<html><head><meta http-equiv="Content-Type" content="text/html charset=utf-8"></head><body style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class=""><meta http-equiv="Content-Type" content="text/html charset=utf-8" class=""><div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">Thanks very much Will.<div class=""><br class=""><div class=""><blockquote type="cite" class=""><div class="">On 11 Dec 2017, at 13:37, William Moore (Staff) <<a href="mailto:W.Moore@dundee.ac.uk" class="">W.Moore@dundee.ac.uk</a>> wrote:</div><br class="Apple-interchange-newline"><div class="">
<meta http-equiv="Content-Type" content="text/html; charset=utf-8" class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Eilidh,
<div class=""><br class="">
</div>
<div class="">I’ve opened at PR for this in web: <a href="https://github.com/openmicroscopy/openmicroscopy/pull/5598" class="">https://github.com/openmicroscopy/openmicroscopy/pull/5598</a> and Jean-Marie tells me</div>
<div class="">that it should also be doable in Insight, so I’ve created a card at</div>
<div class=""><a href="https://trello.com/c/C3EqebXJ/61-script-parameter-password" class="">https://trello.com/c/C3EqebXJ/61-script-parameter-password</a></div>
<div class="">These are likely to be included in the next release of OMERO.</div>
<div class=""><br class="">
</div>
<div class="">Apart from the visibility of the password in the script UI, it’s important to be aware of other places that the password</div>
<div class="">could be exposed to others:</div>
<div class=""><br class="">
</div>
<div class=""> - The connection between Insight and OMERO is not encrypted by default (except for the login). We’ll look at using encrypted connection when submitting script parameters containing passwords, but in the meantime there is the potential for this
data to be read.</div>
<div class=""> - Make sure you’re not logging or printing the script params (as we do in many of our example scripts). Currently, Blitz.log and Processor.log don’t log script params but make sure you don’t log them yourself.</div>
<div class=""> - If you’re using the webclient, you should use https to encrypt the connection between the browser and OMERO.web.</div>
<div class=""> - Currently in webcilent, errors in the handling of script submission are not handled well (display error on page instead of displaying feedback error submission page). This shouldn’t lead to any exposure of passwords, but be careful not to submit
feedback etc that contains the password and if you think you might have done, then be sure to change your password.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
</div>
<div class="">Regards,</div>
<div class=""><br class="">
</div>
<div class=""> Will.</div>
<div class=""><br class="">
</div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 8 Dec 2017, at 11:55, Eilidh Troup <<a href="mailto:e.troup@epcc.ed.ac.uk" class="">e.troup@epcc.ed.ac.uk</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class="">
<div style="word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;" class="">
Hi Josh,
<div class=""><br class="">
</div>
<div class="">Thanks very much. This is a screenshot from running the script in OMERO.insight. I’d like the text entered in the password to be hidden, like this *****.</div>
<div class=""><br class="">
</div>
<div class="">Eilidh </div>
<div class=""><br class="">
</div>
<div class=""><span id="cid:881F9A84-7937-4D81-8216-A1844F3F04F5@ed.ac.uk" class=""><PastedGraphic-2.png></span></div>
<div class=""><br class="">
<div class="">
<blockquote type="cite" class="">
<div class="">On 7 Dec 2017, at 14:39, Josh Moore <<a href="mailto:josh@glencoesoftware.com" class="">josh@glencoesoftware.com</a>> wrote:</div>
<br class="Apple-interchange-newline">
<div class=""><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Hi
Eilidh,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">On
Tue, Dec 5, 2017 at 10:51 PM, Eilidh Troup <</span><a href="mailto:e.troup@epcc.ed.ac.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">e.troup@epcc.ed.ac.uk</a><span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">>
wrote:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
Hi Josh,<br class="">
<br class="">
Thanks for your help. I can now transfer an image from one OMERO to another<br class="">
: )<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Congratulations.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
I’ve put the latest version of the script at<br class="">
<a href="https://github.com/SynthSys/omero-user-scripts/blob/master/Export_to_other_omero.py" class="">https://github.com/SynthSys/omero-user-scripts/blob/master/Export_to_other_omero.py</a><br class="">
<br class="">
I’ve got more questions though:<br class="">
How can I find the managed repository directory? (Something like<br class="">
omero.managed.dir, Default: ${omero.data.dir}/ManagedRepository ?)<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">In
[2]: client.sf.getConfigService().getConfigValue("omero.managed.dir")</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
How can I hide the password text entry?<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Where
are you seeing password text entry?</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
How can I get the newly created image id? It is printed to stdout as<br class="">
"Image:920" for example, but I don't know how to get hold of that number in<br class="">
my script.<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">You
can use something like:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> import
sys</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> old_stdout
= sys.stdout</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> sys.stdout
= open(temporary_file_name, "w")</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> try:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> #
do import</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> finally:</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class=""> sys.stdout
= old_stdout</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
Also, the docker script you sent didn’t quite work (don’t worry about it<br class="">
though, I got what I needed from your example) - I got this error when I ran<br class="">
the python script:<br class="">
<br class="">
bash-4.2$ python /gist/export_to_remote_omero.py<br class="">
Traceback (most recent call last):<br class="">
</blockquote>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
::Glacier2::PermissionDeniedException<br class="">
{<br class="">
reason = internal server error<br class="">
}<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">Alright.
