<html><head></head><body><div style="font-family: Verdana;font-size: 12.0px;"><div>Hi Andrea, Julio, Josh,</div>
<div> </div>
<div>Thanks for all this. I'll have to talk this through and think about which way to go.</div>
<div>Give me a few days. I'll get back to you about this.</div>
<div> </div>
<div>Best regards,</div>
<div>Olaf</div>
<div> </div>
<div>———<br/>
Olaf Selchow<br/>
Microscopy & BioImaging Consulting<br/>
<a href="mailto:microscopy@olafselchow.de">microscopy@olafselchow.de</a></div>
<div>
<div>
<div name="quote" style="margin:10px 5px 5px 10px; padding: 10px 0 10px 10px; border-left:2px solid #C3D9E5; word-wrap: break-word; -webkit-nbsp-mode: space; -webkit-line-break: after-white-space;">
<div style="margin:0 0 10px 0;"><b>Gesendet:</b> Donnerstag, 07. Dezember 2017 um 16:55 Uhr<br/>
<b>Von:</b> "Andrea Falconi" <andrea.falconi@gmail.com><br/>
<b>An:</b> "OME User Support List" <ome-users@lists.openmicroscopy.org.uk><br/>
<b>Betreff:</b> Re: [ome-users] OMERO import - txt format</div>
<div name="quoted-content">
<div>Hi guys,
<div> </div>
<div>Re: mount point. Yes, Smuggler actually supports it already:</div>
<div> </div>
<div>* <a href="https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/file/RemotePathResolver.java" target="_blank">https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/file/RemotePathResolver.java</a></div>
<div> </div>
<div>Re: adding <span style="font-size: 12.8px;">--transfer=ln or --transfer=ln_s to </span><span style="font-size: 12.8px;">the command. Yes, the easiest way I can think of is to hard-code it just for testing. This is the file to hack:</span></div>
<div> </div>
<div><span style="font-size: 12.8px;">* <a href="https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java" target="_blank">https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java</a></span></div>
<div> </div>
<div>In principle, you could just add an application argument here:</div>
<div> </div>
<div>* <a href="https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java#L99" target="_blank">https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java#L99</a></div>
<div> </div>
<div>e.g.</div>
<div> </div>
<div><font face="monospace, monospace"> .addApplicationArgument(arg("--transfer=ln</font><span style="font-family: monospace , monospace;">"));</span></div>
<div> </div>
<div><font face="arial, helvetica, sans-serif">Then like I said your users could just use our modified version of OMERO.Insight as an import GUI. Note that the Smuggler sever process will have to be given the right permissions to write to the OMERO repo as documented here</font></div>
<div> </div>
<div><span style="font-size: 12.8px;">* </span><a href="https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html" style="font-size: 12.8px;" target="_blank">https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html</a></div>
<div> </div>
<div>Let me know if you decide to go down this road so I can give you more details about it.</div>
<div> </div>
<div>Cheers</div>
<div> </div>
<div>/a</div>
</div>
<div class="gmail_extra">
<div class="gmail_quote">On 7 December 2017 at 16:14, Julio MATEOS_LANGERAK <span><<a href="mailto:julio.mateos-langerak@igh.cnrs.fr" onclick="parent.window.location.href='julio.mateos-langerak@igh.cnrs.fr'; return false;" target="_blank">julio.mateos-langerak@igh.cnrs.fr</a>></span> wrote:
<blockquote class="gmail_quote" style="margin: 0 0 0 0.8ex;border-left: 1.0px rgb(204,204,204) solid;padding-left: 1.0ex;">
<div>Hi,
<div> </div>
<div>
<div>
<div>
<div class="h5">
<blockquote>
<div>On 7 Dec 2017, at 15:24, Josh Moore <<a href="mailto:josh@glencoesoftware.com" onclick="parent.window.location.href='josh@glencoesoftware.com'; return false;" target="_blank">josh@glencoesoftware.com</a>> wrote:</div>
<div><span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">Hi both,</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">On Wed, Dec 6, 2017 at 3:20 PM, Andrea Falconi <</span><a href="mailto:andrea.falconi@gmail.com" onclick="parent.window.location.href='andrea.falconi@gmail.com'; return false;" style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;" target="_blank">andrea.falconi@gmail.com</a><span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">> wrote:</span>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">Hello Olaf,<br/>
<br/>
In a nutshell, I don't think there's an out-of-the box solution that would<br/>
be a good fit for your use case---I obviously stand to be corrected.</blockquote>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">I agree. I think there are workarounds that may solve part of your</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">issues or the beginnings of solutions, but we won't have a full</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">solution until later in 2018 at the earliest.</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">But if<br/>
