<div dir="ltr"><div>Simon-<br><br></div>An in-place (symlink) import of the same file from local disk works as expected:<br><br><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><span style="font-family:monospace,monospace"><font size="2">[inplace_user@nunstudy-omero ~]$ omero import -- --transfer=ln_s /tmp/571.svs<br>Using session 452a4118-5a9e-4fce-9cb6-23fc52509d30 (dunn0172@localhost:4064). Id le timeout: 10 min. Current group: Nun Study<br>15:42:05.592 [main] INFO ome.formats.importer.ImportConfig - OMERO Version: 5.3 .5-ice36-b73<br>15:42:05.615 [main] INFO ome.formats.importer.ImportConfig - Bioformats version : 5.5.3 revision: 7bed1b04d071667d7b8a2e8c5d42f05fbfc07ecc date: 5 July 2017<br>15:42:05.687 [main] INFO o.f.importer.cli.CommandLineImporter - Setting transfe r to ln_s<br>15:42:05.689 [main] DEBUG o.f.i.transfers.AbstractFileTransfer - Loading file tr ansfer class ln_s<br>15:42:05.693 [main] INFO o.f.importer.cli.CommandLineImporter - Log levels -- B io-Formats: null OMERO.importer: null<br>15:42:05.844 [main] DEBUG ome.formats.importer.ImportConfig - Loaded savedDirect ory from ome.formats.importer.util.IniFileLoader@27c20538<br>15:42:05.844 [main] DEBUG ome.formats.importer.ImportConfig - Loaded savedDirect ory from default<br>15:42:05.866 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.i n.SlideBook6Reader<br>java.lang.ClassNotFoundException: loci.formats.in.SlideBook6Reader<br> at java.net.URLClassLoader.findClass(URLClassLoader.java:381) ~[na:1.8.0 _151]<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:424) ~[na:1.8.0_151]<br> at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:335) ~[na:1. 8.0_151]<br> at java.lang.ClassLoader.loadClass(ClassLoader.java:357) ~[na:1.8.0_151]<br> at java.lang.Class.forName0(Native Method) ~[na:1.8.0_151]<br> at java.lang.Class.forName(Class.java:264) ~[na:1.8.0_151]<br> at loci.formats.ClassList.parseLine(ClassList.java:196) [formats-api.jar :5.5.3]<br> at loci.formats.ClassList.parseFile(ClassList.java:258) [formats-api.jar :5.5.3]<br> at loci.formats.ClassList.<init>(ClassList.java:138) [formats-api.jar:5. 5.3]<br> at loci.formats.ClassList.<init>(ClassList.java:122) [formats-api.jar:5. 5.3]<br> at loci.formats.ImageReader.getDefaultReaderClasses(ImageReader.java:79) [formats-api.jar:5.5.3]<br> at ome.formats.importer.OMEROWrapper.createReader(OMEROWrapper.java:131) [blitz.jar:na]<br> at ome.formats.importer.OMEROWrapper.<init>(OMEROWrapper.java:93) [blitz .jar:na]<br> at ome.formats.importer.OMEROWrapper.<init>(OMEROWrapper.java:89) [blitz .jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.<init>(CommandLineImport er.java:141) [blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter .java:955) [blitz.jar:na]<br>15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUtil - processor is INTEL_6 4 os.arch is amd64<br>15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUtil - architecture is LINU X_64 <a href="http://os.name">os.name</a> is linux<br>15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUtil - architecture is LINU X_64 <a href="http://os.name">os.name</a> is linux<br>15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUtil - platform specific pa th is META-INF/lib/linux_64/<br>15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExtractor - mappedLib is li bturbojpeg.so<br>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<br>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<br>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'<br>15:42:06.242 [main] INFO o.formats.importer.ImportCandidates - Depth: 4 Metadat a Level: MINIMUM<br>15:42:06.244 [main] DEBUG o.formats.importer.cli.ErrorHandler - SCANNING: Depth: 0 Num: 1 Tot: n/a File: /tmp/571.svs<br>15:42:06.245 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre am.raw -> null<br>15:42:06.246 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre am.raw -> null<br>15:42:06.248 [main] DEBUG loci.formats.Memoizer - skipping memo: no directory gi ven<br>15:42:06.256 [main] DEBUG loci.common.NIOByteBufferProvider - Using mapped byte buffer? false<br>15:42:06.334 [main] INFO loci.formats.ImageReader - SVSReader initializing /tmp /571.svs<br>15:42:06.334 [main] DEBUG loci.formats.FormatHandler - SVSReader initializing /t mp/571.svs<br>15:42:06.334 [main] DEBUG loci.formats.FormatHandler - loci.formats.in.SVSReader .initFile(/tmp/571.svs)<br>15:42:06.336 [main] INFO loci.formats.in.MinimalTiffReader - Reading IFDs<br>15:42:06.340 [main] INFO loci.formats.in.MinimalTiffReader - Populating metadat a<br>15:42:06.425 [main] DEBUG loci.formats.in.MinimalTiffReader - Found IFD with JPE G 2000 compression<br>15:42:06.427 [main] INFO l.formats.in.JPEG2000MetadataParser - Unknown JPEG 200 0 box 0x2f00 at 16<br>15:42:06.428 [main] INFO l.formats.in.JPEG2000MetadataParser - File is a raw co destream not a JP2.