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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Hi Again,<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">We seem to be running into a problem in that certain OMERO figures are not being converted to PDFs using your gist script (you posted
way back last year, see below) but some figures convert fine. Below is the error. We are using OMERO 5.4.5 and OMERO Figure version 3.1.1.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Job 1472150 ready<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Waiting....<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Callback received: FINISHED<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Figure file: 2109025<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Traceback (most recent call last):<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> File "gist.py", line 84, in <module><o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"> figure_name = str(id)+"_"+figure_pdf.getFile().getName()<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">AttributeError: 'NoneType' object has no attribute 'getFile'<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">I have attached the json of both files. 2086989 converts to pdf and 2100620 doesn’t convert.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Both figures look fine and PDFs download ok using the web client.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Thanks for any help!<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Steve<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">----------------------------------<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Head of Computational Biology Research Group
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">MRC Weatherall Institute of Molecular Medicine
<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US">Oxford<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">www.cbrg.ox.ac.uk<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></p>
<p class="MsoNormal"><a name="_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></a></p>
<p class="MsoNormal"><span style="mso-bookmark:_MailEndCompose"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D;mso-fareast-language:EN-US"><o:p> </o:p></span></span></p>
<span style="mso-bookmark:_MailEndCompose"></span>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> ome-users <ome-users-bounces@lists.openmicroscopy.org.uk>
<b>On Behalf Of </b>William Moore (Staff)<br>
<b>Sent:</b> 01 November 2017 14:20<br>
<b>To:</b> OME User Support List <ome-users@lists.openmicroscopy.org.uk><br>
<b>Subject:</b> Re: [ome-users] OMERO Figure Download<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
<p class="MsoNormal">Hi Steve, <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">By default the timeout is 10 minutes.<o:p></o:p></p>
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<p class="MsoNormal">This can be set on the server by an admin with (milliseconds)<o:p></o:p></p>
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<pre style="line-height:15.0pt;background:#F8F9F9;border:none;padding:0cm;border-top-left-radius: 2px;border-top-right-radius: 2px;border-bottom-right-radius: 2px;border-bottom-left-radius: 2px;word-wrap: normal;max-height: 516px;orphans: 2;widows: 2;overflow:auto"><code><span style="font-size:10.5pt;font-family:"Lucida Console";color:#4D4D4D;border:none windowtext 1.0pt;padding:0cm">$ bin/omero config set omero.sessions.timeout 85000000</span></code><span style="font-size:10.5pt;font-family:"Lucida Console";color:#333333"><o:p></o:p></span></pre>
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<p class="MsoNormal">and this will then apply to ALL server sessions.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">An admin can also set the timeout for an individual session in the CLI with (seconds)<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">$ bin/omero sessions timeout 1000<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">but unfortunately non-admins can’t do this.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">There may be other ways you could keep a session alive if needed by “pinging” from a client?<o:p></o:p></p>
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<p class="MsoNormal">e.g. "watch -n 60 omero login” but I haven’t tried this.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Regards,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<blockquote style="margin-top:5.0pt;margin-bottom:5.0pt">
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<p class="MsoNormal">On 1 Nov 2017, at 13:02, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk">stephen.taylor@imm.ox.ac.uk</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Will,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">If I set up a session, how long does it last? Do you need to set the length for time out?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Kind regards and thanks,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Steve</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>William Moore (Staff)<br>
<b>Sent:</b><span class="apple-converted-space"> </span>01 November 2017 12:24<br>
<b>To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Steve,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> I’m afraid we don’t support token authentication yet, although we have been discussing it…<o:p></o:p></p>
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<p class="MsoNormal"><a href="https://trello.com/c/CbRYR7Ty/34-session-issues"><span style="color:purple">https://trello.com/c/CbRYR7Ty/34-session-issues</span></a><o:p></o:p></p>
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<p class="MsoNormal">I’ve added your request to that card.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">The next best thing you can do is to use an existing session ID to join a session (like a short-lived token).<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">You can get a session key when you login from the command line<o:p></o:p></p>
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<p class="MsoNormal">$ bin/omero login<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Or if you’re already logged-in, you can do<o:p></o:p></p>
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<p class="MsoNormal">$ bin/omero sessions key<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Then use that in your script to connect.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">conn = BlitzGateway(host="localhost", port=4064)<o:p></o:p></p>
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<p class="MsoNormal">conn.connect(SESSION_ID)<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I updated <a href="https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6"><span style="color:purple">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</span></a><o:p></o:p></p>
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<p class="MsoNormal">to show this.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">It would be better to add command line arguments to your script instead of<o:p></o:p></p>
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<p class="MsoNormal">hard-coding it.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Regards,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On 31 Oct 2017, at 11:48, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk"><span style="color:purple">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Will,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Sorry for my slow reply. I haven’t been able to reproduce this as again so may be just a blip when the machine is under load. I have noticed some of the PDFs
