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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 Will,<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">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?
<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">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.<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,<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>
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<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>
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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 [mailto:ome-users-bounces@lists.openmicroscopy.org.uk]
<b>On Behalf Of </b>William Moore (Staff)<br>
<b>Sent:</b> 24 October 2017 10:39<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"> 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">On 20 Oct 2017, at 16:34, 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,</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
[<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span style="color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a>]<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 <<a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="color:purple">ome-users@lists.openmicroscopy.org.uk</span></a>><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
[<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk"><span style="color:purple">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a>]<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 <<a href="mailto:ome-users@lists.openmicroscopy.org.uk"><span style="color:purple">ome-users@lists.openmicroscopy.org.uk</span></a>><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 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"> <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"> <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">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"> <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>
----------------------------------<br>
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>
<br>
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<p class="MsoNormal"><br>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica",sans-serif">_______________________________________________<br>
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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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