From 361e4d7055993d1ba5bb600f120d0706f2bede5b Mon Sep 17 00:00:00 2001 From: William Moore Date: Thu, 15 Jun 2023 15:41:02 +0100 Subject: [PATCH 1/2] Use cli_login in channel_minmax_to_table.py --- .../scripts/channel_minmax_to_table.py | 21 ++++++------------- 1 file changed, 6 insertions(+), 15 deletions(-) diff --git a/maintenance/scripts/channel_minmax_to_table.py b/maintenance/scripts/channel_minmax_to_table.py index fdad6fea..8a1d68bc 100644 --- a/maintenance/scripts/channel_minmax_to_table.py +++ b/maintenance/scripts/channel_minmax_to_table.py @@ -21,6 +21,7 @@ import argparse import omero +from omero.cli import cli_login from omero.rtypes import rstring import omero.grid from omero.gateway import BlitzGateway @@ -29,11 +30,10 @@ NAMESPACE = "openmicroscopy.org/omero/bulk_annotations" -def run(username, password, plate_id, host, port): +def run(plate_id): - conn = BlitzGateway(username, password, host=host, port=port) - try: - conn.connect() + with cli_login() as cli: + conn = BlitzGateway(client_obj=cli._client) query_service = conn.getQueryService() # Create a name for the Original File @@ -109,22 +109,13 @@ def run(username, password, plate_id, host, port): print("save link...") conn.getUpdateService().saveAndReturnObject(link) - except Exception as exc: - print("Error while changing names: %s" % str(exc)) - finally: - conn.close() - def main(args): parser = argparse.ArgumentParser() - parser.add_argument('username') - parser.add_argument('password') parser.add_argument('plate_id') - 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.username, args.password, args.plate_id, args.server, args.port) + + run(args.plate_id) if __name__ == '__main__': From 2444e09fb4b230448ba654edaccbfb5bd77c4748 Mon Sep 17 00:00:00 2001 From: William Moore Date: Thu, 15 Jun 2023 15:41:27 +0100 Subject: [PATCH 2/2] Fix closing of table before getOriginalFile() --- maintenance/scripts/channel_minmax_to_table.py | 5 +++-- 1 file changed, 3 insertions(+), 2 deletions(-) diff --git a/maintenance/scripts/channel_minmax_to_table.py b/maintenance/scripts/channel_minmax_to_table.py index 8a1d68bc..cd5baa26 100644 --- a/maintenance/scripts/channel_minmax_to_table.py +++ b/maintenance/scripts/channel_minmax_to_table.py @@ -94,10 +94,11 @@ def run(plate_id): print("Adding data: ", len(data)) table.addData(data) - table.close() - print("table closed...") + # get original file before closing... orig_file = table.getOriginalFile() + table.close() + fileAnn = omero.model.FileAnnotationI() fileAnn.ns = rstring(NAMESPACE) fileAnn.setFile(omero.model.OriginalFileI(orig_file.id.val, False))