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<p>Dear Will,</p>
<p>thanks for your advice! Please find my answers inlined.</p>
<p>Best, Martin<br>
</p>
<br>
<div class="moz-cite-prefix">On 01.08.2017 13:17, William Moore
(Staff) wrote:<br>
</div>
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8">
Hi Martin,
<div class=""><br class="">
</div>
<div class=""> When you say you removed and installed omero-figure
AND the web app,</div>
<div class="">I’m assuming you mean this (with a couple of other
config settings):</div>
<div class=""><br class="">
</div>
<div class=""><span style="color: rgb(34, 34, 34); font-family:
Monaco, 'Bitstream Vera Sans Mono', 'Lucida Console',
Terminal, monospace; font-size: 14px; orphans: 2; widows: 2;
background-color: rgb(255, 255, 255);" class="">pip install
omero-figure</span></div>
<div class=""><span style="color: rgb(34, 34, 34); font-family:
Monaco, 'Bitstream Vera Sans Mono', 'Lucida Console',
Terminal, monospace; font-size: 14px; orphans: 2; widows: 2;
background-color: rgb(255, 255, 255);" class="">bin/omero
config append omero.web.apps '"omero_figure"'</span></div>
</blockquote>
Yes.<br>
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<div class=""><br class="">
</div>
<div class="">Just wanted to be sure you’re not also downloading
the app and adding it to PYTHONPATH</div>
<div class="">as you had to do for previous releases.</div>
</blockquote>
No, there are no old PYTHONPATH / manually installed plugin relicts.<br>
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<div class=""><br class="">
</div>
<div class="">When you’re looking for channel sliders and buttons
in the Preview panel,</div>
<div class="">these will only show if you have 1 image selected OR
if all the selected</div>
<div class="">images have the same number of channels.</div>
<div class=""><br class="">
</div>
<div class="">Does that explain the problem?</div>
</blockquote>
No, selecting any number of images (0,1, or more) doesn't change it.
<br>
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<div class=""><br class="">
</div>
<div class="">If not, I wonder if you could open your browser’s
dev tools (in Firefox or Chrome you can right-click anywhere on</div>
<div class="">the page and choose the “Inspect Element” option to
open dev tools).</div>
<div class="">Then look in the Console and Network tabs when you
refresh the page and select images</div>
<div class="">and see if there’s any errors there when you’re
seeing the problem.</div>
</blockquote>
In the dev tools console tab I see:<br>
<br>
Use of getPreventDefault() is deprecated. Use defaultPrevented
instead. new<br>
Empty string passed to getElementById(). jquery-1.11.1.js:2798:12<br>
XML Parsing Error: not well-formed<br>
Location:
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825">http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825</a><br>
Line Number 1, Column 1: 3315:1:1<br>
TypeError: this.template is not a function[Learn More]
figure.js:6863:24<br>
render
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24">http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24</a><br>
render
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52">http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52</a><br>
triggerEvents
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32">http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32</a><br>
trigger
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19">http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19</a><br>
notifySelectionChange
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13">http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13</a><br>
later
<a class="moz-txt-link-freetext" href="http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25">http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25</a><br>
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<div class=""><br class="">
</div>
<div class="">Could you send us a screenshot of what you’re
seeing.</div>
</blockquote>
Uploaded to my QA account (user mwlotzka) screenshots with the info,
the preview and the labels tab:<br>
screenshot_OMERO_figure_info_seems_OK.png<br>
screenshot_OMERO_figure_preview_missing_buttons_and_sliders.png<br>
screenshot_OMERO_figure_labels_missing_everything.png
<blockquote type="cite"
