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Channel minmax to table fixes #93

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Channel minmax to table fixes #93

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361e4d7
Use cli_login in channel_minmax_to_table.py
will-moore Jun 15, 2023
2444e09
Fix closing of table before getOriginalFile()
will-moore Jun 15, 2023
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26 changes: 9 additions & 17 deletions maintenance/scripts/channel_minmax_to_table.py
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Original file line number Diff line number Diff line change
Expand Up @@ -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
Expand All @@ -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
Expand Down Expand Up @@ -94,10 +94,11 @@ def run(username, password, plate_id, host, port):

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))
Expand All @@ -109,22 +110,13 @@ 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__':
Expand Down