def get_eval_flag_dict(eval_mode):
"""Get a dictionary of evaluation flags.
:param eval_mode:
Valid evaluation mode (base, draft, final, auto, misc, custom)
:type eval_mode: str
:returns: Dictionary of boolean values.
:rtype: dict
"""
# Base dictionary with all flags set to True.
dict = {}
for key in EVAL_FLAGS:
dict[key] = True
# Auto-annotations.
if eval_mode == "draft":
dict["check_locus_tag"] = False
dict["check_trna"] = False
dict["import_locus_tag"] = False
dict["check_id_typo"] = False
dict["check_host_typo"] = False
dict["check_author"] = False
dict["check_description"] = False
dict["check_coords"] = False
# Manual annotations.
elif eval_mode == "final":
dict["import_locus_tag"] = False
# SEA-PHAGES GenBank records.
elif eval_mode == "auto":
dict["check_locus_tag"] = False
dict["check_description_field"] = False
dict["check_replace"] = False
dict["check_trna"] = False
dict["check_id_typo"] = False
dict["check_host_typo"] = False
dict["check_author"] = False
dict["check_description"] = False
dict["check_description_tally"] = False
dict["check_gene"] = False
dict["check_coords"] = False
# Non-SEA-PHAGES GenBank records.
elif eval_mode == "misc":
dict["check_locus_tag"] = False
# TODO below should probably be True, but it causes problems
# when checking the current genome, GNM2_001, since these are not 'draft'
# genomes.
dict["check_replace"] = False
dict["check_trna"] = False
dict["check_id_typo"] = False
dict["check_host_typo"] = False
dict["check_author"] = False
dict["check_description"] = False
dict["check_description_tally"] = False
dict["check_gene"] = False
# Custom QC settings. User can select the settings, so it is initialized as
# a copy of the base eval_mode. The user can provide the
# customized combination of options.
elif eval_mode == "custom":
for key in dict.keys():
prompt = f"Eval_flag: {key}. {EVAL_FLAGS[key]}"
response = basic.ask_yes_no(prompt=prompt, response_attempt=3)
if response is None:
print("The default setting for this eval_flag will be used.")
else:
dict[key] = response
elif eval_mode == "base":
pass
else:
print("A valid eval_mode has not been selected.")
return dict
def test_ask_yes_no_5(self, input_mock):
"""Verify output when attempts = 3 and
user provides valid response on last attempt."""
input_mock.side_effect = ["invalid", "invalid", "Y"]
response = basic.ask_yes_no(response_attempt=3)
self.assertTrue(response)
def test_ask_yes_no_4(self, input_mock):
"""Verify output when user answers provides invalid response."""
response = basic.ask_yes_no()
self.assertIsNone(response)
def test_ask_yes_no_3(self, input_mock):
"""Verify output when user answers provides exit response."""
response = basic.ask_yes_no(response_attempt=3)
self.assertIsNone(response)
def test_ask_yes_no_2(self, input_mock):
"""Verify output when user answers provides NO response."""
response = basic.ask_yes_no()
self.assertFalse(response)
def test_ask_yes_no_1(self, input_mock):
"""Verify output when user answers provides YES response."""
response = basic.ask_yes_no()
self.assertTrue(response)