class ParticipantSummaryDaoTest(NdbTestBase):
def setUp(self):
super(ParticipantSummaryDaoTest, self).setUp(use_mysql=True)
self.dao = ParticipantSummaryDao()
self.order_dao = BiobankOrderDao()
self.measurement_dao = PhysicalMeasurementsDao()
self.participant_dao = ParticipantDao()
self.no_filter_query = Query([], None, 2, None)
self.one_filter_query = Query([FieldFilter("participantId", Operator.EQUALS, 1)],
None, 2, None)
self.two_filter_query = Query([FieldFilter("participantId", Operator.EQUALS, 1),
FieldFilter("hpoId", Operator.EQUALS, PITT_HPO_ID)],
None, 2, None)
self.ascending_biobank_id_query = Query([], OrderBy("biobankId", True), 2, None)
self.descending_biobank_id_query = Query([], OrderBy("biobankId", False), 2, None)
self.enrollment_status_order_query = Query([], OrderBy("enrollmentStatus", True), 2, None)
self.hpo_id_order_query = Query([], OrderBy("hpoId", True), 2, None)
self.first_name_order_query = Query([], OrderBy("firstName", True), 2, None)
def assert_no_results(self, query):
results = self.dao.query(query)
self.assertEquals([], results.items)
self.assertIsNone(results.pagination_token)
def assert_results(self, query, items, pagination_token=None):
results = self.dao.query(query)
self.assertListAsDictEquals(items, results.items)
self.assertEquals(pagination_token, results.pagination_token,
"Pagination tokens don't match; decoded = %s, %s" %
(_decode_token(pagination_token), _decode_token(results.pagination_token)))
def test_query_with_total(self):
num_participants = 5
query = Query([], None, 10, None, include_total=True)
results = self.dao.query(query)
self.assertEqual(results.total, 0)
for i in range(num_participants):
participant = Participant(participantId=i, biobankId=i)
self._insert(participant)
results = self.dao.query(query)
self.assertEqual(results.total, num_participants)
def testQuery_noSummaries(self):
self.assert_no_results(self.no_filter_query)
self.assert_no_results(self.one_filter_query)
self.assert_no_results(self.two_filter_query)
self.assert_no_results(self.ascending_biobank_id_query)
self.assert_no_results(self.descending_biobank_id_query)
def _insert(self, participant, first_name=None, last_name=None):
self.participant_dao.insert(participant)
summary = self.participant_summary(participant)
if first_name:
summary.firstName = first_name
if last_name:
summary.lastName = last_name
self.dao.insert(summary)
return participant
def testQuery_oneSummary(self):
participant = Participant(participantId=1, biobankId=2)
self._insert(participant)
summary = self.dao.get(1)
self.assert_results(self.no_filter_query, [summary])
self.assert_results(self.one_filter_query, [summary])
self.assert_no_results(self.two_filter_query)
self.assert_results(self.ascending_biobank_id_query, [summary])
self.assert_results(self.descending_biobank_id_query, [summary])
def testUnicodeNameRoundTrip(self):
name = self.fake.first_name()
with self.assertRaises(UnicodeEncodeError):
str(name) # sanity check that the name contains non-ASCII
participant = self._insert(Participant(participantId=1, biobankId=2))
summary = self.dao.get(participant.participantId)
summary.firstName = name
self.dao.update(summary)
fetched_summary = self.dao.get(participant.participantId)
self.assertEquals(name, fetched_summary.firstName)
def testQuery_twoSummaries(self):
participant_1 = Participant(participantId=1, biobankId=2)
self._insert(participant_1, 'Alice', 'Smith')
participant_2 = Participant(participantId=2, biobankId=1)
self._insert(participant_2, 'Zed', 'Zebra')
ps_1 = self.dao.get(1)
ps_2 = self.dao.get(2)
self.assert_results(self.no_filter_query, [ps_1, ps_2])
self.assert_results(self.one_filter_query, [ps_1])
self.assert_no_results(self.two_filter_query)
self.assert_results(self.ascending_biobank_id_query, [ps_2, ps_1])
