[ome-devel] How to migrate OMERO.figure

Wed Nov 26 14:43:17 GMT 2014

Hah, that sure is interesting!

I will definitely put it on the path as well, but still “in theory”, I would expect a similar behaviour.

Thanks for figuring this out!

Best,

On 26 Nov 2014, at 15:12, Douglas Russell <douglas.russell at bioch.ox.ac.uk<mailto:douglas.russell at bioch.ox.ac.uk>> wrote:

Ok, I see the problem which I would consider a bug as I would not expect different behaviour in these two cases.

Check this out:

Run `$OMERO_PREFIX/bin/omero web config apache`

Results: OMERO.server is used in paths.

Run `cd $OMERO_PREFIX && bin/omero web config apache`

Results: OMERO.server-5.0.5-blabla is used in paths.

Personally I have $OMERO_PREFIX/bin added to my local path so I would always just do the following, so I've never seen this behaviour before.

`omero web config apache`

Cheers,

Douglas

On 26 November 2014 at 14:02, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:
Hi Doug,

0 [15:00:36] omerou at lcsbomero(uni,DomU) localadmin> echo $OMERO_PREFIX
/var/lib/apps/OMERO/OMERO.server

and OMERO.server is a symlink to the actual version.

However, when running bin/omero web config apache from within OMERO.server the result contains the actual path, not the symlink.

eg

cd $OMERO_PREFIX
bin/omero web config apache

output contains OMERO.server-5.0.5-blabla rather than OMERO.server.

Did we miss something here?

Best,

On 26 Nov 2014, at 14:38, Douglas Russell <douglas.russell at bioch.ox.ac.uk<mailto:douglas.russell at bioch.ox.ac.uk>> wrote:

Hi Chris,

Looking at what happened, I think maybe you are using an OMERO_PREFIX (or possibly OMERO_HOME) that points to the specific server directory (OMERO.server-5.0.6-blalba) rather than the symlink OMERO.server. Might want to check that to avoid being bitten again later.

Cheers,

Douglas

On 26 November 2014 at 11:55, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:
Hi Will,

Thank you! It turns out that when you do bin/omero web config apache from OMERO.server he will generate using the target folder, e.g. OMERO.server-5.0.6-blalba and not OMERO.server. For small updates I had not deemed necessary to re-create the web config file for apache. So in fact, we were running 5.0.6 core on 5.0.5 web files which could not work obviously.

I have now replaced all special instances in the apache conf with OMERO.server which should then always take the new files instead.

Consequently, csrf is loaded now and Figure works again!

Looking forward to new updates soon :)

Kind Regards,

—
Christophe

On 25 Nov 2014, at 18:00, William Moore <will at lifesci.dundee.ac.uk<mailto:will at lifesci.dundee.ac.uk>> wrote:

Hi Christophe,

 I don't know why the ome.csrf.js is returning a 404.
Presumably the rest of your OMERO 5.0.6 web client is working OK? If so, this should
all be using the same ome.csrf.js from the same location.

Can you confirm that the rest of your OMERO.web 5.0.6 is working OK?
Can you access the file directly at  <your-server>/static/webgateway/js/ome.csrf.js ?

E.g. http://trout.openmicroscopy.org/merge/static/webgateway/js/ome.csrf.js

Can you check the header of your OMERO.figure html page and see if the csrf.js script url
matches the url in the header of your other OMERO.web pages?

You should see these two lines together in all the pages:

<script type="text/javascript" src="/static/3rdparty/jquery-1.7.2.js"></script>
<script type="text/javascript" src="/static/webgateway/js/ome.csrf.js"></script>

 Hopefully you can figure out why this is failing to load in OMERO.figure.

 Regards,

  Will.

On 25 Nov 2014, at 16:30, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:

Hi Will,

You are correct. I get a 403 Denied error, and upon further inspection I get a 404 on ome.csrf.js.

I guess I am missing that file, but I’m not sure why…

Could you elucidate?

Thank you,

—
Christophe

On 18 Nov 2014, at 17:41, William Moore <will at lifesci.dundee.ac.uk<mailto:will at lifesci.dundee.ac.uk>> wrote:

Hi Christophe,

 It sounds like POST requests were failing, possibly due to the upgrade to 5.0.6 where the server now protects against csrf attacks.

It may be that OMERO.figure was not adding the csrf token to these POSTs.
Is it possible that the OMERO.figure page was not refreshed after upgrading OMERO?
This would mean that the required ome.csrf.js Javascript file wouldn't have been loaded.
Or maybe something else is failing here.

I'm afraid there's no real error handling for the AJAX calls within OMERO.figure yet, but
you may be able to get more details from the browser console.
I don't know what browser you're on, but all modern browsers will have some developer tools
that allow you to see AJAX or other errors, usually under the Console or Network tabs.
You can see response codes, error messages etc.

If you have an opportunity to try the upgrade again sometime, hopefully a full refresh of the page
will fix the issue, or if not then let us know if you can get any more error info.

 Thanks,

   Will.

On 18 Nov 2014, at 16:19, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:

Hi Will,

What happened was that when I click Export PDF, nothing happened. There were also no activities in the main OMEROweb.
Further, when clicking “Save”, nothing happened at all, eg nothing was saved.

I quickly returned to 5.0.5 then, as this is our prod env and I did not want to leave it “not working” for a longer while.

Also, do you have any instructions on putting the plugin centrally?  How about the export to pdf.py, is it also possible to put it in a central place?
Is this a valid approach for all plugins? If there is a dev doc I have overseen, please forgive ☺

Thank you for your help,

--
Christophe

From: William Moore [mailto:will@<mailto:will@>lifesci.dundee.ac.uk<http://lifesci.dundee.ac.uk/>]
Sent: mardi 18 novembre 2014 00:11
To: Christophe TREFOIS
Cc: ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
Subject: Re: [ome-devel] How to migrate OMERO.figure

Hi Christophe,

 How does the PDF generation fail?

If the "Export PDF" button is enabled then the script has been found.
If you click this but the blue 'Download' button never appears, you can go to the main webclient
and click on the 'Activities' button (beside the top-right search field) to see more
details on all scripts.

You may prefer to put the /figure app in a separate location, in any directory that's on your $PYTHONPATH
then you won't have to move it on each OMERO upgrade.

Anyway, let me know if you have any more details on what's failing,

 Cheers,

   Will.

On 17 Nov 2014, at 22:34, Christophe TREFOIS <christophe.trefois at uni.lu<mailto:christophe.trefois at uni.lu>> wrote:

Dear Will,

Do you know how to properly migrate OMERO.figure from 5.0.5 – 5.0.6 ?

It seems I copied over content from lib/python/omeroweb/figure and re-imported the .py script.

Yet, I can’t seem to save or to generate PDFs any Figure in 5.0.6 then.

Reverting back 5.0.5 seems to work.

Any suggestions?

Kind Regards,

--
Christophe
_______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

_______________________________________________
ome-devel mailing list
ome-devel at lists.openmicroscopy.org.uk<mailto:ome-devel at lists.openmicroscopy.org.uk>
http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel

-------------- next part --------------
An HTML attachment was scrubbed...
URL: <http://lists.openmicroscopy.org.uk/pipermail/ome-devel/attachments/20141126/20253750/attachment-0001.html>