def tearDown(self):
"""Restore state from any setUp or test steps"""
log.info("Purge test records from the database")
DBUtil.execute \
( """delete from patient_item
where clinical_item_id in
( select clinical_item_id
from clinical_item as ci, clinical_item_category as cic
where ci.clinical_item_category_id = cic.clinical_item_category_id
and cic.source_table = '%s'
);
""" % TEST_SOURCE_TABLE
)
DBUtil.execute \
( """delete from clinical_item
where clinical_item_category_id in
( select clinical_item_category_id
from clinical_item_category
where source_table = '%s'
);
""" % TEST_SOURCE_TABLE
)
DBUtil.execute(
"delete from clinical_item_category where source_table = '%s';" %
TEST_SOURCE_TABLE)
query = SQLQuery()
query.delete = True
query.addFrom("stride_patient")
query.addWhere("pat_id < 0")
DBUtil.execute(query)
DBTestCase.tearDown(self)
def tearDown(self):
"""Restore state from any setUp or test steps"""
log.info("Purge test records from the database")
DBUtil.execute \
( """delete from patient_item
where clinical_item_id in
( select clinical_item_id
from clinical_item as ci, clinical_item_category as cic
where ci.clinical_item_category_id = cic.clinical_item_category_id
and cic.source_table = '%s'
);
""" % TEST_SOURCE_TABLE
)
DBUtil.execute \
( """delete from clinical_item
where clinical_item_category_id in
( select clinical_item_category_id
from clinical_item_category
where source_table = '%s'
);
""" % TEST_SOURCE_TABLE
)
DBUtil.execute(
"delete from clinical_item_category where source_table = '%s';" %
TEST_SOURCE_TABLE)
query = SQLQuery()
query.delete = True
query.addFrom("stride_dx_list")
query.addWhereIn("pat_id", self.patientIdStrList)
DBUtil.execute(query)
query = SQLQuery()
query.delete = True
query.addFrom("stride_icd9_cm")
query.addWhereIn("cui", self.icd9CUIdStrList)
DBUtil.execute(query)
query = SQLQuery()
query.delete = True
query.addFrom("stride_icd10_cm")
query.addWhereIn("order_number", self.icd10_order_number_str_list)
DBUtil.execute(query)
DBTestCase.tearDown(self)
def tearDown(self):
"""Restore state from any setUp or test steps"""
log.info("Purge test records from the database")
query = SQLQuery()
query.delete = True
query.addFrom("access_log")
query.addWhereIn("user_id", self.testUserIDs)
DBUtil.execute(query)
query = SQLQuery()
query.delete = True
query.addFrom("user")
query.addWhereIn("user_id", self.testUserIDs)
DBUtil.execute(query)
DBUtil.execute("drop table %s;" % TEST_SOURCE_TABLE)
DBTestCase.tearDown(self)
def signOrders(self,
userId,
patientId,
currentTime,
orderItemIds,
discontinuePatientOrderIds=None,
conn=None):
"""Commit new order item IDs for the given patient and starting now,
and discontinue (set end date) for any existing orders specified.
Record any patient state transitions the orders would trigger
"""
extConn = True
if conn is None:
conn = self.connFactory.connection()
extConn = False
try:
# Denormalized recording of current patient state to facilitate easy retrieval linked to orders later
patientInfo = self.loadPatientInfo([patientId],
currentTime,
conn=conn)[0]
stateId = patientInfo["sim_state_id"]
postStateIdByItemId = patientInfo["postStateIdByItemId"]
orderItemIdSet = set(
orderItemIds) # Ensure unique and facilitate set operations
insertDict = {
"sim_user_id": userId,
"sim_patient_id": patientId,
"sim_state_id": stateId,
"relative_time_start": currentTime
}
for itemId in orderItemIdSet:
insertDict["clinical_item_id"] = itemId
DBUtil.insertRow("sim_patient_order", insertDict, conn=conn)
# See if any of these new orders triggered state transitions
triggerItemIds = postStateIdByItemId.viewkeys() & orderItemIdSet
while triggerItemIds: # Found a trigger item
triggerItemId = None
if len(
triggerItemIds
) > 1: # Found multiple. Weird. Arbitrarily act on the one that appeared first in the input list
for itemId in orderItemIds:
if itemId in triggerItemIds:
triggerItemId = itemId
break
else:
triggerItemId = triggerItemIds.pop()
postStateId = postStateIdByItemId[triggerItemId]
# Record the state transition
self.recordStateTransition(patientId,
stateId,
postStateId,
currentTime,
conn=conn)
# Reload patientInfo to reflect new patient state
patientInfo = self.loadPatientInfo([patientId],
currentTime,
conn=conn)[0]
stateId = patientInfo["sim_state_id"]
postStateIdByItemId = patientInfo["postStateIdByItemId"]
orderItemIdSet.discard(
triggerItemId
) # Don't keep looking for this one, important to avoid infinite loop
triggerItemIds = postStateIdByItemId.viewkeys(
) & orderItemIdSet
if discontinuePatientOrderIds is not None:
updateDict = {"relative_time_end": currentTime}
for patientOrderId in discontinuePatientOrderIds:
DBUtil.updateRow("sim_patient_order",
updateDict,
patientOrderId,
conn=conn)
# If order is discontinued/cancelled at the same (or before) time of entry,
# take that as a signal to cleanup and delete the record altogether
# (effectively there was no time at which the order was ever allowed to exist)
deleteQuery = SQLQuery()
deleteQuery.delete = True
deleteQuery.addFrom("sim_patient_order")
deleteQuery.addWhereEqual("sim_patient_id", patientId)
deleteQuery.addWhere(
"relative_time_end <= relative_time_start")
DBUtil.execute(deleteQuery, conn=conn)
finally:
conn.commit()
if not extConn:
conn.close()
