def process_genomic_water_line():
"""
Entrypoint, executed as a cron job
"""
genomic_set_id = genomic_set_file_handler.read_genomic_set_from_bucket()
if genomic_set_id is not None:
logging.info('Read input genomic set file successfully.')
dao = GenomicSetDao()
validation.validate_and_update_genomic_set_by_id(genomic_set_id, dao)
genomic_set = dao.get(genomic_set_id)
if genomic_set.genomicSetStatus == GenomicSetStatus.VALID:
genomic_biobank_menifest_handler\
.create_and_upload_genomic_biobank_manifest_file(genomic_set_id)
logging.info(
'Validation passed, generate biobank manifest file successfully.'
)
else:
logging.info('Validation failed.')
genomic_set_file_handler.create_genomic_set_status_result_file(
genomic_set_id)
else:
logging.info('No file found or nothing read from genomic set file')
genomic_biobank_menifest_handler.process_genomic_manifest_result_file_from_bucket(
)
genomic_center_menifest_handler.process_genotyping_manifest_files()
def test_age(self):
now = datetime.datetime(2019, 1, 1)
valid_date_of_birth = datetime.datetime(now.year - 18, now.month,
now.day)
invalid_date_of_birth = datetime.datetime(now.year - 17, now.month,
now.day)
participant_a = self.make_participant()
self.make_summary(participant_a, dateOfBirth=valid_date_of_birth)
participant_b = self.make_participant()
self.make_summary(participant_b, dateOfBirth=invalid_date_of_birth)
genomic_set = self.make_genomic_set()
member_a = self.make_genomic_member(genomic_set, participant_a)
member_b = self.make_genomic_member(genomic_set, participant_b)
with clock.FakeClock(datetime.datetime(2019, 1, 1)):
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member_a = self.genomic_member_dao.get(member_a.id)
current_member_b = self.genomic_member_dao.get(member_b.id)
self.assertEqual(current_member_a.validationStatus,
GenomicSetMemberStatus.VALID)
self.assertEqual(current_member_b.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_AGE,
current_member_b.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_ny_zip_code(self):
participant_a = self.make_participant()
self.make_summary(participant_a, zipCode=None)
participant_b = self.make_participant()
self.make_summary(participant_b, zipCode='')
participant_c = self.make_participant()
self.make_summary(participant_c, zipCode='12345')
genomic_set = self.make_genomic_set()
member_a = self.make_genomic_member(genomic_set, participant_a)
member_b = self.make_genomic_member(genomic_set, participant_b)
member_c = self.make_genomic_member(genomic_set, participant_c)
with clock.FakeClock(datetime.datetime(2019, 1, 1)):
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member_a = self.genomic_member_dao.get(member_a.id)
current_member_b = self.genomic_member_dao.get(member_b.id)
current_member_c = self.genomic_member_dao.get(member_c.id)
self.assertEqual(current_member_a.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_NY_ZIPCODE,
current_member_a.validationFlags)
self.assertEqual(current_member_b.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_NY_ZIPCODE,
current_member_a.validationFlags)
self.assertEqual(current_member_c.validationStatus,
GenomicSetMemberStatus.VALID)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_biobank_status(self):
def make_member(genomic_set, **summary_kwargs):
participant = self.make_participant()
self.make_summary(participant, **summary_kwargs)
return self.make_genomic_member(genomic_set, participant)
kwargs_with_expected_status_and_flags = [
({
'sampleStatus1ED04': SampleStatus.UNSET,
'sampleStatus1SAL2': SampleStatus.UNSET,
'samplesToIsolateDNA': SampleStatus.UNSET,
}, GenomicSetMemberStatus.INVALID,
[GenomicValidationFlag.INVALID_BIOBANK_ORDER]),
({
'sampleStatus1ED04': SampleStatus.RECEIVED,
'sampleStatus1SAL2': SampleStatus.UNSET,
'samplesToIsolateDNA': SampleStatus.UNSET,
}, GenomicSetMemberStatus.INVALID,
[GenomicValidationFlag.INVALID_BIOBANK_ORDER]),
({
'sampleStatus1ED04': SampleStatus.UNSET,
'sampleStatus1SAL2': SampleStatus.RECEIVED,
'samplesToIsolateDNA': SampleStatus.UNSET,
}, GenomicSetMemberStatus.INVALID,
[GenomicValidationFlag.INVALID_BIOBANK_ORDER]),
({
'sampleStatus1ED04': SampleStatus.UNSET,
'sampleStatus1SAL2': SampleStatus.UNSET,
