def _create_sample_from_row(row, biobank_id_prefix):
"""Creates a new BiobankStoredSample object from a CSV row.
Raises:
DataError if the row is invalid.
Returns:
A new BiobankStoredSample, or None if the row should be skipped.
"""
biobank_id_str = row[_Columns.EXTERNAL_PARTICIPANT_ID]
if not biobank_id_str.startswith(biobank_id_prefix):
# This is a biobank sample for another environment. Ignore it.
return None
if _Columns.BIOBANK_ORDER_IDENTIFIER not in row:
return None
biobank_id = from_client_biobank_id(biobank_id_str)
sample = BiobankStoredSample(
biobankStoredSampleId=row[_Columns.SAMPLE_ID],
biobankId=biobank_id,
biobankOrderIdentifier=row[_Columns.BIOBANK_ORDER_IDENTIFIER],
test=row[_Columns.TEST_CODE])
if row[_Columns.PARENT_ID]:
# Skip child samples.
return None
sample.confirmed = _parse_timestamp(row, _Columns.CONFIRMED_DATE, sample)
sample.created = _parse_timestamp(row, _Columns.CREATE_DATE, sample)
return sample
def add_sample(participant, test_code, sample_id, confirmed_time):
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
biobankOrderIdentifier='KIT',
test=test_code,
confirmed=confirmed_time))
def test_dv_order_sample_update(self):
"""
Test Biobank Direct Volunteer order
"""
participant = self.participant_dao.insert(Participant())
self.summary_dao.insert(self.participant_summary(participant))
created_ts = datetime.datetime(2019, 03, 22, 18, 30, 45)
confirmed_ts = datetime.datetime(2019, 03, 23, 12, 13, 00)
bo = self._make_biobank_order(participantId=participant.participantId)
BiobankOrderDao().insert(bo)
boi = bo.identifiers[0]
bss = BiobankStoredSample(biobankStoredSampleId=u'23523523',
biobankId=participant.biobankId,
test=u'1SAL2',
created=created_ts,
biobankOrderIdentifier=boi.value,
confirmed=confirmed_ts)
with self.participant_dao.session() as session:
session.add(bss)
ps = self.summary_dao.get(participant.participantId)
self.assertIsNone(ps.sampleStatusDV1SAL2)
self.assertIsNone(ps.sampleStatusDV1SAL2Time)
self.summary_dao.update_from_biobank_stored_samples()
ps = self.summary_dao.get(participant.participantId)
self.assertEqual(ps.sampleStatus1SAL2, SampleStatus.RECEIVED)
self.assertEqual(ps.sampleStatus1SAL2Time, confirmed_ts)
def test_update_from_samples(self):
# baseline_tests = ['BASELINE1', 'BASELINE2']
baseline_tests = ["1PST8", "2PST8"]
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_baseline_samples = self._insert(Participant(participantId=1, biobankId=11))
p_mixed_samples = self._insert(Participant(participantId=2, biobankId=22))
p_no_samples = self._insert(Participant(participantId=3, biobankId=33))
p_unconfirmed = self._insert(Participant(participantId=4, biobankId=44))
self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 0)
def get_p_baseline_last_modified():
return self.dao.get(p_baseline_samples.participantId).lastModified
p_baseline_last_modified1 = get_p_baseline_last_modified()
sample_dao = BiobankStoredSampleDao()
def add_sample(participant, test_code, sample_id):
TIME = datetime.datetime(2018, 3, 2)
sample_dao.insert(BiobankStoredSample(
biobankStoredSampleId=sample_id, biobankId=participant.biobankId,
biobankOrderIdentifier='KIT', test=test_code, confirmed=TIME))
add_sample(p_baseline_samples, baseline_tests[0], '11111')
add_sample(p_baseline_samples, baseline_tests[1], '22223')
add_sample(p_mixed_samples, baseline_tests[0], '11112')
add_sample(p_mixed_samples, 'NOT1', '44441')
# add unconfirmed sample
sample_dao.insert(BiobankStoredSample(biobankStoredSampleId=55555,
biobankId=p_unconfirmed.biobankId,
biobankOrderIdentifier='KIT', test=baseline_tests[1],
confirmed=None))
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
p_baseline_last_modified2 = get_p_baseline_last_modified()
self.assertNotEquals(p_baseline_last_modified2, p_baseline_last_modified1)
self.assertEquals(self.dao.get(p_baseline_samples.participantId).numBaselineSamplesArrived, 2)
self.assertEquals(self.dao.get(p_mixed_samples.participantId).numBaselineSamplesArrived, 1)
self.assertEquals(self.dao.get(p_no_samples.participantId).numBaselineSamplesArrived, 0)
self.assertEquals(self.dao.get(p_unconfirmed.participantId).numBaselineSamplesArrived, 0)
