def test_catches_bad_argv(self):
with mock.patch.object(logging, 'error') as mock_logging,\
mock.patch.object(sys, 'exit') as mock_exit:
make_examples.main(['make_examples.py', 'extra_arg'])
mock_logging.assert_called_once_with(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"[\'make_examples.py\', \'extra_arg\']".')
mock_exit.assert_called_once_with(errno.ENOENT)
def test_catches_bad_argv(self):
with mock.patch.object(logging, 'error') as mock_logging,\
mock.patch.object(sys, 'exit') as mock_exit:
make_examples.main(['make_examples.py', 'extra_arg'])
mock_logging.assert_called_once_with(
'Command line parsing failure: make_examples does not accept '
'positional arguments but some are present on the command line: '
'"[\'make_examples.py\', \'extra_arg\']".')
mock_exit.assert_called_once_with(errno.ENOENT)
def test_catches_bad_flags(self):
# Set all of the requested flag values.
region = ranges.parse_literal('chr20:10,000,000-10,010,000')
FLAGS.ref = testdata.CHR20_FASTA
FLAGS.reads = testdata.CHR20_BAM
FLAGS.candidates = test_utils.test_tmpfile('vsc.tfrecord')
FLAGS.examples = test_utils.test_tmpfile('examples.tfrecord')
FLAGS.regions = [ranges.to_literal(region)]
FLAGS.partition_size = 1000
FLAGS.mode = 'training'
FLAGS.truth_variants = testdata.TRUTH_VARIANTS_VCF
# This is the bad flag.
FLAGS.confident_regions = ''
with mock.patch.object(logging, 'error') as mock_logging,\
mock.patch.object(sys, 'exit') as mock_exit:
make_examples.main(['make_examples.py'])
mock_logging.assert_called_once_with(
'confident_regions is required when in training mode.')
mock_exit.assert_called_once_with(errno.ENOENT)
def test_catches_bad_flags(self):
# Set all of the requested flag values.
region = ranges.parse_literal('chr20:10,000,000-10,010,000')
FLAGS.ref = test_utils.CHR20_FASTA
FLAGS.reads = test_utils.CHR20_BAM
FLAGS.candidates = test_utils.test_tmpfile('vsc.tfrecord')
FLAGS.examples = test_utils.test_tmpfile('examples.tfrecord')
FLAGS.regions = [ranges.to_literal(region)]
FLAGS.partition_size = 1000
FLAGS.mode = 'training'
FLAGS.truth_variants = test_utils.TRUTH_VARIANTS_VCF
# This is the bad flag.
FLAGS.confident_regions = ''
with mock.patch.object(logging, 'error') as mock_logging,\
mock.patch.object(sys, 'exit') as mock_exit:
make_examples.main(['make_examples.py'])
mock_logging.assert_called_once_with(
'confident_regions is required when in training mode.')
mock_exit.assert_called_once_with(errno.ENOENT)