comparison save_to_db.py @ 5:f934215bdb78 draft default tip

planemo upload for repository https://github.com/brsynth commit 6ae809b563b40bcdb6be2e74fe2a84ddad5484ae

4:c7a7520afb4b

            insert_rows = []

            for gb_file in gb_files:
                # Extract base file name (just the file name, not the full path)
                real_file_name = os.path.basename(gb_file)

                print(f"Processing file: {real_file_name}")  # Debugging: Log the current file

                # Get the corresponding fragment name from the mapping
                fragment_name = file_name_mapping_dict.get(real_file_name)

                if not fragment_name:

    # Load JSON config if provided
    json_config = {}
    if args.json_conf != 'None' or '':
        with open(args.json_conf, "r") as f:
            json_config = json.load(f)

    # Prefer user input; fallback to JSON_ values if not provided
    user_params = {
        "table": args.table,
        "sequence_column": args.sequence_column,

5:f934215bdb78

            insert_rows = []

            for gb_file in gb_files:
                # Extract base file name (just the file name, not the full path)
                real_file_name = os.path.basename(gb_file)
                fragment_name = file_name_mapping_dict.get(real_file_name)

                print(f"Processing file: {real_file_name}({fragment_name})")  # Debugging: Log the current file

                # Get the corresponding fragment name from the mapping
                fragment_name = file_name_mapping_dict.get(real_file_name)

                if not fragment_name:

    # Load JSON config if provided
    json_config = {}
    if args.json_conf != 'None' or '':
        with open(args.json_conf, "r") as f:
            json_config = json.load(f)
        if "execution" in json_config and json_config["execution"] is False:
            print("Execution was blocked by config (execution = false)")
            return

    # Prefer user input; fallback to JSON_ values if not provided
    user_params = {
        "table": args.table,
        "sequence_column": args.sequence_column,