M_baseline_samples = self._insert(Participant(participantId=9, biobankId=99))
add_sample(M_baseline_samples, baseline_tests[0], '999')
M_first_update = self.dao.get(M_baseline_samples.participantId)
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
add_sample(M_baseline_samples, baseline_tests[1], '9999')
M_second_update = self.dao.get(M_baseline_samples.participantId)
# sleep 1 sec to make lastModified different
time.sleep(1)
self.dao.update_from_biobank_stored_samples()
self.assertNotEqual(M_first_update.lastModified, M_second_update.lastModified)
self.assertEquals(get_p_baseline_last_modified(), p_baseline_last_modified2)
def add_sample(test_code, sample_id):
TIME = datetime.datetime(2018, 3, 2)
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
biobankOrderIdentifier='KIT',
test=test_code,
confirmed=TIME))
def _insert_samples(self, participant, tests, sample_ids, confirmed_time,
created_time):
for test_code, sample_id in zip(tests, sample_ids):
self.sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
test=test_code,
confirmed=confirmed_time,
created=created_time))
def test_insert_and_read_sample(self):
sample_id = 'WEB123456'
test_code = '1U234'
now = clock.CLOCK.now()
created = self.dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=self.participant.biobankId,
test=test_code,
confirmed=now))
fetched = self.dao.get(sample_id)
self.assertEquals(test_code, created.test)
self.assertEquals(test_code, fetched.test)
def test_schema(self):
session = self.database.make_session()
hpo = HPO(hpoId=1,
name='UNSET',
displayName='No organization set',
organizationType=OrganizationType.UNSET)
code_book = CodeBook(codeBookId=1,
created=datetime.datetime.now(),
latest=True,
name="pmi",
system="http://foo/bar",
version="v0.1.1")
session.add(hpo)
session.add(code_book)
session.commit()
organization = Organization(organizationId=1,
externalId='org',
displayName='Organization',
hpoId=1)
session.add(organization)
session.commit()
site = Site(siteId=1,
siteName='site',
googleGroup='*****@*****.**',
mayolinkClientNumber=12345,
organizationId=1)
code1 = Code(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
codeHistory1 = CodeHistory(codeId=1,
codeBookId=1,
system="a",
value="b",
shortValue="q",
display=u"c",
topic=u"d",
codeType=CodeType.MODULE,
mapped=True,
created=datetime.datetime.now())
session.add(site)
session.add(code1)
session.add(codeHistory1)
session.commit()
code2 = Code(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
codeHistory2 = CodeHistory(codeId=2,
codeBookId=1,
parentId=1,
system="a",
value="c",
display=u"X",
topic=u"d",
codeType=CodeType.QUESTION,
mapped=True,
created=datetime.datetime.now())
session.add(code2)
session.add(codeHistory2)
session.commit()
code3 = Code(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
codeHistory3 = CodeHistory(codeId=3,
codeBookId=1,
parentId=2,
system="a",
value="d",
display=u"Y",
topic=u"d",
codeType=CodeType.ANSWER,
mapped=False,
created=datetime.datetime.now())
session.add(code3)
session.add(codeHistory3)
session.commit()
session.commit()
p = self._participant_with_defaults(
participantId=1,
version=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
ps = self._participant_summary_with_defaults(
participantId=1,
biobankId=2,
lastModified=datetime.datetime.now(),
hpoId=hpo.hpoId,
firstName=self.fake.first_name(),
middleName=self.fake.first_name(),
lastName=self.fake.last_name(),
email=self.fake.email(),
zipCode='78751',
dateOfBirth=datetime.date.today(),
genderIdentityId=1,
consentForStudyEnrollment=QuestionnaireStatus.SUBMITTED,
consentForStudyEnrollmentTime=datetime.datetime.now(),
numBaselineSamplesArrived=2)
p.participantSummary = ps
session.add(p)
ph = self._participant_history_with_defaults(
participantId=1,
biobankId=2,
clientId='*****@*****.**',
hpoId=hpo.hpoId,
signUpTime=datetime.datetime.now(),
lastModified=datetime.datetime.now())
session.add(ph)
session.commit()
session.add(
BiobankStoredSample(biobankStoredSampleId='WEB1234542',
biobankId=p.biobankId,
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
session.add(
BiobankStoredSample(
biobankStoredSampleId='WEB99999', # Sample ID must be unique.