self.assert_results(self.descending_biobank_id_query, [ps_1, ps_2])
def testQuery_threeSummaries_paginate(self):
participant_1 = Participant(participantId=1, biobankId=4)
self._insert(participant_1, 'Alice', 'Aardvark')
participant_2 = Participant(participantId=2, biobankId=1)
self._insert(participant_2, 'Bob', 'Builder')
participant_3 = Participant(participantId=3, biobankId=3)
self._insert(participant_3, 'Chad', 'Caterpillar')
ps_1 = self.dao.get(1)
ps_2 = self.dao.get(2)
ps_3 = self.dao.get(3)
self.assert_results(self.no_filter_query, [ps_1, ps_2],
_make_pagination_token(['Builder', 'Bob', None, 2]))
self.assert_results(self.one_filter_query, [ps_1])
self.assert_no_results(self.two_filter_query)
self.assert_results(self.ascending_biobank_id_query, [ps_2, ps_3],
_make_pagination_token([3, 'Caterpillar', 'Chad', None, 3]))
self.assert_results(self.descending_biobank_id_query, [ps_1, ps_3],
_make_pagination_token([3, 'Caterpillar', 'Chad', None, 3]))
self.assert_results(_with_token(self.no_filter_query,
_make_pagination_token(['Builder', 'Bob', None, 2])), [ps_3])
self.assert_results(_with_token(self.ascending_biobank_id_query,
_make_pagination_token([3, 'Caterpillar', 'Chad', None, 3])),
[ps_1])
self.assert_results(_with_token(self.descending_biobank_id_query,
_make_pagination_token([3, 'Caterpillar', 'Chad', None, 3])),
[ps_2])
def testQuery_fourFullSummaries_paginate(self):
participant_1 = Participant(participantId=1, biobankId=4)
self._insert(participant_1, 'Bob', 'Jones')
participant_2 = Participant(participantId=2, biobankId=1)
self._insert(participant_2, 'Bob', 'Jones')
participant_3 = Participant(participantId=3, biobankId=3)
self._insert(participant_3, 'Bob', 'Jones')
participant_4 = Participant(participantId=4, biobankId=2)
self._insert(participant_4, 'Bob', 'Jones')
ps_1 = self.dao.get(1)
ps_2 = self.dao.get(2)
ps_3 = self.dao.get(3)
ps_4 = self.dao.get(4)
ps_1.lastName = 'Jones'
ps_1.firstName = 'Bob'
ps_1.dateOfBirth = datetime.date(1978, 10, 9)
ps_1.hpoId = PITT_HPO_ID
self.dao.update(ps_1)
ps_2.lastName = 'Aardvark'
ps_2.firstName = 'Bob'
ps_2.dateOfBirth = datetime.date(1978, 10, 10)
ps_2.enrollmentStatus = EnrollmentStatus.MEMBER
self.dao.update(ps_2)
ps_3.lastName = 'Jones'
ps_3.firstName = 'Bob'
ps_3.dateOfBirth = datetime.date(1978, 10, 10)
ps_3.hpoId = PITT_HPO_ID
ps_3.enrollmentStatus = EnrollmentStatus.MEMBER
self.dao.update(ps_3)
ps_4.lastName = 'Jones'
ps_4.enrollmentStatus = EnrollmentStatus.FULL_PARTICIPANT
self.dao.update(ps_4)
self.assert_results(self.no_filter_query, [ps_2, ps_4],
_make_pagination_token(['Jones', 'Bob', None, 4]))
self.assert_results(self.one_filter_query, [ps_1])
self.assert_results(self.two_filter_query, [ps_1])
self.assert_results(self.ascending_biobank_id_query, [ps_2, ps_4],
_make_pagination_token([2, 'Jones', 'Bob', None, 4]))
self.assert_results(self.descending_biobank_id_query, [ps_1, ps_3],
_make_pagination_token([3, 'Jones', 'Bob', datetime.date(1978, 10, 10), 3]))
self.assert_results(self.hpo_id_order_query, [ps_2, ps_4],
_make_pagination_token([0, 'Jones', 'Bob', None, 4]))
self.assert_results(self.enrollment_status_order_query, [ps_1, ps_2],
_make_pagination_token(['MEMBER', 'Aardvark', 'Bob',
datetime.date(1978, 10, 10), 2]))
self.assert_results(_with_token(self.no_filter_query,
_make_pagination_token(['Jones', 'Bob', None, 4])),
[ps_1, ps_3])
self.assert_results(_with_token(self.ascending_biobank_id_query,
_make_pagination_token([2, 'Jones', 'Bob', None, 4])),
[ps_3, ps_1])
self.assert_results(_with_token(self.descending_biobank_id_query,
_make_pagination_token([3, 'Jones', 'Bob',
datetime.date(1978, 10, 10), 3])),
[ps_4, ps_2])
self.assert_results(_with_token(self.hpo_id_order_query,
_make_pagination_token([0, 'Jones', 'Bob', None, 4])),
[ps_1, ps_3])
self.assert_results(_with_token(self.enrollment_status_order_query,
