[ome-users] Batch import of images AND attachments

[Graeme Ball]

Hi,

as promised, I tidied up the script I was talking about, and it is now
available here:-
  https://github.com/graemeball/omero_scripts/blob/master/iomero.py

It can be used as a command-line importer with options including file
attachments; or alternatively, from a server-side python script or
interactive python shell. It should be quite easy to modify to add
additional features from the Blitz gateway.

Also, I incorporated the advice from this thread to retrieve the image Id
from omero.cli.CLI rather than comparing all images before and after an
upload.

Feel free to use, modify, and let me know if I could do something better.

Best Regards & Merry Christmas :-)

Graeme


On Tue, Dec 10, 2013 at 2:35 PM, Josh Moore <josh at glencoesoftware.com>wrote:

> Hi Graeme,
>
> On Dec 10, 2013, at 3:32 PM, Graeme Ball wrote:
>
> > The biggest problem is that the importer does not seem to return the ID
> of
> > the image after completing the upload, and you need this ID to add your
> > attachments etc.
>
> The stdout from the CLI importer is the ID of the Pixels objects (as
> opposed
> to the Image objects). You can also pipe these values to a file for later
> consumption.
>
>
> > we wanted to do the same thing, and ended up writing a python script that
> > performs the upload in 2 steps:-
> > 1. upload the images using the command line importer (you can invoke it
> > from python)
> > 2. use the Blitz gateway to add attachments and annotations
>
>
> Would you be up for sharing the script?
>
> Cheers,
> ~Josh
>
>
> > Regards,
> >
> > Graeme
> >
> >
> > On Tue, Dec 10, 2013 at 10:26 AM, John Webber (NBI)
> > <John.Webber at nbi.ac.uk>wrote:
> >
> >> Hi all,
> >>
> >>
> >>
> >> I have been using the command line importer to import images into an
> Omero
> >> instance as follows:
> >>
> >>
> >>
> >> bin/omero -s $RemoteHost -u "$User" -w "$Password" -p $Port import -d
> >> $Dataset $File
> >>
> >>
> >>
> >> Can anyone let me know if I can also use this format of command to
> import
> >> ATTACHMENTS to specific images and, if so, please can you advise me of
> the
> >> correct syntax?
> >>
> >>
> >>
> >> If it is not possible to import attachments to specific images, is
> anyone
> >> able to recommend how we can do a batch upload of images AND their
> >> attachments, into Omero?
> >>
> >>
> >> Thanks
> >>
> >> John
> >>
>
>
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