59.336 error: communicator not destroyed during
>>>>> global destruction.
>>>>>
>>>>> [inplace_user at nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0
>>>>> 172admin_3/2018-01/12/11-42-45.714/561.svs
>>>>> lrwxrwxrwx 1 inplace_user inplace_user 46 Jan 12 11:42
>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/12/11-42-45.714/561.svs
>>>>> -> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs
>>>>>
>>>>
>>>> Thanks,
>>>>
>>>> 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)
>>>> -----
>>>> The information transmitted in this e-mail is intended only for the
>>>> person or entity to which it is addressed and may contain confidential
>>>> and/or privileged material, including 'protected health information'. If
>>>> you are not the intended recipient, you are hereby notified that any
>>>> review, retransmission, dissemination, distribution, or copying of this
>>>> message is strictly prohibited. If you have received this communication in
>>>> error, please destroy and delete this message from any computer and contact
>>>> us immediately by return e-mail.
>>>>
>>>> On Fri, Jan 12, 2018 at 4:38 AM, Simon Li <spli at dundee.ac.uk> wrote:
>>>>
>>>>> Hi Brian
>>>>>
>>>>> Systemd services default to a different umask (0002):
>>>>> https://www.freedesktop.org/software/systemd/man/systemd.exe
>>>>> c.html#UMask=
>>>>> If you add "UMask=0022" to the [Service] section of
>>>>> omero-systemd.service (note capitalisation is important), then run
>>>>> "systemctl daemon-reload" to update systemd, and finally restart OMERO, I
>>>>> think this will fix things.
>>>>>
>>>>> I'll check with the rest of out team whether it's safe to update our
>>>>> docs to change the default.
>>>>>
>>>>> Simon
>>>>>
>>>>> On 11 January 2018 at 21:13, Brian Dunnette <dunn0172 at umn.edu> wrote:
>>>>>
>>>>>> Simon-
>>>>>>
>>>>>> Here are the details (to the best of my knowledge) of our server:
>>>>>>
>>>>>> - We're running Red Hat Enterprise v7.4
>>>>>> - OMERO was installed based on the CentOS 7 doc here:
>>>>>> https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/unix/s
>>>>>> erver-centos7-ice36.html
>>>>>> <https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/unix/server-centos7-ice36.html>
>>>>>> - OMERO.admin is started via systemd, using the script from the
>>>>>> docs (https://docs.openmicroscopy.org/omero/5.3.5/_downloads/omer
>>>>>> o-systemd.service)
>>>>>>
>>>>>> Root, /home, /var, and /omero (the binary repository) are each their
>>>>>> own XFS volumes, while the images we're trying to import/link are on an
>>>>>> eNAS (mounted as the omero system user):
>>>>>>
>>>>>> [dunn0172 at nunstudy-omero system]$ grep inplace /etc/passwd /etc/group
>>>>>>> /etc/passwd:inplace_user:x:1003:1003::/home/inplace_user:/bin/bash
>>>>>>> /etc/group:omero:x:1002:inplace_user
>>>>>>> /etc/group:inplace_user:x:1003:
>>>>>>>
>>>>>>> # /etc/fstab
>>>>>>> UUID=e96e0f81-c366-4c30-bc2b-3a6f47d54d13 / xfs
>>>>>>> defaults 0 0
>>>>>>> /dev/mapper/vg_os-home /home xfs
>>>>>>> defaults 0 0
>>>>>>> /dev/mapper/vg_os-var /var xfs
>>>>>>> defaults 0 0
>>>>>>> /dev/mapper/vg_os-swap swap swap
>>>>>>> defaults 0 0
>>>>>>> /dev/mapper/vg_os-omero /omero xfs
>>>>>>> defaults 0 0
>>>>>>> //files.umn.edu/ahc-ns /mnt/ahc-ns/ cifs
>>>>>>> credentials=/root/files.umn.edu.creds,dir_mode=0777,file_mod
>>>>>>> e=0777,sec=ntlmssp,uid=1002,gid=1003 0 0
>>>>>>>
>>>>>>
>>>>>> Thanks,
>>>>>>
>>>>>>
>>>>>> 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)
>>>>>> -----
>>>>>> The information transmitted in this e-mail is intended only for the
>>>>>> person or entity to which it is addressed and may contain confidential
>>>>>> and/or privileged material, including 'protected health information'. If
>>>>>> you are not the intended recipient, you are hereby notified that any
>>>>>> review, retransmission, dissemination, distribution, or copying of this
>>>>>> message is strictly prohibited. If you have received this communication in
>>>>>> error, please destroy and delete this message from any computer and contact
>>>>>> us immediately by return e-mail.
