test-data

#!/bin/bash

# Set up the data structure needed for the tests
# (see setup.csv)

set -e
set -u
set -x

OMERO_DIST=${OMERO_DIST:-/opt/omero/server/OMERO.server}
WORKDIR=$(mktemp -d)

function cleanup {
  rm -rf "$WORKDIR"
  echo "Deleted temp working directory $WORKDIR"
}

trap cleanup EXIT

export PATH=$PATH:${OMERO_DIST}/bin
omero login root@localhost -w omero

# add the root user to a second group
omero group add testGroup
omero group adduser --name testGroup --user-name root 

# create a simple project/dataset/image hierarchy
DATASET=$(omero obj new Dataset name=TestDataset)
PROJECT=$(omero obj new Project name=TestProject)
omero obj new ProjectDatasetLink parent=$PROJECT child=$DATASET
touch "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake"
IMAGE=$(omero import --output=ids  "$WORKDIR/8bit-unsigned&pixelType=uint8&sizeZ=3&sizeC=5&sizeT=7&sizeX=512&sizeY=512.fake" -T Dataset:id:1)

# add some annotations
COMMENT=$(omero obj new CommentAnnotation textValue=BlaBla)
omero obj new ImageAnnotationLink parent=$IMAGE child=$COMMENT
touch "$WORKDIR/test.csv"
FILE=$(omero upload "$WORKDIR/test.csv")
ATTACH=$(omero obj new FileAnnotation file=$FILE)
omero obj new ImageAnnotationLink parent=$IMAGE child=$ATTACH

# import a screen
SCREEN=$(omero obj new Screen name=TestScreen)
touch "$WORKDIR/SPW&plates=1&plateRows=8&plateCols=8&fields=4&plateAcqs=1.fake"
omero import "$WORKDIR/SPW&plates=1&plateRows=8&plateCols=8&fields=4&plateAcqs=1.fake" -T Screen:id:1

# add a map annotation to the screen
MAP=$(omero obj new MapAnnotation)
omero obj map-set $MAP mapValue testkey testvalue
omero obj new ScreenAnnotationLink parent=$SCREEN child=$MAP