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 _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 from_client_json(self,
resource_json,
id_=None,
expected_version=None,
participant_id=None,
client_id=None):
resource = _FhirBiobankOrder(resource_json)
if not resource.created.date: # FHIR warns but does not error on bad date values.
raise BadRequest('Invalid created date %r.' %
resource.created.origval)
order = BiobankOrder(
participantId=participant_id,
created=resource.created.date.replace(tzinfo=None))
if not resource.created_info:
raise BadRequest(
'Created Info is required, but was missing in request.')
order.sourceUsername, order.sourceSiteId = self._parse_handling_info(
resource.created_info)
order.collectedUsername, order.collectedSiteId = self._parse_handling_info(
resource.collected_info)
if order.collectedSiteId is None:
raise BadRequest('Collected site is required in request.')
order.processedUsername, order.processedSiteId = self._parse_handling_info(
resource.processed_info)
order.finalizedUsername, order.finalizedSiteId = self._parse_handling_info(
resource.finalized_info)
# order.finalizedTime uses the time from biobank_ordered_sample.finalized
try:
order.finalizedTime = self.get_random_sample_finalized_time(
resource).date.replace(tzinfo=None)
except AttributeError:
order.finalizedTime = None
if resource.notes:
order.collectedNote = resource.notes.collected
order.processedNote = resource.notes.processed
order.finalizedNote = resource.notes.finalized
if resource.subject != self._participant_id_to_subject(participant_id):
raise BadRequest(
'Participant ID %d from path and %r in request do not match, should be %r.'
% (participant_id, resource.subject,
self._participant_id_to_subject(participant_id)))
self._add_identifiers_and_main_id(order, resource)
self._add_samples(order, resource)
if resource.amendedReason:
order.amendedReason = resource.amendedReason
if resource.amendedInfo:
order.amendedUsername, order.amendedSiteId = self._parse_handling_info(
resource.amendedInfo)
order.version = expected_version
return order
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 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 from_client_json(self,
resource_json,
participant_id=None,
client_id=None):
resource = _FhirBiobankOrder(resource_json)
if not resource.created.date: # FHIR warns but does not error on bad date values.
raise BadRequest('Invalid created date %r.' %
resource.created.origval)
order = BiobankOrder(participantId=participant_id,
created=resource.created.date)
if not resource.created_info:
raise BadRequest(
'Created Info is required, but was missing in request.')
order.sourceUsername, order.sourceSiteId = self._parse_handling_info(
resource.created_info)
order.collectedUsername, order.collectedSiteId = self._parse_handling_info(
resource.collected_info)
order.processedUsername, order.processedSiteId = self._parse_handling_info(
resource.processed_info)
order.finalizedUsername, order.finalizedSiteId = self._parse_handling_info(
resource.finalized_info)
if resource.notes:
order.collectedNote = resource.notes.collected
order.processedNote = resource.notes.processed
order.finalizedNote = resource.notes.finalized
if resource.subject != self._participant_id_to_subject(participant_id):
raise BadRequest(
'Participant ID %d from path and %r in request do not match, should be %r.'
% (participant_id, resource.subject,
self._participant_id_to_subject(participant_id)))
self._add_identifiers_and_main_id(order, resource)
self._add_samples(order, resource)
return order