Source code for schrodinger.application.bioluminate.drivers.io

import logging
import more_itertools
import os
from typing import List

from schrodinger.rdkit import molio


def get_existing_files(files: List[os.PathLike],
                       logger: logging.Logger) -> List[os.PathLike]:
    """
    Filter out files that don't exist and report them as missing.
    """
    missing, existing = map(list,
                            more_itertools.partition(os.path.isfile, files))
    if missing:
        logger.warning('Missing output files:')
        for fname in missing:
            logger.warning(f'  {fname}')
    return existing


def merge_csv_files(csv_files: List[str], merged_file: str,
                    logger: logging.Logger) -> None:
    """
    Merge multiple csv files into a single file.

    :param csv_files: list of csv files to merge
    :param merged_file: the desired output file name
    :param logger: the logger to use for reporting
    """
    csv_files = get_existing_files(csv_files, logger)
    logger.info(f"Recombining output csv files into {merged_file}")
    molio.cat_csv_files(csv_files, merged_file)