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

Martin Wlotzka martin.wlotzka at uni-heidelberg.de
Wed Aug 2 09:21:27 BST 2017 

Dear Will,

thank you very much for your help, that finally pointed me to the source
of the issue:

There was an old figure installation still residing in
OMERO.server/lib/python/omeroweb/static/figure
which was not removed or updated although I removed or updated it via
omero config and pip. So after removing that folder and again
reinstalling figure it works fine now.

Just out of curiosity: Any idea why that old installation remained
despite web app removal / update? I edited the old figure.js by hand at
the time I installed that, might this have caused the remove / update
mechanism to keep it?

Best,
Martin

On 08/01/2017 05:18 PM, William Moore (Staff) wrote:
> Hi Martin,
> 
>  In your dev tools console, could you paste in
> 
> JST["src/templates/image_display_options_template.html”]
> 
> and hit enter:
> I get something like this returned:
> 
>  function(obj) {..
> 
> but I think you might not get this?
> 
> Also, could you open the templates.js in your browser,
> probably at
> http://omero01.urz.uni-heidelberg.de/static/figure/templates.js 
> 
> and search for:
> 
> src/templates/image_display_options_template.html
> 
> you should find this line:
> 
> this["JST"]["src/templates/image_display_options_template.html"] = function(obj) {
> 
> 
> Let me know if you do or not?
> 
> I’m thinking the browser (or something else) has cached an old version
> of this templates.js.
> 
> 
> After uninstalling the figure app, the templates.js at the url above
> should not return (404).
> When you install the figure app again, and do
> 
> bin/omero web start
> 
> or even
> 
> bin/omero syncmedia
> 
> this should copy over the new files from the omero_figure app into your
> static location,
> so you should see this line included…
> 
> Copying
> '/usr/local/lib/python2.7/site-packages/omero_figure/static/figure/templates.js'
> ...
> 
> Hope that helps,
> 
>    Will.
> 
> 
> 
>> On 1 Aug 2017, at 12:58, Martin Wlotzka
>> <martin.wlotzka at uni-heidelberg.de
>> <mailto:martin.wlotzka at uni-heidelberg.de>> wrote:
>>
>> 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
>>>>>>>>>>
>>>>>>>>>> _______________________________________________
>>>>>>>>>> ome-users mailing list
>>>>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>>>>> SC015096
>>>>>>>>> _______________________________________________
>>>>>>>>> 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
>>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>>> SC015096
>>>>>>> _______________________________________________
>>>>>>> ome-users mailing list
>>>>>>> ome-users at lists.openmicroscopy.org.uk
>>>>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>>>> The University of Dundee is a registered Scottish Charity, No:
>>>>>> SC015096
>>>>>> _______________________________________________
>>>>>> 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
>>>>> <mailto: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
>>>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>>>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>>>
>>>
>>> The University of Dundee is a registered Scottish Charity, No: SC015096
>>>
>>>
>>> _______________________________________________
>>> 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
>> <mailto:ome-users at lists.openmicroscopy.org.uk>
>> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
> 
> 
> The University of Dundee is a registered Scottish Charity, No: SC015096
> 
> 
> _______________________________________________
> ome-users mailing list
> ome-users at lists.openmicroscopy.org.uk
> http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users
>

More information about the ome-users mailing list