>>>>>>
>>>>>> On Thu, Jan 11, 2018 at 12:34 PM, Simon Li <spli at dundee.ac.uk> wrote:
>>>>>>
>>>>>>> Hi Brian
>>>>>>>
>>>>>>> Could you give us some details about your OMERO system, including:
>>>>>>> - Operating system and version
>>>>>>> - How you installed OMERO (e.g. manually, scripted, instructions on
>>>>>>> one of our web-pages)
>>>>>>> - How you're starting/stopping OMERO (e.g. manually, systemd,
>>>>>>> upstart)
>>>>>>> - Disk volume mount options
>>>>>>>
>>>>>>> Thanks, Simon
>>>>>>>
>>>>>>> On 11 January 2018 at 17:54, Brian Dunnette <dunn0172 at umn.edu>
>>>>>>> wrote:
>>>>>>>
>>>>>>>> Mark-
>>>>>>>>
>>>>>>>> It appears that the svs file is owned by the omero system user;
>>>>>>>> however, though I ran the chmod/chgrp commands from the inplace-import
>>>>>>>> document (and my umask is 0002), the permissions on new import directories
>>>>>>>> and their files don't seem to be set correctly:
>>>>>>>>
>>>>>>>> [omero at nunstudy-omero ~]$ umask
>>>>>>>>> 0002
>>>>>>>>> [inplace_user at nunstudy-omero 11-43-02.765]$ umask
>>>>>>>>> 0002
>>>>>>>>>
>>>>>>>>> # Change-group script
>>>>>>>>> chgrp inplace_user /omero/ManagedRepository
>>>>>>>>> chmod g+rws /omero/ManagedRepository
>>>>>>>>> chmod g+rws /omero/ManagedRepository/*
>>>>>>>>> chmod g+rws /omero/ManagedRepository/*/*
>>>>>>>>> chmod g+rws /omero/ManagedRepository/*/*/*
>>>>>>>>> chmod g+rws /omero/ManagedRepository/*/*/*/*
>>>>>>>>> chgrp inplace_user /omero/ManagedRepository/*
>>>>>>>>> chgrp inplace_user /omero/ManagedRepository/*/*
>>>>>>>>> chgrp inplace_user /omero/ManagedRepository/*/*/*
>>>>>>>>> chgrp inplace_user /omero/ManagedRepository/*/*/*/*
>>>>>>>>>
>>>>>>>>> [inplace_user at nunstudy-omero 11]$ omero import -- --transfer=ln_s
>>>>>>>>> /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
>>>>>>>>> ...
>>>>>>>>> 11:43:03.083 [main] INFO o.f.i.cli.LoggingImportMonitor -
>>>>>>>>> FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy
>>>>>>>>> /NS-1137/562.svs
>>>>>>>>> 11:43:03.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor -
>>>>>>>>> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
>>>>>>>>> 11:43:03.106 [main] ERROR o.formats.importer.cli.ErrorHandler -
>>>>>>>>> FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs
>>>>>>>>> java.lang.RuntimeException:
>>>>>>>>> ---------------------------------------------------
>>>>>>>>> Check failed: /omero/ManagedRepository/dunn0
>>>>>>>>> 172admin_3/2018-01/11/11-43-02.765/562.svs cannot be modified
>>>>>>>>> locally!