you're willing to roll up your sleeves and write some code you could try one<br/>
of the approaches below.<br/>
<blockquote>is there any existing solution that allows batch import and/or GUI-based<br/>
import with „in-place“ import?</blockquote>
Not that I'm aware of. But I think it shouldn't be too difficult to put<br/>
together a front-end web page that collects import input and then spawns a<br/>
process to run the CLI to do an in-place import as documented here:<br/>
<br/>
* <a href="https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html" target="_blank"> https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html</a><br/>
<br/>
Note that you'll need to set up a suitable environment for this to<br/>
happen---read the instructions carefully ;-)<br/>
<blockquote>Does Smuggler do „in-place“ import too</blockquote>
Not at the moment, but it could be implemented relatively easily---I welcome<br/>
contributions :-)<br/>
As an added benefit, you could then use this modified version OMERO.Insight:<br/>
<br/>
* <a href="https://github.com/MontpellierRessourcesImagerie/openmicroscopy/releases" target="_blank"> https://github.com/MontpellierRessourcesImagerie/openmicroscopy/releases</a><br/>
<br/>
which uses Smuggler's REST API to do offline imports. This is the version<br/>
we're currently using at the CNRS in Montpellier to let our users import<br/>
files into OMERO.<br/>
Like I said both approaches involve writing some code. If you want to do<br/>
that I'll gladly help you out in whichever way I can.</blockquote>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">Andrea, if there's an easy way to add in-place import (which is</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">essentially adding the argument --transfer=ln or --transfer=ln_s to</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">the command), then this might be something Olaf would like to test.</span></div>
</blockquote>
<div> </div>
</div>
</div>
<div>Could the modified insight (or smuggler for that matter) have a configuration option that maps the the local mount point to the mount point seen by OMERO?</div>
<div> </div>
<div><span class="HOEnZb"><font color="#888888">Julio</font></span></div>
<div>
<div class="h5">
<div> </div>
<blockquote>
<div>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">On 6 December 2017 at 14:06, <<a href="mailto:microscopy@olafselchow.de" onclick="parent.window.location.href='microscopy@olafselchow.de'; return false;" target="_blank">microscopy@olafselchow.de</a>> wrote:</blockquote>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">...</span>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">
<blockquote><br/>
Now: is there any existing solution that allows batch import and/or<br/>
GUI-based import with „in-place“ import? Command-line operation is not<br/>
acceptable by the user.<br/>
Does Smuggler do „in-place“ import too? (couldn’t find any comment on this<br/>
on the smuggler description page)<br/>
Anyone out there who has built something on Atom<br/>
(<a href="https://www.medfloss.org/node/695" target="_blank">https://www.medfloss.org/node/695</a>)</blockquote>
</blockquote>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">As far as I know, Atom is unsupported. Happy to be told otherwise.</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">
<blockquote>to make it work with OMERO 5.x and extend to „in-place“?<br/>
<br/>
As a starting point, I would like to get an overview on what is already<br/>
available. (—> Is<br/>
<a href="https://www.openmicroscopy.org/omero/import/" target="_blank">https://www.openmicroscopy.org/omero/import/</a><br/>
a comprehensive list?)</blockquote>
</blockquote>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">More or less. There is some distributed info (email thread and forum</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">posts) about coming up with a cron-like strategy. If this is something</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<span style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;float: none;display: inline;">you'd like to pursue, let us know.</span><br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
<blockquote style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;">
<blockquote>Thanks a lot!<br/>
Olaf</blockquote>
</blockquote>
<br style="font-family: Helvetica;font-size: 12.0px;font-style: normal;font-weight: normal;letter-spacing: normal;text-indent: 0.0px;text-transform: none;white-space: normal;word-spacing: 0.0px;"/>
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