def test_set_base_options(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
ask_ori = msf_cfg.ask
defaults = MacsyDefaults()
resp = [
"Yes", # enter section ?
"ordered", # db_type
"linear", # replicon_topology
"None", # sequence_db
]
g = (r for r in resp)
def fake_ask(*args, **kwargs):
return next(g)
try:
msf_cfg.ask = fake_ask
with self.catch_io(out=True):
msf_cfg.set_base_options(cp, defaults)
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring base options:{msf_cfg.theme.RESET}"
)
self.assertTrue(cp.has_section("base"))
self.assertEqual(cp.get("base", "db_type"), "ordered")
self.assertEqual(cp.get("base", "replicon_topology"), "linear")
self.assertEqual(cp.get("base", "sequence_db"), "None")
finally:
msf_cfg.ask = ask_ori
def test_set_general_options(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
ask_ori = msf_cfg.ask
defaults = MacsyDefaults()
resp = [
"Yes", # enter section ?
'warning', # log_level
0, # worker
True # mute
]
g = (r for r in resp)
def fake_ask(*args, **kwargs):
return next(g)
try:
msf_cfg.ask = fake_ask
with self.catch_io(out=True):
msf_cfg.set_general_options(cp, defaults)
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring general options:{msf_cfg.theme.RESET}"
)
self.assertTrue(cp.has_section("general"))
self.assertEqual(cp.get("general", "log_level"), "warning")
self.assertEqual(cp.get("general", "worker"), "0")
self.assertEqual(cp.get("general", "mute"), "True")
finally:
msf_cfg.ask = ask_ori
def test_set_section_use_defaults(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
sec_name = "new_section"
options = {
'hmmer': {
"question": "that is the question",
"validator": msf_cfg.check_str,
"default": "Yes",
"explanation": ""
}
}
defaults = MacsyDefaults(hmmer="Yes")
with self.catch_io(out=True):
msf_cfg.set_section(sec_name,
options,
cp,
defaults,
use_defaults=True)
stdout = sys.stdout.getvalue().strip()
self.assertTrue(cp.has_section(sec_name))
self.assertFalse(cp.has_option(sec_name, 'hmmer'))
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring new_section options:{msf_cfg.theme.RESET}"
)
def test_ask_default_is_sequence(self):
msf_cfg.theme = msf_cfg.Theme()
resp = msf_cfg.ask("Question",
msf_cfg.check_positive_int, [1, 2, 3],
sequence=True)
self.assertEqual(resp, [1, 2, 3])
def test_ask_use_default(self):
msf_cfg.theme = msf_cfg.Theme()
val = msf_cfg.ask("Question",
msf_cfg.check_bool,
"Yes",
expected=["Yes", "No"],
explanation="bla bla")
self.assertTrue(val)
def test_ask_bad_value(self):
msf_cfg.theme = msf_cfg.Theme()
with self.catch_io(out=True):
with self.assertRaises(RuntimeError) as ctx:
msf_cfg.ask("Question", msf_cfg.check_bool)
self.assertEqual(
str(ctx.exception),
f'{msf_cfg.theme.ERROR}Too many error. Exiting{msf_cfg.theme.RESET}'
)
def test_set_path_options_with_system_models_dir(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
ask_ori = msf_cfg.ask
defaults = MacsyDefaults()
test_dir = os.path.dirname(__file__)
parent = os.path.join(os.path.normpath(os.path.join(test_dir, '..')))
resp = [
"Yes", # enter section ?
[parent, test_dir], # system_models_dir
os.getcwd(), # res_search_dir
"res_search_suffix", # res_search_suffix
"res_extract_suffix", # res_extract_suffix
"profile_suffix"
] # profile_suffix
g = (r for r in resp)
def fake_ask(*args, **kwargs):
return next(g)
try:
msf_cfg.ask = fake_ask
with self.catch_io(out=True):
msf_cfg.set_path_options(cp, defaults)
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring directories options:{msf_cfg.theme.RESET}"
)
self.assertTrue(cp.has_section("directories"))
self.maxDiff = None
self.assertEqual(cp.get("directories", "system_models_dir"),
f"{parent}, {test_dir}")
self.assertEqual(cp.get("directories", "res_search_dir"),
os.getcwd())
self.assertEqual(cp.get("directories", "res_search_suffix"),
"res_search_suffix")
self.assertEqual(cp.get("directories", "res_extract_suffix"),
"res_extract_suffix")
self.assertEqual(cp.get("directories", "profile_suffix"),
"profile_suffix")
finally:
msf_cfg.ask = ask_ori
def test_set_score_options(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
ask_ori = msf_cfg.ask
defaults = MacsyDefaults()
resp = [
"Yes", # enter section ?
0.1, # mandatory_weight
0.2, # accessory_weight
0.3, # exchangeable_weight
0.4, # redundancy_penalty
0.5 # out_of_cluster_weight
]
g = (r for r in resp)
def fake_ask(*args, **kwargs):
return next(g)
try:
msf_cfg.ask = fake_ask
with self.catch_io(out=True):
msf_cfg.set_score_options(cp, defaults)
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring score_opt options:{msf_cfg.theme.RESET}"
)
self.assertTrue(cp.has_section("score_opt"))
self.assertEqual(cp.get("score_opt", "mandatory_weight"), "0.1")
self.assertEqual(cp.get("score_opt", "accessory_weight"), "0.2")
self.assertEqual(cp.get("score_opt", "exchangeable_weight"), "0.3")
self.assertEqual(cp.get("score_opt", "redundancy_penalty"), "0.4")
self.assertEqual(cp.get("score_opt", "out_of_cluster_weight"),
"0.5")
finally:
msf_cfg.ask = ask_ori
def test_set_hmmer_options(self):
msf_cfg.theme = msf_cfg.Theme()
cp = msf_cfg.ConfigParserWithComments()
ask_ori = msf_cfg.ask
defaults = MacsyDefaults()
resp = [
"Yes", # enter section ?
defaults.hmmer, # hmmer exe
True, # no_cut_ga the fake_ask do not perform casting
0.002, # e_value_search,
0.003, # i_evalue_sel,
0.004 # coverage_profile
]
g = (r for r in resp)
def fake_ask(*args, **kwargs):
return next(g)
try:
msf_cfg.ask = fake_ask
with self.catch_io(out=True):
msf_cfg.set_hmmer_options(cp, defaults)
stdout = sys.stdout.getvalue().strip()
self.assertEqual(
stdout,
f"{msf_cfg.theme.SECTION}Configuring hmmer options:{msf_cfg.theme.RESET}"
)
self.assertTrue(cp.has_section("hmmer"))
self.assertFalse(cp.has_option("hmmer", "hmmer"))
# all values are casted in str before inserting in ConfigParser
self.assertEqual(cp.get("hmmer", "no_cut_ga"), 'True')
self.assertEqual(cp.get("hmmer", "e_value_search"), '0.002')
self.assertEqual(cp.get("hmmer", "i_evalue_sel"), '0.003')
self.assertEqual(cp.get("hmmer", "coverage_profile"), '0.004')
finally:
msf_cfg.ask = ask_ori
def test_ask(self):
msf_cfg.theme = msf_cfg.Theme()
resp = msf_cfg.ask("Question", msf_cfg.check_bool)
self.assertTrue(resp)