_make_pagination_token(['MEMBER', 'Aardvark', 'Bob',
datetime.date(1978, 10, 10), 2])),
[ps_3, ps_4])
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 test_update_from_samples_changed_tests(self):
baseline_tests = ["1PST8", "2PST8"]
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
participant = self._insert(Participant(participantId=1, biobankId=11))
self.assertEquals(self.dao.get(participant.participantId).numBaselineSamplesArrived, 0)
sample_dao = BiobankStoredSampleDao()
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))
add_sample(baseline_tests[0], '11111')
add_sample(baseline_tests[1], '22223')
self.dao.update_from_biobank_stored_samples()
summary = self.dao.get(participant.participantId)
init_last_modified = summary.lastModified
self.assertEquals(summary.numBaselineSamplesArrived, 2)
# sleep 1 sec to make lastModified different
time.sleep(1)
# Simulate removal of one of the baseline tests from config.json.
baseline_tests.pop()
config.override_setting(config.BASELINE_SAMPLE_TEST_CODES, baseline_tests)
self.dao.update_from_biobank_stored_samples()
summary = self.dao.get(participant.participantId)
self.assertEquals(summary.numBaselineSamplesArrived, 1)
self.assertNotEqual(init_last_modified, summary.lastModified)
def test_only_update_dna_sample(self):
dna_tests = ["1ED10", "1SAL2"]
config.override_setting(config.DNA_SAMPLE_TEST_CODES, dna_tests)
self.dao.update_from_biobank_stored_samples() # safe noop
p_dna_samples = self._insert(Participant(participantId=1, biobankId=11))
self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)
sample_dao = BiobankStoredSampleDao()
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))
confirmed_time_0 = datetime.datetime(2018, 3, 1)
add_sample(p_dna_samples, dna_tests[0], '11111', confirmed_time_0)
self.dao.update_from_biobank_stored_samples()
self.assertEquals(self.dao.get(p_dna_samples.participantId).samplesToIsolateDNA,
SampleStatus.RECEIVED)
# only update dna sample will not update enrollmentStatusCoreStoredSampleTime
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreStoredSampleTime, None)
self.assertEquals(
self.dao.get(p_dna_samples.participantId).enrollmentStatusCoreOrderedSampleTime, None)
def test_calculate_enrollment_status(self):
self.assertEquals(EnrollmentStatus.FULL_PARTICIPANT,
self.dao.calculate_enrollment_status(True,
NUM_BASELINE_PPI_MODULES,
PhysicalMeasurementsStatus.COMPLETED,
SampleStatus.RECEIVED))
self.assertEquals(EnrollmentStatus.MEMBER,
self.dao.calculate_enrollment_status(True,
NUM_BASELINE_PPI_MODULES - 1,
PhysicalMeasurementsStatus.COMPLETED,
SampleStatus.RECEIVED))
self.assertEquals(EnrollmentStatus.MEMBER,
self.dao.calculate_enrollment_status(True,
NUM_BASELINE_PPI_MODULES,
PhysicalMeasurementsStatus.UNSET,
SampleStatus.RECEIVED))
self.assertEquals(EnrollmentStatus.MEMBER,
self.dao.calculate_enrollment_status(True,
NUM_BASELINE_PPI_MODULES,
PhysicalMeasurementsStatus.COMPLETED,
SampleStatus.UNSET))
self.assertEquals(EnrollmentStatus.INTERESTED,
self.dao.calculate_enrollment_status(False,
NUM_BASELINE_PPI_MODULES,
PhysicalMeasurementsStatus.COMPLETED,
SampleStatus.RECEIVED))
def testUpdateEnrollmentStatus(self):
ehr_consent_time = datetime.datetime(2018, 3, 1)
summary = ParticipantSummary(
participantId=1,
biobankId=2,
consentForStudyEnrollment=QuestionnaireStatus.SUBMITTED,
consentForElectronicHealthRecords=QuestionnaireStatus.SUBMITTED,
consentForElectronicHealthRecordsTime=ehr_consent_time,
enrollmentStatus=EnrollmentStatus.INTERESTED)
self.dao.update_enrollment_status(summary)
self.assertEquals(EnrollmentStatus.MEMBER, summary.enrollmentStatus)
self.assertEquals(ehr_consent_time, summary.enrollmentStatusMemberTime)
def testUpdateEnrollmentStatusLastModified(self):
"""DA-631: enrollment_status update should update last_modified."""
