comparison omero_metadata_upload.py @ 2:e41f70e69349 draft

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 266752b0162fbdb32f132a6702cb661ae36f48f0

1:588d6fa22fc4

import argparse
from datetime import datetime

import ezomero as ez
import pandas as pd

        log_error(f"Connection error: {str(e)}")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Import metadata into OMERO.')
    parser.add_argument('--user', required=True, help='OMERO username')
    parser.add_argument('--pws', required=True, help='OMERO password')
    parser.add_argument('--host', required=True, help='OMERO host')
    parser.add_argument('--port', required=True, type=int, help='OMERO port')
    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'image'],
                        help='Type of OMERO object')
    parser.add_argument('--did', type=int, help='ID of the object (if it exists)')

    parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation')
    parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file')

    args = parser.parse_args()

    metadata_import_ezo(user=args.user, pws=args.pws, host=args.host, port=args.port,
                        obj_type=args.obj_type, did=args.did, ann_type=args.ann_type,
                        ann_file=args.ann_file, an_name=args.an_name, log_file=args.log_file)

2:e41f70e69349

import argparse
import json
from datetime import datetime

import ezomero as ez
import pandas as pd

        log_error(f"Connection error: {str(e)}")


if __name__ == "__main__":
    parser = argparse.ArgumentParser(description='Import metadata into OMERO.')
    parser.add_argument("--credential-file", dest="credential_file", type=str, required=True, help="Credential file (JSON file with username and password for OMERO)")
    parser.add_argument('--host', required=True, help='OMERO host')
    parser.add_argument('--port', required=True, type=int, help='OMERO port')
    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'image'],
                        help='Type of OMERO object')
    parser.add_argument('--did', type=int, help='ID of the object (if it exists)')

    parser.add_argument('--an_name', required=True, help='Namespace or title for the annotation')
    parser.add_argument('--log_file', default='metadata_import_log.txt', help='Path to the log file')

    args = parser.parse_args()

    with open(args.credential_file, 'r') as f:
        crds = json.load(f)

    metadata_import_ezo(user=crds['username'], pws=crds['password'], host=args.host, port=args.port,
                        obj_type=args.obj_type, did=args.did, ann_type=args.ann_type,
                        ann_file=args.ann_file, an_name=args.an_name, log_file=args.log_file)