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Hi Jake,
<div class=""><br class="">
</div>
<div class="">great news for the server start.</div>
<div class="">The `__import__` error indicates something is not properly configured with the webtest web application.</div>
<div class="">Note that the webtest example web application has been removed from the main repository since</div>
<div class="">5.1.0-m2 and need to be checked out separately.</div>
<div class=""><br class="">
</div>
<div class="">In your case, you will need to do one the following to let OMERO.web start:</div>
<div class=""><br class="">
</div>
<div class="">- either remove webtest from the web apps registered in the server configuration</div>
<div class="">$ bin/omero config remove omero.web.apps '”webtest”'</div>
<div class=""><br class="">
</div>
<div class="">
<div class="">- or clone <a href="https://github.com/openmicroscopy/webtest" class="">https://github.com/openmicroscopy/webtest</a>, make sure it is available in your PYTHONPATH</div>
<div class=""> and restart OMERO.web</div>
<div class=""><br class="">
</div>
<div class="">Let us know how this works,</div>
<div class="">Sebastien</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 3 Apr 2015, at 12:40, Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au" class="">jake.carroll@uq.edu.au</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Hi Josh et al.<br class="">
<br class="">
Good news and bad - see way down below.<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
On Fri, Apr 3, 2015 at 2:02 AM, Jake Carroll <<a href="mailto:jake.carroll@uq.edu.au" class="">jake.carroll@uq.edu.au</a>><br class="">
wrote:<br class="">
<blockquote type="cite" class="">Hi.<br class="">
</blockquote>
<br class="">
Hi Jake,<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">We've been running omero 5.xx.xx for a long time now on Ubuntu 14<br class="">
series server environments.<br class="">
<br class="">
I upgraded our development host this morning to omero 5.1.0.<br class="">
<br class="">
For reference, the server:<br class="">
<br class="">
DISTRIB_ID=Ubuntu<br class="">
DISTRIB_RELEASE=14.04<br class="">
DISTRIB_CODENAME=trusty<br class="">
DISTRIB_DESCRIPTION="Ubuntu 14.04.2 LTS"<br class="">
<br class="">
Anyway - after upgrading to omero 5.1.0 in the usual way, I found that<br class="">
running an "omero admin start" end the end paused/failed then killed off<br class="">
remaining daemons/processes. In the master.err I found:<br class="">
<br class="">
<br class="">
omero@omero-devel-relegated:~$ tail -100 OMERO.server/var/log/master.err<br class="">
-! 04/03/15 09:38:20.041 OMERO.Glacier2: warning: unable to contact<br class="">
permissions verifier `BlitzVerifier@BlitzAdapters'<br class="">
Reference.cpp:1663: Ice::NoEndpointException:<br class="">
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @<br class="">
BlitzAdapters'<br class="">
-! 04/03/15 09:38:20.043 OMERO.Glacier2: warning: unable to contact<br class="">
session manager `BlitzManager@BlitzAdapters'<br class="">
Reference.cpp:1663: Ice::NoEndpointException:<br class="">
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @<br class="">
BlitzAdapters'<br class="">
-! 04/03/15 09:49:40.137 OMERO.Glacier2: warning: unable to contact<br class="">
permissions verifier `BlitzVerifier@BlitzAdapters'<br class="">
Reference.cpp:1663: Ice::NoEndpointException:<br class="">
no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @<br class="">
BlitzAdapters'<br class="">
-! 04/03/15 09:49:40.139 OMERO.Glacier2: warning: unable to contact<br class="">
session manager `BlitzManager@BlitzAdapters'<br class="">
Reference.cpp:1663: Ice::NoEndpointException:<br class="">
no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @<br class="">
BlitzAdapters'<br class="">
<br class="">
I'd not seen this behavior before.<br class="">
<br class="">
Ideas?<br class="">
</blockquote>
<br class="">
I don't think this would be related to the Ubuntu version and is more<br class="">
likely a configuration issue, perhaps something we need to explain<br class="">
better in the upgrade guide.<br class="">
<br class="">
<blockquote type="cite" class="">From what 5.0 version were you upgrading? Did you change any other<br class="">
</blockquote>
dependencies at the same time, e.g. Ice 3.4 to 3.5? Are there any<br class="">
errors in var/log/Blitz-0.log?<br class="">
</blockquote>
<br class="">
