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Hi Martin,
<div class=""><br class="">
</div>
<div class=""> Yes, as it says on the collect static docs:</div>
<div class=""><a href="https://docs.djangoproject.com/en/1.8/ref/contrib/staticfiles/#collectstatic" class="">https://docs.djangoproject.com/en/1.8/ref/contrib/staticfiles/#collectstatic</a></div>
<div class=""><br class="">
</div>
<div class=""><span style="color: rgb(12, 60, 38); font-family: Roboto, Corbel, Avenir, 'Lucida Grande', 'Lucida Sans', sans-serif; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">On subsequent </span><code class="literal docutils" style="font-family: 'Fira Mono', Consolas, Menlo, Monaco, 'Courier New', Courier, monospace; font-size: 14px; text-rendering: optimizespeed; color: rgb(12, 75, 51); font-weight: 700; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><span class="pre" style="text-rendering: optimizespeed;">collectstatic</span></code><span style="color: rgb(12, 60, 38); font-family: Roboto, Corbel, Avenir, 'Lucida Grande', 'Lucida Sans', sans-serif; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""> runs
(if </span><code class="literal docutils" style="font-family: 'Fira Mono', Consolas, Menlo, Monaco, 'Courier New', Courier, monospace; font-size: 14px; text-rendering: optimizespeed; color: rgb(12, 75, 51); font-weight: 700; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><span class="pre" style="text-rendering: optimizespeed;">STATIC_ROOT</span></code><span style="color: rgb(12, 60, 38); font-family: Roboto, Corbel, Avenir, 'Lucida Grande', 'Lucida Sans', sans-serif; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class=""> isn’t
empty), files are copied</span></div>
<div class=""><span style="color: rgb(12, 60, 38); font-family: Roboto, Corbel, Avenir, 'Lucida Grande', 'Lucida Sans', sans-serif; font-size: 14px; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);" class="">only if they have a modified timestamp
greater than the timestamp of the file in </span><code class="literal docutils" style="font-family: 'Fira Mono', Consolas, Menlo, Monaco, 'Courier New', Courier, monospace; font-size: 14px; text-rendering: optimizespeed; color: rgb(12, 75, 51); font-weight: 700; orphans: 2; widows: 2; background-color: rgb(255, 255, 255);"><span class="pre" style="text-rendering: optimizespeed;">STATIC_ROOT</span></code></div>
<div class="">
<div style="orphans: 2; widows: 2;" class=""><br class="">
</div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""> So that would explain why editing the file could cause it to be ignored for the update.</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""><br class="">
</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""> Cheers,</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""><br class="">
</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""> Will.</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""><br class="">
</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""><br class="">
</span></div>
<div style="orphans: 2; widows: 2;" class=""><span style="orphans: auto; widows: auto;" class=""><br class="">
</span></div>
<div>
<blockquote type="cite" class="">
<div class="">On 2 Aug 2017, at 09:21, Martin Wlotzka <<a href="mailto:martin.wlotzka@uni-heidelberg.de" class="">martin.wlotzka@uni-heidelberg.de</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">Dear Will,<br class="">
<br class="">
thank you very much for your help, that finally pointed me to the source<br class="">
of the issue:<br class="">
<br class="">
There was an old figure installation still residing in<br class="">
OMERO.server/lib/python/omeroweb/static/figure<br class="">
which was not removed or updated although I removed or updated it via<br class="">
omero config and pip. So after removing that folder and again<br class="">
reinstalling figure it works fine now.<br class="">
<br class="">
Just out of curiosity: Any idea why that old installation remained<br class="">
despite web app removal / update? I edited the old figure.js by hand at<br class="">
the time I installed that, might this have caused the remove / update<br class="">
mechanism to keep it?<br class="">
<br class="">
Best,<br class="">
Martin<br class="">
<br class="">
On 08/01/2017 05:18 PM, William Moore (Staff) wrote:<br class="">
<blockquote type="cite" class="">Hi Martin,<br class="">
<br class="">
In your dev tools console, could you paste in<br class="">
<br class="">
JST["src/templates/image_display_options_template.html”]<br class="">
<br class="">
and hit enter:<br class="">
I get something like this returned:<br class="">
<br class="">
function(obj) {..<br class="">
<br class="">
but I think you might not get this?<br class="">
<br class="">
Also, could you open the templates.js in your browser,<br class="">
probably at<br class="">
<a href="http://omero01.urz.uni-heidelberg.de/static/figure/templates.js" class="">http://omero01.urz.uni-heidelberg.de/static/figure/templates.js</a>
<br class="">
<br class="">
and search for:<br class="">
<br class="">
src/templates/image_display_options_template.html<br class="">
<br class="">
you should find this line:<br class="">
<br class="">
this["JST"]["src/templates/image_display_options_template.html"] = function(obj) {<br class="">
<br class="">
<br class="">
Let me know if you do or not?<br class="">
<br class="">
I’m thinking the browser (or something else) has cached an old version<br class="">
of this templates.js.<br class="">
<br class="">
<br class="">
After uninstalling the figure app, the templates.js at the url above<br class="">
should not return (404).<br class="">
When you install the figure app again, and do<br class="">
<br class="">
bin/omero web start<br class="">
<br class="">
or even<br class="">
<br class="">
bin/omero syncmedia<br class="">
<br class="">
this should copy over the new files from the omero_figure app into your<br class="">
static location,<br class="">
so you should see this line included…<br class="">
<br class="">
Copying<br class="">
'/usr/local/lib/python2.7/site-packages/omero_figure/static/figure/templates.js'<br class="">
...<br class="">
<br class="">
Hope that helps,<br class="">
<br class="">
Will.<br class="">
<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On 1 Aug 2017, at 12:58, Martin Wlotzka<br class="">
<<a href="mailto:martin.wlotzka@uni-heidelberg.de" class="">martin.wlotzka@uni-heidelberg.de</a><br class="">
