<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">https://docs.openmicroscopy.org/omero/5.3.5/sysadmins/unix/server-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">https://docs.openmicroscopy.org/omero/5.3.5/_downloads/omero-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:1003:1003::/home/inplace_user:/bin/bash<br>/etc/group:omero:x:1002:inplace_user<br>/etc/group:inplace_user:x:1003:<br><br># /etc/fstab<br>UUID=e96e0f81-c366-4c30-bc2b-3a6f47d54d13 / 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">files.umn.edu/ahc-ns</a> /mnt/ahc-ns/ cifs credentials=/root/files.umn.edu.creds,dir_mode=0777,file_mode=0777,sec=ntlmssp,uid=1002,gid=1003 0 0<br></span></font></blockquote><div><br></div><div></div><div>Thanks, <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 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:0 0 0 .8ex;border-left:1px #ccc solid;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="h5">
<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:0 0 0 .8ex;border-left:1px #ccc solid;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-<wbr>02.765/562.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-<wbr>02.765/<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_5622562909497765594m_8605135310308664991gmail_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>
<div>
<div class="m_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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">
Dear Brian,<span><br>
<br>
<blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;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:0 0 0 .8ex;border-left:1px #ccc solid;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">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>