<br>15:42:06.447 [main] DEBUG loci.common.services.ServiceFactory - Loaded propertie s from: services.properties<br>15:42:06.448 [main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.POIService and implementation class loci.formats .services.POIServiceImpl<br>15:42:06.448 [main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.MDBService and implementation class loci.formats .services.MDBServiceImpl<br>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<br>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<br>15:42:06.450 [main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.WlzService and implementation class loci.formats .services.WlzServiceImpl<br>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<br>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<br>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<br>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<br>15:42:06.453 [main] DEBUG loci.common.services.ServiceFactory - Added interface interface loci.formats.services.LuraWaveService and implementation class <a href="http://loci.fo">loci.fo</a> rmats.services.LuraWaveServiceImpl<br>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<br>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<br>15:42:06.493 [main] INFO loci.formats.in.BaseTiffReader - Populating OME metada ta<br>15:42:06.496 [main] DEBUG loci.formats.Memoizer - start[1516138926248] time[247] tag[loci.formats.Memoizer.setId]<br>15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre am.raw -> null<br>15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre am.raw -> null<br>15:42:06.510 [main] DEBUG o.formats.importer.cli.ErrorHandler - SCANNING: Depth: 0 Num: 1 Tot: 1 File: /tmp/571.svs<br>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]<br>15:42:06.698 [main] ERROR ome.system.UpgradeCheck - Error reading from url: http ://<a href="http://upgrade.openmicroscopy.org.uk?version=5.3.5-ice36-b73;os.name=Linux;os.arch=a">upgrade.openmicroscopy.org.uk?version=5.3.5-ice36-b73;os.name=Linux;os.arch=a</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)"<br>15:42:06.773 [main] INFO ome.formats.OMEROMetadataStoreClient - Attempting init ial SSL connection to localhost:4064<br>15:42:07.295 [main] INFO ome.formats.OMEROMetadataStoreClient - Insecure connec tion requested, falling back<br>15:42:07.351 [main] DEBUG ome.formats.OMEROMetadataStoreClient - closing client session.<br>15:42:07.360 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client closed.<br>15:42:07.605 [main] INFO ome.formats.OMEROMetadataStoreClient - Server: 5.3.5<br>15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - Client: 5.3.5-i ce36-b73<br>15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - Java Version: 1 .8.0_151<br>15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS Name: Linux<br>15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS Arch: amd64<br>15:42:07.606 [main] INFO ome.formats.OMEROMetadataStoreClient - OS Version: 3.1 0.0-693.5.2.el7.x86_64<br>15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary - Main file: /tmp/5 71.svs<br>15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary - Used files before :<br>15:42:07.704 [main] DEBUG ome.formats.importer.ImportLibrary - /tmp/571.svs<br>15:42:07.708 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPAR ATION<br>15:42:07.735 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized current op erating system as being Linux<br>15:42:08.068 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_START<br>15:42:08.077 [main] INFO o.f.i.transfers.SymlinkFileTransfer - Transferring /tm p/571.svs...