<<a href="mailto:martin.wlotzka@uni-heidelberg.de" class="">mailto:martin.wlotzka@uni-heidelberg.de</a>>> wrote:<br class="">
<br class="">
Dear Will,<br class="">
<br class="">
thanks for your advice! Please find my answers inlined.<br class="">
<br class="">
Best, Martin<br class="">
<br class="">
<br class="">
On 01.08.2017 13:17, William Moore (Staff) wrote:<br class="">
<blockquote type="cite" class="">Hi Martin,<br class="">
<br class="">
When you say you removed and installed omero-figure AND the web app,<br class="">
I’m assuming you mean this (with a couple of other config settings):<br class="">
<br class="">
pip install omero-figure<br class="">
bin/omero config append omero.web.apps '"omero_figure"'<br class="">
</blockquote>
Yes.<br class="">
<blockquote type="cite" class=""><br class="">
Just wanted to be sure you’re not also downloading the app and adding<br class="">
it to PYTHONPATH<br class="">
as you had to do for previous releases.<br class="">
</blockquote>
No, there are no old PYTHONPATH / manually installed plugin relicts.<br class="">
<blockquote type="cite" class=""><br class="">
When you’re looking for channel sliders and buttons in the Preview panel,<br class="">
these will only show if you have 1 image selected OR if all the selected<br class="">
images have the same number of channels.<br class="">
<br class="">
Does that explain the problem?<br class="">
</blockquote>
No, selecting any number of images (0,1, or more) doesn't change it.<br class="">
<blockquote type="cite" class=""><br class="">
If not, I wonder if you could open your browser’s dev tools (in<br class="">
Firefox or Chrome you can right-click anywhere on<br class="">
the page and choose the “Inspect Element” option to open dev tools).<br class="">
Then look in the Console and Network tabs when you refresh the page<br class="">
and select images<br class="">
and see if there’s any errors there when you’re seeing the problem.<br class="">
</blockquote>
In the dev tools console tab I see:<br class="">
<br class="">
Use of getPreventDefault() is deprecated. Use defaultPrevented<br class="">
instead. new<br class="">
Empty string passed to getElementById(). jquery-1.11.1.js:2798:12<br class="">
XML Parsing Error: not well-formed<br class="">
Location:<br class="">
<a href="http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825" class="">http://omero01.urz.uni-heidelberg.de/figure/imgData/3315/?_=1501587400825</a><br class="">
Line Number 1, Column 1: 3315:1:1<br class="">
TypeError: this.template is not a function[Learn More] figure.js:6863:24<br class="">
render<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:6863:24<br class="">
render<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:5301:52<br class="">
triggerEvents<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:203:32<br class="">
trigger<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/backbone-1.0.0.js:146:19<br class="">
notifySelectionChange<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/figure.js:686:13<br class="">
later<br class="">
http://omero01.urz.uni-heidelberg.de/static/figure/3rdparty/underscore-1.3.3.js:561:25<br class="">
<blockquote type="cite" class=""><br class="">
Could you send us a screenshot of what you’re seeing.<br class="">
</blockquote>
Uploaded to my QA account (user mwlotzka) screenshots with the info,<br class="">
the preview and the labels tab:<br class="">
screenshot_OMERO_figure_info_seems_OK.png<br class="">
screenshot_OMERO_figure_preview_missing_buttons_and_sliders.png<br class="">
screenshot_OMERO_figure_labels_missing_everything.png<br class="">
<blockquote type="cite" class=""><br class="">
Hope that helps,<br class="">
<br class="">
Will.<br class="">
<br class="">
<br class="">
<blockquote type="cite" class="">On 31 Jul 2017, at 15:18, Martin Wlotzka<br class="">
<martin.wlotzka@uni-heidelberg.de<br class="">
<mailto:martin.wlotzka@uni-heidelberg.de>> wrote:<br class="">
<br 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<br class="">
and edit<br class="">
the channels, which implies your Figure issue is not related to<br class="">
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<br class="">
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<br class="">
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="">
https://docs.openmicroscopy.org/omero/5.3.3/sysadmins/unix/install-web/walk<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="">
http://www.twitter.com/openmicroscopy<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="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
k.h.gillen@dundee.ac.uk> 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<br class="">
of your<br class="">
OMEROweb.log and your NGINX log. Perhaps there¹s something in the<br class="">
NGINX<br class="">
log, for example, which is showing 404s or 5xx responses which<br class="">
might point<br class="">
to what is going on.<br class="">
<br class="">
You can send us logs via http://qa.openmicroscopy.org.uk/qa/upload/<br class="">
<br class="">
It¹d be interesting to hear if anyone else has come across this<br class="">
one. My<br class="">
own OMERO server upgraded to this version without issues on<br class="">
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="">
http://www.twitter.com/openmicroscopy<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="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
martin.wlotzka@uni-heidelberg.de> 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 /<br class="">
sliders<br class="">
were there in 3.1.0. I already tried downgrading again, but that<br class="">
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="">
http://www.twitter.com/openmicroscopy<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="">
<ome-users-bounces@lists.openmicroscopy.org.uk on behalf of<br class="">
martin.wlotzka@uni-heidelberg.de> 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"<br class="">
window.<br class="">
There is only the zoom slider, no matter how many images I add<br class="">
to the<br class="">
page, and how many of them I select for editing. Any idea what<br class="">
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="">
_______________________________________________<br class="">
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</blockquote>
The University of Dundee is a registered Scottish Charity, No:<br class="">
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