def test_main(self):
args_list = ["-d", "vert", "-if", "my_fake_file"]
args = cg.build_parser().parse_args(args_list)
logger.debug(
"unhappy path - input file list only contains 1 entry - args: {}".
format(args))
cg.main(args)
args_list[2] = "--file_wildcard"
args_list[3] = "not_going_to_find_this_file_3874873784378389"
args = cg.build_parser().parse_args(args_list)
logger.debug(
"unhappy path - file_wildcard does not match any files - args: {}"
.format(args))
with self.assertRaises(Exception) as context:
cg.main(args)
self.assertIsNotNone(context.exception)
logger.debug("context.exception: {}".format(context.exception))
self.assertIn("No files were found", str(context.exception),
"the expected exception was not thrown")
args_list[
3] = "functional_tests/test_concat_gctoo_test_main_fake_empty_file.gct"
args = cg.build_parser().parse_args(args_list)
logger.debug(
"unhappy path - file_wildcard matches just 1 file - args: {}".
format(args))
cg.main(args)
def test_main(self):
test_dir = "functional_tests/test_concat_gctoo/test_main"
g_a = pg.parse(os.path.join(test_dir, "a.gct"))
logger.debug("g_a: {}".format(g_a))
g_b = pg.parse(os.path.join(test_dir, "b.gct"))
logger.debug("g_b: {}".format(g_b))
save_build_parser = cg.build_parser
class MockParser:
def __init__(self, args):
self.args = args
def parse_args(self, unused):
return self.args
#unhappy path - write out error report file
expected_output_file = tempfile.mkstemp()[1]
logger.debug(
"unhappy path - write out error report file - expected_output_file: {}"
.format(expected_output_file))
args = save_build_parser().parse_args([
"-d", "horiz", "-if", g_a.src, g_b.src, "-o", "should_not_be_used",
"-ot", "gct", "-erof", expected_output_file
])
logger.debug("args: {}".format(args))
my_mock_parser = MockParser(args)
cg.build_parser = lambda: my_mock_parser
with self.assertRaises(
cg.MismatchCommonMetadataConcatGctooException) as context:
cg.main()
self.assertTrue(os.path.exists(expected_output_file))
report_df = pd.read_csv(expected_output_file, sep="\t")
logger.debug("report_df:\n{}".format(report_df))
self.assertEqual(2, report_df.shape[0])
os.remove(expected_output_file)
print()
print()
print()
#happy path
args.remove_all_metadata_fields = True
args.error_report_output_file = None
expected_output_file = tempfile.mkstemp(suffix=".gct")[1]
logger.debug("happy path - expected_output_file: {}".format(
expected_output_file))
args.out_name = expected_output_file
my_mock_parser = MockParser(args)
cg.buid_parser = lambda: my_mock_parser
cg.main()
self.assertTrue(os.path.exists(expected_output_file))
r = pg.parse(expected_output_file)
logger.debug("happy path -r:\n{}".format(r))
logger.debug("r.data_df:\n{}".format(r.data_df))
self.assertEqual((2, 4), r.data_df.shape)
self.assertEqual({"a", "b", "g", "f"}, set(r.data_df.columns))
self.assertEqual({"rid1", "rid2"}, set(r.data_df.index))
#cleanup
os.remove(expected_output_file)
cg.build_parser = save_build_parser