biobankId=p.
biobankId, # Participant ID and test may be duplicated.
biobankOrderIdentifier='KIT',
test='1UR10',
confirmed=datetime.datetime.utcnow()))
pm = PhysicalMeasurements(physicalMeasurementsId=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=False,
logPosition=LogPosition())
pm2 = PhysicalMeasurements(physicalMeasurementsId=2,
participantId=1,
created=datetime.datetime.now(),
resource='blah',
final=True,
amendedMeasurementsId=1,
logPosition=LogPosition())
session.add(pm)
session.add(pm2)
session.commit()
q1 = Measurement(measurementId=3,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value3')
session.add(q1)
session.commit()
m1 = Measurement(measurementId=1,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
bodySiteCodeSystem='bodySiteCodeSystem',
bodySiteCodeValue='bodySiteCodeValue',
valueString='a',
valueDecimal=1.2,
valueUnit='cm',
valueCodeSystem='valueCodeSystem',
valueCodeValue='value',
valueDateTime=datetime.datetime.now(),
qualifierId=q1.measurementId)
session.add(m1)
session.commit()
m2 = Measurement(measurementId=2,
physicalMeasurementsId=pm.physicalMeasurementsId,
codeSystem='codeSystem',
codeValue='codeValue',
measurementTime=datetime.datetime.now(),
valueCodeSystem='valueCodeSystem',
valueCodeValue='value2',
parentId=m1.measurementId,
qualifierId=q1.measurementId)
session.add(m2)
session.commit()
q = Questionnaire(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh = QuestionnaireHistory(questionnaireId=1,
version=1,
created=datetime.datetime.now(),
lastModified=datetime.datetime.now(),
resource='what?')
qh.questions.append(
QuestionnaireQuestion(questionnaireQuestionId=1,
questionnaireId=1,
questionnaireVersion=1,
linkId="1.2.3",
codeId=2,
repeats=True))
qh.concepts.append(
QuestionnaireConcept(questionnaireConceptId=1,
questionnaireId=1,
questionnaireVersion=1,
codeId=1))
session.add(q)
session.add(qh)
session.commit()
qr = QuestionnaireResponse(questionnaireResponseId=1,
questionnaireId=1,
questionnaireVersion=1,
participantId=1,
created=datetime.datetime.now(),
resource='blah')
qr.answers.append(
QuestionnaireResponseAnswer(questionnaireResponseAnswerId=1,
questionnaireResponseId=1,
questionId=1,
endTime=datetime.datetime.now(),
valueSystem='a',
valueCodeId=3,
valueDecimal=123,
valueString=self.fake.first_name(),
valueDate=datetime.date.today()))
session.add(qr)
session.commit()
mv = MetricsVersion(metricsVersionId=1,
inProgress=False,
complete=True,
date=datetime.datetime.utcnow(),
dataVersion=1)
session.add(mv)
session.commit()
mb = MetricsBucket(metricsVersionId=1,
date=datetime.date.today(),
hpoId='PITT',
metrics='blah')
session.add(mb)
session.commit()
def _create_data(self):
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 1, name='AZ_TUCSON_2'))
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 4, name='TEST'))
SqlTestBase.setup_codes(
ANSWER_FIELD_TO_QUESTION_CODE.values() + [EHR_CONSENT_QUESTION_CODE],
code_type=CodeType.QUESTION)
SqlTestBase.setup_codes(
FIELD_TO_QUESTIONNAIRE_MODULE_CODE.values(), code_type=CodeType.MODULE)
