def test_createschema_empty_pairs(test_args, expected):
with pytest.raises(SystemExit) as e:
with patch.object(sys, 'argv', test_args):
chewBBACA.main()
assert e.type == SystemExit
assert expected in e.value.code
def test_modules_exit_codes(test_args, expected):
with pytest.raises(SystemExit) as e:
with patch.object(sys, 'argv', test_args):
chewBBACA.main()
assert e.type == SystemExit
assert e.value.code == expected
def test_allelecall_valid(test_args, expected):
with patch.object(sys, 'argv', test_args):
capture = py.io.StdCapture()
chewBBACA.main()
stdout, stderr = capture.reset()
# check text printed to stdout
assert 'Writing output files' in stdout
# check output files
for root, dirs, files in os.walk(test_args[7]):
output_files = [os.path.join(root, file)
for file in files
if 'logging_info.txt' != file]
expected_files = [os.path.join(expected, file)
for file in os.listdir(expected)
if 'logging_info.txt' != file]
files = output_files + expected_files
basename_dict = {}
for f in files:
basename = os.path.basename(f)
basename_dict.setdefault(basename, []).append(f)
# assert that files in each pair are equal
file_cmps = []
for k, v in basename_dict.items():
file_cmps.append(filecmp.cmp(v[0], v[1], shallow=False))
assert all(file_cmps) is True
def test_invalid_input(test_args, expected):
# create empty dir for empty dir test
if 'empty_dir' in test_args[3] and os.path.isdir(test_args[3]) is False:
os.mkdir(test_args[3])
with pytest.raises(SystemExit) as e:
with patch.object(sys, 'argv', test_args):
chewBBACA.main()
assert e.type == SystemExit
assert expected in e.value.code
def test_schemaEvaluator_invalid_input(test_args, expected):
with pytest.raises(SystemExit) as e:
with patch.object(sys, "argv", test_args):
chewBBACA.main()
try:
shutil.rmtree(test_args[5])
except Exception as e2:
pass
assert e.type == SystemExit
assert expected in e.value.code
def test_createschema_valid(test_args, expected):
with patch.object(sys, 'argv', test_args):
capture = py.io.StdCapture()
chewBBACA.main()
stdout, stderr = capture.reset()
# check output files
schema_seed = os.path.join(test_args[5], 'schema_seed')
output_files = [
os.path.join(schema_seed, file) for file in os.listdir(schema_seed)
if 'short' != file
]
output_files.sort()
expected_seed = os.path.join(expected, 'schema_seed')
expected_files = [
os.path.join(expected_seed, file) for file in os.listdir(expected_seed)
if 'short' != file
]
expected_files.sort()
# get config files
genes_lists = [output_files.pop(0), expected_files.pop(0)]
schemas_configs = [output_files.pop(0), expected_files.pop(0)]
# compare configs
assert pickle_loader(genes_lists[0]).sort() == pickle_loader(
genes_lists[1]).sort()
assert pickle_loader(schemas_configs[0]) == pickle_loader(
schemas_configs[1])
files = output_files + expected_files
basename_dict = {}
for f in files:
basename = os.path.basename(f)
basename_dict.setdefault(basename, []).append(f)
# assert that files in each pair are equal
file_cmps = []
for k, v in basename_dict.items():
file_cmps.append(filecmp.cmp(v[0], v[1], shallow=False))
assert all(file_cmps) is True
def test_schemaEvaluator_valid(test_args, expected):
with patch.object(sys, "argv", test_args):
capture = py.io.StdCapture()
chewBBACA.main()
stdout, stderr = capture.reset()
# check if the report has been created
assert "The report has been created." in stdout
# check output HTML files
output_html_files = [
os.path.join(test_args[5], "html_files", file)
for file in os.listdir(os.path.join(test_args[5], "html_files"))
]
output_html_files.sort()
expected_html_files = [
