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Hi Steve,
<div class=""><br class="">
</div>
<div class=""> It looks like the figure is getting created OK since you get the ID returned.</div>
<div class="">So it’s probably a permissions issue due to the figure file getting created</div>
<div class="">in a different group from the group that the figure file itself is in.</div>
<div class=""><br class="">
</div>
<div class="">In the gist, we switch to the group that the figure.json file is in, but it’s possible</div>
<div class="">that the PDF is created in a different group.</div>
<div class="">The export script tries to save exported figures to the same group as the first image in the figure.</div>
<div class=""><br class="">
</div>
<div class="">Anyway, you can repeat this line:</div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">conn.</span><span class="pl-c1" style="box-sizing: border-box; color: rgb(0, 92, 197); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);">SERVICE_OPTS</span><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">.setOmeroGroup(</span><span class="pl-k" style="box-sizing: border-box; color: rgb(215, 58, 73); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);">-</span><span class="pl-c1" style="box-sizing: border-box; color: rgb(0, 92, 197); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);">1</span><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">)</span></div>
<div class=""><br class="">
</div>
<div class="">Right before this line:</div>
<div class=""><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">figure_pdf
</span><span class="pl-k" style="box-sizing: border-box; color: rgb(215, 58, 73); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);">=</span><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">
conn.getObject(</span><span class="pl-s" style="box-sizing: border-box; color: rgb(3, 47, 98); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);"><span class="pl-pds" style="box-sizing: border-box;">"</span>FileAnnotation<span class="pl-pds" style="box-sizing: border-box;">"</span></span><span style="color: rgb(36, 41, 46); font-family: SFMono-Regular, Consolas, 'Liberation Mono', Menlo, Courier, monospace; orphans: 2; white-space: pre; widows: 2; background-color: rgb(255, 255, 255);" class="">,
figure_id)</span></div>
<div class=""><br class="">
</div>
<div class="">So hopefully that should find the newly created PDF OK.</div>
<div class=""><br class="">
</div>
<div class="">I’ve updated the gist at <a href="https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6" class="">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</a> with</div>
<div class="">this change.</div>
<div class=""><br class="">
</div>
<div class="">Let us know if that doesn’t work?</div>
<div class="">Regards,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div>
<blockquote type="cite" class="">
<div class="">On 6 Apr 2018, at 17:28, 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">
<div class="">
<div class="WordSection1" style="page: WordSection1; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;">
<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="">Hi Again,<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="">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 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="">Job 1472150 ready<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="">Waiting....<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="">Callback received: FINISHED<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="">Figure file: 2109025<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="">Traceback (most recent call last):<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 "gist.py", line 84, in <module><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=""> figure_name = str(id)+"_"+figure_pdf.getFile().getName()<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="">AttributeError: 'NoneType' object has no attribute 'getFile'<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="">I have attached the json of both files. 2086989 converts to pdf and 2100620 doesn’t convert.<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="">Both figures look fine and PDFs download ok using the web client.<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 for any help!<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="">Steve<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="">----------------------------------<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="">Head of Computational Biology Research Group<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="">MRC Weatherall Institute of Molecular Medicine<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="">Oxford<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=""><a href="http://www.cbrg.ox.ac.uk/" style="color: purple; text-decoration: underline;" class="">www.cbrg.ox.ac.uk</a><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=""> </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="">
<a name="_MailEndCompose" class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></a></div>
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
<span class=""><span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span></span></div>
<span class=""></span>
<div style="border-style: none none none solid; border-left-color: blue; border-left-width: 1.5pt; padding: 0cm 0cm 0cm 4pt;" class="">
<div class="">
<div style="border-style: solid none none; border-top-color: rgb(225, 225, 225); border-top-width: 1pt; padding: 3pt 0cm 0cm;" class="">
<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="">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>01 November 2017 14:20<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>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
By default the timeout is 10 minutes.<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="">
This can be set on the server by an admin with (milliseconds)<o:p class=""></o:p></div>
</div>
<div class="">
<div style="border: 1pt solid rgb(226, 228, 230); padding: 6pt 8pt; background-color: rgb(248, 249, 249); background-position: initial initial; background-repeat: initial initial;" class="">
<pre style="margin: 0cm 0cm 0.0001pt; font-size: 10pt; font-family: 'Courier New'; line-height: 15pt; background-color: rgb(248, 249, 249); 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; background-position: initial initial; background-repeat: initial initial;" class=""><code style="font-family: 'Courier New';" class=""><span style="font-size: 10.5pt; font-family: 'Lucida Console'; color: rgb(77, 77, 77); border: 1pt none windowtext; padding: 0cm;" class="">$ bin/omero config set omero.sessions.timeout 85000000</span></code><span style="font-size: 10.5pt; font-family: 'Lucida Console'; color: rgb(51, 51, 51);" class=""><o:p class=""></o:p></span></pre>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
and this will then apply to ALL server sessions.<o:p class=""></o:p></div>
</div>
</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>
</div>
