[ome-users] In-place import from CIFS share fails with permission error
Brian Dunnette
dunn0172 at umn.edu
Tue Jan 16 21:50:50 GMT 2018
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>(CommandLineImport
> er.java:141) [blitz.jar:na]
> at
> ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter
> .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/turbojpeg.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/turbojpeg.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/libturbojpeg8961843198283737496.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.version=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=e42776463f16e21dc0c56e232b14b
> 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/dunn0172_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)
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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/dunn0172admin_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.NativeConstructorAccessorImpl.newInstance0(Native
>>> Method) ~[na:1.8.0_151]
>>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Native
>>> ConstructorAccessorImpl.java:62) ~[na:1.8.0_151]
>>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De
>>> legatingConstructorAccessorImpl.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.tran
>>> sfer(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]
>>> 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.NativeConstructorAccessorImpl.newInstance0(Native
>>> Method) ~[na:1.8.0_151]
>>> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Native
>>> ConstructorAccessorImpl.java:62) ~[na:1.8.0_151]
>>> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(De
>>> legatingConstructorAccessorImpl.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.tran
>>> sfer(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]
>>> 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
>
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