[ome-users] OMERO import - txt format

Fri Dec 8 14:40:29 GMT 2017

Again .... message went out as html. Sorry ... here's the txt.

Hi Andrea, Julio, Josh,

Thanks for all this. I'll have to talk this through and think about which way to go.
Give me a few days. I'll get back to you about this.

Best regards,
Olaf

———
Olaf Selchow
Microscopy & BioImaging Consulting
microscopy at olafselchow.de

Gesendet: Donnerstag, 07. Dezember 2017 um 16:55 Uhr
Von: "Andrea Falconi" <andrea.falconi at gmail.com>
An: "OME User Support List" <ome-users at lists.openmicroscopy.org.uk>
Betreff: Re: [ome-users] OMERO import - txt format

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[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[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[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[mailto:julio.mateos-langerak at igh.cnrs.fr]> wrote:
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[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 tooNot 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[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[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/[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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