<br>15:42:08.156 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /tmp/571.svs<br>15:42:10.456 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES upl oaded: 313025695 of: 313025695 bytes (ETA: 0' 0")<br>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<br>15:42:12.967 [main] DEBUG o.f.importer.transfers.TransferState - checksums: clie nt=e42776463f16e21dc0c56e232b14b7f89be0053b,server=e42776463f16e21dc0c56e232b14b 7f89be0053b<br>15:42:12.967 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: /tmp/571.svs<br>15:42:15.511 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_END<br>15:42:15.736 [main] INFO o.f.i.cli.LoggingImportMonitor - IMPORT_STARTED Logfil e: 4294<br>15:42:16.307 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - ME TADATA_IMPORTED Step: 1 of 5 Logfile: 4294<br>15:42:17.411 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - PI XELDATA_PROCESSED Step: 2 of 5 Logfile: 4294<br>15:42:18.501 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - TH UMBNAILS_GENERATED Step: 3 of 5 Logfile: 4294<br>15:42:18.529 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - ME TADATA_PROCESSED Step: 4 of 5 Logfile: 4294<br>15:42:18.548 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - OB JECTS_RETURNED Step: 5 of 5 Logfile: 4294<br>15:42:18.751 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - IM PORT_DONE Imported file: /tmp/571.svs<br>Image:151,152,153<br>Other imported objects:<br>Fileset:303<br>15:42:18.754 [Ice.ThreadPool.Client-1] INFO o.formats.importer.cli.ErrorHandler - Number of errors: 0<br><br>==> Summary<br>1 file uploaded, 1 fileset created, 3 images imported, 0 errors in 0:00:11.056<br>15:42:18.793 [main] DEBUG ome.formats.OMEROMetadataStoreClient - closing client session.<br>15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient - client closed.<br>15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient - Logout called, shutting keep alive down.<br>15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStoreClient - keepalive shut down.<br><br>[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0172_102/2018-01/16/15-42-07.816<br>total 0<br>drwxrwsr-x 2 omero inplace_user 21 Jan 16 15:42 .<br>drwxrwsr-x 4 omero inplace_user 70 Jan 16 15:42 ..<br>lrwxrwxrwx 1 inplace_user inplace_user 12 Jan 16 15:42 571.svs -> /tmp/571.svs</font></span><br><br></blockquote><div><br></div><div>Maybe a problem with the permissions on (or otherwise reading from) the external fileshare?</div><div><br></div><div><blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex"><font size="2"><span style="font-family:monospace,monospace">[inplace_user@nunstudy-omero ~]$ ls -la /mnt/ahc-ns/Pathology/NunStudy/NS-1137/<br>total 15180800<br>drwxrwxrwx 2 omero inplace_user 0 Jan 10 11:16 .<br>drwxrwxrwx 2 omero inplace_user 0 Sep 14 2015 ..<br>-rwxrwxrwx 1 omero inplace_user 313025695 Feb 17 2009 571.svs<br>-rwxrwxrwx 1 omero inplace_user 302926913 Feb 17 2009 572.svs</span></font></blockquote><div><br></div><div>Thanks again for your help! <br></div><br></div></div><div class="gmail_extra"><br clear="all"><div><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><span style="font-size:10pt;font-family:Arial,sans-serif">Brian Dunnette</span></p><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><span style="font-size:10pt;font-family:Arial,sans-serif">Digital Imaging & Info Tech</span><u></u><u></u></p><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><span style="font-size:10pt;font-family:Arial,sans-serif"><a href="http://pathology.umn.edu" target="_blank">Lab Medicine and Pathology</a></span><u></u><u></u></p><p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)"><span style="font-size:10pt;font-family:Arial,sans-serif">University of Minnesota</span><u></u><u></u></p><div><br></div><a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a><br>(612) 424-8187 (Mobile)<br>(612) 624-6176 (Office)<br><div>-----</div>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. </div></div></div></div></div>
<br><div class="gmail_quote">On Mon, Jan 15, 2018 at 7:24 AM, Simon Li <span dir="ltr"><<a href="mailto:spli@dundee.ac.uk" target="_blank">spli@dundee.ac.uk</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">
