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<p class="MsoNormal">All,<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Sorry for another email from me - I do not seem to be getting very far with Omero today!<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have stopped both web and admin for version 4.4.8 of OMERO.server, and I have stopped the HTTPD service.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I have downloaded and unpacked version 4.4.6 of OMERO.Server into /opt. I therefore now have the following:<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"> <span style="font-size:9.0pt">
/opt/OMERO.server-4.4.6-ice33-b102 <o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">And /opt/OMERO.server-4.4.8-ice33-b256<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">I believe that I have all of my environment variables set correctly, and the correct software versions, for example:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo $PATH
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/local/bin:/bin:/usr/bin:/home/omero/bin:/usr/java/default/bin:/usr/java/default/bin:/usr/share/Ice-3.3.1/bin<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo $PYTHONPATH
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/lib/python2.4<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo $LD_LIBRARY_PATH
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/share/java:/usr/lib/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo $ICE_HOME
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/share/Ice-3.3.1<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo $DYLD_LIBRARY_PATH
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/share/java:/usr/lib/<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">java –version </span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> java version "1.7.0_07"<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt;text-indent:36.0pt"><span style="font-size:9.0pt">Java(TM) SE Runtime Environment (build 1.7.0_07-b10)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt;text-indent:36.0pt"><span style="font-size:9.0pt">Java HotSpot(TM) 64-Bit Server VM (build 23.3-b01, mixed mode)<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">python –V
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> Python 2.4.3<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo JAVA_HOME </span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/java/default<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:36.0pt"><span style="font-size:9.0pt">echo JRE_HOME
</span><span style="font-size:9.0pt;font-family:Wingdings">à</span><span style="font-size:9.0pt"> /usr/java/default<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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.<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">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:<o:p></o:p></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">[omero@v0324 OMERO.server-4.4.6-ice33-b102]$ bin/omero admin diagnostics<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">Error loading: /opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/cli.py", line 1138, in loadpath<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> execfile( str(pathobj), loc )<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py", line 434<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> finally:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> ^<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">Error loading: /opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/node.py<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/cli.py", line 1138, in loadpath<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> execfile( str(pathobj), loc )<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/node.py", line 17, in ?<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> from omero.plugins.admin import AdminControl<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> File "/opt/OMERO.server-4.4.6-ice33-b102/lib/python/omero/plugins/admin.py", line 434<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> finally:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> ^<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">SyntaxError: invalid syntax<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">usage: bin/omero [-h] [-v] [-d DEBUG] [--path PATH] [-C] [-s SERVER] [-p PORT]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> [-g GROUP] [-u USER] [-w PASSWORD] [-k KEY]<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> <subcommand> ...<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">bin/omero: error: argument <subcommand>: invalid choice: 'admin'<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"><o:p> </o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">choose from:<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> cecog, chgrp, config, db, delete, download, export, group, help,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> hql, import, ldap, load, login, logout, perf, quit, script, search,<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt"> server, sessions, shell, testengine, upload, user, version, web<o:p></o:p></span></p>
<p class="MsoNormal" style="margin-left:72.0pt"><span style="font-size:9.0pt">[omero@v0324 OMERO.server-4.4.6-ice33-b102]$<o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Can anyone give me any pointers as to why this is not working?<o:p></o:p></p>
<p class="MsoNormal"><br>
Thanks<o:p></o:p></p>
<p class="MsoNormal">John<o:p></o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-size:10.0pt;font-family:"Arial","sans-serif";color:#4F81BD;mso-fareast-language:EN-GB">-------------------------------------------------------------------------------------------------------------------------------------------- </span></b><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><b><span style="font-family:"Arial","sans-serif";color:#548DD4;mso-fareast-language:EN-GB">John Webber<br>
</span></b><span style="color:#1F497D;mso-fareast-language:EN-GB">Computing and Information Services</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NBI Partnership Ltd</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich Research park</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Colney Lane</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Norwich</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">NR4 7UH</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">E-Mail:
<a href="mailto:john.webber@nbi.ac.uk"><span style="color:blue">john.webber@nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Web:
<a href="http://www.nbi.ac.uk"><span style="color:blue">http://www.nbi.ac.uk</span></a></span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal" style="line-height:12.0pt;background:white"><span style="color:#1F497D;mso-fareast-language:EN-GB">Tel: +44(0)1603 450 818</span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><span style="color:#1F497D;mso-fareast-language:EN-GB"> </span><span style="color:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><i><span style="color:#1F497D;mso-fareast-language:EN-GB">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:#0F126F;mso-fareast-language:EN-GB"><o:p></o:p></span></p>
<p class="MsoNormal"><o:p> </o:p></p>
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