def test_simple(self):
parser = smu_parser_lib.SmuParser(
os.path.join(TESTDATA_PATH, MAIN_DAT_FILE))
conformer, _ = next(parser.process_stage2())
expected = get_file_contents(os.path.join(TESTDATA_PATH, ATOMIC_INPUT))
writer = smu_writer_lib.AtomicInputWriter()
smu_writer_lib.check_dat_formats_match(
expected,
writer.process(conformer).splitlines())
def __init__(self, output_path):
"""Creates AtomicInputOutputter.
Args:
output_path: directory to write output files to
"""
self.output_path = output_path
if output_path and not os.path.isdir(self.output_path):
raise ValueError(
'Atomic input requires directory as output path, got {}'.
format(self.output_path))
self.atomic_writer = smu_writer_lib.AtomicInputWriter()
def main(argv):
if len(argv) > 1:
raise app.UsageError('Too many command-line arguments.')
atomic_writer = smu_writer_lib.AtomicInputWriter()
file_count = 0
conformer_count = 0
mismatches = 0
for filepath in gfile.glob(FLAGS.input_glob):
logging.info('Processing file %s', filepath)
file_count += 1
smu_parser = smu_parser_lib.SmuParser(filepath)
for conformer, _ in smu_parser.process_stage2():
conformer_count += 1
actual_contents = atomic_writer.process(conformer)
expected_fn = atomic_writer.get_filename_for_atomic_input(
conformer)
with gfile.GFile(os.path.join(FLAGS.atomic_input_dir,
expected_fn)) as expected_f:
expected_contents = expected_f.readlines()
try:
smu_writer_lib.check_dat_formats_match(
expected_contents, actual_contents.splitlines())
except smu_writer_lib.DatFormatMismatchError as e:
mismatches += 1
print(e)
if FLAGS.output_dir:
with gfile.GFile(
os.path.join(
FLAGS.output_dir,
atomic_writer.get_filename_for_atomic_input(
conformer)), 'w') as f:
f.write(actual_contents)
status_str = ('COMPLETE: Read %d files, %d conformers, %d mismatches\n' %
(file_count, conformer_count, mismatches))
logging.info(status_str)
print(status_str)