[ome-users] CLI importing (arbitrary) file annotations

[Colin Blackburn (Staff)]

Hi Niko,

On 19/07/2016 16:45, "ome-users on behalf of Niko Ehrenfeuchter"
<ome-users-bounces at lists.openmicroscopy.org.uk on behalf of
nikolaus.ehrenfeuchter at unibas.ch> wrote:

>Dear all,
>
>I'm feeling a bit stupid but I couldn't find anything in the docs about
>importing file annotations using the command line interface.
>
>Our use case is to attach some text and Excel files to a dataset - is
>this doable using the CLI?


Yes it is doable from the CLI, I covered it in a workshop presentation at
this year's users' meeting:

http://downloads.openmicroscopy.org/presentations/2016/Users-Meeting/Worksh
ops/CLI-Data-Interaction/#/


You'd do something like this:

$ bin/omero upload analysis.csv
Uploaded analysis.csv as 275
$ bin/omero obj new FileAnnotation file=OriginalFile:275
  FileAnnotation:5
  $ bin/omero obj new DatasetAnnotationLink parent=Dataset:51
child=FileAnnotation:5
  DatasetAnnotationLink:2



>From 5.3 the slightly idiosyncratic output of 'upload' is rationalised to:

$ bin/omero upload analysis.csv
OriginalFile:275


so that the returned value can be more easily used as input to other
commands.

The presentations are probably ahead of the docs here. I'll check if we
have a card and look at improving the docs with some concrete examples.

>Thanks a lot,
>~Niko

Cheers,

Colin


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