<div>
<div>Hi Brian<br>
<br>
</div>
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.<br>
<br>
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.<span class="HOEnZb"><font color="#888888"><br>
<br>
</font></span></div><span class="HOEnZb"><font color="#888888">
Simon<br>
<div><br>
<br>
</div>
</font></span></div><div><div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On 12 January 2018 at 17:49, Brian Dunnette <span dir="ltr">
<<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div dir="ltr">
<div>Simon-<br>
<br>
</div>
Thanks for the tip - however, when I add "UMask=0022" to the systemd file and reload the service, I get the same error:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
[Service]<br>
UMask=0022<br>
<br>
[dunn0172@nunstudy-omero system]$ sudo systemctl daemon-reload && sudo systemctl reload-or-restart omero-admin<br>
[inplace_user@nunstudy-omero ~]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
...<br>
11:36:07.268 [main] INFO o.f.i.transfers.SymlinkFileTra<wbr>nsfer - Transferring /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs...<br>
11:36:07.388 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
11:36:07.422 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
11:36:07.422 [main] ERROR o.formats.importer.cli.ErrorHa<wbr>ndler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
java.lang.RuntimeException:<br>
------------------------------<wbr>---------------------<br>
Check failed: /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-36-<wbr>06.810/561.svs cannot be modified locally!<span><br>
You likely do not have access to the ManagedRepository for in-place import.<br>
Aborting...<br>
<br>
</span>[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-36-<wbr>06.810/561.svs<br>
-rw-r--r-- 1 omero inplace_user 36 Jan 12 11:36 /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-36-<wbr>06.810/561.svs<br>
</blockquote>
<div><br>
</div>
<div>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?):</div>
<div><br>
</div>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>[Service]<br>
UMask=0002<br>
<br>
[dunn0172@nunstudy-omero system]$ sudo systemctl daemon-reload && sudo systemctl reload-or-restart omero-admin<br>
<br>
[inplace_user@nunstudy-omero ~]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
...<br>
11:42:46.521 [main] INFO o.f.i.transfers.SymlinkFileTra<wbr>nsfer - Transferring /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs...<br>
11:42:46.778 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
11:42:59.066 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 342957409 of: 342957409 bytes (ETA: 0' 0")<br>
11:42:59.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
11:42:59.105 [main] ERROR o.formats.importer.cli.ErrorHa<wbr>ndler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
omero.ResourceError: null<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance0(<wbr>Native Method) ~[na:1.8.0_151]<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance(Native<wbr>ConstructorAccessorImpl.java:<wbr>62) ~[na:1.8.0_151]<br>
at sun.reflect.DelegatingConstruc<wbr>torAccessorImpl.newInstance(De<wbr>legatingConstructorAccessorImp<wbr>l.java:45) ~[na:1.8.0_151]<br>
at java.lang.reflect.Constructor.<wbr>newInstance(Constructor.java:4<wbr>23) ~[na:1.8.0_151]<br>
at java.lang.Class.newInstance(Cl<wbr>ass.java:442) ~[na:1.8.0_151]<br>
at IceInternal.BasicStream.create<wbr>UserException(BasicStream.<wbr>java:2779) ~[ice.jar:na]<br>
at IceInternal.BasicStream.access<wbr>$300(BasicStream.java:14) ~[ice.jar:na]<br>
at IceInternal.BasicStream$Encaps<wbr>Decoder10.throwException(<wbr>BasicStream.java:3298) ~[ice.jar:na]<br>
at IceInternal.BasicStream.throwE<wbr>xception(BasicStream.java:<wbr>2291) ~[ice.jar:na]<br>
at IceInternal.OutgoingAsync.thro<wbr>wUserException(OutgoingAsync.<wbr>java:399) ~[ice.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.end_save(<wbr>RawFileStorePrxHelper.java:<wbr>724) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.<wbr>java:611) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.<wbr>java:598) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.TransferState.save(TransferSt<wbr>ate.java:128) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.AbstractFileTransfer.finish(A<wbr>bstractFileTransfer.java:114) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.AbstractExecFileTransfer.tran<wbr>sfer(AbstractExecFileTransfer.<wbr>java:70) ~[blitz.jar:na]<span><br>