participant = self._insert(Participant(participantId=6, biobankId=66))
# collect current modified and enrollment status
summary = self.dao.get(participant.participantId)
test_dt = datetime.datetime(2018, 11, 1)
def reset_summary():
# change summary so enrollment status will be changed from INTERESTED to MEMBER.
summary.enrollmentStatus = EnrollmentStatus.INTERESTED
summary.lastModified = test_dt
summary.consentForStudyEnrollment = QuestionnaireStatus.SUBMITTED
summary.consentForElectronicHealthRecords = QuestionnaireStatus.SUBMITTED
summary.physicalMeasurementsStatus = PhysicalMeasurementsStatus.COMPLETED
summary.samplesToIsolateDNA = SampleStatus.RECEIVED
self.dao.update(summary)
## Test Step 1: Validate update_from_biobank_stored_samples() changes lastModified.
reset_summary()
# Update and reload summary record
self.dao.update_from_biobank_stored_samples(participant_id=participant.participantId)
summary = self.dao.get(participant.participantId)
# Test that status has changed and lastModified is also different
self.assertEquals(EnrollmentStatus.MEMBER, summary.enrollmentStatus)
self.assertNotEqual(test_dt, summary.lastModified)
## Test Step 2: Validate that update_enrollment_status() changes the lastModified property.
reset_summary()
summary = self.dao.get(participant.participantId)
self.assertEqual(test_dt, summary.lastModified)
# update_enrollment_status() does not touch the db, it only modifies object properties.
self.dao.update_enrollment_status(summary)
self.assertEquals(EnrollmentStatus.MEMBER, summary.enrollmentStatus)
self.assertNotEqual(test_dt, summary.lastModified)
def testNumberDistinctVisitsCounts(self):
self.participant = self._insert(Participant(participantId=7, biobankId=77))
# insert biobank order
order = self.order_dao.insert(self._make_biobank_order())
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
cancel_request = cancel_biobank_order()
# cancel biobank order
self.order_dao.update_with_patch(order.biobankOrderId, cancel_request, order.version)
summary = self.dao.get(self.participant.participantId)
# distinct count should be 0
self.assertEquals(summary.numberDistinctVisits, 0)
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_1.isoformat()))
# insert physical measurement
measurement = self.measurement_dao.insert(self._make_physical_measurements())
summary = self.dao.get(self.participant.participantId)
# count should be 1
self.assertEquals(summary.numberDistinctVisits, 1)
# cancel the measurement
cancel_measurement = get_restore_or_cancel_info()
with self.measurement_dao.session() as session:
self.measurement_dao.update_with_patch(measurement.physicalMeasurementsId, session,
cancel_measurement)
summary = self.dao.get(self.participant.participantId)
# count should be 0
self.assertEquals(summary.numberDistinctVisits, 0)
with clock.FakeClock(TIME_1):
self.order_dao.insert(self._make_biobank_order(biobankOrderId='2', identifiers=[
BiobankOrderIdentifier(system='b', value='d')], samples=[BiobankOrderedSample(
biobankOrderId='2',
test=BIOBANK_TESTS[0],
description='description',
processingRequired=True)]))
with clock.FakeClock(TIME_2):
self.measurement_dao.insert(self._make_physical_measurements(
physicalMeasurementsId=2))
summary = self.dao.get(self.participant.participantId)
