[ome-users] OMERO.figure >> buttons and sliders in Preview window missing

Mon Jul 31 15:18:05 BST 2017

Dear Kenny,

I tried a complete requirements check and OMERO.figure reinstall
(removed the web app, removed omero-figure via pip, server reboot,
installed omero-figure and web app again), but that didn't change
anything. The channel sliders and buttons are still missing.

I uploaded the pip freeze output, the omero config output, the
master.err and the Blitz log to OMERO QA. Hope you can find something...

Best regards,

Martin

On 24.07.2017 15:30, Martin Wlotzka wrote:
> Hi Kenny,
>
> yes there are indeed pyramid issues with Leica .lif images. However, I
> uploaded the good/bad pyramid files for the other mailing list post on
> "Pyramids, fast/slow rendering and image size".
>
> Regarding the OMERO.figure issue, I uploaded the nginx logs and the
> OMERO.web log:
>
> nginx_access.log
> nginx_error.log
> OMEROweb_inspect_figure_missing_buttons.log
>
> Thanks for the hint on the OMERO.web requirements, I'll check that.
>
> Best regards,
> Martin
>
> On 24.07.2017 12:14, Kenneth Gillen (Staff) wrote:
>> Hi Martin,
>>
>>> Leica_16bit_bad_pyramid.lif
>> Is this a file you’d expect OMERO to import, and properly render? The
>> filename, `bad_pyramid` suggests you know of issues. I.e. is this
>> something you`d like to the Bio-Formats team to look at?  (a separate
>> issue to the OMERO.figure issue perhaps?)
>>
>> For me, this image loads in an OMERO 5.3.3 with Figure 3.1.1 server,
>> though (perhaps suggested by the filename), looks odd: yellowish
>> background, random spots. However, I can add labels, rotate, zoom and edit
>> the channels, which implies your Figure issue is not related to the image,
>> but to the setup of Figure.
>>
>>> Leica_8bit_good_pyramid.lif
>> And this second image, when loading into the same server, I see error:
>> `Image Leica_8bit_good_pyramid.lif is too big for OMERO.figure`. Is it
>> happily loaded by your own OMERO.figure?
>>
>>
>> The next thing I can think of is that some OMERO.web requirements are not
>> satisfied.
>>
>> If you could confirm which versions of the OMERO.web requirements
>> OMERO.web is configured to use, we can rule that out:
>>
>> e.g. your equivalent of: ~omero/omerowebvenv/bin/pip freeze
>>
>> Which will determine if you need to re-install/upgrade the OMERO.web
>> requirements, outlined in the install docs ubuntu walkthrough [1].
>>
>> If re-installing the web requirements doesn’t yield and instant result, if
>> you could also send us your OMERO configuration via omero config get
>> --hide-password, and your server’s Blitz-0.log, and master.err
>>
>>
>> [1]
>> https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk
>> through/omeroweb-install-ubuntu-ice3.6.html or
>>
>> All the best,
>>
>> Kenny
>>
>> --
>>
>> Kenneth Gillen
>>
>>
>> OME System Administrator
>>
>> Wellcome Trust Centre for Gene Regulation & Expression
>> School of Life Sciences
>> CTIR 2
>> University of Dundee
>> Dow Street
>> Dundee  DD1 5EH
>> United Kingdom
>>
>> Tel: +44 (0) 1382 388797
>>
>>
>> http://www.twitter.com/openmicroscopy
>>
>> ----
>>
>> Dear Kenny,
>>
>> I've uploaded the logs:
>>
>> nginx_access.log
>> nginx_error.log
>>
>> OMEROweb_inspect_figure_missing_buttons.log
>>
>> I also tried reinstalling, but that didn't change anything.
>>
>> Best,
>>
>> Martin
>>
>>
>>
>>
>>
>>
>>
>> On 19/07/2017 17:08, "ome-users on behalf of Kenneth Gillen (Staff)"
>> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
>> k.h.gillen at dundee.ac.uk> wrote:
>>
>>> It would be worth retrying the install of the plugin at the least.
>>>
>>> Then I¹d be thinking about at least sending us a .tar.gz or .zip of your
>>> OMEROweb.log and your NGINX log. Perhaps there¹s something in the NGINX
>>> log, for example, which is showing 404s or 5xx responses which might point
>>> to what is going on.
>>>
>>> You can send us logs via http://qa.openmicroscopy.org.uk/qa/upload/
>>>
>>> It¹d be interesting to hear if anyone else has come across this one. My
>>> own OMERO server upgraded to this version without issues on RHEL7, rather
>>> than Ubuntu.
>>>
>>>
>>> All the best,
>>>
>>> Kenny
>>>
>>> --
>>>
>>> Kenneth Gillen
>>>
>>> OME System Administrator
>>>
>>> Wellcome Trust Centre for Gene Regulation & Expression
>>> School of Life Sciences
>>> CTIR 2
>>> University of Dundee
>>> Dow Street
>>> Dundee  DD1 5EH
>>> United Kingdom
>>>
>>> Tel: +44 (0) 1382 388797
>>>
>>>
>>> http://www.twitter.com/openmicroscopy
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>>
>>> On 19/07/2017 15:08, "ome-users on behalf of Martin Wlotzka"
>>> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
>>> martin.wlotzka at uni-heidelberg.de> wrote:
>>>
>>>> Hi Kenny,
>>>>
>>>> yes I recently upgraded from 3.1.0 to 3.1.1, and the buttons / sliders
>>>> were there in 3.1.0. I already tried downgrading again, but that didn't
>>>> bring them back.
>>>>
>>>> -- Martin
>>>>
>>>>
>>>> On 19.07.2017 15:55, Kenneth Gillen (Staff) wrote:
>>>>> Hi Martin,
>>>>>
>>>>> Has OMERO.figure always been like this on this server? Was it, for
>>>>> example, installed, or upgraded recently?
>>>>>
>>>>> Many thanks
>>>>>
>>>>> Kenny
>>>>>
>>>>> --
>>>>>
>>>>> Kenneth Gillen
>>>>>
>>>>>
>>>>> OME System Administrator
>>>>>
>>>>> Wellcome Trust Centre for Gene Regulation & Expression
>>>>> School of Life Sciences
>>>>> CTIR 2
>>>>> University of Dundee
>>>>> Dow Street
>>>>> Dundee  DD1 5EH
>>>>> United Kingdom
>>>>>
>>>>> Tel: +44 (0) 1382 388797
>>>>>
>>>>>
>>>>> http://www.twitter.com/openmicroscopy
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>>
>>>>> On 19/07/2017 14:28, "ome-users on behalf of Martin Wlotzka"
>>>>> <ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
>>>>> martin.wlotzka at uni-heidelberg.de> wrote:
>>>>>
>>>>>> Dear all,
>>>>>>
>>>>>> when I open images in OMERO.figure, the sliders and buttons for
>>>>>> channel
>>>>>> adjustment, image rotation etc. are missing in the "Preview" window.
>>>>>> There is only the zoom slider, no matter how many images I add to the
>>>>>> page, and how many of them I select for editing. Any idea what could
>>>>>> be
>>>>>> the reason?
>>>>>>
>>>>>> I run OMERO 5.3.3 and Figure 3.1.1. on Ubuntu 16.04.
>>>>>>
>>>>>> Best regards,
>>>>>>
>>>>>> Martin
>>>>>>
>>>>>> _______________________________________________
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