[ome-users] OMERO import - txt format

[Josh Moore]

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.



> 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