<div dir="ltr">Hi Chris,<div><br></div><div>Looking at what happened, I think maybe you are using an OMERO_PREFIX (or possibly OMERO_HOME) that points to the specific server directory (<span style="font-family:arial,sans-serif;font-size:13px">OMERO.server-5.0.6-blalba) rather than the symlink OMERO.server. Might want to check that to avoid being bitten again later.</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Cheers,</span></div><div><span style="font-family:arial,sans-serif;font-size:13px"><br></span></div><div><span style="font-family:arial,sans-serif;font-size:13px">Douglas</span></div><div class="gmail_extra"><br><div class="gmail_quote">On 26 November 2014 at 11:55, Christophe TREFOIS <span dir="ltr"><<a href="mailto:christophe.trefois@uni.lu" target="_blank">christophe.trefois@uni.lu</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">



<div style="word-wrap:break-word">
Hi Will,
<div><br>
</div>
<div>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.</div>
<div><br>
</div>
<div>I have now replaced all special instances in the apache conf with OMERO.server which should then always take the new files instead.</div>
<div><br>
</div>
<div>Consequently, csrf is loaded now and Figure works again!</div>
<div><br>
</div>
<div>Looking forward to new updates soon :)</div>
<div><br>
</div>
<div>Kind Regards,</div>
<div><br>
</div>
<div>—</div><span><font color="#888888">
<div>Christophe</div></font></span><div><div>
<div><br>
<div>
<blockquote type="cite">
<div>On 25 Nov 2014, at 18:00, William Moore <<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</a>> wrote:</div>
<br>
<div>
<div style="word-wrap:break-word">
Hi Christophe,
<div><br>
</div>
<div> I don't know why the ome.csrf.js is returning a 404.</div>
<div>Presumably the rest of your OMERO 5.0.6 web client is working OK? If so, this should</div>
<div>all be using the same ome.csrf.js from the same location.</div>
<div><br>
</div>
<div>Can you confirm that the rest of your OMERO.web 5.0.6 is working OK?</div>
<div>Can you access the file directly at  <your-server>/static/webgateway/js/ome.csrf.js ?</div>
<div><br>
</div>
<div>E.g. <a href="http://trout.openmicroscopy.org/merge/static/webgateway/js/ome.csrf.js" target="_blank">http://trout.openmicroscopy.org/merge/static/webgateway/js/ome.csrf.js</a></div>
<div><br>
</div>
<div>Can you check the header of your OMERO.figure html page and see if the csrf.js script url</div>
<div>matches the url in the header of your other OMERO.web pages?</div>
<div><br>
</div>
<div></div>
<div>You should see these two lines together in all the pages:</div>
<div><br>
</div>
<div>
<div><script type="text/javascript" src="/static/3rdparty/jquery-1.7.2.js"></script></div>
<div><script type="text/javascript" src="/static/webgateway/js/ome.csrf.js"></script></div>
</div>
<div><br>
</div>
<div> Hopefully you can figure out why this is failing to load in OMERO.figure.</div>
<div><br>
</div>
<div> Regards,</div>
<div><br>
</div>
<div>  Will.</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>On 25 Nov 2014, at 16:30, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" target="_blank">christophe.trefois@uni.lu</a>> wrote:</div>
<br>
<blockquote type="cite">
<div style="word-wrap:break-word">
Hi Will,
<div><br>
</div>
<div>You are correct. I get a 403 Denied error, and upon further inspection I get a 404 on ome.csrf.js.</div>
<div><br>
</div>
<div>I guess I am missing that file, but I’m not sure why…</div>
<div><br>
</div>
<div>Could you elucidate?</div>
<div><br>
</div>
<div>Thank you,</div>
<div><br>
</div>
<div>—</div>
<div>Christophe</div>
<div><br>
</div>
<div><br>
</div>
<div>
<div>
<blockquote type="cite">
<div>On 18 Nov 2014, at 17:41, William Moore <<a href="mailto:will@lifesci.dundee.ac.uk" target="_blank">will@lifesci.dundee.ac.uk</a>> wrote:</div>
<br>
<div>
<div style="word-wrap:break-word">
Hi Christophe,
<div><br>
</div>
<div> It sounds like POST requests were failing, possibly due to the upgrade to 5.0.6 where the server now protects against csrf attacks.</div>
<div><br>
</div>
<div>It may be that OMERO.figure was not adding the csrf token to these POSTs.</div>
<div>Is it possible that the OMERO.figure page was not refreshed after upgrading OMERO?</div>
<div>This would mean that the required ome.csrf.js Javascript file wouldn't have been loaded.</div>
<div>Or maybe something else is failing here.</div>
<div><br>
</div>
<div>I'm afraid there's no real error handling for the AJAX calls within OMERO.figure yet, but</div>
<div>you may be able to get more details from the browser console.</div>
<div>I don't know what browser you're on, but all modern browsers will have some developer tools</div>
<div>that allow you to see AJAX or other errors, usually under the Console or Network tabs.</div>
<div>You can see response codes, error messages etc.</div>
<div><br>
</div>
<div>If you have an opportunity to try the upgrade again sometime, hopefully a full refresh of the page</div>
<div>will fix the issue, or if not then let us know if you can get any more error info.</div>
<div><br>
</div>
<div> Thanks,</div>
<div><br>
</div>
<div>   Will.</div>
<div><br>
</div>
<div><br>
</div>
<div><br>
<div>
<div>
<div>On 18 Nov 2014, at 16:19, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" target="_blank">christophe.trefois@uni.lu</a>> wrote:</div>
<br>
<blockquote type="cite">
<div lang="FR-BE" link="blue" vlink="purple" style="font-family:Helvetica;font-size:inherit;font-style:normal;font-variant:normal;font-weight:normal;letter-spacing:normal;line-height:normal;text-align:-webkit-auto;text-indent:0px;text-transform:none;white-space:normal;word-spacing:0px">
