[ome-users] OMERO.figure >> buttons and sliders in Preview window missing
William Moore (Staff)
W.Moore at dundee.ac.uk
Fri Aug 4 12:44:58 BST 2017
Hi Martin,
Yes, as it says on the collect static docs:
https://docs.djangoproject.com/en/1.8/ref/contrib/staticfiles/#collectstatic
On subsequent collectstatic runs (if STATIC_ROOT isn’t empty), files are copied
only if they have a modified timestamp greater than the timestamp of the file in STATIC_ROOT
So that would explain why editing the file could cause it to be ignored for the update.
Cheers,
Will.
On 2 Aug 2017, at 09:21, Martin Wlotzka <martin.wlotzka at uni-heidelberg.de<mailto:martin.wlotzka at uni-heidelberg.de>> wrote:
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>
<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
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