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Hi Steve,
<div class=""><br class="">
</div>
<div class=""> I tried a simple modification to my script to export and download a handful of figures</div>
<div class="">sequentially, and this seemed to work OK.</div>
<div class="">Could you share your script and give us an idea of how many figures you</div>
<div class="">can export before you see this ConnectionRefusedException?</div>
<div class=""><br class="">
</div>
<div class="">Also, any other info you think might be relevant?</div>
<div class="">Timing of export (do the figures contain large numbers of images), reproducibility of</div>
<div class="">this issue (do you always get this error at the same point, or just occasionally) etc.</div>
<div class=""><br class="">
</div>
<div class=""> Thanks,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 20 Oct 2017, at 16:34, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" class="">stephen.taylor@imm.ox.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi,<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Ah. Spoke to soon.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Got an new error when I set a batch job to run multiple figures.<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Waiting....<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Traceback (most recent call last):<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> File "figure2png.py", line 88, in <module><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> while proc.poll() is None:<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> File "/opt/OMERO.py-5.3.5-ice35-b73/lib/python/omero_Scripts_ice.py", line 691, in poll<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> return _M_omero.grid.Process._op_poll.invoke(self, ((), _ctx))<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Ice.UnknownLocalException: exception ::Ice::UnknownLocalException<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">{<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> unknown = Network.cpp:2381: Ice::ConnectionRefusedException:<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">connection refused: Connection refused<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">}<o:p class=""></o:p></span></div>
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<a name="_MailEndCompose" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></a></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Any idea?<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Steve<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>Stephen Taylor<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>20 October 2017 14:04<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download<o:p class=""></o:p></span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Hi Will,<o:p class=""></o:p></span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks! This seems to fix things.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Steve<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<b class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">From:</span></b><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""><span class="Apple-converted-space"> </span>ome-users [<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</a>]<span class="Apple-converted-space"> </span><b class="">On
Behalf Of<span class="Apple-converted-space"> </span></b>William Moore (Staff)<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>17 October 2017 11:37<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>OME User Support List <<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class="">ome-users@lists.openmicroscopy.org.uk</a>><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download<o:p class=""></o:p></span></div>
</div>
</div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Hi Steve,<span class="Apple-converted-space"> </span><o:p class=""></o:p></div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
I think you must have also updated OMERO.figure too, since the return key changed in OMERO.figure 3.1.0: <o:p class=""></o:p></div>
</div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<a href="https://github.com/ome/omero-figure/commit/6d07fc88" style="color: purple; text-decoration: underline;" class="">https://github.com/ome/omero-figure/commit/6d07fc88</a><o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
You now need to use “New_Figure” everywhere instead of “File_Annotation”).<o:p class=""></o:p></div>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Apologies for not anticipating that this would be a breaking change.<o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
I’ll update the gist.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Hope that works,<o:p class=""></o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Regards,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Will.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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<o:p class=""> </o:p></div>
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<blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class="">
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
On 17 Oct 2017, at 08:27, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" style="color: purple; text-decoration: underline;" class="">stephen.taylor@imm.ox.ac.uk</a>> wrote:<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
Hi,<br class="">
<br class="">
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" style="color: purple; text-decoration: underline;" class="">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</a>).<br class="">
<br class="">
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 class="">
<br class="">
I am using running the script on Ubuntu and using the OMERO.py-5.3.5-ice35-b73 libs.<br class="">
<br class="">
Kind regards and thanks,<br class="">
<br class="">
Steve<br class="">
----------------------------------<br class="">
Head of Computational Biology Research Group<span class="Apple-converted-space"> </span><br class="">
MRC Weatherall Institute of Molecular Medicine<span class="Apple-converted-space"> </span><br class="">
Oxford<br class="">
<a href="http://www.cbrg.ox.ac.uk/" style="color: purple; text-decoration: underline;" class="">www.cbrg.ox.ac.uk</a><br class="">
<br class="">
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