# A PM on another day should add a new distinct count.
self.assertEquals(summary.numberDistinctVisits, 2)
with clock.FakeClock(TIME_3):
self.order_dao.insert(self._make_biobank_order(biobankOrderId='3', identifiers=[
BiobankOrderIdentifier(system='s', value='s')], samples=[BiobankOrderedSample(
biobankOrderId ='3',
finalized=TIME_3,
test=BIOBANK_TESTS[1],
description='another description',
processingRequired=False)]))
# a physical measurement on same day as biobank order does not add distinct visit.
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=6))
# another biobank order on the same day should also not add a distinct visit
self.order_dao.insert(self._make_biobank_order(biobankOrderId='7', identifiers=[
BiobankOrderIdentifier(system='x', value='x')], samples=[BiobankOrderedSample(
biobankOrderId ='7',
finalized=TIME_3,
test=BIOBANK_TESTS[1],
description='another description',
processingRequired=False)]))
summary = self.dao.get(self.participant.participantId)
# 1 from each of TIME_1 TIME_2 TIME_3
self.assertEquals(summary.numberDistinctVisits, 3)
def test_qa_scenarios_for_pmb_visits(self):
""" PDR at https://docs.google.com/document/d/1sL54f-I91RvhjIprrdbwD8TlR9Jq91MX2ELf1EtJdxc/edit#heading=h.bqo8kt3igsrw<Paste> """
self.participant = self._insert(Participant(participantId=6, biobankId=66))
# test scenario 1
with clock.FakeClock(TIME_4):
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_4.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=666,
participantId=self.participant.participantId,
finalized=TIME_4))
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
with clock.FakeClock(TIME_5):
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_5.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=669,
finalized=TIME_5))
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 2)
# test scenario 2
with clock.FakeClock(TIME_6):
self.participant = self._insert(Participant(participantId=9, biobankId=13))
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_6.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=8,
finalized=TIME_6))
self.order_dao.insert(self._make_biobank_order(biobankOrderId='2', identifiers=[
BiobankOrderIdentifier(system='b', value='d')], samples=[BiobankOrderedSample(
biobankOrderId='2',
finalized=TIME_7,
test=BIOBANK_TESTS[0],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 2
self.assertEquals(summary.numberDistinctVisits, 2)
# test scenario 3
with clock.FakeClock(TIME_6):
self.participant = self._insert(Participant(participantId=66, biobankId=42))
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_6.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=12,
createdSiteId=2,
finalized=TIME_6))
self.order_dao.insert(self._make_biobank_order(biobankOrderId='18', finalizedSiteId=1, identifiers=[
BiobankOrderIdentifier(system='x', value='y')], samples=[BiobankOrderedSample(
biobankOrderId='18',
finalized=TIME_6,
test=BIOBANK_TESTS[0],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 1
self.assertEquals(summary.numberDistinctVisits, 1)
# test scenario 4
with clock.FakeClock(TIME_8):
self.participant = self._insert(Participant(participantId=6613, biobankId=142))
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_8.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=129,
finalized=TIME_8))
order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='999', identifiers=[
BiobankOrderIdentifier(system='s', value='s')], samples=[BiobankOrderedSample(
biobankOrderId='999',
finalized=TIME_8,
test=BIOBANK_TESTS[1],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 1
self.assertEquals(summary.numberDistinctVisits, 1)
# change finalized time, recalculating count
with self.order_dao.session() as session:
existing_order = copy.deepcopy(order)
order.samples[0].finalized = TIME_9
self.order_dao._do_update(session, order, existing_order)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