'samplesToIsolateDNA': SampleStatus.RECEIVED,
}, GenomicSetMemberStatus.INVALID,
[GenomicValidationFlag.INVALID_BIOBANK_ORDER]),
({
'sampleStatus1ED04': SampleStatus.RECEIVED,
'sampleStatus1SAL2': SampleStatus.UNSET,
'samplesToIsolateDNA': SampleStatus.RECEIVED,
}, GenomicSetMemberStatus.VALID, []),
({
'sampleStatus1ED04': SampleStatus.UNSET,
'sampleStatus1SAL2': SampleStatus.RECEIVED,
'samplesToIsolateDNA': SampleStatus.RECEIVED,
}, GenomicSetMemberStatus.VALID, []),
]
genomic_set = self.make_genomic_set()
runs = [
(make_member(genomic_set, **kwargs), kwargs, status, flags)
for kwargs, status, flags in kwargs_with_expected_status_and_flags
]
validate_and_update_genomic_set_by_id(genomic_set.id)
for member, kwargs, expected_status, expected_flags in runs:
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus, expected_status)
for flag in expected_flags:
self.assertIn(flag, current_member.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_test_defaults_are_valid(self):
participant = self.make_participant()
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus,
GenomicSetMemberStatus.VALID)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus, GenomicSetStatus.VALID)
def test_invalid_does_not_update_validated_time(self):
participant = self.make_participant(
withdrawalStatus=WithdrawalStatus.NO_USE)
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validatedTime, None)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.validatedTime, None)
def test_valid_does_update_validated_time(self):
participant = self.make_participant()
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
now = datetime.datetime(2019, 1, 1)
with clock.FakeClock(now):
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validatedTime, now)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.validatedTime, now)
def test_consent_null(self):
participant = self.make_participant()
self.make_summary(participant, consentForStudyEnrollmentTime=None)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_CONSENT,
current_member.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_transaction(self):
participant = self.make_participant()
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
with mock.patch('genomic.validation.GenomicSetDao.update_with_session'
) as mocked_set_update:
mocked_set_update.side_effect = Exception('baz')
with clock.FakeClock(datetime.datetime(2019, 1, 1)):
with self.assertRaises(Exception):
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus, None)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus, None)
def test_withdrawn(self):
participant = self.make_participant(
withdrawalStatus=WithdrawalStatus.NO_USE)
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set, participant)
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_WITHDRAW_STATUS,
current_member.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_sexatbirth(self):
participant = self.make_participant()
self.make_summary(participant)
genomic_set = self.make_genomic_set()
member = self.make_genomic_member(genomic_set,
participant,
sexAtBirth='foo')
validate_and_update_genomic_set_by_id(genomic_set.id)
current_member = self.genomic_member_dao.get(member.id)
self.assertEqual(current_member.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_SEX_AT_BIRTH,
current_member.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)
def test_duplicate(self):
participant = self.make_participant()
self.make_summary(participant)
genomic_set_a = self.make_genomic_set(
genomicSetName='A', genomicSetStatus=GenomicSetStatus.VALID)
self.make_genomic_member(genomic_set_a, participant)
genomic_set_b = self.make_genomic_set(genomicSetName='B')
member_b = self.make_genomic_member(genomic_set_b, participant)
validate_and_update_genomic_set_by_id(genomic_set_b.id)
current_member = self.genomic_member_dao.get(member_b.id)
self.assertEqual(current_member.validationStatus,
GenomicSetMemberStatus.INVALID)
self.assertIn(GenomicValidationFlag.INVALID_DUP_PARTICIPANT,
current_member.validationFlags)
current_set = self.genomic_set_dao.get(genomic_set_b.id)
self.assertEqual(current_set.genomicSetStatus,
GenomicSetStatus.INVALID)