def test_not_valid_input(monkeypatch):
print("test not valid input")
dbpath_tmp = os.path.join(tmpdir, "customdb.fas.nsq")
with open(dbpath_tmp, "w") as f:
f.write(">mockDB")
try:
mock = batchassist_mock(nodef_input, wrong_input)
monkeypatch.setattr('builtins.input', mock.prompt_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "3")
if os.path.isfile(configpath):
os.remove(configpath)
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "4")
if os.path.isfile(configpath):
os.remove(configpath)
mock = batchassist_mock(nodef_input, wrong_input2)
monkeypatch.setattr('builtins.input', mock.prompt_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "7")
if os.path.isfile(configpath):
os.remove(configpath)
finally:
if os.path.isfile(dbpath_tmp):
os.remove(dbpath_tmp)
def test_nodefault(monkeypatch):
G.create_directory(tmpdir)
dbpath_tmp = os.path.join(tmpdir, "customdb.fas.nsq")
with open(dbpath_tmp, "w") as f:
f.write(">mockDB")
try:
monkeypatch.setattr('builtins.input', nodef_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "3")
if os.path.isfile(configpath):
os.remove(configpath)
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "4")
if os.path.isfile(configpath):
os.remove(configpath)
monkeypatch.setattr('builtins.input', nodef_input2)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "8")
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "9")
finally:
if os.path.isfile(dbpath_tmp):
os.remove(dbpath_tmp)
def test_sys_exit(monkeypatch):
monkeypatch.setattr('builtins.input', fail_input)
with pytest.raises(SystemExit):
conf_from_file = Config()
monkeypatch.setattr('builtins.input', fail_startinput)
with pytest.raises(SystemExit):
conf_from_file = Config()
def test_start_unknown(monkeypatch):
print("Start unknown")
mock = batchassist_mock(start_oneinput, start_unknown)
monkeypatch.setattr('builtins.input', mock.prompt_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "8")
def test_default_input(monkeypatch):
monkeypatch.setattr('builtins.input', alldef_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "0")
defdir = os.path.join("/", "Lactobacillus_curvatus")
if os.path.isdir(defdir):
shutil.rmtree(defdir)
def test_start_wrong(monkeypatch):
print("Start wrong")
mock = batchassist_mock(save_wronginput, start_wronginput)
monkeypatch.setattr('builtins.input', mock.prompt_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "8")
if os.path.isfile(configpath):
os.remove(configpath)
def test_start_all(monkeypatch):
monkeypatch.setattr('builtins.input', start_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "8")
if os.path.isfile(configpath):
os.remove(configpath)
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "9")
if os.path.isfile(configpath):
os.remove(configpath)
def test_incomplete_config(monkeypatch):
testfile = os.path.join(
"/", "primerdesign", "test", "Lactobacillus_curvatus",
"config", "config.json")
incomplete_dict = {
"target": "lactobacillus_curvatus", "path": "/primerdesign/test"}
with open(testfile, "w") as f:
f.write(json.dumps(incomplete_dict))
monkeypatch.setattr('builtins.input', start_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "5")
def test_offline(monkeypatch):
monkeypatch.setattr('builtins.input', offline_input)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "1")
if os.path.isfile(configpath):
os.remove(configpath)
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "2")
if os.path.isfile(configpath):
os.remove(configpath)
monkeypatch.setattr('builtins.input', offline_input2)
conf_from_file = Config()
configpath = get_config_from_file(conf_from_file)[0]
compare_configfiles(reference_dict, configpath, "1")
if os.path.isfile(configpath):
os.remove(configpath)
configpath = get_config_from_file(conf_from_file)[1]
compare_configfiles(reference_dict, configpath, "2")
if os.path.isfile(configpath):
os.remove(configpath)