# change test, should not change count.
with self.order_dao.session() as session:
existing_order = copy.deepcopy(order)
order.samples[0].test = BIOBANK_TESTS[0]
self.order_dao._do_update(session, order, existing_order)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
# test scenario 5
with clock.FakeClock(TIME_12):
self.participant = self._insert(Participant(participantId=3000, biobankId=2019))
self.order_dao.insert(self._make_biobank_order(biobankOrderId='700', identifiers=[
BiobankOrderIdentifier(system='n', value='s')], samples=[BiobankOrderedSample(
biobankOrderId='700',
finalized=TIME_10,
test=BIOBANK_TESTS[1],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 1
self.assertEquals(summary.numberDistinctVisits, 1)
other_order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='701', identifiers=[
BiobankOrderIdentifier(system='n', value='t')], samples=[BiobankOrderedSample(
biobankOrderId='701',
finalized=TIME_11,
test=BIOBANK_TESTS[1],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 2
self.assertEquals(summary.numberDistinctVisits, 2)
order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='702', identifiers=[
BiobankOrderIdentifier(system='n', value='u')], samples=[BiobankOrderedSample(
biobankOrderId='702',
finalized=TIME_12,
test=BIOBANK_TESTS[1],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 3
self.assertEquals(summary.numberDistinctVisits, 3)
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_12.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=120,
finalized=TIME_12))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 3
self.assertEquals(summary.numberDistinctVisits, 3)
cancel_request = cancel_biobank_order()
# cancel biobank order with PM on same day
self.order_dao.update_with_patch(order.biobankOrderId, cancel_request, order.version)
summary = self.dao.get(self.participant.participantId)
# distinct count should be 3 (the PM on same day still counts)
self.assertEquals(summary.numberDistinctVisits, 3)
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_1.isoformat()))
self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=150,
finalized=TIME_1))
summary = self.dao.get(self.participant.participantId)
# distinct count should be 4
self.assertEquals(summary.numberDistinctVisits, 4)
# cancel order with pm on different day
self.order_dao.update_with_patch(other_order.biobankOrderId, cancel_request, order.version)
summary = self.dao.get(self.participant.participantId)
# distinct count should be 3
self.assertEquals(summary.numberDistinctVisits, 3)
def test_pm_restore_cancel_biobank_restore_cancel(self):
self.participant = self._insert(Participant(participantId=9, biobankId=13))
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_4.isoformat()))
measurement = self.measurement_dao.insert(self._make_physical_measurements(physicalMeasurementsId=669,
finalized=TIME_4))
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
with clock.FakeClock(TIME_5):
order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='2', identifiers=[
BiobankOrderIdentifier(system='b', value='d')], samples=[BiobankOrderedSample(
biobankOrderId='2',
finalized=TIME_5,
test=BIOBANK_TESTS[0],
description='description',
processingRequired=True)]))
with clock.FakeClock(TIME_7):
summary = self.dao.get(self.participant.participantId)
# distinct count should be 2
self.assertEquals(summary.numberDistinctVisits, 2)
# cancel the measurement
cancel_measurement = get_restore_or_cancel_info()
with self.measurement_dao.session() as session:
self.measurement_dao.update_with_patch(measurement.physicalMeasurementsId, session,
cancel_measurement)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
with clock.FakeClock(TIME_7):
restore_measurement = get_restore_or_cancel_info(status='restored')
with self.measurement_dao.session() as session:
self.measurement_dao.update_with_patch(measurement.physicalMeasurementsId, session,
restore_measurement)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 2)
cancel_request = cancel_biobank_order()
order = self.order_dao.update_with_patch(order.biobankOrderId, cancel_request, order.version)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
restore_order = get_restore_or_cancel_info(status='restored')
restore_order['amendedReason'] = 'some reason'
self.order_dao.update_with_patch(order.biobankOrderId, restore_order, order.version)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 2)
def test_amending_biobank_order_distinct_visit_count(self):
self.participant = self._insert(Participant(participantId=9, biobankId=13))
with clock.FakeClock(TIME_5):
order = self.order_dao.insert(self._make_biobank_order(biobankOrderId='2', identifiers=[
BiobankOrderIdentifier(system='b', value='d')], samples=[BiobankOrderedSample(
biobankOrderId='2',
finalized=TIME_5,
test=BIOBANK_TESTS[0],
description='description',
processingRequired=True)]))
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
with clock.FakeClock(TIME_7):
amend_order = self._get_amended_info(order)
with self.order_dao.session() as session:
self.order_dao._do_update(session, amend_order, order)
# Shouldn't change on a simple amendment (unless finalized time on samples change)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 1)
with clock.FakeClock(TIME_7_5):
cancel_request = cancel_biobank_order()
order = self.order_dao.update_with_patch(order.biobankOrderId, cancel_request, order.version)
# A cancelled order (even after amending) should reduce count (unless some other valid order on same day)
summary = self.dao.get(self.participant.participantId)
self.assertEquals(summary.numberDistinctVisits, 0)
@staticmethod
def _get_amended_info(order):
amendment = dict(amendedReason='I had to change something', amendedInfo={
"author": {
"system": "https://www.pmi-ops.org/healthpro-username",
"value": "*****@*****.**"
},
"site": {
"system": "https://www.pmi-ops.org/site-id",
"value": "hpo-site-monroeville"
}
})
order.amendedReason = amendment['amendedReason']
order.amendedInfo = amendment['amendedInfo']
return order
def _make_biobank_order(self, **kwargs):
"""Makes a new BiobankOrder (same values every time) with valid/complete defaults.