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
An admin can also set the timeout for an individual session in the CLI with (seconds)<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="">
<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="">
$ bin/omero sessions timeout 1000<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="">
<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="">
but unfortunately non-admins can’t do this.<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="">
<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="">
There may be other ways you could keep a session alive if needed by “pinging” from a client?<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="">
e.g. "watch -n 60 omero login” but I haven’t tried this.<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="">
<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="">
Regards,<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="">
<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="">
Will.<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="">
<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="">
<o:p class=""> </o:p></div>
<div class="">
<blockquote style="margin-top: 5pt; margin-bottom: 5pt;" class="">
<div class="">
<div style="margin: 0cm 0cm 0.0001pt; font-size: 12pt; font-family: 'Times New Roman', serif;" class="">
On 1 Nov 2017, at 13:02, 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>
</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 class="">
<div class="">
<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="">Hi Will,</span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Thanks.</span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">If I set up a session, how long does it last? Do you need to set the length for time out?</span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Kind regards and thanks,</span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Steve</span><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="">
<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><o:p class=""></o:p></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 class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">]<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>01 November 2017 12:24<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p class=""></o:p></div>
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Hi Steve,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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I’m afraid we don’t support token authentication yet, although we have been discussing it…<o:p class=""></o:p></div>
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<a href="https://trello.com/c/CbRYR7Ty/34-session-issues" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">https://trello.com/c/CbRYR7Ty/34-session-issues</span></a><o:p class=""></o:p></div>
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I’ve added your request to that card.<o:p class=""></o:p></div>
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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 class=""></o:p></div>
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You can get a session key when you login from the command line<o:p class=""></o:p></div>
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$ bin/omero login<o:p class=""></o:p></div>
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Or if you’re already logged-in, you can do<o:p class=""></o:p></div>
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$ bin/omero sessions key<o:p class=""></o:p></div>
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Then use that in your script to connect.<o:p class=""></o:p></div>
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conn = BlitzGateway(host="localhost", port=4064)<o:p class=""></o:p></div>
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conn.connect(SESSION_ID)<o:p class=""></o:p></div>
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I updated <a href="https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</span></a><o:p class=""></o:p></div>
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to show this.<o:p class=""></o:p></div>
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It would be better to add command line arguments to your script instead of<o:p class=""></o:p></div>
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hard-coding it.<o:p class=""></o:p></div>
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Regards,<o:p class=""></o:p></div>
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Will.<o:p class=""></o:p></div>
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On 31 Oct 2017, at 11:48, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<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,</span><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=""> </span><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="">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 class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">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 class=""></o:p></div>
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<span style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><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="">Thanks,</span><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="">Steve</span><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=""> </span><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=""> </span><o:p class=""></o:p></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 class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">]<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>24 October 2017 10:39<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>OME User Support List <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p class=""></o:p></div>
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Hi Steve,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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I tried a simple modification to my script to export and download a handful of figures<o:p class=""></o:p></div>
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sequentially, and this seemed to work OK.<o:p class=""></o:p></div>
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Could you share your script and give us an idea of how many figures you<o:p class=""></o:p></div>
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can export before you see this ConnectionRefusedException?<o:p class=""></o:p></div>
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Also, any other info you think might be relevant?<o:p class=""></o:p></div>
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Timing of export (do the figures contain large numbers of images), reproducibility of<o:p class=""></o:p></div>
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this issue (do you always get this error at the same point, or just occasionally) etc.<o:p class=""></o:p></div>
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Thanks,<o:p class=""></o:p></div>
