<div dir="ltr"><div><div><div>Simon-<br><br></div>1. I've uploaded the relevant portion of Blitz-0.log (for 1/10-1/12) via the QA site - hope this is of some help!<br><br></div>2. Yes, this seems to work fine - no error messages when cat-ing the SVS file as the omero user.<br><br></div>3. I've set the mount permissions to read-only as you suggested - it seems to read the file data, but still ends with the "cannot flush" error:<br><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">[inplace_user@nunstudy-omero ~]$ ls -la /mnt/ahc-ns/Pathology/NunStudy/NS-1137/<br>total 15180800<br>dr-xr-xr-x 2 omero inplace_user 0 Jan 10 11:16 .<br>dr-xr-xr-x 2 omero inplace_user 0 Sep 14 2015 ..<br>-r--r--r-- 1 omero inplace_user 342957409 Feb 17 2009 561.svs<br> <br>[inplace_user@nunstudy-omero ~]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>...<br>14:42:40.573 [main] DEBUG ome.formats.importer.ImportLibrary - Main file: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>14:42:40.574 [main] DEBUG ome.formats.importer.ImportLibrary - Used files before:<br>14:42:40.574 [main] DEBUG ome.formats.importer.ImportLibrary - /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>14:42:40.577 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPARATION<br>14:42:40.604 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized current operating system as being Linux<br>14:42:40.974 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_START<br>14:42:40.995 [main] INFO o.f.i.transfers.SymlinkFileTransfer - Transferring /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs...<br>14:42:41.079 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>14:42:53.904 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES uploaded: 342957409 of: 342957409 bytes (ETA: 0' 0")<br>14:42:53.943 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>14:42:53.944 [main] ERROR o.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/561.svs<br>omero.ResourceError: null<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_151]<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_151]<br> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_151]<br> at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_151]<br> at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_151]<br> at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]<br> at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]<br> at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]<br> at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]<br> at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]<br> at omero.api.RawFileStorePrxHelper.end_save(RawFileStorePrxHelper.java:724) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:611) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:598) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.TransferState.save(TransferState.java:128) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:114) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:70) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437) [blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511) [blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289) [blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]<br>14:42:53.949 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_ERROR<br>14:42:53.949 [main] ERROR ome.formats.importer.ImportLibrary - Error on import: cannot flush /omero/ManagedRepository/dunn0172_102/2018-01/17/14-42-40.678/561.svs: java.io.IOException: Permission denied<br>omero.ResourceError: null<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method) ~[na:1.8.0_151]<br> at sun.reflect.NativeConstructorAccessorImpl.newInstance(NativeConstructorAccessorImpl.java:62) ~[na:1.8.0_151]<br> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(DelegatingConstructorAccessorImpl.java:45) ~[na:1.8.0_151]<br> at java.lang.reflect.Constructor.newInstance(Constructor.java:423) ~[na:1.8.0_151]<br> at java.lang.Class.newInstance(Class.java:442) ~[na:1.8.0_151]<br> at IceInternal.BasicStream.createUserException(BasicStream.java:2779) ~[ice.jar:na]<br> at IceInternal.BasicStream.access$300(BasicStream.java:14) ~[ice.jar:na]<br> at IceInternal.BasicStream$EncapsDecoder10.throwException(BasicStream.java:3298) ~[ice.jar:na]<br> at