Kwargs pass through to BiobankOrder constructor, overriding defaults.
"""
for k, default_value in (
('biobankOrderId', '1'),
('created', clock.CLOCK.now()),
('participantId', self.participant.participantId),
('sourceSiteId', 1),
('sourceUsername', '*****@*****.**'),
('collectedSiteId', 1),
('collectedUsername', '*****@*****.**'),
('processedSiteId', 1),
('processedUsername', '*****@*****.**'),
('finalizedSiteId', 2),
('finalizedUsername', '*****@*****.**'),
('identifiers', [BiobankOrderIdentifier(system='a', value='c')]),
('samples', [BiobankOrderedSample(
biobankOrderId='1',
test=BIOBANK_TESTS[0],
description='description',
finalized=TIME_1,
processingRequired=True)])):
if k not in kwargs:
kwargs[k] = default_value
return BiobankOrder(**kwargs)
def _make_physical_measurements(self, **kwargs):
"""Makes a new PhysicalMeasurements (same values every time) with valid/complete defaults.
Kwargs pass through to PM constructor, overriding defaults.
"""
for k, default_value in (
('physicalMeasurementsId', 1),
('participantId', self.participant.participantId),
('resource', self.measurement_json),
('createdSiteId', 1),
('finalized', TIME_3),
('finalizedSiteId', 2)):
if k not in kwargs:
kwargs[k] = default_value
return PhysicalMeasurements(**kwargs)
class PhysicalMeasurementsDaoTest(SqlTestBase):
def setUp(self):
super(PhysicalMeasurementsDaoTest, self).setUp()
self.participant = Participant(participantId=1, biobankId=2)
ParticipantDao().insert(self.participant)
self.dao = PhysicalMeasurementsDao()
self.participant_summary_dao = ParticipantSummaryDao()
self.measurement_json = json.dumps(load_measurement_json(self.participant.participantId,
TIME_1.isoformat()))
self.biobank = BiobankOrderDao()
def test_from_client_json(self):
measurement = PhysicalMeasurementsDao.from_client_json(json.loads(self.measurement_json))
self.assertIsNotNone(measurement.createdSiteId)
self.assertIsNotNone(measurement.finalizedSiteId)
def _make_physical_measurements(self, **kwargs):
"""Makes a new PhysicalMeasurements (same values every time) with valid/complete defaults.
Kwargs pass through to PM constructor, overriding defaults.
