<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'. 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 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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