at ome.formats.importer.ImportLib<wbr>rary.uploadFile(ImportLibrary.<wbr>java:437) [blitz.jar:na]<br>
at ome.formats.importer.ImportLib<wbr>rary.importImage(ImportLibrary<wbr>.java:511) [blitz.jar:na]<br>
at ome.formats.importer.ImportLib<wbr>rary.importCandidates(ImportLi<wbr>brary.java:289) [blitz.jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.start(CommandLi<wbr>neImporter.java:289) [blitz.jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.main(CommandLin<wbr>eImporter.java:958) [blitz.jar:na]<br>
</span>11:42:59.110 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_ERROR<br>
11:42:59.110 [main] ERROR ome.formats.importer.ImportLib<wbr>rary - Error on import: cannot flush /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-42-<wbr>45.714/561.svs: java.io.IOException: Permission denied<br>
omero.ResourceError: null<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance0(<wbr>Native Method) ~[na:1.8.0_151]<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance(Native<wbr>ConstructorAccessorImpl.java:<wbr>62) ~[na:1.8.0_151]<br>
at sun.reflect.DelegatingConstruc<wbr>torAccessorImpl.newInstance(De<wbr>legatingConstructorAccessorImp<wbr>l.java:45) ~[na:1.8.0_151]<br>
at java.lang.reflect.Constructor.<wbr>newInstance(Constructor.java:4<wbr>23) ~[na:1.8.0_151]<br>
at java.lang.Class.newInstance(Cl<wbr>ass.java:442) ~[na:1.8.0_151]<br>
at IceInternal.BasicStream.create<wbr>UserException(BasicStream.<wbr>java:2779) ~[ice.jar:na]<br>
at IceInternal.BasicStream.access<wbr>$300(BasicStream.java:14) ~[ice.jar:na]<br>
at IceInternal.BasicStream$Encaps<wbr>Decoder10.throwException(<wbr>BasicStream.java:3298) ~[ice.jar:na]<br>
at IceInternal.BasicStream.throwE<wbr>xception(BasicStream.java:<wbr>2291) ~[ice.jar:na]<br>
at IceInternal.OutgoingAsync.thro<wbr>wUserException(OutgoingAsync.<wbr>java:399) ~[ice.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.end_save(<wbr>RawFileStorePrxHelper.java:<wbr>724) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.<wbr>java:611) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.<wbr>java:598) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.TransferState.save(TransferSt<wbr>ate.java:128) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.AbstractFileTransfer.finish(A<wbr>bstractFileTransfer.java:114) ~[blitz.jar:na]<br>
at ome.formats.importer.transfers<wbr>.AbstractExecFileTransfer.tran<wbr>sfer(AbstractExecFileTransfer.<wbr>java:70) ~[blitz.jar:na]<span><br>
at ome.formats.importer.ImportLib<wbr>rary.uploadFile(ImportLibrary.<wbr>java:437) ~[blitz.jar:na]<br>
at ome.formats.importer.ImportLib<wbr>rary.importImage(ImportLibrary<wbr>.java:511) ~[blitz.jar:na]<br>
at ome.formats.importer.ImportLib<wbr>rary.importCandidates(ImportLi<wbr>brary.java:289) ~[blitz.jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.start(CommandLi<wbr>neImporter.java:289) [blitz.jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.main(CommandLin<wbr>eImporter.java:958) [blitz.jar:na]<br>
</span>11:42:59.110 [main] INFO ome.formats.importer.ImportLib<wbr>rary - Exiting on error<br>
<br>
==> Summary<br>
0 files uploaded, 0 filesets created, 0 images imported, 1 error in 0:00:13.564<br>
11:42:59.166 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - closing client session.<br>
11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - client closed.<br>
11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - Logout called, shutting keep alive down.<br>
11:42:59.190 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - keepalive shut down.<br>
!! 01/12/18 11:42:59.336 error: communicator not destroyed during global destruction.<br>
<br>
[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-42-<wbr>45.714/561.svs<br>
lrwxrwxrwx 1 inplace_user inplace_user 46 Jan 12 11:42 /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-42-<wbr>45.714/561.svs -> /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/561.svs<br>
