cli.py

import argparse
import logging
from pathlib import Path
import sys

from rmmd.update import AbortedByUser, UpdateOptions, update
from rmmd.validate import RmmdValidationError, validate_rmmd

def _add_validate_args(parser: argparse.ArgumentParser):
    parser.add_argument(
        '--schema',
        help='Path to schema file',
        metavar='SCHEMA',
        required=True,
        type=Path)
    parser.add_argument(
        'rmmd',
        help='Path to RMMD file to validate',
        metavar='RMMD',
        type=Path)
    

def _add_update_args(parser: argparse.ArgumentParser):
    parser.add_argument(
        'source',
        help='File to take data from',
        metavar='SOURCE',
        type=Path)
    parser.add_argument(
        'target',
        help='File to update (will be overwritten!)',
        metavar='TARGET',
        type=Path)
    parser.add_argument(
        '--root',
        help='Root directory of the project. Default: current working directory.',
        metavar='ROOT',
        type=Path,
        default=Path.cwd()
    )
    parser.add_argument(
        '--species',
        help='Path to JSON/YAML file containing species information',
        metavar='SPECIES_FILE',
        type=Path,
        default=None
    )
    ## mutually exclusive group:
    backup_grp = parser.add_mutually_exclusive_group()
    backup_grp.add_argument(
        '--backup',
        help='Create a backup of the target file',
        action='store_true',
        dest='backup',
        default=True
    )
    backup_grp.add_argument(
        '--no-backup',
        help='Do not create a backup of the target file',
        action='store_false',
        dest='backup',
        default=True
    )
    
def _parent_parser() -> argparse.ArgumentParser:
    parent_parser = argparse.ArgumentParser(add_help=False)
    parent_parser.add_argument(
        '-v', '--verbose',
        help='Enable verbose logging',
        action='store_true'
    )

    return parent_parser

def main():
    logger = logging.getLogger()
    logger.setLevel(logging.INFO)
    formatter = logging.Formatter('%(message)s')
    # use sdtout as logging.INFO is used as standard output for user
    handler = logging.StreamHandler(stream=sys.stdout)
    handler.setFormatter(formatter)
    logger.addHandler(handler)

    parent = _parent_parser()   # contains arguments that should always be there
    parser = argparse.ArgumentParser(parents=[parent])
    subparsers = parser.add_subparsers(dest='_cmd_')

    validate_parser = subparsers.add_parser('validate', parents= [parent])
    _add_validate_args(validate_parser)

    update_parser = subparsers.add_parser('update', parents= [parent])
    _add_update_args(update_parser)

    args = parser.parse_args()

    if args.verbose:
        logger.setLevel(logging.DEBUG)


    if args._cmd_ == 'validate':
        try:
            validate_rmmd(args.rmmd, args.schema)
        except RmmdValidationError as err:
            logging.error(err)
            exit(1)
        except Exception as err:
            logging.error(err)
            logging.debug('An error occurred.', exc_info=err)
            exit(1)
        else:
            logging.info('Validation successful.')
    elif args._cmd_ == 'update':
        try:
            opts = UpdateOptions(
                root=args.root,
                species_json=args.species,
                backup=args.backup
            )
            update(args.source, args.target, opts)
        except AbortedByUser as err:
            logging.info(err)
            exit(0)
        except Exception as err:
            logging.error(err)
            logging.debug('An error occurred.', exc_info=err)
            exit(1)
    else:
        parser.print_help()

if __name__ == '__main__':
    main()