[ome-users] OMERO import - txt format

[Andrea Falconi]

Hi guys,

Re: mount point. Yes, Smuggler actually supports it already:

*
https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/file/RemotePathResolver.java

Re: adding --transfer=ln or --transfer=ln_s to the command. Yes, the
easiest way I can think of is to hard-code it just for testing. This is the
file to hack:

*
https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java

In principle, you could just add an application argument here:

*
https://github.com/c0c0n3/omero-ms-queue/blob/master/components/server/src/main/java/ome/smuggler/core/service/omero/impl/ImporterCommandBuilder.java#L99

e.g.

    .addApplicationArgument(arg("--transfer=ln"));

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

* https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-place-import.html

Let me know if you decide to go down this road so I can give you more
details about it.

Cheers

/a

On 7 December 2017 at 16:14, Julio MATEOS_LANGERAK <
julio.mateos-langerak at igh.cnrs.fr> wrote:

> Hi,
>
> On 7 Dec 2017, at 15:24, Josh Moore <josh at glencoesoftware.com> wrote:
>
> Hi both,
>
> On Wed, Dec 6, 2017 at 3:20 PM, Andrea Falconi <andrea.falconi at gmail.com>
> wrote:
>
> Hello Olaf,
>
> In a nutshell, I don't think there's an out-of-the box solution that would
> be a good fit for your use case---I obviously stand to be corrected.
>
>
> I agree. I think there are workarounds that may solve part of your
> issues or the beginnings of solutions, but we won't have a full
> solution until later in 2018 at the earliest.
>
>
> But if
> you're willing to roll up your sleeves and write some code you could try
> one
> of the approaches below.
>
> is there any existing solution that allows batch import and/or GUI-based
> import with „in-place“ import?
>
> Not that I'm aware of. But I think it shouldn't be too difficult to put
> together a front-end web page that collects import input and then spawns a
> process to run the CLI to do an in-place import as documented here:
>
> * https://docs.openmicroscopy.org/omero/5.4.1/sysadmins/in-
> place-import.html
>
> Note that you'll need to set up a suitable environment for this to
> happen---read the instructions carefully ;-)
>
> Does Smuggler do „in-place“ import too
>
> Not at the moment, but it could be implemented relatively easily---I
> welcome
> contributions :-)
> As an added benefit, you could then use this modified version
> OMERO.Insight:
>
> * https://github.com/MontpellierRessourcesImagerie/openmicroscopy/releases
>
> which uses Smuggler's REST API to do offline imports. This is the version
> we're currently using at the CNRS in Montpellier to let our users import
> files into OMERO.
> Like I said both approaches involve writing some code. If you want to do
> that I'll gladly help you out in whichever way I can.
>
>
> Andrea, if there's an easy way to add in-place import (which is
> essentially adding the argument --transfer=ln or --transfer=ln_s to
> the command), then this might be something Olaf would like to test.
>
>
> 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?
>
> Julio
>
>
> On 6 December 2017 at 14:06, <microscopy at olafselchow.de> wrote:
>
> ...
>
>
> Now: is there any existing solution that allows batch import and/or
> GUI-based import with „in-place“ import? Command-line operation is not
> acceptable by the user.
> Does Smuggler do „in-place“ import too? (couldn’t find any comment on this
> on the smuggler description page)
> Anyone out there who has built something on Atom
> (https://www.medfloss.org/node/695)
>
>
> As far as I know, Atom is unsupported. Happy to be told otherwise.
>
>
> to make it work with OMERO 5.x and extend to „in-place“?
>
> As a starting point, I would like to get an overview on what is already
> available. (—> Is
> https://www.openmicroscopy.org/omero/import/
> a comprehensive list?)
>
>
>
> More or less. There is some distributed info (email thread and forum
> posts) about coming up with a cron-like strategy. If this is something
> you'd like to pursue, let us know.
>
>
> Thanks a lot!
> Olaf
>
>
> ~Josh
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