[ome-users] In-place import from CIFS share fails with permission error
Simon Li
spli at dundee.ac.uk
Wed Jan 17 14:30:13 GMT 2018
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<mailto: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<http://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<http://os.name> is linux
15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUtil - architecture is LINU X_64 os.name<http://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<http://loci.formats.in>.MinimalTiffReader - Reading IFDs
15:42:06.340 [main] INFO loci.formats.in<http://loci.formats.in>.MinimalTiffReader - Populating metadat a
15:42:06.425 [main] DEBUG loci.formats.in<http://loci.formats.in>.MinimalTiffReader - Found IFD with JPE G 2000 compression
15:42:06.427 [main] INFO l.formats.in<http://l.formats.in>.JPEG2000MetadataParser - Unknown JPEG 200 0 box 0x2f00 at 16
15:42:06.428 [main] INFO l.formats.in<http://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<http://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<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<mailto:dunn0172 at umn.edu>
(612) 424-8187<tel:(612)%20424-8187> (Mobile)
(612) 624-6176<tel:(612)%20624-6176> (Office)
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On Mon, Jan 15, 2018 at 7:24 AM, Simon Li <spli at dundee.ac.uk<mailto: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<mailto: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/dunn0172admin_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(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]
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/dunn0172admin_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(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]
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/dunn0172admin_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<mailto:dunn0172 at umn.edu>
(612) 424-8187<tel:(612)%20424-8187> (Mobile)
(612) 624-6176<tel:(612)%20624-6176> (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<mailto:spli at dundee.ac.uk>> wrote:
Hi Brian
Systemd services default to a different umask (0002): https://www.freedesktop.org/software/systemd/man/systemd.exec.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<mailto: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/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/omero-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<http://files.umn.edu/ahc-ns> /mnt/ahc-ns/ cifs credentials=/root/files.umn.edu.creds,dir_mode=0777,file_mode=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<mailto:dunn0172 at umn.edu>
(612) 424-8187<tel:(612)%20424-8187> (Mobile)
(612) 624-6176<tel:(612)%20624-6176> (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<mailto: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<mailto: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/dunn0172admin_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<mailto:dunn0172 at umn.edu>
(612) 424-8187<tel:(612)%20424-8187> (Mobile)
(612) 624-6176<tel:(612)%20624-6176> (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<mailto: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
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