OMERO.script which merges duplicate Tags and moves Images ONLY to remaining Tag.

Merge_Tags.py

#!/usr/bin/env python
# -*- coding: utf-8 -*-
# -----------------------------------------------------------------------------
#   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.
# 
# ------------------------------------------------------------------------------

"""This script merges duplicate Tags and moves Images to remaining Tag."""
# https://www.openmicroscopy.org/community/viewtopic.php?f=4&t=8478&p=19225#p19225


from omero.gateway import BlitzGateway
from omero import ValidationException
from omero.model import TagAnnotationI, ImageAnnotationLinkI, ImageI
from omero.rtypes import rstring
import omero.scripts as scripts

def merge_tags(conn, params):
    """Merge tags and return a message."""
    tag_text = params['Tag_Name']
    updateService = conn.getUpdateService()

    # Find Tags by Name
    tags = conn.getObjects("TagAnnotation", attributes={"textValue": tag_text})
    tags = list(tags)

    if len(tags) < 2:
        return "Found fewer than 2 Tags of %s " % tag_text

    # Keep the first tag, delete others, moving links to new tag
    to_keep = tags[0]
    print 'to keep', to_keep.id, to_keep.textValue

    to_delete = []

    # Go through all the tags we're deleting...
    for tag in tags[1:]:
        print "Transfer images from Tag:", tag.id
        # Create new links between 'to_keep' and tagged objects
        # Just handle images for now...
        for link in conn.getAnnotationLinks("Image", ann_ids=[tag.id]):
            new_link = ImageAnnotationLinkI()
            new_link.child = TagAnnotationI(to_keep.id, False)
            new_link.parent = ImageI(link.parent.id, False)
            try:
                updateService.saveObject(new_link)
            except ValidationException:
                # Ignore failures where link already exists
                print "   link already exists to image: %s" % link.parent.id
        to_delete.append(tag.id)

    # Do the deletion
    print "Deleting Tags", to_delete
    conn.deleteObjects("Annotation", to_delete)

    return "Deleted %s Tags" % len(to_delete)


def run_script():
    """The main entry point of the script, as called by the client."""
    client = scripts.client(
        'Merge_Tags.py',
        """Delete duplicate Tags, moving Images to remaining Tag""",

        scripts.String(
            "Tag_Name", optional=False, grouping="1",
            description="Name of the Tags you want to merge."),

        authors=["William Moore", "OME Team"],
        institutions=["University of Dundee"],
        contact="[email protected]",
    )

    try:
        conn = BlitzGateway(client_obj=client)

        script_params = client.getInputs(unwrap=True)
        print script_params

        # call the main script
        message = merge_tags(conn, script_params)

        # Return message
        client.setOutput("Message", rstring(message))

    finally:
        client.closeSession()


if __name__ == "__main__":
    run_script()