</div>
</blockquote>
<div><br>
</div>
<div>Thanks, <br>
</div>
</div>
<div class="gmail_extra"><span><br clear="all">
<div>
<div class="m_-6071734035117955650m_-7026116517787571893gmail_signature" data-smartmail="gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Brian Dunnette</span></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Digital Imaging & Info Tech</span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif"><a href="http://pathology.umn.edu" target="_blank">Lab Medicine and Pathology</a></span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">University of Minnesota</span><u></u><u></u></p>
<div><br>
</div>
<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a><br>
<a href="tel:(612)%20424-8187" value="+16124248187" target="_blank">(612) 424-8187</a> (Mobile)<br>
<a href="tel:(612)%20624-6176" value="+16126246176" target="_blank">(612) 624-6176</a> (Office)<br>
<div>-----</div>
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. </div>
</div>
</div>
</div>
</div>
<br>
</span>
<div>
<div class="m_-6071734035117955650h5">
<div class="gmail_quote">On Fri, Jan 12, 2018 at 4:38 AM, Simon Li <span dir="ltr">
<<a href="mailto:spli@dundee.ac.uk" target="_blank">spli@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
<div>
<div dir="ltr">
<div>
<div>
<div>Hi Brian<br>
<br>
</div>
Systemd services default to a different umask (0002): <a href="https://www.freedesktop.org/software/systemd/man/systemd.exec.html#UMask=" target="_blank">
https://www.freedesktop.org/so<wbr>ftware/systemd/man/systemd.exe<wbr>c.html#UMask=</a><br>
</div>
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.<br>
<br>
</div>
I'll check with the rest of out team whether it's safe to update our docs to change the default.<span class="m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888"><br>
</font></span>
<div><span class="m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888"></font></span>
<div><span class="m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Simon<br>
</div>
</font></span>
<div>
<div class="m_-6071734035117955650m_-7026116517787571893h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On 11 January 2018 at 21:13, Brian Dunnette <span dir="ltr">
<<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Simon-<br>
<br>
</div>
Here are the details (to the best of my knowledge) of our server:<br>
</div>
<ul>
<li>We're running Red Hat Enterprise v7.4</li><li>OMERO was installed based on the CentOS 7 doc here: <a href="https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/unix/server-centos7-ice36.html" target="_blank">
https://docs.openmicroscopy.or<wbr>g/omero/5.3.5/sysadmins/unix/s<wbr>erver-centos7-ice36.html</a></li><li>OMERO.admin is started via systemd, using the script from the docs (<a href="https://docs.openmicroscopy.org/omero/5.3.5/_downloads/omero-systemd.service" target="_blank">https://docs.openmicroscopy.o<wbr>rg/omero/5.3.5/_downloads/omer<wbr>o-systemd.service</a>)</li></ul>
</div>
</div>
</div>
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):<br>
<div><br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<font size="2"><span style="font-family:monospace,monospace">[dunn0172@nunstudy-omero system]$ grep inplace /etc/passwd /etc/group<br>
/etc/passwd:inplace_user:x:100<wbr>3:1003::/home/inplace_user:/bi<wbr>n/bash<br>
/etc/group:omero:x:1002:inplac<wbr>e_user<br>
/etc/group:inplace_user:x:1003<wbr>:<br>
<br>
# /etc/fstab<br>
UUID=e96e0f81-c366-4c30-bc2b-3<wbr>a6f47d54d13 / xfs defaults 0 0<br>
/dev/mapper/vg_os-home /home xfs defaults 0 0<br>
/dev/mapper/vg_os-var /var xfs defaults 0 0<br>
/dev/mapper/vg_os-swap swap swap defaults 0 0<br>
/dev/mapper/vg_os-omero /omero xfs defaults 0 0<br>
//<a href="http://files.umn.edu/ahc-ns" target="_blank">files.umn.edu/ahc-ns</a> /mnt/ahc-ns/ cifs credentials=/root/files.umn.ed<wbr>u.creds,dir_mode=0777,file_mod<wbr>e=0777,sec=ntlmssp,uid=1002,gi<wbr>d=1003 0 0<br>
</span></font></blockquote>
<div><br>
</div>
<div></div>
<div>Thanks, <br>
</div>
<br>
</div>
</div>
<div class="gmail_extra"><span class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-"><br clear="all">
<div>