"""
for k, default_value in (
('physicalMeasurementsId', 1),
('participantId', self.participant.participantId),
('resource', self.measurement_json),
('createdSiteId', 1),
('finalizedSiteId', 2)):
if k not in kwargs:
kwargs[k] = default_value
return PhysicalMeasurements(**kwargs)
def testInsert_noParticipantId(self):
with self.assertRaises(BadRequest):
self.dao.insert(self._make_physical_measurements(participantId=None))
def testInsert_wrongParticipantId(self):
with self.assertRaises(BadRequest):
self.dao.insert(self._make_physical_measurements(participantId=2))
def _with_id(self, resource, id_):
measurements_json = json.loads(resource)
measurements_json['id'] = id_
return json.dumps(measurements_json)
def testInsert_noSummary(self):
with self.assertRaises(BadRequest):
self.dao.insert(self._make_physical_measurements())
def _make_summary(self):
self.participant_summary_dao.insert(self.participant_summary(self.participant))
def testInsert_rightParticipantId(self):
self._make_summary()
summary = ParticipantSummaryDao().get(self.participant.participantId)
self.assertIsNone(summary.physicalMeasurementsStatus)
with FakeClock(TIME_2):
measurements = self.dao.insert(self._make_physical_measurements())
expected_measurements = PhysicalMeasurements(
physicalMeasurementsId=1,
participantId=self.participant.participantId,
resource=self._with_id(self.measurement_json, '1'),
created=TIME_2,
finalized=TIME_1,
final=True,
logPositionId=1,
createdSiteId=1,
finalizedSiteId=2)
self.assertEquals(expected_measurements.asdict(), measurements.asdict())
measurements = self.dao.get(measurements.physicalMeasurementsId)
self.assertEquals(expected_measurements.asdict(), measurements.asdict())
# Completing physical measurements changes the participant summary status
summary = ParticipantSummaryDao().get(self.participant.participantId)
self.assertEquals(PhysicalMeasurementsStatus.COMPLETED, summary.physicalMeasurementsStatus)
self.assertEquals(TIME_2, summary.physicalMeasurementsTime)
self.assertEquals(TIME_2, summary.lastModified)
def test_backfill_is_noop(self):
self._make_summary()
measurements_id = self.dao.insert(self._make_physical_measurements()).physicalMeasurementsId
orig_measurements = self.dao.get_with_children(measurements_id).asdict()
self.dao.backfill_measurements()
backfilled_measurements = self.dao.get_with_children(measurements_id).asdict()
# Formatting of resource gets changed, so test it separately as parsed JSON.
self.assertEquals(
json.loads(orig_measurements['resource']),
json.loads(backfilled_measurements['resource']))
del orig_measurements['resource']
del backfilled_measurements['resource']
self.assertEquals(orig_measurements, backfilled_measurements)
def testInsert_withdrawnParticipantFails(self):
self.participant.withdrawalStatus = WithdrawalStatus.NO_USE
ParticipantDao().update(self.participant)
self._make_summary()
summary = ParticipantSummaryDao().get(self.participant.participantId)
self.assertIsNone(summary.physicalMeasurementsStatus)
with self.assertRaises(Forbidden):
self.dao.insert(self._make_physical_measurements())
def testInsert_getFailsForWithdrawnParticipant(self):
self._make_summary()
self.dao.insert(self._make_physical_measurements())
self.participant.version += 1
self.participant.withdrawalStatus = WithdrawalStatus.NO_USE
ParticipantDao().update(self.participant)
with self.assertRaises(Forbidden):
self.dao.get(1)
with self.assertRaises(Forbidden):
self.dao.query(Query([FieldFilter('participantId', Operator.EQUALS,
self.participant.participantId)],
None, 10, None))
def testInsert_duplicate(self):
self._make_summary()
with FakeClock(TIME_2):
measurements = self.dao.insert(self._make_physical_measurements())
with FakeClock(TIME_3):
measurements_2 = self.dao.insert(self._make_physical_measurements())
self.assertEquals(measurements.asdict(), measurements_2.asdict())
def testInsert_amend(self):
self._make_summary()
with FakeClock(TIME_2):
measurements = self.dao.insert(self._make_physical_measurements(
physicalMeasurementsId=1))
amendment_json = load_measurement_json_amendment(self.participant.participantId,
measurements.physicalMeasurementsId,
TIME_2)
with FakeClock(TIME_3):
new_measurements = self.dao.insert(self._make_physical_measurements(
physicalMeasurementsId=2, resource=json.dumps(amendment_json)))
measurements = self.dao.get(measurements.physicalMeasurementsId)
amended_json = json.loads(measurements.resource)
self.assertEquals('amended', amended_json['entry'][0]['resource']['status'])
self.assertEquals('1', amended_json['id'])
amendment_json = json.loads(new_measurements.resource)
self.assertEquals('2', amendment_json['id'])
self.assertTrue(new_measurements.final)
self.assertEquals(TIME_3, new_measurements.created)