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)
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=u'description', finalized=self.TIME_1, processingRequired=True) ])): if k not in kwargs: kwargs[k] = default_value return BiobankOrder(**kwargs)
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. """ participantId = kwargs['participantId'] modified = datetime.datetime(2019, 03, 25, 15, 59, 30) for k, default_value in ( ('biobankOrderId', u'1'), ('created', clock.CLOCK.now()), # ('participantId', self.participant.participantId), ('sourceSiteId', 1), ('sourceUsername', u'*****@*****.**'), ('collectedSiteId', 1), ('collectedUsername', u'*****@*****.**'), ('processedSiteId', 1), ('processedUsername', u'*****@*****.**'), ('finalizedSiteId', 2), ('finalizedUsername', u'*****@*****.**'), ('version', 1), ('identifiers', [BiobankOrderIdentifier(system=u'a', value=u'c')]), ('samples', [ BiobankOrderedSample(test=u'1SAL2', description=u'description', processingRequired=True) ]), ('dvOrders', [ BiobankDVOrder(participantId=participantId, modified=modified, version=1) ])): if k not in kwargs: kwargs[k] = default_value return BiobankOrder(**kwargs)
def test_cancelled_order_removes_from_participant_summary(self): ParticipantSummaryDao().insert(self.participant_summary(self.participant)) samples = [BiobankOrderedSample( test=self._B_TEST, processingRequired=True, description=u'new sample')] biobank_order_id = 2 with clock.FakeClock(self.TIME_1): order_1 = self.dao.insert(self._make_biobank_order()) with clock.FakeClock(self.TIME_2): self.dao.insert(self._make_biobank_order(samples=samples, biobankOrderId=biobank_order_id, identifiers=[ BiobankOrderIdentifier(system='z', value='x')])) cancelled_request = self._get_cancel_patch() ps_dao = ParticipantSummaryDao().get(self.participant.participantId) self.assertEqual(ps_dao.sampleOrderStatus1ED10, OrderStatus.FINALIZED) self.assertEqual(ps_dao.sampleOrderStatus1ED10Time, self.TIME_2) self.assertEqual(ps_dao.sampleOrderStatus2ED10, OrderStatus.CREATED) self.assertEqual(ps_dao.sampleOrderStatus2ED10Time, self.TIME_2) self.dao.update_with_patch(order_1.biobankOrderId, cancelled_request, order_1.version) ps_dao = ParticipantSummaryDao().get(self.participant.participantId) self.assertEqual(ps_dao.sampleOrderStatus1ED10, None) self.assertEqual(ps_dao.sampleOrderStatus1ED10Time, None) # should not remove the other order self.assertEqual(ps_dao.sampleOrderStatus2ED10, OrderStatus.CREATED) self.assertEqual(ps_dao.sampleOrderStatus2ED10Time, self.TIME_2) self.assertEqual(ps_dao.biospecimenCollectedSiteId, 1) self.assertEqual(ps_dao.biospecimenFinalizedSiteId, 2) self.assertEqual(ps_dao.biospecimenProcessedSiteId, 1) self.assertEqual(ps_dao.biospecimenStatus, OrderStatus.FINALIZED)
def test_store_invalid_test(self): with self.assertRaises(BadRequest): self.dao.insert( self._make_biobank_order(samples=[ BiobankOrderedSample(test='InvalidTestName', processingRequired=True, description=u'tested it') ]))
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 _insert_order(self, participant, order_id, tests, order_time, finalized_tests=None, kit_id=None, tracking_number=None, collected_note=None, processed_note=None, finalized_note=None): order = BiobankOrder(biobankOrderId=order_id, participantId=participant.participantId, sourceSiteId=1, finalizedSiteId=2, collectedSiteId=1, finalizedUsername='******', created=order_time, collectedNote=collected_note, processedNote=processed_note, finalizedNote=finalized_note, samples=[]) id_1 = BiobankOrderIdentifier( system="https://orders.mayomedicallaboratories.com", value=order_id) id_2 = BiobankOrderIdentifier(system="https://www.pmi-ops.org", value='O%s' % order_id) order.identifiers.append(id_1) order.identifiers.append(id_2) if kit_id: order.identifiers.append( BiobankOrderIdentifier(system=_KIT_ID_SYSTEM, value=kit_id)) if tracking_number: order.identifiers.append( BiobankOrderIdentifier(system=_TRACKING_NUMBER_SYSTEM, value=tracking_number)) for test_code in tests: finalized_time = order_time if finalized_tests and not test_code in finalized_tests: finalized_time = None order.samples.append( BiobankOrderedSample(biobankOrderId=order.biobankOrderId, test=test_code, description=u'test', processingRequired=False, collected=order_time, processed=order_time, finalized=finalized_time)) return self.order_dao.insert(order)