IceInternal.BasicStream.throwException(BasicStream.java:2291) ~[ice.jar:na]<br> at IceInternal.OutgoingAsync.throwUserException(OutgoingAsync.java:399) ~[ice.jar:na]<br> at omero.api.RawFileStorePrxHelper.end_save(RawFileStorePrxHelper.java:724) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:611) ~[blitz.jar:na]<br> at omero.api.RawFileStorePrxHelper.save(RawFileStorePrxHelper.java:598) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.TransferState.save(TransferState.java:128) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractFileTransfer.finish(AbstractFileTransfer.java:114) ~[blitz.jar:na]<br> at ome.formats.importer.transfers.AbstractExecFileTransfer.transfer(AbstractExecFileTransfer.java:70) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.uploadFile(ImportLibrary.java:437) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importImage(ImportLibrary.java:511) ~[blitz.jar:na]<br> at ome.formats.importer.ImportLibrary.importCandidates(ImportLibrary.java:289) ~[blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.start(CommandLineImporter.java:289) [blitz.jar:na]<br> at ome.formats.importer.cli.CommandLineImporter.main(CommandLineImporter.java:958) [blitz.jar:na]<br>14:42:53.949 [main] INFO ome.formats.importer.ImportLibrary - Exiting on error</span></font><br></blockquote><div><br></div><div>Thanks, <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 Wed, Jan 17, 2018 at 8:30 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>
I've had a discussion with the rest of the team and came up with the following. Could you please:<br>
</div>
<div><br>
</div>
1. Send us your server Blitz-0.log corresponding to the failed import, either copy the relevant lines or upload the whole file to
<a href="https://www.openmicroscopy.org/qa2/qa/upload/" target="_blank">https://www.openmicroscopy.<wbr>org/qa2/qa/upload/</a></div>
<div>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.<br>
</div>
<br>
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<wbr>/NS-1137/561.svs > /dev/null<br>
<div>
<div>
<div>If this fails it suggests the CIFS mount options are incorrect, or the file permissions on the remote filesystem are blocking access.</div>
<div><br>
</div>
<div>3. Change your CIFS mount options to read-only (<font size="2"><span style="font-family:monospace,monospace">dir_mode=0555,file_mode=0444</span></font>) 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.<br>
</div>
<div><br>
</div>
<div>Many thanks</div><span class="HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Simon<br>
</div>
</font></span></div>
</div><div><div class="h5">
<div class="gmail_extra"><br>
<div class="gmail_quote">On 16 January 2018 at 21:50, 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>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-9cb6-23fc52<wbr>509d30 (dunn0172@localhost:4064). Id <wbr> le timeout: 10 min. Current group: Nun Study<br>
15:42:05.592 [main] INFO ome.formats.importer.ImportCon<wbr>fig - OMERO Version: 5.3 <wbr> .5-ice36-b73<br>
15:42:05.615 [main] INFO ome.formats.importer.ImportCon<wbr>fig - Bioformats version <wbr> : 5.5.3 revision: 7bed1b04d071667d7b8a2e8c5d42f0<wbr>5fbfc07ecc date: 5 July 2017<br>
15:42:05.687 [main] INFO o.f.importer.cli.CommandLineIm<wbr>porter - Setting transfe <wbr> r to ln_s<br>
15:42:05.689 [main] DEBUG o.f.i.transfers.AbstractFileTr<wbr>ansfer - Loading file tr <wbr> ansfer class ln_s<br>
15:42:05.693 [main] INFO o.f.importer.cli.CommandLineIm<wbr>porter - Log levels -- B <wbr> io-Formats: null OMERO.importer: null<br>
15:42:05.844 [main] DEBUG ome.formats.importer.ImportCon<wbr>fig - Loaded savedDirect <wbr> ory from ome.formats.importer.util.IniF<wbr>ileLoader@27c20538<br>
15:42:05.844 [main] DEBUG ome.formats.importer.ImportCon<wbr>fig - Loaded savedDirect <wbr> ory from default<br>
15:42:05.866 [main] DEBUG loci.formats.ClassList - Could not find loci.formats.i <wbr> n.SlideBook6Reader<span class="m_-5508117184170654899gmail-"><br>
java.lang.ClassNotFoundExcepti<wbr>on: <a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.SlideBook6Read<wbr>er<br>
at java.net.URLClassLoader.findCl<wbr>ass(URLClassLoader.java:381) ~[na:1.8.0 <wbr> _151]<br>
