[ome-users] OMERO import - txt format

[Julio MATEOS_LANGERAK]

Hi,

On 7 Dec 2017, at 15:24, Josh Moore <josh at glencoesoftware.com<mailto:josh at glencoesoftware.com>> wrote:

Hi both,

On Wed, Dec 6, 2017 at 3:20 PM, Andrea Falconi <andrea.falconi at gmail.com<mailto: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<mailto: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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