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

Tue Aug 1 12:58:30 BST 2017

Dear Will,

thanks for your advice! Please find my answers inlined.

Best, Martin

On 01.08.2017 13:17, William Moore (Staff) wrote:
> Hi Martin,
>
>  When you say you removed and installed omero-figure AND the web app,
> I’m assuming you mean this (with a couple of other config settings):
>
> pip install omero-figure
> bin/omero config append omero.web.apps '"omero_figure"'
Yes.
>
> Just wanted to be sure you’re not also downloading the app and adding
> it to PYTHONPATH
> as you had to do for previous releases.
No, there are no old PYTHONPATH / manually installed plugin relicts.
>
> When you’re looking for channel sliders and buttons in the Preview panel,
> these will only show if you have 1 image selected OR if all the selected
> images have the same number of channels.
>
> Does that explain the problem?
No, selecting any number of images (0,1, or more) doesn't change it.
>
> If not, I wonder if you could open your browser’s dev tools (in
> Firefox or Chrome you can right-click anywhere on
> the page and choose the “Inspect Element” option to open dev tools).
> Then look in the Console and Network tabs when you refresh the page
> and select images
> and see if there’s any errors there when you’re seeing the problem.
In the dev tools console tab I see:

Use of getPreventDefault() is deprecated.  Use defaultPrevented
instead.  new
Empty string passed to getElementById(). jquery-1.11.1.js:2798:12
XML Parsing Error: not well-formed
Location:
http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825
Line Number 1, Column 1:  3315:1:1
TypeError: this.template is not a function[Learn More]  figure.js:6863:24
    render
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24
    render
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52
    triggerEvents
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32
    trigger
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19
    notifySelectionChange
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13
    later
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25
>
> Could you send us a screenshot of what you’re seeing.
Uploaded to my QA account (user mwlotzka) screenshots with the info, the
preview and the labels tab:
screenshot_OMERO_figure_info_seems_OK.png
screenshot_OMERO_figure_preview_missing_buttons_and_sliders.png
screenshot_OMERO_figure_labels_missing_everything.png
>
>  Hope that helps,
>
>   Will.
>
>
>> On 31 Jul 2017, at 15:18, Martin Wlotzka
>> <martin.wlotzka at uni-heidelberg.de
>> <mailto:martin.wlotzka at uni-heidelberg.de>> wrote:
>>
>> 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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