delete_annotations.py

# -----------------------------------------------------------------------------
#  Copyright (C) 2018 University of Dundee. All rights reserved.
#
#
#  This program is free software; you can redistribute it and/or modify
#  it under the terms of the GNU General Public License as published by
#  the Free Software Foundation; either version 2 of the License, or
#  (at your option) any later version.
#  This program is distributed in the hope that it will be useful,
#  but WITHOUT ANY WARRANTY; without even the implied warranty of
#  MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#  GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License along
# with this program; if not, write to the Free Software Foundation, Inc.,
#  51 Franklin Street, Fifth Floor, Boston, MA 02110-1301 USA.
#
# ------------------------------------------------------------------------------

# Delete Annotations of a particular namespace from all Images in a Dataset
# The namespace can be also "none"
# Examples
# delete_annotations.py --anntype file --namespace none pwd datasetname
# will delete all FileAnnotations on images of
# a given dataset regardless of namespace
#
# delete_annotations.py pwd datasetname
# will delete all MapAnnotations with
# namespace omero.batch_roi_export.map_ann

import argparse
from omero.gateway import BlitzGateway
import omero


def run(name, password, dataset_name, anntype, ns, host, port):

    conn = BlitzGateway(name, password, host=host, port=port)
    try:
        conn.connect()
        datasets = conn.getObjects("Dataset",
                                   attributes={"name": dataset_name})
        for dataset in datasets:
            print(dataset.getId())
            ann_ids = []
            given_type = None
            if anntype == "map":
                given_type = omero.model.MapAnnotationI
            if anntype == "file":
                given_type = omero.model.FileAnnotationI
            if ns == "none":
                ns = None
            for image in dataset.listChildren():
                for a in image.listAnnotations(ns):
                    if a.OMERO_TYPE == given_type:
                        print(a.getId(), a.OMERO_TYPE, a.ns)
                        ann_ids.append(a.id)
            # Delete the annotations link to the dataset
            for a in dataset.listAnnotations(ns):
                if a.OMERO_TYPE == given_type:
                    print(a.getId(), a.OMERO_TYPE, a.ns)
                    ann_ids.append(a.id)
            if len(ann_ids) > 0:
                print("Deleting %s annotations..." % len(ann_ids))
                conn.deleteObjects('Annotation', ann_ids, wait=True)
    except Exception as exc:
        print("Error while deleting annotations: %s" % str(exc))
    finally:
        conn.close()


def main(args):
    parser = argparse.ArgumentParser()
    parser.add_argument('password')
    parser.add_argument('datasetname')
    parser.add_argument('--name', default="trainer-1",
                        help="The user deleting the annotations")
    parser.add_argument('--anntype', default="map",
                        help="The type of the annotations")
    parser.add_argument('--namespace',
                        default="omero.batch_roi_export.map_ann",
                        help="The namespace of the annotations")
    parser.add_argument('--server', default="workshop.openmicroscopy.org",
                        help="OMERO server hostname")
    parser.add_argument('--port', default=4064, help="OMERO server port")
    args = parser.parse_args(args)
    run(args.name, args.password, args.datasetname, args.anntype,
        args.namespace, args.server, args.port)


if __name__ == '__main__':
    import sys
    main(sys.argv[1:])