# Import codes for white and female, but not male or black.
SqlTestBase.setup_codes([
RACE_WHITE_CODE, CONSENT_PERMISSION_YES_CODE, RACE_NONE_OF_THESE_CODE,
PMI_PREFER_NOT_TO_ANSWER_CODE, CONSENT_PERMISSION_NO_CODE, 'female', 'PIIState_VA',
PMI_SKIP_CODE
], code_type=CodeType.ANSWER)
participant_dao = ParticipantDao()
questionnaire_id = self.create_questionnaire('questionnaire3.json')
questionnaire_id_2 = self.create_questionnaire('questionnaire4.json')
questionnaire_id_3 = self.create_questionnaire('all_consents_questionnaire.json')
pl_tucson = make_primary_provider_link_for_name('AZ_TUCSON')
pl_test = make_primary_provider_link_for_name('TEST')
pl_pitt = make_primary_provider_link_for_name('PITT')
with FakeClock(TIME):
participant = Participant(participantId=1, biobankId=2, providerLink=pl_tucson)
participant_dao.insert(participant)
self.send_consent('P1', email='*****@*****.**')
# Participant 2 starts out unpaired; later gets paired automatically when their physical
# measurements come in.
participant2 = Participant(participantId=2, biobankId=3)
participant_dao.insert(participant2)
self.send_consent('P2', email='*****@*****.**')
# Test HPO affiliation; this test participant is ignored.
participant3 = Participant(participantId=3, biobankId=4, providerLink=pl_test)
participant_dao.insert(participant3)
self.send_consent('P3', email='*****@*****.**')
# example.com e-mail; this test participant is ignored, too.
participant4 = Participant(participantId=4, biobankId=5, providerLink=pl_pitt)
participant_dao.insert(participant4)
self.send_consent('P4', email='*****@*****.**')
participant5 = Participant(participantId=5, biobankId=6, providerLink=pl_tucson)
participant_dao.insert(participant5)
self.send_consent('P5', email='*****@*****.**')
with FakeClock(TIME_2):
# FIXME: The test passes, but the following "update" doesn't actually make much sense. The
# providerlink is not changed but the HPO ID actually is (at this point in time
# `participant.hpoId` evaluates to 4, which is the value given in `unit_test_util.AZ_HPO_ID`).
# The original intent of the test is not clear.
# This update to participant has no effect, as the HPO ID didn't change.
participant = self._participant_with_defaults(
participantId=1, version=1, biobankId=2,
hpoId=3, # <<<< Had to add hpoId here, default is UNSET_HPO_ID
providerLink=pl_tucson
)
participant_dao.update(participant)
self.submit_questionnaire_response('P1', questionnaire_id,
race_code=RACE_WHITE_CODE,
gender_code='male',
state=PMI_SKIP_CODE,
date_of_birth=datetime.date(1980, 1, 2))
self.submit_questionnaire_response('P2', questionnaire_id,
race_code=RACE_NONE_OF_THESE_CODE,
gender_code=None,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P5', questionnaire_id,
race_code=PMI_SKIP_CODE,
gender_code=PMI_SKIP_CODE,
state=None,
date_of_birth=None)
with FakeClock(TIME_3):
# Re-pair the original participant
participant.version = 2
participant.providerLink = pl_pitt
participant_dao.update(participant)
self.send_post('Participant/P2/PhysicalMeasurements', load_measurement_json(2))
self.send_post('Participant/P2/BiobankOrder', load_biobank_order_json(2))
self.submit_questionnaire_response('P1', questionnaire_id,
race_code='black',
gender_code='female',
state=None,
date_of_birth=datetime.date(1980, 1, 3))
self.submit_questionnaire_response('P2', questionnaire_id,
race_code=None,
gender_code=PMI_PREFER_NOT_TO_ANSWER_CODE,
state=None,
date_of_birth=None)
self.submit_questionnaire_response('P2', questionnaire_id_2,
race_code=None,
gender_code=None,
state='PIIState_VA',
date_of_birth=None)
self.submit_consent_questionnaire_response('P1', questionnaire_id_3,
CONSENT_PERMISSION_NO_CODE)
self.submit_consent_questionnaire_response('P2', questionnaire_id_3,
CONSENT_PERMISSION_YES_CODE)
sample_dao = BiobankStoredSampleDao()
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='abc',
biobankId=2,
biobankOrderIdentifier='KIT',
test='test',
confirmed=TIME_2))
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='def',
biobankId=3,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME_2))
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='xyz',
biobankId=4,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME_2))
def _create_data(self):
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 1, name='AZ_TUCSON'))
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 2, name='TEST'))
SqlTestBase.setup_codes(
ANSWER_FIELD_TO_QUESTION_CODE.values() + [EHR_CONSENT_QUESTION_CODE],
code_type=CodeType.QUESTION)
SqlTestBase.setup_codes(
FIELD_TO_QUESTIONNAIRE_MODULE_CODE.values(), code_type=CodeType.MODULE)
