def _refresh_participant_summary(self, session, obj):
# called when cancelled/restored
participant_summary_dao = ParticipantSummaryDao()
participant_summary = participant_summary_dao.get_for_update(
session, obj.participantId)
non_cancelled_orders = self._get_non_cancelled_biobank_orders(
session, obj.participantId)
participant_summary.biospecimenStatus = OrderStatus.UNSET
participant_summary.biospecimenOrderTime = None
participant_summary.biospecimenSourceSiteId = None
participant_summary.biospecimenCollectedSiteId = None
participant_summary.biospecimenProcessedSiteId = None
participant_summary.biospecimenFinalizedSiteId = None
participant_summary.lastModified = clock.CLOCK.now()
for sample in obj.samples:
status_field = 'sampleOrderStatus' + sample.test
setattr(participant_summary, status_field, OrderStatus.UNSET)
setattr(participant_summary, status_field + 'Time', None)
if len(non_cancelled_orders) > 0:
for order in non_cancelled_orders:
self._set_participant_summary_fields(order,
participant_summary)
participant_summary_dao.update_enrollment_status(participant_summary)
def _update_participant_summary(self, session, obj):
participant_summary_dao = ParticipantSummaryDao()
participant_summary = participant_summary_dao.get_for_update(
session, obj.participantId)
if not participant_summary:
raise BadRequest(
"Can't submit biospecimens for participant %s without consent"
% obj.participantId)
raise_if_withdrawn(participant_summary)
self._set_participant_summary_fields(obj, participant_summary)
participant_summary_dao.update_enrollment_status(participant_summary)
def _update_participant_summary(self, session, obj):
""" called on insert"""
participant_summary_dao = ParticipantSummaryDao()
participant_summary = participant_summary_dao.get_for_update(
session, obj.participantId)
if not participant_summary:
raise BadRequest(
"Can't submit biospecimens for participant %s without consent"
% obj.participantId)
raise_if_withdrawn(participant_summary)
self._set_participant_summary_fields(obj, participant_summary)
participant_summary_dao.update_enrollment_status(participant_summary)
finalized_time = self.get_random_sample_finalized_time(obj)
is_distinct_visit = ParticipantSummaryDao().calculate_distinct_visits(
participant_summary.participantId, finalized_time,
obj.biobankOrderId)
if is_distinct_visit:
participant_summary.numberDistinctVisits += 1
def _refresh_participant_summary(self, session, obj):
# called when cancelled/restored/amended
participant_summary_dao = ParticipantSummaryDao()
participant_summary = participant_summary_dao.get_for_update(
session, obj.participantId)
non_cancelled_orders = self._get_non_cancelled_biobank_orders(
session, obj.participantId)
participant_summary.biospecimenStatus = OrderStatus.UNSET
participant_summary.biospecimenOrderTime = None
participant_summary.biospecimenSourceSiteId = None
participant_summary.biospecimenCollectedSiteId = None
participant_summary.biospecimenProcessedSiteId = None
participant_summary.biospecimenFinalizedSiteId = None
finalized_time = self.get_random_sample_finalized_time(obj)
amendment = False
if not finalized_time:
amendment = True
is_distinct_visit = ParticipantSummaryDao().calculate_distinct_visits(
participant_summary.participantId, finalized_time,
obj.biobankOrderId, amendment)
if is_distinct_visit and obj.orderStatus != BiobankOrderStatus.CANCELLED:
participant_summary.numberDistinctVisits += 1
if (obj.orderStatus == BiobankOrderStatus.CANCELLED
and participant_summary.numberDistinctVisits > 0
and is_distinct_visit):
participant_summary.numberDistinctVisits -= 1
participant_summary.lastModified = clock.CLOCK.now()
for sample in obj.samples:
status_field = 'sampleOrderStatus' + sample.test
setattr(participant_summary, status_field, OrderStatus.UNSET)
setattr(participant_summary, status_field + 'Time', None)
if len(non_cancelled_orders) > 0:
for order in non_cancelled_orders:
self._set_participant_summary_fields(order,
participant_summary)
participant_summary_dao.update_enrollment_status(participant_summary)
def _update_participant_summary(self, session, obj):
participant_summary_dao = ParticipantSummaryDao()
participant_summary = participant_summary_dao.get_for_update(
session, obj.participantId)
if not participant_summary:
raise BadRequest(
"Can't submit biospecimens for participant %s without consent"
% obj.participantId)
raise_if_withdrawn(participant_summary)
participant_summary.biospecimenStatus = OrderStatus.FINALIZED
participant_summary.biospecimenOrderTime = obj.created
participant_summary.biospecimenSourceSiteId = obj.sourceSiteId
participant_summary.biospecimenCollectedSiteId = obj.collectedSiteId
participant_summary.biospecimenProcessedSiteId = obj.processedSiteId
participant_summary.biospecimenFinalizedSiteId = obj.finalizedSiteId
participant_summary.lastModified = clock.CLOCK.now()
for sample in obj.samples:
status_field = 'sampleOrderStatus' + sample.test
status, time = self._get_order_status_and_time(sample, obj)
setattr(participant_summary, status_field, status)
setattr(participant_summary, status_field + 'Time', time)