def _do_update_with_patch(self, session, order, resource,
expected_version):
self._validate_patch_update(order, resource, expected_version)
order.lastModified = clock.CLOCK.now()
order.logPosition = LogPosition()
order.version += 1
if resource['status'].lower() == 'cancelled':
order.amendedReason = resource['amendedReason']
order.cancelledUsername = resource['cancelledInfo']['author'][
'value']
order.cancelledSiteId = get_site(resource['cancelledInfo'])
order.cancelledTime = clock.CLOCK.now()
order.orderStatus = BiobankOrderStatus.CANCELLED
elif resource['status'].lower() == 'restored':
order.amendedReason = resource['amendedReason']
order.restoredUsername = resource['restoredInfo']['author'][
'value']
order.restoredSiteId = get_site(resource['restoredInfo'])
order.restoredTime = clock.CLOCK.now()
order.orderStatus = BiobankOrderStatus.UNSET
else:
raise BadRequest(
'status must be restored or cancelled for patch request.')
super(BiobankOrderDao, self)._do_update(session, order, resource)
self._update_history(session, order)
self._refresh_participant_summary(session, order)
return order
def insert_with_session(self, session, obj):
obj.version = 1
if obj.logPosition is not None:
raise BadRequest('%s.logPosition must be auto-generated.' %
self.model_type.__name__)
obj.logPosition = LogPosition()
if obj.biobankOrderId is None:
raise BadRequest('Client must supply biobankOrderId.')
existing_order = self.get_with_children_in_session(
session, obj.biobankOrderId)
if existing_order:
existing_order_dict = self._order_as_dict(existing_order)
new_dict = self._order_as_dict(obj)
if existing_order_dict == new_dict:
# If an existing matching order exists, just return it without trying to create it again.
return existing_order
else:
raise Conflict('Order with ID %s already exists' %
obj.biobankOrderId)
self._update_participant_summary(session, obj)
inserted_obj = super(BiobankOrderDao,
self).insert_with_session(session, obj)
if inserted_obj.collectedSiteId is not None:
ParticipantDao().add_missing_hpo_from_site(
session, inserted_obj.participantId,
inserted_obj.collectedSiteId)
self._update_history(session, obj)
return inserted_obj
def insert_with_session(self, session, obj):
is_amendment = False
obj.logPosition = LogPosition()
obj.final = True
obj.created = clock.CLOCK.now()
resource_json = json.loads(obj.resource)
finalized_date = resource_json['entry'][0]['resource'].get('date')
if finalized_date:
obj.finalized = parse_date(finalized_date)
for extension in resource_json['entry'][0]['resource'].get(
'extension', []):
url = extension.get('url')
if url not in _ALL_EXTENSIONS:
logging.info(
'Ignoring unsupported extension for PhysicalMeasurements: %r. Expected one of: %s',
url, _ALL_EXTENSIONS)
continue
if url == _AMENDMENT_URL:
self._update_amended(obj, extension, url, session)
is_amendment = True
break
participant_summary = self._update_participant_summary(
session, obj, is_amendment)
existing_measurements = (session.query(PhysicalMeasurements).filter(
PhysicalMeasurements.participantId == obj.participantId).all())
if existing_measurements:
new_dict = self._measurements_as_dict(obj)
for measurements in existing_measurements:
if self._measurements_as_dict(measurements) == new_dict:
# If there are already measurements that look exactly like this, return them
# without inserting new measurements.
return measurements
PhysicalMeasurementsDao.set_measurement_ids(obj)
inserted_obj = super(PhysicalMeasurementsDao,
self).insert_with_session(session, obj)
if not is_amendment: # Amendments aren't expected to have site ID extensions.
if participant_summary.biospecimenCollectedSiteId is None:
ParticipantDao().add_missing_hpo_from_site(
session, inserted_obj.participantId,
inserted_obj.finalizedSiteId)
# Flush to assign an ID to the measurements, as the client doesn't provide one.
session.flush()
# Update the resource to contain the ID.
resource_json['id'] = str(obj.physicalMeasurementsId)
obj.resource = json.dumps(resource_json)
return obj
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 _do_update(self, session, order, existing_obj):
order.lastModified = clock.CLOCK.now()
order.biobankOrderId = existing_obj.biobankOrderId
order.orderStatus = BiobankOrderStatus.AMENDED
if hasattr(existing_obj, 'amendedInfo'
) and existing_obj.amendedInfo.get('author') is not None:
order.amendedUsername = existing_obj.amendedInfo.get('author').get(
'value')
if hasattr(existing_obj, 'amendedInfo'):
order.amendedSiteId = get_site(existing_obj.amendedInfo)
order.amendedTime = clock.CLOCK.now()
order.logPosition = LogPosition()
order.version += 1
# Ensure that if an order was previously cancelled/restored those columns are removed.
self._clear_cancelled_and_restored_fields(order)
super(BiobankOrderDao, self)._do_update(session, order, existing_obj)
session.add(order.logPosition)
self._refresh_participant_summary(session, order)
self._update_history(session, order)
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()