def test_convert_other_sex(other_sex_case_output: str):
"""Test to validate a case when the is set to 'other'"""
cases = json.loads(other_sex_case_output)
case = cases[0]
# GIVEN a case that has parent set to None
assert case["individuals"][0]["sex"] == "other"
# WHEN validating the output with model
case_obj = ScoutExportCase(**case)
# THEN assert that the sex has been converted to "0"
assert case_obj.dict()["individuals"][0]["sex"] == "0"
def test_validate_empty_diagnosis_phenotypes(none_case_output: str):
"""Test to validate a case when the diagnosis phenotypes is a empty list"""
cases = json.loads(none_case_output)
case = cases[0]
# GIVEN a case that has parent set to None
assert case["diagnosis_phenotypes"] == []
# WHEN validating the output with model
case_obj = ScoutExportCase(**case)
# THEN assert diagnosis phenotypes is set to None
assert case_obj.dict()["diagnosis_phenotypes"] == []
def test_validate_case_parents_none(none_case_output: str):
"""Test to validate a case when there are mandatory fields with the value None"""
cases = json.loads(none_case_output)
case = cases[0]
# GIVEN a case that has parent set to None
assert case["individuals"][0]["father"] is None
assert case["individuals"][0]["mother"] is None
# WHEN validating the output with model
case_obj = ScoutExportCase(**case)
# THEN assert father is set to None
assert case_obj.dict()["individuals"][0]["father"] == "0"
assert case_obj.dict()["individuals"][0]["mother"] == "0"
def test_validate_case_father_none(none_case_output: str):
"""Test to validate a case when there are mandatory fields with the value None"""
cases = json.loads(none_case_output)
case = cases[0]
# GIVEN a case that has parent set to None
assert case["individuals"][0]["father"] is None
# WHEN validating the output with model
case_obj = ScoutExportCase(**case)
case_dict = case_obj.dict()
# THEN assert father is set to None
assert case_dict["individuals"][0]["father"] == "0"
# THEN assert that '_id' has been changed to 'id'
assert "_id" not in case_dict
assert "id" in case_dict
def get_cases(
self,
case_id: Optional[str] = None,
reruns: bool = False,
finished: bool = False,
status: Optional[str] = None,
days_ago: int = None,
) -> List[ScoutExportCase]:
"""Interact with cases existing in the database."""
# These commands can be run with `scout export cases`
get_cases_command = ["export", "cases", "--json"]
if case_id:
get_cases_command.extend(["--case-id", case_id])
elif status:
get_cases_command.extend(["--status", status])
elif finished:
get_cases_command.append("--finished")
if reruns:
LOG.info("Fetching cases that are reruns")
get_cases_command.append("--reruns")
if days_ago:
get_cases_command.extend(["--within-days", str(days_ago)])
try:
self.process.run_command(get_cases_command)
if not self.process.stdout:
return []
except CalledProcessError:
LOG.info("Could not find cases")
return []
cases = []
for case_export in json.loads(self.process.stdout):
LOG.info("Validating case %s", case_export.get("_id"))
case_obj = ScoutExportCase(**case_export)
cases.append(case_obj)
return cases
def fixture_scout_export_case_missing_bam(
scout_export_case_data: dict) -> ScoutExportCase:
"""Returns a export case object where one individual is missing bam file"""
scout_export_case_data["individuals"][1].pop("bam_file")
return ScoutExportCase(**scout_export_case_data)
def fixture_scout_export_case(scout_export_case_data: dict) -> ScoutExportCase:
"""Returns a export case object"""
return ScoutExportCase(**scout_export_case_data)
def fixture_scout_export_case_no_causatives(
scout_export_case_data: dict) -> ScoutExportCase:
"""Returns a export case object without causatives"""
scout_export_case_data.pop("causatives")
return ScoutExportCase(**scout_export_case_data)