>>>>>>>>> You likely do not have access to the ManagedRepository for
>>>>>>>>> in-place import.
>>>>>>>>> Aborting...
>>>>>>>>>
>>>>>>>>> [inplace_user at nunstudy-omero ~]$ ls -la
>>>>>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/
>>>>>>>>> total 0
>>>>>>>>> drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 .
>>>>>>>>> drwxrwsr-x 3 omero inplace_user 21 Jan 10 11:22 ..
>>>>>>>>> drwxrwsr-x 3 omero inplace_user 26 Jan 10 11:22 10
>>>>>>>>> drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 11
>>>>>>>>>
>>>>>>>>> [inplace_user at nunstudy-omero ~]$ ls -la
>>>>>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/11/
>>>>>>>>> total 0
>>>>>>>>> drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 .
>>>>>>>>> drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 ..
>>>>>>>>> drwxrwxr-x 2 omero inplace_user 21 Jan 11 11:40 11-40-49.349
>>>>>>>>> drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 11-43-02.765
>>>>>>>>>
>>>>>>>>> [inplace_user at nunstudy-omero ~]$ ls -la
>>>>>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/11/11-43-02.765/
>>>>>>>>> total 4
>>>>>>>>> drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 .
>>>>>>>>> drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 ..
>>>>>>>>> -rw-r--r-- 1 omero inplace_user 36 Jan 11 11:43 562.svs
>>>>>>>>>
>>>>>>>>>
>>>>>>>> Suggestions?
>>>>>>>>
>>>>>>>> Thanks,
>>>>>>>>
>>>>>>>> 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)
>>>>>>>> -----
>>>>>>>> The information transmitted in this e-mail is intended only for the
>>>>>>>> person or entity to which it is addressed and may contain confidential
>>>>>>>> and/or privileged material, including 'protected health information'. If
>>>>>>>> you are not the intended recipient, you are hereby notified that any
>>>>>>>> review, retransmission, dissemination, distribution, or copying of this
>>>>>>>> message is strictly prohibited. If you have received this communication in
>>>>>>>> error, please destroy and delete this message from any computer and contact
>>>>>>>> us immediately by return e-mail.
>>>>>>>>
>>>>>>>> On Thu, Jan 11, 2018 at 4:35 AM, Mark Carroll <
>>>>>>>> m.t.b.carroll at dundee.ac.uk> wrote:
>>>>>>>>
>>>>>>>>> Dear Brian,
>>>>>>>>>
>>>>>>>>> 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).
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> 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.
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>> Is this file owned by the omero system user? Is the inplace_user
>>>>>>>>> able to:
>>>>>>>>>
>>>>>>>>> * append to it?
>>>>>>>>> * delete it?
>>>>>>>>> * create another file in that same
>>>>>>>>> /omero/ManagedRepository/dunn0172admin_3/2018-01/10/11-15-14.918/
>>>>>>>>> directory?
>>>>>>>>>
>>>>>>>>> -- Mark
>>>>>>>>>
>>>>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>>>>> SC015096
>>>>>>>>> _______________________________________________
>>>>>>>>> ome-users mailing list
>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>> _______________________________________________
>>>>>>>> ome-users mailing list
>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>>> SC015096
>>>>>>>
>>>>>>> _______________________________________________
>>>>>>> ome-users mailing list
>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>
>>>>>>>
>>>>>>
>>>>>> _______________________________________________
>>>>>> ome-users mailing list
>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>
>>>>>>
>>>>>
>>>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>>>
>>>>> _______________________________________________
>>>>> ome-users mailing list
>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>
>>>>>
>>>>
>>>> _______________________________________________
>>>> ome-users mailing list
>>>> ome-users at lists.openmicroscopy.org.uk
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>
>>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>
>>
>
> The University of Dundee is a registered Scottish Charity, No: SC015096
>
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>
>
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