def test_run_madeline(mocker, trio, madeline_output):
"""Test to run the madeline call from api"""
# GIVEN a ped stream and a madeline process mock
config = {"madeline_exe": "madeline"}
madeline_api = MadelineAPI(config)
mocker.patch.object(Process, "run_command")
# WHEN running the madeline command
outpath = madeline_api.run("a family", trio, madeline_output)
# THEN assert a madeline xml file is returned
assert outpath.endswith(".xml")
def madeline_api(self) -> MadelineAPI:
api = self.__dict__.get("madeline_api_")
if api is None:
LOG.debug("Instantiating madeline api")
api = MadelineAPI(config=self.dict())
self.madeline_api_ = api
return api
def fixture_madeline_api() -> MadelineAPI:
"""Return a madeline API with mocked process"""
binary_path = "madeline"
config = {"madeline_exe": binary_path}
madeline_api: MadelineAPI = MadelineAPI(config)
madeline_process: ProcessMock = ProcessMock(binary=binary_path)
madeline_api.process = madeline_process
return madeline_api
def madeline_input(proband: dict) -> List[str]:
"""return a iterable with madeline formated lines"""
individuals = [proband]
case_id = "test"
_input = []
for line in MadelineAPI.make_ped(case_id, individuals):
_input.append(line)
return _input
def madeline_input(proband):
"""return a iterable with madeline formated lines"""
inds = [proband]
case_id = "test"
_input = []
for line in MadelineAPI.make_ped(case_id, inds):
_input.append(line)
return _input
def test_generate_madeline_input_none_status(madeline_columns, proband):
"""Test generate input for madeline"""
# GIVEN a case id and a list of ind dicts
proband["status"] = None
case_id = "test"
inds = [proband]
# WHEN generating madeline formated lines
madeline_lines = MadelineAPI.make_ped(case_id, inds)
# Skip the header line
next(madeline_lines)
# Convert line to dict
ind_info = get_ind_info(madeline_columns.keys(), next(madeline_lines))
# THEN assert that the status is "."
assert ind_info["status"] == "."
def test_generate_madeline_input_no_inds(madeline_columns):
"""Test generate input for madeline when no individuals"""
# GIVEN a case id and a empty list of inds
case_id = "test"
inds = []
# WHEN generating madeline formated lines
res = MadelineAPI.make_ped(case_id, inds)
# THEN assert that only the header line was generated
i = 0
header_line = None
for i, line in enumerate(res, 1):
header_line = line
assert header_line == "\t".join(madeline_columns.values())
# THEN assert only the header line is returned
assert i == 1
def test_generate_madeline_input_no_mother(madeline_columns, proband):
"""Test generate input for madeline when mother is missing"""
# GIVEN a family id and a ind with unknown mother
family_id = "test"
proband.pop("mother")
inds = [proband]
# WHEN generating madeline formated lines
madeline_lines = MadelineAPI.make_ped(family_id, inds)
i = 0
for i, line in enumerate(madeline_lines, 1):
if i == 1:
continue
ind_info = get_ind_info(madeline_columns.keys(), line)
# THEN assert that the mother is set to '.', meaning no mother exists
assert ind_info["mother"] == "."
def test_generate_madeline_input_no_sex(madeline_columns, proband):
"""Test generate input for madeline when sex is missing"""
# GIVEN a case id and a ind with unknown sex
case_id = "test"
proband["sex"] = "unknown"
inds = [proband]
# WHEN generating madeline formated lines
madeline_lines = MadelineAPI.make_ped(case_id, inds)
i = 0
for i, line in enumerate(madeline_lines, 1):
if i == 1:
continue
ind_info = get_ind_info(madeline_columns.keys(), line)
# THEN assert that sex is set to '.', meaning sex is unknown
assert ind_info["sex"] == "."
def test_generate_madeline_input(madeline_columns, proband):
"""Test generate input for madeline"""
# GIVEN a case id and a list of ind dicts
case_id = "test"
inds = [proband]
# WHEN generating madeline formated lines
madeline_lines = MadelineAPI.make_ped(case_id, inds)
# Skip the header line
next(madeline_lines)
# Convert line to dict
ind_info = get_ind_info(madeline_columns.keys(), next(madeline_lines))
# THEN assert that the case id is included
assert ind_info["case"] == case_id
# THEN assert that the ind id information is correct
assert ind_info["sample"] == proband["sample"]
# THEN assert that the is converted to madeline format
assert ind_info["sex"] == "F"
def test_generate_madeline_input_non_existing_status(madeline_columns,
proband):
"""Test generate input for madeline"""
# GIVEN an individual without status
proband.pop("status")
assert "status" not in proband
family_id = "test"
# GIVEN a family id and a list of ind dicts
inds = [proband]
# WHEN generating madeline formated lines
madeline_lines = MadelineAPI.make_ped(family_id, inds)
# Skip the header line
next(madeline_lines)
# Convert line to dict
ind_info = get_ind_info(madeline_columns.keys(), next(madeline_lines))
# THEN assert that the status is "."
assert ind_info["status"] == "."