Delete rnd

maintenance/scripts/delete_rendering.py

@@ -0,0 +1,87 @@
+#!/usr/bin/env python
+# -*- coding: utf-8 -*-
+#
+# -----------------------------------------------------------------------------
+#   Copyright (C) 2017 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 finds all rendering on images from a dataset specified
+by dataset id or dataset name and deletes these rendering settings.
+"""
+
+import argparse
+import omero
+from omero.gateway import BlitzGateway
+
+
+def run(name, password, dataset_name, dataset_id, host, port):
+
+    conn = BlitzGateway(name, password, host=host, port=port)
+    try:
+        conn.connect()
+        datasets = []
+        if dataset_id >= 0:
+            datasets.append(conn.getObject("Dataset", dataset_id))
+        else:
+            datasets = conn.getObjects("Dataset",
+                                       attributes={"name": dataset_name})
+
+        for dataset in datasets:
+            print(dataset.getId())
+            for image in dataset.listChildren():
+                pixels = image.getPrimaryPixels()
+                pixId = pixels.getId()
+                print(pixId)
+                params = omero.sys.ParametersI()
+                query = "from RenderingDef where pixels.id = '%s'" % pixId
+                query_service = conn.getQueryService()
+                result = query_service.findAllByQuery(query, params,
+                                                      conn.SERVICE_OPTS)
+                if result is not None:
+                    rnd_ids = [rnd.id.val for rnd in result]
+                    if len(rnd_ids) > 0:
+                        print("Deleting %s rnds..." % len(rnd_ids))
+                        print(rnd_ids)
+                        conn.deleteObjects("RenderingDef", rnd_ids, wait=True)
+
+    except Exception as exc:
+        print("Error while deleting rendering: %s" % str(exc))
+    finally:
+        conn.close()
+
+
+def main(args):
+    parser = argparse.ArgumentParser()
+    parser.add_argument('password')
+    parser.add_argument('--datasetid', default=-1,
+                        help="The ID of the dataset")
+    parser.add_argument('--datasetname', default="",
+                        help="The name of the dataset")
+    parser.add_argument('--name', default="trainer-1",
+                        help="The user deleting the rois")
+    parser.add_argument('--server', default="outreach.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.datasetid,
+        args.server, args.port)
+
+
+if __name__ == '__main__':
+    import sys
+    main(sys.argv[1:])

maintenance/scripts/delete_rendering.sh

@@ -0,0 +1,31 @@
+#!/bin/bash
+#
+# This script deletes rnd settings on images in specified Datasets.
+# Datasets can be specified either by name, such as
+# DATASETNAME=svs bash delete_rendering.sh
+# or by IDs (one or more, separated by comma), such as
+# DATASETID=1868,2073 bash delete_rendering.sh
+
+echo Starting
+OMEROPATH=${OMEROPATH:-/opt/omero/server/OMERO.server/bin/omero}
+PASSWORD=${PASSWORD:-ome}
+HOST=${HOST:-outreach.openmicroscopy.org}
+DATASETNAME=${DATASETNAME:-siRNAi-HeLa}
+DATASETIDS=${DATASETID:-none}
+NUMBER=${NUMBER:-50}
+OMEUSER=${OMEUSER:-trainer-1}
+
+$OMEROPATH login -u $OMEUSER -s $HOST -w $PASSWORD
+if [ "$DATASETIDS" = "none" ]
+then
+    result=`$OMEROPATH hql --ids-only --limit 1000 --style plain -q --all "SELECT id from Dataset WHERE name = '$DATASETNAME'" | cut -f 2 -d , | tr '\n' ,`
+    dataset_number=`echo $result | tr -cd , | wc -c | sed -e 's/[[:space:]]*//'`
+    datasetids=`echo $result | sed -e 's/,$//'`
+else
+    datasetids=$DATASETIDS
+    dataset_number="specified datasets"
+fi
+echo 'Deleting rnd settings on '"$dataset_number"' Datasets:' $datasetids
+$OMEROPATH delete --report Dataset/RenderingDef:$datasetids
+$OMEROPATH logout
+echo Stopping