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Hi John
<div><br>
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<div>This sounds familiar- it was due to a bug in 4.4.6 with Python 2.4:
<div><a href="http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-March/003593.html">http://lists.openmicroscopy.org.uk/pipermail/ome-users/2013-March/003593.html</a></div>
<div><br>
</div>
<div>Simon</div>
<div><br>
<div>
<div>On 9 Jul 2013, at 15:53, "John Webber (NBI)" <<a href="mailto:John.Webber@nbi.ac.uk">John.Webber@nbi.ac.uk</a>></div>
<div> wrote:</div>
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All,</div>
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</div>
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Sorry for another email from me - I do not seem to be getting very far with Omero today!</div>
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<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
Due to issues with the LDAP authentication (as per my last email) for OMERO.server version 4.4.8, I thought I would attempt to use a previous version of OMERO.server (4.4.6) that I already have running on another server. To this end I have therefore downloaded
OMERO.server 4.4.6 and have started to switch to this version on my server.</div>
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</div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
I have stopped both web and admin for version 4.4.8 of OMERO.server, and I have stopped the HTTPD service.</div>
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</div>
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I have downloaded and unpacked version 4.4.6 of OMERO.Server into /opt. I therefore now have the following:</div>
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<span class="Apple-converted-space"> </span><span style="font-size:9pt">/opt/OMERO.server-4.4.6-ice33-b102 </span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">And /opt/OMERO.server-4.4.8-ice33-b256</span></div>
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</div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
I believe that I have all of my environment variables set correctly, and the correct software versions, for example:</div>
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<span style="font-size:9pt"> </span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo $PATH<span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/local/bin:/bin:/usr/bin:/home/omero/bin:/usr/java/default/bin:/usr/java/default/bin:/usr/share/Ice-3.3.1/bin</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo $PYTHONPATH<span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/lib/python2.4</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo $LD_LIBRARY_PATH <span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/share/java:/usr/lib/</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo $ICE_HOME<span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/share/Ice-3.3.1</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo $DYLD_LIBRARY_PATH<span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/share/java:/usr/lib/</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">java –version </span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span> java version "1.7.0_07"</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif; text-indent:36pt">
<span style="font-size:9pt">Java(TM) SE Runtime Environment (build 1.7.0_07-b10)</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif; text-indent:36pt">
<span style="font-size:9pt">Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">python –V<span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span> Python 2.4.3</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo JAVA_HOME </span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/java/default</span></div>
<div style="margin:0cm 0cm 0.0001pt 36pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">echo JRE_HOME <span class="Apple-converted-space"> </span></span><span style="font-size:9pt; font-family:Wingdings">à</span><span style="font-size:9pt"><span class="Apple-converted-space"> </span>/usr/java/default</span></div>
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</div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
Now, as the “omero” user, I am attempting to run : “bin/omero admin diagnostics” for both version of OMERO.server. For the version of Omero that I started on this server with, (4.4.8), this command runs correctly and I see the diagnostic information for
OMERO.server, as per the attached file.</div>
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</div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
However, when I attempt to run : “bin/omero admin diagnostics” for the older version of OMERO.server (4.4.6), I see the following errors:</div>
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<span style="font-size:9pt">[omero@v0324 OMERO.server-4.4.6-ice33-b102]$ bin/omero admin diagnostics</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">Error loading: /opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py</span></div>
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<span style="font-size:9pt">Traceback (most recent call last):</span></div>
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<span style="font-size:9pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/cli.py", line 1138, in loadpath</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> execfile( str(pathobj), loc )</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py", line 434</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> finally:</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> ^</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">SyntaxError: invalid syntax</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">Error loading: /opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/node.py</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">Traceback (most recent call last):</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/cli.py", line 1138, in loadpath</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> execfile( str(pathobj), loc )</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/node.py", line 17, in ?</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> from omero.plugins.admin import AdminControl</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py", line 434</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> finally:</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> ^</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">SyntaxError: invalid syntax</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">usage: bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-C] [-s SERVER] [-p PORT]</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> [-g GROUP] [-u USER] [-w PASSWORD] [-k KEY]</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> <subcommand> ...</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">bin/omero: error: argument <subcommand>: invalid choice: 'admin'</span></div>
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<span style="font-size:9pt"> </span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">choose from:</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> cecog, chgrp, config, db, delete, download, export, group, help,</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> hql, import, ldap, load, login, logout, perf, quit, script, search,</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt"> server, sessions, shell, testengine, upload, user, version, web</span></div>
<div style="margin:0cm 0cm 0.0001pt 72pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="font-size:9pt">[omero@v0324 OMERO.server-4.4.6-ice33-b102]$</span></div>
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</div>
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Can anyone give me any pointers as to why this is not working?</div>
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<br>
Thanks</div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
John</div>
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</div>
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<b><span style="font-size:10pt; font-family:Arial,sans-serif; color:rgb(79,129,189)">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<b><span style="font-family:Arial,sans-serif; color:rgb(84,141,212)">John Webber<br>
</span></b><span style="color:rgb(31,73,125)">Computing and Information Services</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">NBI Partnership Ltd</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">Norwich Research park</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">Colney Lane</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">Norwich</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">NR4 7UH</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)"> </span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">E-Mail: <span class="Apple-converted-space"> </span><a href="mailto:john.webber@nbi.ac.uk" style="color:rgb(149,79,114); text-decoration:underline"><span style="color:blue">john.webber@nbi.ac.uk</span></a></span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">Web: <span class="Apple-converted-space"> </span><a href="http://www.nbi.ac.uk/" style="color:rgb(149,79,114); text-decoration:underline"><span style="color:blue">http://www.nbi.ac.uk</span></a></span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif; line-height:12pt; background-color:white">
<span style="color:rgb(31,73,125)">Tel: +44(0)1603 450 818</span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
<span style="color:rgb(31,73,125)"> </span><span style="color:rgb(15,18,111)"></span></div>
<div style="margin:0cm 0cm 0.0001pt; font-size:11pt; font-family:Calibri,sans-serif">
<i><span style="color:rgb(31,73,125)">The NBI Partnership Ltd provides non-scientific services to the Institute of Food Research, the John Innes Centre, The Genome Analysis Centre and The Sainsbury Laboratory</span></i><span style="color:rgb(15,18,111)"></span></div>
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</div>
</div>
<span><admin.diagnostics.txt></span>_______________________________________________<br>
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</blockquote>
</div>
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<span style="font-size:10pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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