os.path.join(expected, "html_files", file)
for file in os.listdir(os.path.join(expected, "html_files"))
]
expected_html_files.sort()
output_prot_files = [
os.path.join(
test_args[5], "SchemaEvaluator_pre_computed_data", "prot_files", file
)
for file in os.listdir(
os.path.join(
test_args[5], "SchemaEvaluator_pre_computed_data", "prot_files"
)
)
if "exceptions" != file
]
output_prot_files.sort()
html_files = output_html_files + expected_html_files
basename_html_dict = {}
for f1 in html_files:
basename1 = os.path.basename(f1)
basename_html_dict.setdefault(basename1, []).append(f1)
# assert that files in each pair are equal
file_cmps_html = []
for k, v in basename_html_dict.items():
file_cmps_html.append(filecmp.cmp(v[0], v[1], shallow=False))
assert all(file_cmps_html) is True
# check output MAIN files
output_main_files = [
os.path.join(test_args[5], "SchemaEvaluator_pre_computed_data", file)
for file in os.listdir(
os.path.join(test_args[5], "SchemaEvaluator_pre_computed_data")
)
if "prot_files" != file
]
output_main_files.sort()
expected_main_files = [
os.path.join(expected, "SchemaEvaluator_pre_computed_data", file)
for file in os.listdir(
os.path.join(expected, "SchemaEvaluator_pre_computed_data")
)
if "prot_files" != file
]
expected_main_files.sort()
main_files = output_main_files + expected_main_files
basename_main_dict = {}
for f2 in main_files:
basename2 = os.path.basename(f2)
basename_main_dict.setdefault(basename2, []).append(f2)
# assert that files in each pair are equal
file_cmps_main = []
for k2, v2 in basename_main_dict.items():
file_cmps_main.append(filecmp.cmp(v2[0], v2[1], shallow=False))
assert all(file_cmps_main) is True
# check output PROTEIN files
output_prot_files = [
os.path.join(
test_args[5], "SchemaEvaluator_pre_computed_data", "prot_files", file
)
for file in os.listdir(
os.path.join(
test_args[5], "SchemaEvaluator_pre_computed_data", "prot_files"
)
)
if "exceptions" != file
]
output_prot_files.sort()
expected_prot_files = [
os.path.join(expected, "SchemaEvaluator_pre_computed_data", "prot_files", file)
for file in os.listdir(
os.path.join(expected, "SchemaEvaluator_pre_computed_data", "prot_files")
)
if "exceptions" != file
]
expected_prot_files.sort()
prot_files = output_prot_files + expected_prot_files
basename_prot_dict = {}
for f in prot_files:
basename3 = os.path.basename(f)
basename_prot_dict.setdefault(basename3, []).append(f)
# assert that files in each pair are equal
file_cmps_prot = []
for k3, v3 in basename_prot_dict.items():
file_cmps_prot.append(filecmp.cmp(v3[0], v3[1], shallow=False))
assert all(file_cmps_prot) is True
# check output EXCEPTION files
output_exc_files = [
os.path.join(
test_args[5],
"SchemaEvaluator_pre_computed_data",
"prot_files",
"exceptions",
file,
)
for file in os.listdir(
os.path.join(
test_args[5],
"SchemaEvaluator_pre_computed_data",
"prot_files",
"exceptions",
)
)
]
output_exc_files.sort()
expected_exc_files = [
os.path.join(
expected,
"SchemaEvaluator_pre_computed_data",
"prot_files",
"exceptions",
file,
)
for file in os.listdir(
os.path.join(
expected,
"SchemaEvaluator_pre_computed_data",
"prot_files",
"exceptions",
)
)
]
expected_exc_files.sort()
exc_files = output_exc_files + expected_exc_files
basename_exc_dict = {}
for f in exc_files:
basename4 = os.path.basename(f)
basename_exc_dict.setdefault(basename4, []).append(f)
# assert that files in each pair are equal
file_cmps_exc = []
for k4, v4 in basename_exc_dict.items():
file_cmps_exc.append(filecmp.cmp(v4[0], v4[1], shallow=False))
assert all(file_cmps_exc) is True