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

Sebastien Besson (Staff) s.besson at dundee.ac.uk
Fri Apr 3 12:53:00 BST 2015 

Hi Jake,

great news for the server start.
The `__import__` error indicates something is not properly configured with the webtest web application.
Note that the webtest example web application has been removed from the main repository since
5.1.0-m2 and need to be checked out separately.

In your case, you will need to do one the following to let OMERO.web start:

- either remove webtest from the web apps registered in the server configuration
$  bin/omero config remove omero.web.apps '”webtest”'

- or clone https://github.com/openmicroscopy/webtest, make sure it is available in your PYTHONPATH
  and restart OMERO.web

Let us know how this works,
Sebastien

On 3 Apr 2015, at 12:40, Jake Carroll <jake.carroll at uq.edu.au<mailto: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<mailto: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<mailto:josh at glencoesoftware.com>>
To: OME User Support List <ome-users at lists.openmicroscopy.org.uk<mailto: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<mailto: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<mailto: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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