[ome-devel] CLI import, exception when trying to add annotation link

[Sebastien Besson (Staff)]

Hi Niko,

looking at the source code, are you linking the image to a comment annotation or a different
type of annotation?
At the moment, the `—annotation_link` option in the importer code can only handle comment
annotations (and we may have suggested the opposite during the meeting, apologies if that
was the case) - see
https://github.com/openmicroscopy/openmicroscopy/blob/v5.1.2/components/blitz/src/ome/formats/importer/cli/CommandLineImporter.java#L843

If you want to create a link to a different type of annotation, your best current solution using the
current state might be to do the following post-import:
1- parse the output of bin/omero import to retrieve the image id - see for instance
https://github.com/sbesson/openmicroscopy/blob/v5.1.2/examples/Training/training_setup.sh#L52
2- call bin/omero obj in a separate command to link the image to the know annotation e.g.
$ bin/omero obj new ImageAnnotationLink parent=Image:iid child=FileAnnotation:fid

Best,
Sebastien

On 4 Jun 2015, at 21:40, Niko Ehrenfeuchter <nikolaus.ehrenfeuchter at unibas.ch<mailto:nikolaus.ehrenfeuchter at unibas.ch>> wrote:





Am I doing something wrong?

A quick guess from the road: is the annotation in another group?

I don't think so, as another image in this  dataset has the very same annotation - set via the webclient. At least if I remember correctly.

I'll double check tomorrow, iirc the webclient shows all those properties when hovering with the mouse over an annotation, right?

Cheers
Niko
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