cite="mid:F57549EE-BDD7-4208-B7D0-797A3D674660@dundee.ac.uk">
<div class=""><br class="">
</div>
<div class=""> Hope that helps,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 31 Jul 2017, at 15:18, Martin Wlotzka <<a
href="mailto:martin.wlotzka@uni-heidelberg.de" class=""
moz-do-not-send="true">martin.wlotzka@uni-heidelberg.de</a>>
wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Kenny,<br class="">
<br class="">
I tried a complete requirements check and OMERO.figure
reinstall<br class="">
(removed the web app, removed omero-figure via pip, server
reboot,<br class="">
installed omero-figure and web app again), but that didn't
change<br class="">
anything. The channel sliders and buttons are still
missing.<br class="">
<br class="">
I uploaded the pip freeze output, the omero config output,
the<br class="">
master.err and the Blitz log to OMERO QA. Hope you can
find something...<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Martin<br class="">
<br class="">
<br class="">
On 24.07.2017 15:30, Martin Wlotzka wrote:<br class="">
<blockquote type="cite" class="">Hi Kenny,<br class="">
<br class="">
yes there are indeed pyramid issues with Leica .lif
images. However, I<br class="">
uploaded the good/bad pyramid files for the other
mailing list post on<br class="">
"Pyramids, fast/slow rendering and image size".<br
class="">
<br class="">
Regarding the OMERO.figure issue, I uploaded the nginx
logs and the<br class="">
OMERO.web log:<br class="">
<br class="">
nginx_access.log<br class="">
nginx_error.log<br class="">
OMEROweb_inspect_figure_missing_buttons.log<br class="">
<br class="">
Thanks for the hint on the OMERO.web requirements, I'll
check that.<br class="">
<br class="">
Best regards,<br class="">
Martin<br class="">
<br class="">
On 24.07.2017 12:14, Kenneth Gillen (Staff) wrote:<br
class="">
<blockquote type="cite" class="">Hi Martin,<br class="">
<br class="">
<blockquote type="cite" class="">Leica_16bit_bad_pyramid.lif<br
class="">
</blockquote>
Is this a file you’d expect OMERO to import, and
properly render? The<br class="">
filename, `bad_pyramid` suggests you know of issues.
I.e. is this<br class="">
something you`d like to the Bio-Formats team to look
at? (a separate<br class="">
issue to the OMERO.figure issue perhaps?)<br class="">
<br class="">
For me, this image loads in an OMERO 5.3.3 with Figure
3.1.1 server,<br class="">
though (perhaps suggested by the filename), looks odd:
yellowish<br class="">
background, random spots. However, I can add labels,
rotate, zoom and edit<br class="">
the channels, which implies your Figure issue is not
related to the image,<br class="">
but to the setup of Figure.<br class="">
<br class="">
<blockquote type="cite" class="">Leica_8bit_good_pyramid.lif<br
class="">
</blockquote>
And this second image, when loading into the same
server, I see error:<br class="">
`Image Leica_8bit_good_pyramid.lif is too big for
OMERO.figure`. Is it<br class="">
happily loaded by your own OMERO.figure?<br class="">
<br class="">
<br class="">
The next thing I can think of is that some OMERO.web
requirements are not<br class="">
satisfied.<br class="">
<br class="">
If you could confirm which versions of the OMERO.web
requirements<br class="">
OMERO.web is configured to use, we can rule that out:<br
class="">
<br class="">
e.g. your equivalent of: ~omero/omerowebvenv/bin/pip
freeze<br class="">
<br class="">
Which will determine if you need to re-install/upgrade
the OMERO.web<br class="">
requirements, outlined in the install docs ubuntu
walkthrough [1].<br class="">
<br class="">
If re-installing the web requirements doesn’t yield
and instant result, if<br class="">
you could also send us your OMERO configuration via
omero config get<br class="">
--hide-password, and your server’s Blitz-0.log, and
master.err<br class="">
<br class="">
<br class="">
[1]<br class="">
<a
href="https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk"
class="" moz-do-not-send="true">https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk</a><br
class="">
through/omeroweb-install-ubuntu-ice3.6.html or<br
class="">
<br class="">
All the best,<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation &
Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><br class="">
<br class="">
----<br class="">
<br class="">
Dear Kenny,<br class="">