at java.lang.ClassLoader.loadClas<wbr>s(ClassLoader.java:424) ~[na:1.8.0_151]<br>
at sun.misc.Launcher$AppClassLoad<wbr>er.loadClass(Launcher.java:<wbr>335) ~[na:1. <wbr> 8.0_151]<br>
at java.lang.ClassLoader.loadClas<wbr>s(ClassLoader.java:357) ~[na:1.8.0_151]<br>
at java.lang.Class.forName0(Nativ<wbr>e Method) ~[na:1.8.0_151]<br>
at java.lang.Class.forName(Class.<wbr>java:264) ~[na:1.8.0_151]<br>
at loci.formats.ClassList.parseLi<wbr>ne(ClassList.java:196) [formats-api.jar <wbr> :5.5.3]<br>
at loci.formats.ClassList.parseFi<wbr>le(ClassList.java:258) [formats-api.jar <wbr> :5.5.3]<br>
at loci.formats.ClassList.<init>(<wbr>ClassList.java:138) [formats-api.jar:5. <wbr> 5.3]<br>
at loci.formats.ClassList.<init>(<wbr>ClassList.java:122) [formats-api.jar:5. <wbr> 5.3]<br>
at loci.formats.ImageReader.getDe<wbr>faultReaderClasses(ImageReader<wbr>.java:79) <wbr> [formats-api.jar:5.5.3]<br>
at ome.formats.importer.OMEROWrap<wbr>per.createReader(OMEROWrapper.<wbr>java:131) <wbr> [blitz.jar:na]<br>
</span> at ome.formats.importer.OMEROWrap<wbr>per.<init>(OMEROWrapper.java:<wbr>93) [blitz <wbr> .jar:na]<span class="m_-5508117184170654899gmail-"><br>
at ome.formats.importer.OMEROWrap<wbr>per.<init>(OMEROWrapper.java:<wbr>89) [blitz <wbr> .jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.<init>(CommandL<wbr>ineImport <wbr> er.java:141) [blitz.jar:na]<br>
at ome.formats.importer.cli.Comma<wbr>ndLineImporter.main(CommandLin<wbr>eImporter <wbr> .java:955) [blitz.jar:na]<br>
</span>15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUti<wbr>l - processor is INTEL_6 <wbr> 4 os.arch is amd64<br>
15:42:06.213 [main] DEBUG o.s.nativelib.NativeLibraryUti<wbr>l - architecture is LINU <wbr> X_64
<a href="http://os.name" target="_blank">os.name</a> is linux<br>
15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUti<wbr>l - architecture is LINU <wbr> X_64
<a href="http://os.name" target="_blank">os.name</a> is linux<br>
15:42:06.216 [main] DEBUG o.s.nativelib.NativeLibraryUti<wbr>l - platform specific pa <wbr> th is META-INF/lib/linux_64/<br>
15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExt<wbr>ractor - mappedLib is li <wbr> bturbojpeg.so<br>
15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExt<wbr>ractor - URL is jar:file <wbr> :/home/omero/OMERO.server-5.3.<wbr>5-ice36-b73/lib/client/turbojp<wbr>eg.jar!/META-INF/lib <wbr>
/linux_64/libturbojpeg.so<br>
15:42:06.216 [main] DEBUG o.scijava.nativelib.BaseJniExt<wbr>ractor - URL path is fil <wbr> e:/home/omero/OMERO.server-5.3<wbr>.5-ice36-b73/lib/client/turboj<wbr>peg.jar!/META-INF/li <wbr>
b/linux_64/libturbojpeg.so<br>
15:42:06.219 [main] DEBUG o.scijava.nativelib.BaseJniExt<wbr>ractor - Extracting 'jar <wbr> :file:/home/omero/OMERO.server<wbr>-5.3.5-ice36-b73/lib/client/<wbr>turbojpeg.jar!/META-IN <wbr>
F/lib/linux_64/libturbojpeg.so<wbr>' to '/tmp/libturbojpeg896184319828<wbr>3737496.so'<br>
15:42:06.242 [main] INFO o.formats.importer.ImportCandi<wbr>dates - Depth: 4 Metadat <wbr> a Level: MINIMUM<br>
15:42:06.244 [main] DEBUG o.formats.importer.cli.ErrorHa<wbr>ndler - SCANNING: Depth: <wbr> 0 Num: 1 Tot: n/a File: /tmp/571.svs<br>
15:42:06.245 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre <wbr> am.raw -> null<br>
15:42:06.246 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre <wbr> am.raw -> null<br>
15:42:06.248 [main] DEBUG loci.formats.Memoizer - skipping memo: no directory gi <wbr> ven<br>
15:42:06.256 [main] DEBUG loci.common.NIOByteBufferProvi<wbr>der - Using mapped byte <wbr> buffer? false<br>
15:42:06.334 [main] INFO loci.formats.ImageReader - SVSReader initializing /tmp <wbr> /571.svs<br>
15:42:06.334 [main] DEBUG loci.formats.FormatHandler - SVSReader initializing /t <wbr> mp/571.svs<br>
15:42:06.334 [main] DEBUG loci.formats.FormatHandler - loci.formats.in.SVSReader <wbr> <wbr> .initFile(/tmp/571.svs)<br>
15:42:06.336 [main] INFO <a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.MinimalTiffRea<wbr>der - Reading IFDs<br>
15:42:06.340 [main] INFO <a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.MinimalTiffRea<wbr>der - Populating metadat <wbr> a<br>
15:42:06.425 [main] DEBUG <a href="http://loci.formats.in" target="_blank">loci.formats.in</a>.MinimalTiffRea<wbr>der - Found IFD with JPE <wbr> G 2000 compression<br>
