comparison COBRAxy/fromCSVtoCOBRA_beta.py @ 453:51f794fff930 draft

Uploaded

452:40a8eeb5f614

import utils.reaction_parsing as reactionUtils
import utils.model_utils as modelUtils

ARGS : argparse.Namespace
def process_args(args: List[str] = None) -> argparse.Namespace:
    """
    Parse command-line arguments for CustomDataGenerator.
    """

    parser = argparse.ArgumentParser(
        usage="%(prog)s [options]",
        description="Generate custom data from a given model"
    )

    parser.add_argument("--out_log", type=str, required=True,
                        help="Output log file")

    parser.add_argument("--input", type=str,
                        help="Input tabular file")
    
    parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
                        help="Model format (SBML, JSON, MATLAB, YAML)")

    parser.add_argument("--output", type=str,
                        help="Output model file")
    
    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
                        help="Tool directory (passed from Galaxy as $__tool_directory__)")
    


    return parser.parse_args(args)

###############################- ENTRY POINT -################################
def main(args:List[str] = None) -> None:
    """
    Initializes everything and sets the program in motion based on the fronted input arguments.
    
    Returns:
        None
    """
    # get args from frontend (related xml)
    global ARGS
    ARGS = process_args(args)

    model = modelUtils.build_cobra_model_from_csv(ARGS.model_upload)


    if ARGS.format == "sbml":
        cobra.io.write_sbml_model(model, ARGS.output)
    elif ARGS.format == "json":
        cobra.io.save_json_model(model, ARGS.output)
    elif ARGS.format == "mat":
        cobra.io.save_matlab_model(model, ARGS.output)
    elif ARGS.format == "yaml":
        cobra.io.save_yaml_model(model, ARGS.output)

if __name__ == '__main__':
    main()

453:51f794fff930

import utils.reaction_parsing as reactionUtils
import utils.model_utils as modelUtils

ARGS : argparse.Namespace
def process_args(args: List[str] = None) -> argparse.Namespace:
    parser = argparse.ArgumentParser(
    usage="%(prog)s [options]",
    description="Convert a tabular/CSV file to a COBRA model"
    )


    parser.add_argument("--out_log", type=str, required=True,
    help="Output log file")


    parser.add_argument("--input", type=str, required=True,
    help="Input tabular file (CSV/TSV)")


    parser.add_argument("--format", type=str, required=True, choices=["sbml", "json", "mat", "yaml"],
    help="Model format (SBML, JSON, MATLAB, YAML)")


    parser.add_argument("--output", type=str, required=True,
    help="Output model file path")


    parser.add_argument("--tool_dir", type=str, default=os.path.dirname(__file__),
    help="Tool directory (passed from Galaxy as $__tool_directory__)")


    return parser.parse_args(args)


###############################- ENTRY POINT -################################

def main(args: List[str] = None) -> None:
    global ARGS
    ARGS = process_args(args)

    # configure logging to the requested log file (overwrite each run)
    logging.basicConfig(filename=ARGS.out_log,
                        level=logging.DEBUG,
                        format='%(asctime)s %(levelname)s: %(message)s',
                        filemode='w')

    logging.info('Starting fromCSVtoCOBRA tool')
    logging.debug('Args: input=%s format=%s output=%s tool_dir=%s', ARGS.input, ARGS.format, ARGS.output, ARGS.tool_dir)

    try:
        # Basic sanity checks
        if not os.path.exists(ARGS.input):
            logging.error('Input file not found: %s', ARGS.input)
            print(f"ERROR: Input file not found: {ARGS.input}", file=sys.stderr)
            sys.exit(2)

        out_dir = os.path.dirname(os.path.abspath(ARGS.output))
        if out_dir and not os.path.isdir(out_dir):
            try:
                os.makedirs(out_dir, exist_ok=True)
                logging.info('Created missing output directory: %s', out_dir)
            except Exception as e:
                logging.exception('Cannot create output directory: %s', out_dir)
                print(f"ERROR: Cannot create output directory: {out_dir}", file=sys.stderr)
                sys.exit(3)

        # Build the model from the CSV (NOTE: use ARGS.input here)
        model = modelUtils.build_cobra_model_from_csv(ARGS.input)

        # Save model in requested format
        if ARGS.format == "sbml":
            cobra.io.write_sbml_model(model, ARGS.output)
        elif ARGS.format == "json":
            cobra.io.save_json_model(model, ARGS.output)
        elif ARGS.format == "mat":
            cobra.io.save_matlab_model(model, ARGS.output)
        elif ARGS.format == "yaml":
            cobra.io.save_yaml_model(model, ARGS.output)
        else:
            logging.error('Unknown format requested: %s', ARGS.format)
            print(f"ERROR: Unknown format: {ARGS.format}", file=sys.stderr)
            sys.exit(4)

        logging.info('Model successfully written to %s (format=%s)', ARGS.output, ARGS.format)

    except Exception:
        # Log full traceback to the out_log so Galaxy users/admins can see what happened
        logging.exception('Unhandled exception in fromCSVtoCOBRA')
        traceback.print_exc(file=sys.stderr)
        sys.exit(1)


if __name__ == '__main__':
    main()