<br class="">
I've uploaded the logs:<br class="">
<br class="">
nginx_access.log<br class="">
nginx_error.log<br class="">
<br class="">
OMEROweb_inspect_figure_missing_buttons.log<br
class="">
<br class="">
I also tried reinstalling, but that didn't change
anything.<br class="">
<br class="">
Best,<br class="">
<br class="">
Martin<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 17:08, "ome-users on behalf of Kenneth
Gillen (Staff)"<br class="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on
behalf of<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:k.h.gillen@dundee.ac.uk">k.h.gillen@dundee.ac.uk</a>> wrote:<br class="">
<br class="">
<blockquote type="cite" class="">It would be worth
retrying the install of the plugin at the least.<br
class="">
<br class="">
Then I¹d be thinking about at least sending us a
.tar.gz or .zip of your<br class="">
OMEROweb.log and your NGINX log. Perhaps there¹s
something in the NGINX<br class="">
log, for example, which is showing 404s or 5xx
responses which might point<br class="">
to what is going on.<br class="">
<br class="">
You can send us logs via
<a class="moz-txt-link-freetext" href="http://qa.openmicroscopy.org.uk/qa/upload/">http://qa.openmicroscopy.org.uk/qa/upload/</a><br
class="">
<br class="">
It¹d be interesting to hear if anyone else has come
across this one. My<br class="">
own OMERO server upgraded to this version without
issues on RHEL7, rather<br class="">
than Ubuntu.<br class="">
<br class="">
<br class="">
All the best,<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation &
Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 15:08, "ome-users on behalf of Martin
Wlotzka"<br class="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on
behalf of<br class="">
<a class="moz-txt-link-abbreviated" href="mailto:martin.wlotzka@uni-heidelberg.de">martin.wlotzka@uni-heidelberg.de</a>> wrote:<br
class="">
<br class="">
<blockquote type="cite" class="">Hi Kenny,<br
class="">
<br class="">
yes I recently upgraded from 3.1.0 to 3.1.1, and
the buttons / sliders<br class="">
were there in 3.1.0. I already tried downgrading
again, but that didn't<br class="">
bring them back.<br class="">
<br class="">
-- Martin<br class="">
<br class="">
<br class="">
On 19.07.2017 15:55, Kenneth Gillen (Staff) wrote:<br
class="">
<blockquote type="cite" class="">Hi Martin,<br
class="">
<br class="">
Has OMERO.figure always been like this on this
server? Was it, for<br class="">
example, installed, or upgraded recently?<br
class="">
<br class="">
Many thanks<br class="">
<br class="">
Kenny<br class="">
<br class="">
--<br class="">
<br class="">
Kenneth Gillen<br class="">
<br class="">
<br class="">
OME System Administrator<br class="">
<br class="">
Wellcome Trust Centre for Gene Regulation &
Expression<br class="">
School of Life Sciences<br class="">
CTIR 2<br class="">
University of Dundee<br class="">
Dow Street<br class="">
Dundee DD1 5EH<br class="">
United Kingdom<br class="">
<br class="">
Tel: +44 (0) 1382 388797<br class="">
<br class="">
<br class="">
<a class="moz-txt-link-freetext" href="http://www.twitter.com/openmicroscopy">http://www.twitter.com/openmicroscopy</a><br
class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
<br class="">
On 19/07/2017 14:28, "ome-users on behalf of
Martin Wlotzka"<br class="">
<<a class="moz-txt-link-abbreviated" href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk">ome-users-bounces@lists.openmicroscopy.org.uk</a> on behalf of<br
class="">
<a class="moz-txt-link-abbreviated" href="mailto:martin.wlotzka@uni-heidelberg.de">martin.wlotzka@uni-heidelberg.de</a>> wrote:<br
class="">
<br class="">
<blockquote type="cite" class="">Dear all,<br
class="">
<br class="">
when I open images in OMERO.figure, the
sliders and buttons for<br class="">
channel<br class="">
adjustment, image rotation etc. are missing in
the "Preview" window.<br class="">
There is only the zoom slider, no matter how
many images I add to the<br class="">
page, and how many of them I select for
editing. Any idea what could<br class="">
be<br class="">
the reason?<br class="">
<br class="">
I run OMERO 5.3.3 and Figure 3.1.1. on Ubuntu
16.04.<br class="">
<br class="">
Best regards,<br class="">
<br class="">
Martin<br class="">
<br class="">
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