comparison omero_metadata_upload.py @ 5:f5c4f523432d draft default tip

planemo upload for repository https://github.com/Helmholtz-UFZ/galaxy-tools/tree/main/tools/omero commit 3f4e79a4e8350481f3c8d70bc64f01b4cb0a4bf0

4:7a94eb8c345d

            elif ann_type == "table":
                id_tb_ann = ez.post_table(conn, df, object_type=obj_type, object_id=int(did), title=an_name,
                                          headers=True)
                tb_dict = ez.get_table(conn, id_tb_ann)
                return tb_dict
        except Exception as e:
            log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}")
            return None

    def log_error(message):

    if ann_type == "table":
        data_dict = df.to_dict(orient='records')
    elif ann_type == "KV":
        data_dict = {col: df[col].iloc[0] for col in df.columns}

    try:
        with ez.connect(user, pws, "", host, port, secure=True) as conn:
            if obj_type == "project":
                if did is None:

    parser.add_argument('--port', required=True, type=int, help='OMERO port')
    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate',
                                                              'well ', 'image'],
                        help='Type of OMERO object')
    parser.add_argument('--did', type=int, help='ID of the object (if it exists)')
    parser.add_argument('--ann_type', required=True, choices=['table', 'KV'], help='Annotation type')
    parser.add_argument('--ann_file', required=True, help='Path to the annotation file')
    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()

5:f5c4f523432d

            elif ann_type == "table":
                id_tb_ann = ez.post_table(conn, df, object_type=obj_type, object_id=int(did), title=an_name,
                                          headers=True)
                tb_dict = ez.get_table(conn, id_tb_ann)
                return tb_dict
            elif ann_type == "attachement":
                id_file_attach = ez.post_file_annotation(conn, file_path=data_dict, ns=an_name, object_type=obj_type, object_id=int(did))
                return id_file_attach
        except Exception as e:
            log_error(f"Error uploading metadata for {obj_type} with ID {did}: {str(e)}")
            return None

    def log_error(message):

    if ann_type == "table":
        data_dict = df.to_dict(orient='records')
    elif ann_type == "KV":
        data_dict = {col: df[col].iloc[0] for col in df.columns}
    elif ann_type == "attachement":
        data_dict = ann_file

    try:
        with ez.connect(user, pws, "", host, port, secure=True) as conn:
            if obj_type == "project":
                if did is None:

    parser.add_argument('--port', required=True, type=int, help='OMERO port')
    parser.add_argument('--obj_type', required=True, choices=['project', 'screen', 'dataset', 'plate',
                                                              'well ', 'image'],
                        help='Type of OMERO object')
    parser.add_argument('--did', type=int, help='ID of the object (if it exists)')
    parser.add_argument('--ann_type', required=True, choices=['table', 'KV', "attachement"], help='Annotation type')
    parser.add_argument('--ann_file', required=True, help='Path to the annotation file')
    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()