pb_assembly/FALCON/falcon_kit/mains/cromwell_symlink.py

import argparse
import logging
import os
import sys
from .. import io

LOG = logging.getLogger()


def symlink(actual, symbolic=None, force=True):
    """Symlink into cwd, relatively.
    symbolic name is basename(actual) if not provided.
    If not force, raise when already exists and does not match.
    But ignore symlink to self.
    """
    # COPIED VERBATIM FROM ./dazzler.py
    symbolic = os.path.basename(actual) if not symbolic else symbolic
    if os.path.abspath(actual) == os.path.abspath(symbolic):
        LOG.warning('Cannot symlink {!r} as {!r}, itself.'.format(actual, symbolic))
        return
    rel = os.path.relpath(actual)
    if force:
        LOG.info('ln -sf {} {}'.format(rel, symbolic))
        if os.path.lexists(symbolic):
            if os.readlink(symbolic) == rel:
                return
            else:
                os.unlink(symbolic)
    else:
        LOG.info('ln -s {} {}'.format(rel, symbolic))
        if os.path.lexists(symbolic):
            if os.readlink(symbolic) != rel:
                msg = '{!r} already exists as {!r}, not {!r}'.format(
                        symbolic, os.readlink(symbolic), rel)
                raise Exception(msg)
            else:
                LOG.info('{!r} already points to {!r}'.format(symbolic, rel))
                return
    os.symlink(rel, symbolic)


def run(input_fns):
    for fn in input_fns:
        symlink(fn)


class HelpF(argparse.RawTextHelpFormatter, argparse.ArgumentDefaultsHelpFormatter):
    pass


def parse_args(argv):
    description = 'Symlink into current directory. This helps keep command-lines short later.'
    epilog = ''
    parser = argparse.ArgumentParser(
        description=description,
        epilog=epilog,
        formatter_class=HelpF,
    )
    parser.add_argument(
        'input_fns', nargs='*',
        help='These will be symlinked according to their basenames.')

    args = parser.parse_args(argv[1:])
    return args


def main(argv=sys.argv):
    args = parse_args(argv)
    logging.basicConfig(level=logging.INFO)
    run(**vars(args))


if __name__ == '__main__':  # pragma: no cover
    main()