Good news - I got the omero admin component up and running. Simply put I<br class="">
had to run the database scripted upgrade, as per the documentation.<br class="">
<br class="">
Bad news: However, when I attempt an Œomero web start¹<br class="">
<br class="">
root@omero-devel-relegated:~# su - omero<br class="">
omero@omero-devel-relegated:~$ omero web start<br class="">
Traceback (most recent call last):<br class="">
File "manage.py", line 56, in <module><br class="">
execute_from_command_line(sys.argv)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/core/management/__init__.py",<br class="">
line 399, in execute_from_command_line<br class="">
utility.execute()<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/core/management/__init__.py",<br class="">
line 392, in execute<br class="">
self.fetch_command(subcommand).run_from_argv(self.argv)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/core/management/base.py", line<br class="">
242, in run_from_argv<br class="">
self.execute(*args, **options.__dict__)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/core/management/base.py", line<br class="">
280, in execute<br class="">
translation.activate('en-us')<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/utils/translation/__init__.py",<br class="">
line 130, in activate<br class="">
return _trans.activate(language)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py<br class="">
", line 188, in activate<br class="">
_active.value = translation(language)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py<br class="">
", line 177, in translation<br class="">
default_translation = _fetch(settings.LANGUAGE_CODE)<br class="">
File <br class="">
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py<br class="">
", line 159, in _fetch<br class="">
app = import_module(appname)<br class="">
File "/home/omero/OMERO.server/lib/python/django/utils/importlib.py",<br class="">
line 40, in import_module<br class="">
__import__(name)<br class="">
ImportError: No module named webtest<br class="">
<br class="">
<br class="">
<br class="">
Thoughts?</div>
</blockquote>
<blockquote type="cite" class="">
<div class=""><br class="">
-jc<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class=""><br class="">
Cheers,<br class="">
~Josh.<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">Thanks, all!<br class="">
<br class="">
-jc<br class="">
</blockquote>
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
Message: 6<br class="">
Date: Fri, 3 Apr 2015 09:57:21 +0200<br class="">
From: Josh Moore <<a href="mailto:josh@glencoesoftware.com" class="">josh@glencoesoftware.com</a>><br class="">
To: OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
Subject: Re: [ome-users] Bioformats: is it possible to create a<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span>pyramidal tiled OME-TIFF using bfconvert<br class="">
Message-ID:<br class="">
<span class="Apple-tab-span" style="white-space:pre"></span><<a href="mailto:CAD3Ea=U4x=rZvOLcOYsEqRUHsm-sP6vi3ncUp=fLiPYgtRr4gw@mail.gmail.com" class="">CAD3Ea=U4x=rZvOLcOYsEqRUHsm-sP6vi3ncUp=fLiPYgtRr4gw@mail.gmail.com</a>><br class="">
Content-Type: text/plain; charset=UTF-8<br class="">
<br class="">
Hi Dmitry,<br class="">
<br class="">
On Fri, Apr 3, 2015 at 6:15 AM, Dmitry Fedorov <<a href="mailto:fedorov@ece.ucsb.edu" class="">fedorov@ece.ucsb.edu</a>><br class="">
wrote:<br class="">
<blockquote type="cite" class="">Dear bioformatters, Melissa,<br class="">
<br class="">
Congratulations on your 5.1 release and thank you very much for fixing<br class="">
-z<br class="">
and -timepoint in bfconvert. It's working great and really improves our<br class="">
user<br class="">
experience!<br class="">
</blockquote>
<br class="">
It's great to hear that. It makes the effort worth it! Thanks.<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">I wanted to ask if it is possible to instruct bfconvert to generate a<br class="">
pyramidal tiled OME-TIFF file. Something like:<br class="">
-bigtiff -compression LZW -pyramid -tile 256<br class="">
</blockquote>
<br class="">
It's not currently, no, but I've certainly jotted down your interest.<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">Thank you,<br class="">
dmitry<br class="">
</blockquote>
<br class="">
Cheers,<br class="">
~Josh<br class="">
<br class="">
<br class="">
------------------------------<br class="">
<br class="">
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