<div class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-m_-9178000793618904860gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Brian Dunnette</span></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Digital Imaging & Info Tech</span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif"><a href="http://pathology.umn.edu" target="_blank">Lab Medicine and Pathology</a></span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">University of Minnesota</span><u></u><u></u></p>
<div><br>
</div>
<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a><br>
<a href="tel:(612)%20424-8187" value="+16124248187" target="_blank">(612) 424-8187</a> (Mobile)<br>
<a href="tel:(612)%20624-6176" value="+16126246176" target="_blank">(612) 624-6176</a> (Office)<br>
<div>-----</div>
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. </div>
</div>
</div>
</div>
</div>
<br>
</span>
<div>
<div class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-h5">
<div class="gmail_quote">On Thu, Jan 11, 2018 at 12:34 PM, Simon Li <span dir="ltr">
<<a href="mailto:spli@dundee.ac.uk" target="_blank">spli@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div>
<div dir="ltr">
<div>
<div>
<div>
<div>
<div>Hi Brian<br>
<br>
</div>
Could you give us some details about your OMERO system, including:<br>
</div>
- Operating system and version<br>
</div>
- How you installed OMERO (e.g. manually, scripted, instructions on one of our web-pages)<br>
</div>
- How you're starting/stopping OMERO (e.g. manually, systemd, upstart)</div>
<div>- Disk volume mount options<br>
</div>
<div><br>
</div>
Thanks, Simon<br>
</div>
<div>
<div class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-m_-9178000793618904860h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On 11 January 2018 at 17:54, Brian Dunnette <span dir="ltr">
<<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div dir="ltr">
<div>Mark-<br>
<br>
</div>
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:<br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<div><span style="font-family:monospace,monospace"><font size="2">[omero@nunstudy-omero ~]$ umask<br>
0002<br>
[inplace_user@nunstudy-omero 11-43-02.765]$ umask<br>
0002<br>
<br>
</font></span></div>
<span style="font-family:monospace,monospace"><font size="2"># Change-group script<br>
chgrp inplace_user /omero/ManagedRepository<br>
chmod g+rws /omero/ManagedRepository<br>
chmod g+rws /omero/ManagedRepository/*<br>
chmod g+rws /omero/ManagedRepository/*/*<br>
chmod g+rws /omero/ManagedRepository/*/*/*<br>
chmod g+rws /omero/ManagedRepository/*/*/*<wbr>/*<br>
chgrp inplace_user /omero/ManagedRepository/*<br>
chgrp inplace_user /omero/ManagedRepository/*/*<br>
chgrp inplace_user /omero/ManagedRepository/*/*/*<br>
chgrp inplace_user /omero/ManagedRepository/*/*/*<wbr>/*<br>
<br>
[inplace_user@nunstudy-omero 11]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/562.svs<br>
...<br>
11:43:03.083 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/562.svs<br>
11:43:03.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/562.svs<br>
11:43:03.106 [main] ERROR o.formats.importer.cli.ErrorHa<wbr>ndler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy<wbr>/NS-1137/562.svs<br>
java.lang.RuntimeException:<br>
------------------------------<wbr>---------------------<br>
Check failed: /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/11/11-43-02<wbr>.765/562.svs cannot be modified locally!<span><br>
You likely do not have access to the ManagedRepository for in-place import.<br>
</span>Aborting...<br>
<br>
[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/<br>
total 0<br>
drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 .<br>
drwxrwsr-x 3 omero inplace_user 21 Jan 10 11:22 ..<br>
drwxrwsr-x 3 omero inplace_user 26 Jan 10 11:22 10<br>
<span style="color:rgb(255,0,0)">drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 11</span><br>
<br>
[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/11/<br>
total 0<br>
drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 .<br>
drwxrwsr-x 4 omero inplace_user 26 Jan 11 11:40 ..<br>
drwxrwxr-x 2 omero inplace_user 21 Jan 11 11:40 11-40-49.349<br>
<span style="color:rgb(255,0,0)">drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 11-43-02.765</span></font></span>