# Import codes for white and female, but not male or black.
SqlTestBase.setup_codes(
[
RACE_WHITE_CODE, CONSENT_PERMISSION_YES_CODE,
CONSENT_PERMISSION_NO_CODE, 'female', 'PIIState_VA'
],
code_type=CodeType.ANSWER)
participant_dao = ParticipantDao()
questionnaire_id = self.create_questionnaire('questionnaire3.json')
questionnaire_id_2 = self.create_questionnaire('questionnaire4.json')
questionnaire_id_3 = self.create_questionnaire(
'all_consents_questionnaire.json')
with FakeClock(TIME):
participant = Participant(
participantId=1,
biobankId=2,
providerLink=make_primary_provider_link_for_name('AZ_TUCSON'))
participant_dao.insert(participant)
self.send_consent('P1', email='*****@*****.**')
with FakeClock(TIME):
# Participant 2 starts out unpaired; later gets paired automatically when their physical
# measurements come in.
participant2 = Participant(
participantId=2,
biobankId=3)
participant_dao.insert(participant2)
self.send_consent('P2', email='*****@*****.**')
with FakeClock(TIME):
# Test HPO affiliation; this test participant is ignored.
participant3 = Participant(participantId=3, biobankId=4,
providerLink=make_primary_provider_link_for_name('TEST'))
participant_dao.insert(participant3)
self.send_consent('P3', email='*****@*****.**')
# example.com e-mail; this test participant is ignored, too.
participant4 = Participant(participantId=4, biobankId=5,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant4)
self.send_consent('P4', email='*****@*****.**')
with FakeClock(TIME_2):
# This update to participant has no effect, as the HPO ID didn't change.
participant = self._participant_with_defaults(
participantId=1, version=1, biobankId=2,
providerLink=make_primary_provider_link_for_name('AZ_TUCSON'))
participant_dao.update(participant)
self.submit_questionnaire_response('P1', questionnaire_id,
RACE_WHITE_CODE, 'male', None,
datetime.date(1980, 1, 2))
self.submit_questionnaire_response('P2', questionnaire_id, None, None,
None, None)
with FakeClock(TIME_3):
participant = self._participant_with_defaults(
participantId=1,
version=2,
biobankId=2,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.update(participant)
self.send_post('Participant/P2/PhysicalMeasurements',
load_measurement_json(2))
self.send_post('Participant/P2/BiobankOrder', load_biobank_order_json(2))
self.submit_questionnaire_response('P1', questionnaire_id, 'black',
'female', None,
datetime.date(1980, 1, 3))
self.submit_questionnaire_response('P2', questionnaire_id_2, None, None,
'PIIState_VA', None)
self._submit_consent_questionnaire_response('P1', questionnaire_id_3,
CONSENT_PERMISSION_NO_CODE)
self._submit_consent_questionnaire_response('P2', questionnaire_id_3,
CONSENT_PERMISSION_YES_CODE)
sample_dao = BiobankStoredSampleDao()
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='abc',
biobankId=2,
test='test',
confirmed=TIME_2))
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='def',
biobankId=3,
test='1SAL',
confirmed=TIME_2))
def _create_data(self):
HPODao().insert(HPO(hpoId=AZ_HPO_ID + 1, name='AZ_TUCSON_2'))
HPODao().insert(HPO(hpoId=PITT_HPO_ID + 4, name='TEST'))
SqlTestBase.setup_codes(
ANSWER_FIELD_TO_QUESTION_CODE.values() + [EHR_CONSENT_QUESTION_CODE],
code_type=CodeType.QUESTION)
SqlTestBase.setup_codes(
FIELD_TO_QUESTIONNAIRE_MODULE_CODE.values(), code_type=CodeType.MODULE)
