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

Fri Apr 3 12:53:29 BST 2015

Hi Jake,

Sorry - go the wrong order on the command. 
It should be

$ bin/omero config remove omero.web.apps '"webtest"'

 Cheers,

   Will.

On 3 Apr 2015, at 12:51, William Moore <will at lifesci.dundee.ac.uk> wrote:

> Hi Jake,
> 
> It seems you've got the 'webtest' web app listed in your installed apps, but it isn't
> available on your $PYTHONPATH.
> 
> To confirm, can you do:
> 
> $ bin/omero config get omero.web.apps
> 
> Do you see 'webtest' listed?
> 
> If so, and you want to uninstall it, you can do this (NB: single and double quotes on '"wettest"')
> 
> $ bin/omero config remove '"webtest"' omero.web.apps
> 
> Alternatively, you should make sure that the 'webtest' directory of the webtest app is in
> a directory that is on your $PYTHONPATH.
> 
> Hope that helps,
> 
>   Will.
> 
> 
> 
> On 3 Apr 2015, at 12:40, Jake Carroll <jake.carroll at uq.edu.au> wrote:
> 
>> Hi Josh et al.
>> 
>> Good news and bad - see way down below.
>> 
>>> 
>>> On Fri, Apr 3, 2015 at 2:02 AM, Jake Carroll <jake.carroll at uq.edu.au>
>>> wrote:
>>>> Hi.
>>> 
>>> Hi Jake,
>>> 
>>> 
>>>> We've been running omero 5.xx.xx for a long time now on Ubuntu 14
>>>> series server environments.
>>>> 
>>>> I upgraded our development host this morning to omero 5.1.0.
>>>> 
>>>> For reference, the server:
>>>> 
>>>> DISTRIB_ID=Ubuntu
>>>> DISTRIB_RELEASE=14.04
>>>> DISTRIB_CODENAME=trusty
>>>> DISTRIB_DESCRIPTION="Ubuntu 14.04.2 LTS"
>>>> 
>>>> Anyway - after upgrading to omero 5.1.0 in the usual way, I found that
>>>> running an "omero admin start" end the end paused/failed then killed off
>>>> remaining daemons/processes. In the master.err I found:
>>>> 
>>>> 
>>>> omero at omero-devel-relegated:~$ 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
>>> 
>>> 
>>> ------------------------------
>>> 
>>> Subject: Digest Footer
>>> 
>>> _______________________________________________
>>> ome-users mailing list
>>> ome-users at lists.openmicroscopy.org.uk
>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>> 
>>> 
>>> ------------------------------
>>> 
>>> End of ome-users Digest, Vol 121, Issue 4
>>> *****************************************
>> 
>> _______________________________________________
>> ome-users mailing list
>> ome-users at lists.openmicroscopy.org.uk
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users