<br>
<br>
</blockquote>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
<span style="font-family:monospace,monospace"><font size="2">[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/11/11-43-02<wbr>.765/<br>
total 4<br>
drwxr-sr-x 2 omero inplace_user 21 Jan 11 11:43 .<br>
drwxr-sr-x 4 omero inplace_user 46 Jan 11 11:43 ..<br>
<span style="color:rgb(255,0,0)">-rw-r--r-- 1 omero inplace_user 36 Jan 11 11:43 562.svs</span></font></span><span style="color:rgb(255,0,0)"><br>
</span><br>
</blockquote>
<div><br>
</div>
<div>Suggestions?</div>
<div><br>
</div>
<div>Thanks,<br>
</div>
</div>
<div class="gmail_extra"><br clear="all">
<div>
<div class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-m_-9178000793618904860m_5622562909497765594m_8605135310308664991gmail_signature">
<div dir="ltr">
<div>
<div dir="ltr">
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Brian Dunnette</span></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">Digital Imaging & Info Tech</span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif"><a href="http://pathology.umn.edu" target="_blank">Lab Medicine and Pathology</a></span><u></u><u></u></p>
<p style="margin:0px;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px;background-color:rgb(255,255,255)">
<span style="font-size:10pt;font-family:Arial,sans-serif">University of Minnesota</span><u></u><u></u></p>
<div><br>
</div>
<a href="mailto:dunn0172@umn.edu" target="_blank">dunn0172@umn.edu</a><br>
<a href="tel:(612)%20424-8187" value="+16124248187" target="_blank">(612) 424-8187</a> (Mobile)<br>
<a href="tel:(612)%20624-6176" value="+16126246176" target="_blank">(612) 624-6176</a> (Office)<br>
<div>-----</div>
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. </div>
</div>
</div>
</div>
</div>
<div>
<div class="m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-m_-9178000793618904860m_5622562909497765594h5">
<br>
<div class="gmail_quote">On Thu, Jan 11, 2018 at 4:35 AM, Mark Carroll <span dir="ltr">
<<a href="mailto:m.t.b.carroll@dundee.ac.uk" target="_blank">m.t.b.carroll@dundee.ac.uk</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Dear Brian,<span><br>
<br>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
We're attempting to do an in-place import of SVS files from a CIFS share<br>
into our new OMERO 5.3.5 install, and followed the in-place import guide<br>
(set up the inplace_user user & group, gave them ownership of the<br>
ManagedRepository, verified that inplace_user can create a directory in<br>
ManagedRepository and the omero system user can delete it).<br>
</blockquote>
<br>
</span><span>
<blockquote class="gmail_quote" style="margin:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);padding-left:1ex">
Check failed:<br>
/omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/10/11-15-14<wbr>.918/561.svs<br>
cannot be modified locally!<br>
<br>
You likely do not have access to the ManagedRepository for in-place<br>
import.<br>
</blockquote>
<br>
</span>Is this file owned by the omero system user? Is the inplace_user able to:<br>
<br>
* append to it?<br>
* delete it?<br>
* create another file in that same<br>
/omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/10/11-15-14<wbr>.918/ directory?<br>
<br>
-- Mark<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
</div>
</div>
</div>
<div>
<div class="m_-6071734035117955650m_-7026116517787571893h5"><br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
<br>
</blockquote>
</div>
<br>
</div>
</div>
</div>
<br>
______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" target="_blank">ome-users@lists.openmicroscopy<wbr>.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.or<wbr>g.uk/mailman/listinfo/ome-user<wbr>s</a><br>
<br>
</blockquote>
</div>
<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div></div></div>
<br>______________________________<wbr>_________________<br>
ome-users mailing list<br>
<a href="mailto:ome-users@lists.openmicroscopy.org.uk">ome-users@lists.<wbr>openmicroscopy.org.uk</a><br>
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" rel="noreferrer" target="_blank">http://lists.openmicroscopy.<wbr>org.uk/mailman/listinfo/ome-<wbr>users</a><br>
<br></blockquote></div><br></div>