15:42:06.427 [main] INFO <a href="http://l.formats.in" target="_blank">l.formats.in</a>.JPEG2000MetadataP<wbr>arser - Unknown JPEG 200 <wbr> 0 box 0x2f00 at 16<br>
15:42:06.428 [main] INFO <a href="http://l.formats.in" target="_blank">l.formats.in</a>.JPEG2000MetadataP<wbr>arser - File is a raw co <wbr> destream not a JP2.<br>
15:42:06.447 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Loaded propertie <wbr> s from: services.properties<br>
15:42:06.448 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.POIServi<wbr>ce and implementation class loci.formats <wbr> .services.POIServiceImpl<br>
15:42:06.448 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.MDBServi<wbr>ce and implementation class loci.formats <wbr> .services.MDBServiceImpl<br>
15:42:06.448 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.JPEGTurb<wbr>oService and implementation class loci.f <wbr> ormats.services.JPEGTurboServi<wbr>ceImpl<br>
15:42:06.449 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.JAIIIOSe<wbr>rvice and implementation class loci.form <wbr> ats.services.JAIIIOServiceImpl<br>
15:42:06.450 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.WlzServi<wbr>ce and implementation class loci.formats <wbr> .services.WlzServiceImpl<br>
15:42:06.451 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.JHDFServ<wbr>ice and implementation class loci.format <wbr> s.services.JHDFServiceImpl<br>
15:42:06.451 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.NetCDFSe<wbr>rvice and implementation class loci.form <wbr> ats.services.NetCDFServiceImpl<br>
15:42:06.452 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.EXIFServ<wbr>ice and implementation class loci.format <wbr> s.services.EXIFServiceImpl<br>
15:42:06.452 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.MetakitS<wbr>ervice and implementation class loci.for <wbr> mats.services.MetakitServiceIm<wbr>pl<br>
15:42:06.453 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.LuraWave<wbr>Service and implementation class
<a href="http://loci.fo" target="_blank">loci.fo</a> <wbr> rmats.services.LuraWaveService<wbr>Impl<br>
15:42:06.454 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.OMEXMLSe<wbr>rvice and implementation class loci.form <wbr> ats.services.OMEXMLServiceImpl<br>
15:42:06.455 [main] DEBUG loci.common.services.ServiceFa<wbr>ctory - Added interface <wbr> interface loci.formats.services.JPEGXRSe<wbr>rvice and implementation class loci.form <wbr> ats.services.JPEGXRServiceImpl<br>
15:42:06.493 [main] INFO loci.formats.in.BaseTiffReader - Populating OME metada <wbr> ta<br>
15:42:06.496 [main] DEBUG loci.formats.Memoizer - start[1516138926248] time[247] <wbr> tag[loci.formats.Memoizer.setI<wbr>d]<br>
15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre <wbr> am.raw -> null<br>
15:42:06.509 [main] DEBUG loci.common.Location - Location.mapFile: embedded-stre <wbr> am.raw -> null<br>
15:42:06.510 [main] DEBUG o.formats.importer.cli.ErrorHa<wbr>ndler - SCANNING: Depth: <wbr> 0 Num: 1 Tot: 1 File: /tmp/571.svs<br>
15:42:06.511 [main] INFO o.formats.importer.ImportCandi<wbr>dates - 1 file(s) parsed <wbr> 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 <wbr> ://<a href="http://upgrade.openmicroscopy.org.uk?version=5.3.5-ice36-b73;os.name=Linux;os.arch=a" target="_blank">upgrade.openmicroscopy.org.<wbr>uk?version=5.3.5-ice36-b73;os.<wbr>name=Linux;os.arch=a</a> <wbr>
md64;os.version=3.10.0-693.5.2<wbr>.el7.x86_64;java.runtime.versi<wbr>on=1.8.0_151-b12;jav <wbr> a.vm.vendor=Oracle+Corporation "Connection refused (Connection refused)"<br>
15:42:06.773 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - Attempting init <wbr> ial SSL connection to localhost:4064<br>
15:42:07.295 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - Insecure connec <wbr> tion requested, falling back<br>
15:42:07.351 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - closing client <wbr> session.<br>
15:42:07.360 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - client closed.<br>
15:42:07.605 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - Server: 5.3.5<br>
15:42:07.606 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - Client: 5.3.5-i <wbr> ce36-b73<br>
