<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/*/*/*/*<br>chgrp inplace_user /omero/ManagedRepository/*<br>chgrp inplace_user /omero/ManagedRepository/*/*<br>chgrp inplace_user /omero/ManagedRepository/*/*/*<br>chgrp inplace_user /omero/ManagedRepository/*/*/*/*<br><br>[inplace_user@nunstudy-omero 11]$ omero import -- --transfer=ln_s /mnt/ahc-ns/Pathology/NunStudy/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/NS-1137/562.svs<br>11:43:03.105 [main] DEBUG o.f.i.cli.LoggingImportMonitor - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs<br>11:43:03.106 [main] ERROR o.formats.importer.cli.ErrorHandler - FILE_EXCEPTION: /mnt/ahc-ns/Pathology/NunStudy/NS-1137/562.svs<br>java.lang.RuntimeException:<br>---------------------------------------------------<br>Check failed: /omero/ManagedRepository/dunn0172admin_3/2018-01/11/11-43-02.765/562.svs cannot be modified locally!<br>You likely do not have access to the ManagedRepository for in-place import.<br>Aborting...<br><br>[inplace_user@nunstudy-omero ~]$ ls -la /omero/ManagedRepository/dunn0172admin_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/dunn0172admin_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/dunn0172admin_3/2018-01/11/11-43-02.765/<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="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'. 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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:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">Dear Brian,<span class=""><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 class=""><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-<wbr>14.918/561.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-<wbr>14.918/ directory?<br>
<br>
-- Mark<br>
<br>
The University of Dundee is a registered Scottish Charity, No: SC015096<br>
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