[ome-devel] How to migrate OMERO.figure

Wed Nov 26 13:38:35 GMT 2014

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>
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>
> 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>
> 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>
> 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>
> 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 J
>
>  Thank you for your help,
>
>  --
>  Christophe
>
>   *From:* William Moore [mailto:will at lifesci.dundee.ac.uk]
> *Sent:* mardi 18 novembre 2014 00:11
> *To:* Christophe TREFOIS
> *Cc:* 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>
> 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
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