don’t download and when I look at the ids in OMERO.figure it says ‘Data missing’. Does this mean that an image has been removed from a database which is breaking things?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">On another note, does OMERO support token based authentication? There has been a concern from sys admins here that we are logging in with a username and password
every time.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Steve</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>William Moore (Staff)<br>
<b>Sent:</b><span class="apple-converted-space"> </span>24 October 2017 10:39<br>
<b>To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Hi Steve,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> I tried a simple modification to my script to export and download a handful of figures<o:p></o:p></p>
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<p class="MsoNormal">sequentially, and this seemed to work OK.<o:p></o:p></p>
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<p class="MsoNormal">Could you share your script and give us an idea of how many figures you<o:p></o:p></p>
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<p class="MsoNormal">can export before you see this ConnectionRefusedException?<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">Also, any other info you think might be relevant?<o:p></o:p></p>
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<p class="MsoNormal">Timing of export (do the figures contain large numbers of images), reproducibility of<o:p></o:p></p>
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<p class="MsoNormal">this issue (do you always get this error at the same point, or just occasionally) etc.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> Thanks,<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">On 20 Oct 2017, at 16:34, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk"><span style="color:purple">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Ah. Spoke to soon.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Got an new error when I set a batch job to run multiple figures.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Waiting....</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Traceback (most recent call last):</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> File "figure2png.py", line 88, in <module></span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> while proc.poll() is None:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> File "/opt/OMERO.py-5.3.5-ice35-b73/lib/python/omero_Scripts_ice.py", line 691, in poll</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> return _M_omero.grid.Process._op_poll.invoke(self, ((), _ctx))</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Ice.UnknownLocalException: exception ::Ice::UnknownLocalException</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">{</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> unknown = Network.cpp:2381: Ice::ConnectionRefusedException:</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">connection refused: Connection refused</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">}</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Any idea?</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Steve</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>Stephen Taylor<br>
<b>Sent:</b><span class="apple-converted-space"> </span>20 October 2017 14:04<br>
<b>To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Hi Will,</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Thanks! This seems to fix things.</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D">Steve</span><o:p></o:p></p>
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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:#1F497D"> </span><o:p></o:p></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">From:</span></b><span class="apple-converted-space"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif"> </span></span><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">]<span class="apple-converted-space"> </span><b>On
Behalf Of<span class="apple-converted-space"> </span></b>William Moore (Staff)<br>
<b>Sent:</b><span class="apple-converted-space"> </span>17 October 2017 11:37<br>
<b>To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif;color:purple">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size:11.0pt;font-family:"Calibri",sans-serif">><br>
<b>Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p></o:p></p>
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<p class="MsoNormal">Hi Steve,<span class="apple-converted-space"> </span><o:p></o:p></p>
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<p class="MsoNormal"> I think you must have also updated OMERO.figure too, since the return key changed in OMERO.figure 3.1.0: <o:p></o:p></p>
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<p class="MsoNormal"><a href="https://github.com/ome/omero-figure/commit/6d07fc88"><span style="color:purple">https://github.com/ome/omero-figure/commit/6d07fc88</span></a><o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">You now need to use “New_Figure” everywhere instead of “File_Annotation”).<o:p></o:p></p>
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<p class="MsoNormal">Apologies for not anticipating that this would be a breaking change.<o:p></o:p></p>
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<p class="MsoNormal"> <o:p></o:p></p>
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<p class="MsoNormal">I’ll update the gist.<o:p></o:p></p>
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<p class="MsoNormal"> Hope that works,<o:p></o:p></p>
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<p class="MsoNormal"> Regards,<o:p></o:p></p>
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<p class="MsoNormal"> Will.<o:p></o:p></p>
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<p class="MsoNormal">On 17 Oct 2017, at 08:27, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk"><span style="color:purple">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal">Hi,<br>
<br>
Earlier this year Will kindly helped me write a script to download data from OMERO figure (see<a href="https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6"><span style="color:purple">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</span></a>).<br>
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Our OMERO server just got updated to version 5.3.5. Now line 53, if rv.get('File_Annotation'):, returns None so it never gets to the download step. Please can someone advise how I can debug this because AFAIK the figures look ok and I am a bit stuck what to
do next.<br>
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I am using running the script on Ubuntu and using the OMERO.py-5.3.5-ice35-b73 libs.<br>
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Kind regards and thanks,<br>
<br>
Steve<br>
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Head of Computational Biology Research Group<span class="apple-converted-space"> </span><br>
MRC Weatherall Institute of Molecular Medicine<span class="apple-converted-space"> </span><br>
Oxford<br>
<a href="http://www.cbrg.ox.ac.uk/"><span style="color:purple">www.cbrg.ox.ac.uk</span></a><br>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p></o:p></p>
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<span style="font-size:10.0pt">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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