[ome-users] omero 5.1.0 server might be broken on Ubuntu 14.0.4.x

[Jake Carroll]

Hi Josh et al.

Good news and bad - see way down below.

>
>On Fri, Apr 3, 2015 at 2:02 AM, Jake Carroll <jake.carroll at uq.edu.au>
>wrote:
>> Hi.
>
>Hi Jake,
>
>
>> We've been running omero 5.xx.xx for a long time now on Ubuntu 14
>>series server environments.
>>
>> I upgraded our development host this morning to omero 5.1.0.
>>
>> For reference, the server:
>>
>> DISTRIB_ID=Ubuntu
>> DISTRIB_RELEASE=14.04
>> DISTRIB_CODENAME=trusty
>> DISTRIB_DESCRIPTION="Ubuntu 14.04.2 LTS"
>>
>> Anyway - after upgrading to omero 5.1.0 in the usual way, I found that
>>running an "omero admin start" end the end paused/failed then killed off
>>remaining daemons/processes. In the master.err I found:
>>
>>
>> omero at omero-devel-relegated:~$ tail -100 OMERO.server/var/log/master.err
>> -! 04/03/15 09:38:20.041 OMERO.Glacier2: warning: unable to contact
>>permissions verifier `BlitzVerifier at BlitzAdapters'
>>    Reference.cpp:1663: Ice::NoEndpointException:
>>    no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @
>>BlitzAdapters'
>> -! 04/03/15 09:38:20.043 OMERO.Glacier2: warning: unable to contact
>>session manager `BlitzManager at BlitzAdapters'
>>    Reference.cpp:1663: Ice::NoEndpointException:
>>    no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @
>>BlitzAdapters'
>> -! 04/03/15 09:49:40.137 OMERO.Glacier2: warning: unable to contact
>>permissions verifier `BlitzVerifier at BlitzAdapters'
>>    Reference.cpp:1663: Ice::NoEndpointException:
>>    no suitable endpoint available for proxy `BlitzVerifier -t -e 1.1 @
>>BlitzAdapters'
>> -! 04/03/15 09:49:40.139 OMERO.Glacier2: warning: unable to contact
>>session manager `BlitzManager at BlitzAdapters'
>>    Reference.cpp:1663: Ice::NoEndpointException:
>>    no suitable endpoint available for proxy `BlitzManager -t -e 1.1 @
>>BlitzAdapters'
>>
>> I'd not seen this behavior before.
>>
>> Ideas?
>
>I don't think this would be related to the Ubuntu version and is more
>likely a configuration issue, perhaps something we need to explain
>better in the upgrade guide.
>
>>From what 5.0 version were you upgrading? Did you change any other
>dependencies at the same time, e.g. Ice 3.4 to 3.5? Are there any
>errors in var/log/Blitz-0.log?

Good news - I got the omero admin component up and running. Simply put I
had to run the database scripted upgrade, as per the documentation.

Bad news: However, when I attempt an Œomero web start¹

root at omero-devel-relegated:~# su - omero
omero at omero-devel-relegated:~$ omero web start
Traceback (most recent call last):
  File "manage.py", line 56, in <module>
    execute_from_command_line(sys.argv)
  File 
"/home/omero/OMERO.server/lib/python/django/core/management/__init__.py",
line 399, in execute_from_command_line
    utility.execute()
  File 
"/home/omero/OMERO.server/lib/python/django/core/management/__init__.py",
line 392, in execute
    self.fetch_command(subcommand).run_from_argv(self.argv)
  File 
"/home/omero/OMERO.server/lib/python/django/core/management/base.py", line
242, in run_from_argv
    self.execute(*args, **options.__dict__)
  File 
"/home/omero/OMERO.server/lib/python/django/core/management/base.py", line
280, in execute
    translation.activate('en-us')
  File 
"/home/omero/OMERO.server/lib/python/django/utils/translation/__init__.py",
 line 130, in activate
    return _trans.activate(language)
  File 
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py
", line 188, in activate
    _active.value = translation(language)
  File 
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py
", line 177, in translation
    default_translation = _fetch(settings.LANGUAGE_CODE)
  File 
"/home/omero/OMERO.server/lib/python/django/utils/translation/trans_real.py
", line 159, in _fetch
    app = import_module(appname)
  File "/home/omero/OMERO.server/lib/python/django/utils/importlib.py",
line 40, in import_module
    __import__(name)
ImportError: No module named webtest



Thoughts?

-jc



>
>Cheers,
>~Josh.
>
>
>> Thanks, all!
>>
>> -jc
>
>
>------------------------------
>
>Message: 6
>Date: Fri, 3 Apr 2015 09:57:21 +0200
>From: Josh Moore <josh at glencoesoftware.com>
>To: OME User Support List <ome-users at lists.openmicroscopy.org.uk>
>Subject: Re: [ome-users] Bioformats: is it possible to create a
>	pyramidal tiled OME-TIFF using bfconvert
>Message-ID:
>	<CAD3Ea=U4x=rZvOLcOYsEqRUHsm-sP6vi3ncUp=fLiPYgtRr4gw at mail.gmail.com>
>Content-Type: text/plain; charset=UTF-8
>
>Hi Dmitry,
>
>On Fri, Apr 3, 2015 at 6:15 AM, Dmitry Fedorov <fedorov at ece.ucsb.edu>
>wrote:
>> Dear bioformatters, Melissa,
>>
>> Congratulations on your 5.1 release and thank you very much for fixing
>>-z
>> and -timepoint in bfconvert. It's working great and really improves our
>>user
>> experience!
>
>It's great to hear that. It makes the effort worth it! Thanks.
>
>
>> I wanted to ask if it is possible to instruct bfconvert to generate a
>> pyramidal tiled OME-TIFF file. Something like:
>> -bigtiff -compression LZW -pyramid -tile 256
>
>It's not currently, no, but I've certainly jotted down your interest.
>
>
>> Thank you,
>> dmitry
>
>Cheers,
>~Josh
>
>
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