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

Fri Apr 3 12:51:48 BST 2015

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
>> 
>> 
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>> 
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