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Will.<o:p class=""></o:p></div>
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On 20 Oct 2017, at 16:34, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<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,</span><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="">Ah. Spoke to soon.</span><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="">Got an new error when I set a batch job to run multiple figures.</span><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="">Waiting....</span><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="">Traceback (most recent call last):</span><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=""> File "figure2png.py", line 88, in <module></span><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=""> while proc.poll() is None:</span><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=""> File "/opt/OMERO.py-5.3.5-ice35-b73/lib/python/omero_Scripts_ice.py", line 691, in poll</span><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=""> return _M_omero.grid.Process._op_poll.invoke(self, ((), _ctx))</span><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="">Ice.UnknownLocalException: exception ::Ice::UnknownLocalException</span><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="">{</span><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=""> unknown = Network.cpp:2381: Ice::ConnectionRefusedException:</span><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="">connection refused: Connection refused</span><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="">}</span><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="">Any idea?</span><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="">Steve</span><o:p class=""></o:p></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 class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">]<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 <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><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,</span><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="">Thanks! This seems to fix things.</span><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="">Steve</span><o:p class=""></o:p></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 class="apple-converted-space"><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class=""> </span></span><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">ome-users
[</span><a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">]<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 <</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif; color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><span lang="EN-US" style="font-size: 11pt; font-family: Calibri, sans-serif;" class="">><br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>Re: [ome-users] OMERO Figure Download</span><o:p class=""></o:p></div>
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Hi Steve,<span class="apple-converted-space"> </span><o:p class=""></o:p></div>
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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>
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<a href="https://github.com/ome/omero-figure/commit/6d07fc88" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">https://github.com/ome/omero-figure/commit/6d07fc88</span></a><o:p class=""></o:p></div>
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You now need to use “New_Figure” everywhere instead of “File_Annotation”).<o:p class=""></o:p></div>
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Apologies for not anticipating that this would be a breaking change.<o:p class=""></o:p></div>
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I’ll update the gist.<o:p class=""></o:p></div>
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Hope that works,<o:p class=""></o:p></div>
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Regards,<o:p class=""></o:p></div>
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Will.<o:p class=""></o:p></div>
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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=""><span style="color: purple;" class="">stephen.taylor@imm.ox.ac.uk</span></a>> wrote:<o:p class=""></o:p></div>
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Hi,<br class="">
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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=""><span style="color: purple;" class="">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</span></a>).<br class="">
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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 class="">
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I am using running the script on Ubuntu and using the OMERO.py-5.3.5-ice35-b73 libs.<br class="">
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Kind regards and thanks,<br class="">
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Steve<br class="">
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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=""><span style="color: purple;" class="">www.cbrg.ox.ac.uk</span></a><br class="">
<br class="">
_______________________________________________<br class="">
ome-users mailing list<br class="">
<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-users</span></a><o:p class=""></o:p></div>
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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<span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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<span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class="">_______________________________________________<br class="">
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</span><a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="font-size: 9pt; font-family: Helvetica, sans-serif; color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a><span style="font-size: 9pt; font-family: Helvetica, sans-serif;" class=""><br class="">
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<span style="font-size: 10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span><o:p class=""></o:p></div>
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<span id="cid:3A5C685D-4CF0-49E3-8F59-C27AD253C89D@home"><2086989.json></span><span id="cid:6A99A1E4-1919-4206-9B29-25105FBDD3A0@home"><2100620.json></span><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">_______________________________________________</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<a href="mailto:ome-users@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline; font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">ome-users@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant: normal; font-weight: normal; letter-spacing: normal; line-height: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
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<span style="font-size:10pt;">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
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