def test_with_empty_args():
"""
User passes no args, should produce a usage statement and then
raise SystemExit. Usage statement will appear
"""
parser = create_parser()
with pytest.raises(SystemExit):
parser.parse_args()
def pipeline_wd(self, tmpdir_factory):
wd = tmpdir_factory.mktemp("pdbechem_test")
parser = create_parser()
args = parser.parse_args(["-o", str(wd), test_cut_down_components_cif])
m = PDBeChemManager()
m.run(args.components_cif, args.output_dir)
return args.output_dir
def pipeline_wd(self, tmpdir_factory):
wd = tmpdir_factory.mktemp('pdbechem_test')
parser = create_parser()
args = parser.parse_args(['-o', str(wd), test_cut_down_components_cif])
check_args(args)
m = PDBeChemManager()
m.run_pipeline(args)
return str(wd)
def test_with_problematic_cif_7om(tmpdir):
"""
7OM caused problems because it lacks an inchikey
and this used to cause a crash
"""
cif_file = cif_filename('7OM')
test_output_dir = tmpdir.mkdir('test_process_components_cif_70M')
parser = create_parser()
args = parser.parse_args([cif_file, '-o', str(test_output_dir)])
m = PDBeChemManager()
m.run_pipeline(args)
assert os.path.isdir(
test_output_dir
), f'output directory {str(test_output_dir)} must be created'
def test_input_file_that_cannot_exist_raises_system_exit():
parser = create_parser()
args = parser.parse_args(
['-o foo', '/////impossible_to_open_file', '--debug'])
with pytest.raises(SystemExit):
check_args(args)
def test_input_file_that_cannot_exist_raises_system_exit():
parser = create_parser()
with pytest.raises(SystemExit):
parser.parse_args(
["-o foo", "/////impossible_to_open_file", "--debug"])