[ome-users] Batch import of images AND attachments

[Jason Swedlow]

Hi Graeme

Thanks for the early Christmas present!  Sounds great!

Cheers,

Jason

Centre for Gene Regulation & Expression | Open Microscopy Environment | University of Dundee

On 25 Dec 2013 00:02, Graeme Ball <graemeball at googlemail.com> wrote:
>
> 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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