If you'd like to investigate further, we'll need the server logs.</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
Thanks,<br class="">
Eilidh<br class="">
</blockquote>
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">All
the best,</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">~Josh</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<blockquote type="cite" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">
On 10 Nov 2017, at 09:22, Josh Moore <<a href="mailto:josh@glencoesoftware.com" class="">josh@glencoesoftware.com</a>> wrote:<br class="">
<br class="">
Hi Elidh,<br class="">
<br class="">
On Thu, Nov 9, 2017 at 5:07 PM, Eilidh Troup <<a href="mailto:e.troup@epcc.ed.ac.uk" class="">e.troup@epcc.ed.ac.uk</a>> wrote:<br class="">
<br class="">
Hi,<br class="">
<br class="">
I’ve run into a similar problem as last time.<br class="">
<br class="">
<br class="">
Turns out, there's a similar solution.<br class="">
<br class="">
I’ve written a script that<br class="">
will upload an image to a remote OMERO server, but only from the python<br class="">
command line, and not from within a script running in a local OMERO. As<br class="">
before, the script will work from the command line or from with OMERO when<br class="">
transferring the image to the local OMERO server. When I try to import an<br class="">
image on the remote server, I get the following error:<br class="">
<br class="">
...<br class="">
<br class="">
<br class="">
The code, and full error output are below.<br class="">
I’ve also put it into a different script on gist that demonstrates the error<br class="">
by running it from within OMERO as a script.<br class="">
<a href="https://gist.github.com/eilidh-t/e763dab7d4f3515cc85b0b6ddfb8d9f4" class="">https://gist.github.com/eilidh-t/e763dab7d4f3515cc85b0b6ddfb8d9f4</a><br class="">
<br class="">
<br class="">
I've update your script:<br class="">
<a href="https://gist.github.com/joshmoore/0c2e5319d8d5ae7f79ee82e3e68b721b" class="">https://gist.github.com/joshmoore/0c2e5319d8d5ae7f79ee82e3e68b721b</a><br class="">
<br class="">
The most important change is:<br class="">
<br class="">
del os.environ["ICE_CONFIG"] before importing<br class="">
<br class="">
which does the equivalent of `Ice.Config=/dev/null` but for the import<br class="">
process. Likely, that should be done closer to the top.<br class="">
<br class="">
Other changes include:<br class="">
<br class="">
* use ome.cli.CLI rather than calling subprocess (simplicity)<br class="">
* only register the script if it doesn't exist (less test mess)<br class="">
* pass a key to not store the root's password (security)<br class="">
* adding a warning about the security whole that this script could<br class="">
cause (security)<br class="">
<br class="">
My general workflow was:<br class="">
<br class="">
* docker-compose up -d<br class="">
* docker-compose exec omero1 bash<br class="">
* cd /opt/omero/server/OMERO.server<br class="">
* export PYTHONPATH=lib/python<br class="">
* python /gist/export_to_remote_omero.py<br class="">
<br class="">
If I needed to change the script, I deleted the uploaded file from<br class="">
lib/script/export_to_remote_omero.py and re-ran.<br class="">
<br class="">
Thanks for your help with this,<br class="">
Eilidh<br class="">
<br class="">
<br class="">
<br class="">
Let us know if that works for you.<br class="">
~J<br class="">
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
<br class="">
<br class="">
<br class="">
The University of Edinburgh is a charitable body, registered in<br class="">
Scotland, with registration number SC005336.<br class="">
<br class="">
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
<br class="">
</blockquote>
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; 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-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<span style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px; float: none; display: inline !important;" class="">ome-devel
mailing list</span><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">ome-devel@lists.openmicroscopy.org.uk</a><br style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; word-spacing: 0px; -webkit-text-stroke-width: 0px;" class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" style="font-family: Helvetica; font-size: 12px; font-style: normal; font-variant-caps: normal; font-weight: normal; letter-spacing: normal; orphans: auto; text-align: start; text-indent: 0px; text-transform: none; white-space: normal; widows: auto; word-spacing: 0px; -webkit-text-size-adjust: auto; -webkit-text-stroke-width: 0px;" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a></div>
</blockquote>
</div>
<br class="">
</div>
</div>
The University of Edinburgh is a charitable body, registered in<br class="">
Scotland, with registration number SC005336.<br class="">
_______________________________________________<br class="">
ome-devel mailing list<br class="">
<a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class="">
<a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class="">
</div>
</blockquote>
</div>
<br class="">
</div>
<br class="">
<span style="font-size:10pt;" class="">The University of Dundee is a registered Scottish Charity, No: SC015096</span>
</div>
_______________________________________________<br class="">ome-devel mailing list<br class=""><a href="mailto:ome-devel@lists.openmicroscopy.org.uk" class="">ome-devel@lists.openmicroscopy.org.uk</a><br class=""><a href="http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel" class="">http://lists.openmicroscopy.org.uk/mailman/listinfo/ome-devel</a><br class=""></div></blockquote></div><br class=""></div></div></body></html>