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Hi Will,<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">What happened was that when I click Export PDF, nothing happened. There were also no activities in the main OMEROweb.<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Further, when clicking “Save”, nothing happened at all, eg nothing was saved.<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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.<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">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?<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Is this a valid approach for all plugins? If there is a dev doc I have overseen, please forgive<span> </span></span><span lang="EN-US" style="font-size:11pt;font-family:Wingdings;color:rgb(31,73,125)">J</span><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"><u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Thank you for your help,<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">--<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)">Christophe<u></u><u></u></span></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif;color:rgb(31,73,125)"> </span></div>
<div>
<div style="border-style:solid none none;border-top-width:1pt;border-top-color:rgb(225,225,225);padding:3pt 0cm 0cm">
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<b><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">From:</span></b><span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"><span> </span>William Moore
 [mailto:<a href="mailto:will@" target="_blank">will@</a><a href="http://lifesci.dundee.ac.uk/" style="color:purple;text-decoration:underline" target="_blank">lifesci.dundee.ac.uk</a>]<span> </span><br>
<b>Sent:</b><span> </span>mardi 18 novembre 2014 00:11<br>
<b>To:</b><span> </span>Christophe TREFOIS<br>
<b>Cc:</b><span> </span><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="color:purple;text-decoration:underline" target="_blank">ome-devel@lists.openmicroscopy.org.uk</a><br>
<b>Subject:</b><span> </span>Re: [ome-devel] How to migrate OMERO.figure<u></u><u></u></span></div>
</div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
Hi Christophe,<u></u><u></u></div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
 How does the PDF generation fail?<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
If the "Export PDF" button is enabled then the script has been found.<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
If you click this but the blue 'Download' button never appears, you can go to the main webclient<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
and click on the 'Activities' button (beside the top-right search field) to see more<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
details on all scripts.<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
You may prefer to put the /figure app in a separate location, in any directory that's on your $PYTHONPATH<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
then you won't have to move it on each OMERO upgrade.<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
Anyway, let me know if you have any more details on what's failing,<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
 Cheers,<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
   Will.<u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
 <u></u><u></u></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<u></u> <u></u></div>
<div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
On 17 Nov 2014, at 22:34, Christophe TREFOIS <<a href="mailto:christophe.trefois@uni.lu" style="color:purple;text-decoration:underline" target="_blank">christophe.trefois@uni.lu</a>> wrote:<u></u><u></u></div>
</div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<br>
<br>
<u></u><u></u></div>
<blockquote style="margin-top:5pt;margin-bottom:5pt">
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif">Dear Will,<u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"> <u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Do you know how to properly migrate OMERO.figure from 5.0.5 – 5.0.6 ?</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">It seems I copied over content from lib/python/omeroweb/figure and re-imported the .py script.</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Yet, I can’t seem to save or to generate PDFs any Figure in 5.0.6 then.</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
<div style="margin:0cm 0cm 0.0001pt;font-size:12pt;font-family:'Times New Roman',serif">
<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
</div>
<div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Reverting back 5.0.5 seems to work.</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Any suggestions?</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Kind Regards,</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif"> </span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">--</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="EN-US" style="font-size:11pt;font-family:Calibri,sans-serif">Christophe</span><span lang="FR-LU" style="font-size:11pt;font-family:Calibri,sans-serif"><u></u><u></u></span></div>
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<span lang="FR-LU" style="font-size:13.5pt;font-family:Helvetica,sans-serif">_______________________________________________<br>
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<u></u> <u></u></div>
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