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Hi Steve,
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<div class=""> I’m afraid we don’t support token authentication yet, although we have been discussing it…</div>
<div class=""><a href="https://trello.com/c/CbRYR7Ty/34-session-issues" class="">https://trello.com/c/CbRYR7Ty/34-session-issues</a></div>
<div class="">I’ve added your request to that card.</div>
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<div class="">The next best thing you can do is to use an existing session ID to join a session (like a short-lived token).</div>
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</div>
<div class="">You can get a session key when you login from the command line</div>
<div class="">$ bin/omero login</div>
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</div>
<div class="">Or if you’re already logged-in, you can do</div>
<div class="">$ bin/omero sessions key</div>
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</div>
<div class="">Then use that in your script to connect.</div>
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</div>
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<div class="">conn = BlitzGateway(host="localhost", port=4064)</div>
<div class="">conn.connect(SESSION_ID)</div>
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<div class="">I updated <a href="https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6" class="">https://gist.github.com/will-moore/d448a7abd57425734aba426f0952eff6</a></div>
<div class="">to show this.</div>
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</div>
<div class="">It would be better to add command line arguments to your script instead of</div>
<div class="">hard-coding it.</div>
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<div class="">Regards,</div>
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<div class=""> Will.</div>
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<blockquote type="cite" class="">
<div class="">On 31 Oct 2017, at 11:48, Stephen Taylor <<a href="mailto:stephen.taylor@imm.ox.ac.uk" class="">stephen.taylor@imm.ox.ac.uk</a>> wrote:</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>
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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="">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 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="">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 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="">Thanks,<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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<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>24 October 2017 10:39<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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<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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<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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<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="">
Also, any other info you think might be relevant?<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="">
Timing of export (do the figures contain large numbers of images), reproducibility of<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="">
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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<o:p class=""> </o:p></div>
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Thanks,<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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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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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="">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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<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=""> </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=""> </span><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="">
<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=""> </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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<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 "figure2png.py", line 88, in <module></span><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="">
<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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<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</span><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="">
<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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<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=""> 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=""> </span><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="">
<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=""> </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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<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
[<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></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=""><span style="color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a>><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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<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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<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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<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=""> </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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<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
[<a href="mailto:ome-users-bounces@lists.openmicroscopy.org.uk" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">mailto:ome-users-bounces@lists.openmicroscopy.org.uk</span></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=""><span style="color: purple;" class="">ome-users@lists.openmicroscopy.org.uk</span></a>><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
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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="">
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