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<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=">
https://www.freedesktop.org/software/systemd/man/systemd.exec.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.<br>
<div>
<div>
<div><br>
</div>
<div>Simon<br>
</div>
<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">
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<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.<wbr>org/omero/5.3.5/sysadmins/<wbr>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" target="_blank">https://docs.openmicroscopy.<wbr>org/omero/5.3.5/_downloads/<wbr>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:<wbr>1003:1003::/home/inplace_user:<wbr>/bin/bash<br>
/etc/group:omero:x:1002:<wbr>inplace_user<br>
/etc/group:inplace_user:x:<wbr>1003:<br>
<br>
# /etc/fstab<br>
UUID=e96e0f81-c366-4c30-bc2b-<wbr>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" target="_blank">files.umn.edu/ahc-ns</a> /mnt/ahc-ns/ cifs credentials=/root/files.umn.<wbr>edu.creds,dir_mode=0777,file_<wbr>mode=0777,sec=ntlmssp,uid=<wbr>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"><span class="gmail-"><br clear="all">
<div>
<div class="gmail-m_-9178000793618904860gmail_signature">
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<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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<div class="gmail-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="gmail-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="gmail-m_-9178000793618904860m_5622562909497765594m_8605135310308664991gmail_signature">
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<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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<div class="gmail-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>
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