15:42:07.606 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - Java Version: 1 <wbr> .8.0_151<br>
15:42:07.606 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - OS Name: Linux<br>
15:42:07.606 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - OS Arch: amd64<br>
15:42:07.606 [main] INFO ome.formats.OMEROMetadataStore<wbr>Client - OS Version: 3.1 <wbr> 0.0-693.5.2.el7.x86_64<br>
15:42:07.704 [main] DEBUG ome.formats.importer.ImportLib<wbr>rary - Main file: /tmp/5 <wbr> 71.svs<br>
15:42:07.704 [main] DEBUG ome.formats.importer.ImportLib<wbr>rary - Used files before <wbr> :<br>
15:42:07.704 [main] DEBUG ome.formats.importer.ImportLib<wbr>rary - /tmp/571.svs<br>
15:42:07.708 [main] INFO o.f.i.cli.LoggingImportMonitor - FILESET_UPLOAD_PREPAR <wbr> ATION<br>
15:42:07.735 [main] DEBUG o.s.blitz.util.CurrentPlatform - recognized current op <wbr> 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.SymlinkFileTra<wbr>nsfer - Transferring /tm <wbr> p/571.svs...<br>
15:42:08.156 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_STARTED: <wbr> /tmp/571.svs<br>
15:42:10.456 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_BYTES upl <wbr> oaded: 313025695 of: 313025695 bytes (ETA: 0' 0")<br>
15:42:12.967 [main] DEBUG o.f.importer.transfers.Transfe<wbr>rState - dunn0172_102/20 <wbr> 18-01/16/15-42-07.816//571.svs id=4295<br>
15:42:12.967 [main] DEBUG o.f.importer.transfers.Transfe<wbr>rState - checksums: clie <wbr> nt=e42776463f16e21dc0c56e232b1<wbr>4b7f89be0053b,server=e42776463<wbr>f16e21dc0c56e232b14b <wbr>
7f89be0053b<br>
15:42:12.967 [main] INFO o.f.i.cli.LoggingImportMonitor - FILE_UPLOAD_COMPLETE: <wbr> /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 <wbr> e: 4294<br>
15:42:16.307 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - ME <wbr> TADATA_IMPORTED Step: 1 of 5 Logfile: 4294<br>
15:42:17.411 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - PI <wbr> XELDATA_PROCESSED Step: 2 of 5 Logfile: 4294<br>
15:42:18.501 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - TH <wbr> UMBNAILS_GENERATED Step: 3 of 5 Logfile: 4294<br>
15:42:18.529 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - ME <wbr> TADATA_PROCESSED Step: 4 of 5 Logfile: 4294<br>
15:42:18.548 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - OB <wbr> JECTS_RETURNED Step: 5 of 5 Logfile: 4294<br>
15:42:18.751 [Ice.ThreadPool.Client-1] INFO o.f.i.cli.LoggingImportMonitor - IM <wbr> 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.ErrorHa<wbr>ndler <wbr> - 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.OMEROMetadataStore<wbr>Client - closing client <wbr> session.<br>
15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - client closed.<br>
15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - Logout called, <wbr> shutting keep alive down.<br>
15:42:18.796 [main] DEBUG ome.formats.OMEROMetadataStore<wbr>Client - keepalive shut <wbr> down.<br>
<br>
[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0<wbr>172_102/2018-01/16/15-42-07.<wbr>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<wbr>/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"><span class="m_-5508117184170654899gmail-"><br clear="all">
<div>
<div class="m_-5508117184170654899gmail-m_-7864205254332027326gmail_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>
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</span>
<div>
<div class="m_-5508117184170654899gmail-h5">
<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:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);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="m_-5508117184170654899gmail-m_-7864205254332027326HOEnZb"><font color="#888888"><br>
<br>
</font></span></div>
<span class="m_-5508117184170654899gmail-m_-7864205254332027326HOEnZb"><font color="#888888">Simon<br>
<div><br>
<br>
</div>
</font></span></div>
<div>
<div class="m_-5508117184170654899gmail-m_-7864205254332027326h5">
<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:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);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_3/2018-01/12/11-36-06<wbr>.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_3/2018-01/12/11-36-06<wbr>.810/561.svs<br>