# Import codes for white and female, but not male or black.
SqlTestBase.setup_codes(
[
RACE_WHITE_CODE, CONSENT_PERMISSION_YES_CODE,
RACE_NONE_OF_THESE_CODE, PMI_PREFER_NOT_TO_ANSWER_CODE,
CONSENT_PERMISSION_NO_CODE, 'female', 'PIIState_VA'
],
code_type=CodeType.ANSWER)
participant_dao = ParticipantDao()
questionnaire_id = self.create_questionnaire('questionnaire3.json')
questionnaire_id_2 = self.create_questionnaire('questionnaire4.json')
questionnaire_id_3 = self.create_questionnaire(
'all_consents_questionnaire.json')
with FakeClock(TIME):
participant = self._participant_with_defaults(
participantId=1,
version=2,
biobankId=2,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant)
self.send_consent('P1', email='*****@*****.**')
# Participant 2 starts out unpaired; later gets paired automatically when their physical
# measurements come in.
participant2 = Participant(participantId=2, biobankId=3)
participant_dao.insert(participant2)
self.send_consent('P2', email='*****@*****.**')
# Test HPO affiliation; this test participant is ignored.
participant3 = Participant(
participantId=3,
biobankId=4,
providerLink=make_primary_provider_link_for_name('TEST'))
participant_dao.insert(participant3)
self.send_consent('P3', email='*****@*****.**')
# example.com e-mail; this test participant is ignored, too.
participant4 = Participant(
participantId=4,
biobankId=5,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant4)
self.send_consent('P4', email='*****@*****.**')
participant5 = Participant(
participantId=5,
biobankId=6,
providerLink=make_primary_provider_link_for_name('PITT'))
participant_dao.insert(participant5)
self.send_consent('P5', email='*****@*****.**')
# A withdrawn participant should be excluded from metrics.
participant6 = Participant(
participantId=6,
biobankId=7,
providerLink=make_primary_provider_link_for_name('PITT')
)
participant_dao.insert(participant6)
self.send_consent('P6', email='*****@*****.**')
participant6.withdrawalStatus=WithdrawalStatus.NO_USE
participant_dao.update(participant6)
self.send_post('Participant/P2/PhysicalMeasurements',
load_measurement_json(2))
self.send_post('Participant/P2/BiobankOrder', load_biobank_order_json(2))
self.submit_questionnaire_response('P1', questionnaire_id,
RACE_WHITE_CODE, 'female', None,
datetime.date(1980, 1, 2))
self.submit_questionnaire_response(
'P2', questionnaire_id, PMI_PREFER_NOT_TO_ANSWER_CODE, 'male', None,
datetime.date(1920, 1, 3))
self.submit_questionnaire_response('P2', questionnaire_id_2, None, None,
'PIIState_VA', None)
self.submit_questionnaire_response('P5', questionnaire_id, None, None,
None, datetime.date(1970, 1, 2))
self.submit_consent_questionnaire_response('P1', questionnaire_id_3,
CONSENT_PERMISSION_NO_CODE)
self.submit_consent_questionnaire_response('P2', questionnaire_id_3,
CONSENT_PERMISSION_YES_CODE)
sample_dao = BiobankStoredSampleDao()
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='abc',
biobankId=2,
biobankOrderIdentifier='KIT',
test='test',
confirmed=TIME))
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='def',
biobankId=3,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME))
# Required to update the HPO linkage (and test filtering for P3).
sample_dao.insert(
BiobankStoredSample(
biobankStoredSampleId='xyz',
biobankId=4,
biobankOrderIdentifier='KIT',
test='1SAL',
confirmed=TIME))
def add_sample(participant, test_code, sample_id):
sample_dao.insert(
BiobankStoredSample(biobankStoredSampleId=sample_id,
biobankId=participant.biobankId,
test=test_code))
def _store_biobank_sample(self, participant, test_code):
BiobankStoredSampleDao().insert(BiobankStoredSample(
biobankStoredSampleId='s' + participant['participantId'] + test_code,
biobankId=participant['biobankId'][1:],
test=test_code,
confirmed=TIME_1))