[ome-users] Multiple groups "in-place import"?

[Sebastien Besson (Staff)]

Evening Konrad,

Reading your code snippet, the modified bash script never invokes a bin omero import command. This explains how you end up with empty folders.

Can you try re-adding the following line:

$OMEROPATH import -d $DatasetId --transfer=ln_s "/OMERO/in-place-import/$FOLDER"

right after the command that links the dataset to the project:

$OMEROPATH obj new ProjectDatasetLink parent=$ProjectId child=$DatasetId

Best,
Sebastien

> On 13 Feb 2019, at 19:59, Kölble, Konrad <Konrad.Koelble at uk-erlangen.de> wrote:
>
> Hi,
> Josh's suggestion modified for testing
> https://raw.githubusercontent.com/ome/training-scripts/master/maintenance/scripts/in_place_import_as.sh
> ...
> echo Starting
> SUDOER=${SUDOER:-GrandImporter}
> OMEROPATH=${OMEROPATH:-/opt/omero/server/OMERO.server/bin/omero}
> PASSWORD=${PASSWORD:-ome}
> HOST=${HOST:-omerotest.uk-erlangen.de}
> PROJECT=${PROJECT:-Lightsheet}
> FOLDER=${FOLDER:-SN120-16}
> NUMBER=${NUMBER:-2}
> OMEUSER=${OMEUSER:-trainer}
> DATATYPE=${DATATYPE:-dataset}
> for ((i=1;i<=$NUMBER;i++));
> do  $OMEROPATH login --sudo ${SUDOER} -u $OMEUSER-$i -s $HOST -w $PASSWORD
>     if [ "$DATATYPE" = "dataset" ]; then
>        ProjectId=$($OMEROPATH obj new Project name=$PROJECT)
>        DatasetId=$($OMEROPATH obj new Dataset name=$FOLDER)
>        $OMEROPATH obj new ProjectDatasetLink parent=$ProjectId child=$DatasetId
>
>     elif [ "$DATATYPE" = "plate" ]; then
>        $OMEROPATH import --transfer=ln_s "/OMERO/in-place-import/$FOLDER"
>
>    fi
>    $OMEROPATH logout
> ...
>
> produces
> "
> Starting
> Created session 7aeb4c20-90c3-4870-ac24-40920388a6f7 (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 7aeb4c20-90c3-4870-ac24-40920388a6f7 (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 7aeb4c20-90c3-4870-ac24-40920388a6f7 (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 7aeb4c20-90c3-4870-ac24-40920388a6f7 (trainer-1 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> ProjectDatasetLink:1738
> Created session 3028a26e-1a12-491a-96c5-c5ef5a08879c (trainer-2 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 3028a26e-1a12-491a-96c5-c5ef5a08879c (trainer-2 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 3028a26e-1a12-491a-96c5-c5ef5a08879c (trainer-2 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> Using session 3028a26e-1a12-491a-96c5-c5ef5a08879c (trainer-2 at omerotest.uk-erlangen.de:4064). Idle timeout: 10 min. Current group: FPBioimage
> ProjectDatasetLink:1739
> Finishing
> "
> and creates projects and folders DEVOID OF images contained in the source.
> What's missing?
>
> Cheers
> Konrad
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