-rw-r--r-- 1 omero inplace_user 36 Jan 12 11:36 /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-36-06<wbr>.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(Nativ<wbr>e Method) ~[na:1.8.0_151]<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance(Native<wbr>ConstructorAccessorImpl.java:6<wbr>2) ~[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.java<wbr>: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(Basic<wbr>Stream.java:3298) ~[ice.jar:na]<br>
at IceInternal.BasicStream.throwE<wbr>xception(BasicStream.java:2291<wbr>) ~[ice.jar:na]<br>
at IceInternal.OutgoingAsync.thro<wbr>wUserException(OutgoingAsync.j<wbr>ava:399) ~[ice.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.end_save(RawFileStorePrxHelp<wbr>er.java:724) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.j<wbr>ava:611) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.j<wbr>ava: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_3/2018-01/12/11-42-45<wbr>.714/561.svs: java.io.IOException: Permission denied<br>
omero.ResourceError: null<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance0(Nativ<wbr>e Method) ~[na:1.8.0_151]<br>
at sun.reflect.NativeConstructorA<wbr>ccessorImpl.newInstance(Native<wbr>ConstructorAccessorImpl.java:6<wbr>2) ~[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.java<wbr>: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(Basic<wbr>Stream.java:3298) ~[ice.jar:na]<br>
at IceInternal.BasicStream.throwE<wbr>xception(BasicStream.java:2291<wbr>) ~[ice.jar:na]<br>
at IceInternal.OutgoingAsync.thro<wbr>wUserException(OutgoingAsync.j<wbr>ava:399) ~[ice.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.end_save(RawFileStorePrxHelp<wbr>er.java:724) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.j<wbr>ava:611) ~[blitz.jar:na]<br>
at omero.api.RawFileStorePrxHelpe<wbr>r.save(RawFileStorePrxHelper.j<wbr>ava: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_3/2018-01/12/11-42-45<wbr>.714/561.svs<br>
lrwxrwxrwx 1 inplace_user inplace_user 46 Jan 12 11:42 /omero/ManagedRepository/dunn0<wbr>172admin_3/2018-01/12/11-42-45<wbr>.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_-5508117184170654899gmail-m_-7864205254332027326m_-6071734035117955650m_-7026116517787571893gmail_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>
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<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:0px 0px 0px 0.8ex;border-left:1px solid rgb(204,204,204);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_-5508117184170654899gmail-m_-7864205254332027326m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888"><br>
</font></span>
<div><span class="m_-5508117184170654899gmail-m_-7864205254332027326m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888"></font></span>
<div><span class="m_-5508117184170654899gmail-m_-7864205254332027326m_-6071734035117955650m_-7026116517787571893HOEnZb"><font color="#888888">
<div><br>
</div>
<div>Simon<br>
</div>
</font></span>
<div>
<div class="m_-5508117184170654899gmail-m_-7864205254332027326m_-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_-5508117184170654899gmail-m_-7864205254332027326m_-6071734035117955650m_-7026116517787571893m_-6793648303585274199gmail-"><br clear="all">
<div>
<div class="m_-5508117184170654899gmail-m_-7864205254332027326m_-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>
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<div class="m_-5508117184170654899gmail-m_-7864205254332027326m_-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_-5508117184170654899gmail-m_-7864205254332027326m_-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_-5508117184170654899gmail-m_-7864205254332027326m_-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>
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<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>
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<br>
</div>
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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</div></div></div><div><div class="h5">
<br>
<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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