def test_schema_biobank_order_and_datetime_roundtrip(self): bo_id = 1 now = isodate.parse_datetime('2016-01-04T10:28:50-04:00') write_session = self.database.make_session() p = self._create_participant(write_session) site = Site(siteId=1, siteName='site', googleGroup='*****@*****.**', mayolinkClientNumber=12345, hpoId=1) write_session.add(site) write_session.commit() bo = BiobankOrder(biobankOrderId=bo_id, participantId=p.participantId, created=now, sourceSiteId=1, version=1, sourceUsername='******', collectedSiteId=1, collectedUsername='******', processedSiteId=1, processedUsername='******', finalizedSiteId=1, finalizedUsername='******', collectedNote=r'written by ' + self.fake.last_name(), processedNote=u'd', finalizedNote=u'e', logPosition=LogPosition()) bo.identifiers.append(BiobankOrderIdentifier(system='a', value='b')) bo.samples.append( BiobankOrderedSample(test='a', description=u'a test invented by ' + self.fake.first_name(), processingRequired=True, collected=now, processed=now, finalized=now)) write_session.add(bo) write_session.commit() read_session = self.database.make_session() bo = read_session.query(BiobankOrder).get(bo_id) self.assertEquals( bo.created.isoformat(), now.astimezone(tzutc()).replace(tzinfo=None).isoformat())
def _add_samples(cls, order, resource): all_tests = sorted([s.test for s in resource.samples]) if len(set(all_tests)) != len(all_tests): raise BadRequest('Duplicate test in sample list for order: %s.' % (all_tests, )) for s in resource.samples: order.samples.append( BiobankOrderedSample(biobankOrderId=order.biobankOrderId, test=s.test, description=s.description, processingRequired=s.processing_required, collected=s.collected and s.collected.date, processed=s.processed and s.processed.date, finalized=s.finalized and s.finalized.date))
def insert_biobank_order(self, pid, resource): obj = BiobankOrder() obj.participantId = long(pid) obj.created = clock.CLOCK.now() obj.created = datetime.datetime.now() obj.orderStatus = BiobankOrderStatus.UNSET obj.biobankOrderId = resource['biobankOrderId'] test = self.get(resource['id']) obj.dvOrders = [test] bod = BiobankOrderDao() obj.samples = [ BiobankOrderedSample(test='1SAL2', processingRequired=False, description=u'salivary pilot kit') ] self._add_identifiers_and_main_id(obj, ObjectView(resource)) bod.insert(obj)
def test_amending_order_participant_summary(self): ParticipantSummaryDao().insert(self.participant_summary(self.participant)) order_1 = self.dao.insert(self._make_biobank_order()) amended_info = self._get_amended_info(order_1) amended_info.sourceSiteId = 2 samples = [BiobankOrderedSample( test=self._B_TEST, processingRequired=True, description=u'new sample')] amended_info.samples = samples with self.dao.session() as session: self.dao._do_update(session, amended_info, order_1) amended_order = self.dao.get(1) self.assertEqual(amended_order.version, 2) ps_dao = ParticipantSummaryDao().get(self.participant.participantId) self.assertEqual(ps_dao.sampleOrderStatus2ED10, OrderStatus.CREATED) self.assertEqual(ps_dao.sampleOrderStatus1ED10, OrderStatus.FINALIZED) self.assertEqual(ps_dao.numberDistinctVisits, 1)
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 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)