def loadPatientOrders(self,
patientId,
currentTime,
loadActive=True,
conn=None):
"""Load orders for the given patient that exist by the specified current time point.
loadActive - Specify whether to load active vs. inactive/completed orders. Set to None to load both
"""
extConn = True
if conn is None:
conn = self.connFactory.connection()
extConn = False
try:
query = SQLQuery()
query.addSelect("po.sim_patient_order_id")
query.addSelect("po.sim_user_id")
query.addSelect("po.sim_patient_id")
query.addSelect("po.sim_state_id")
query.addSelect("po.clinical_item_id")
query.addSelect("po.relative_time_start")
query.addSelect("po.relative_time_end")
query.addSelect("ci.name")
query.addSelect("ci.description")
query.addSelect("cic.source_table")
query.addSelect("cic.description as category_description")
query.addFrom("sim_patient_order as po")
query.addFrom("clinical_item as ci")
query.addFrom("clinical_item_category as cic")
query.addWhere("po.clinical_item_id = ci.clinical_item_id")
query.addWhere(
"ci.clinical_item_category_id = cic.clinical_item_category_id")
query.addWhereEqual("sim_patient_id", patientId)
query.addWhereOp("relative_time_start", "<=", currentTime)
if loadActive: # Filter out inactive orders here.
query.openWhereOrClause()
query.addWhere("relative_time_end is null")
query.addWhereOp("relative_time_end", ">", currentTime)
query.closeWhereOrClause()
#elif loadActive is not None: # Filter out active orders here.
# query.addWhereOp("relative_time_end","<=", currentTime)
if loadActive: # Organize currently active orders by category
query.addOrderBy("cic.description")
query.addOrderBy("ci.description")
query.addOrderBy("relative_time_start")
else: # Otherwise chronologic order
query.addOrderBy("relative_time_start")
query.addOrderBy("cic.description")
query.addOrderBy("ci.description")
dataTable = DBUtil.execute(query,
includeColumnNames=True,
conn=conn)
dataModels = modelListFromTable(dataTable)
return dataModels
finally:
if not extConn:
conn.close()
def loadPendingResultOrders(self, patientId, relativeTime, conn=None):
"""Load all patient orders at the given relativeTime that
are due to yield results, but have not yet.
Include an estimate of time until results available.
"""
extConn = True
if conn is None:
conn = self.connFactory.connection()
extConn = False
try:
query = SQLQuery()
query.addSelect(
"distinct po.clinical_item_id"
) # Distinct so don't report multiple times for panel orders
query.addSelect("po.relative_time_start")
query.addSelect("po.relative_time_end")
query.addSelect("ci.name")
query.addSelect("ci.description")
query.addSelect(
"sorm.turnaround_time"
) # Could have different turnaround times for single order if different sub results. Just report each.
query.addSelect(
"sorm.turnaround_time - (%d - po.relative_time_start) as time_until_result"
% relativeTime) # Calculate time until expect result
query.addFrom("sim_patient_order as po")
query.addFrom("clinical_item as ci")
query.addFrom("sim_order_result_map as sorm")
query.addWhere("po.clinical_item_id = ci.clinical_item_id")
query.addWhere("po.clinical_item_id = sorm.clinical_item_id")
query.addWhereEqual("sim_patient_id", patientId)
# Only catch orders up to the given relativeTime and not cancelled
query.addWhereOp("relative_time_start", "<=", relativeTime)
query.openWhereOrClause()
query.addWhere("relative_time_end is null")
query.addWhereOp("relative_time_end", ">", relativeTime)
query.closeWhereOrClause()
# Only PENDING orders, so don't report orders who results should already be available
query.addWhereOp("sorm.turnaround_time + po.relative_time_start",
">", relativeTime)
query.addOrderBy("time_until_result")
query.addOrderBy("relative_time_start")
query.addOrderBy("ci.name")
dataTable = DBUtil.execute(query,
includeColumnNames=True,
conn=conn)
dataModels = modelListFromTable(dataTable)
return dataModels
finally:
if not extConn:
conn.close()
def loadIVAntibioticItemIds(extractor):
# ivMedCategoryId = 72;
ivMedCategoryId = DBUtil.execute("select clinical_item_category_id from clinical_item_category where description like '%%(Intravenous)'")[0][0];
# Look for any IV antibiotics based on expected names
query = SQLQuery();
query.addSelect("clinical_item_id");
query.addFrom("clinical_item");
query.addWhereEqual("analysis_status", 1);
query.addWhereEqual("clinical_item_category_id", ivMedCategoryId);
query.openWhereOrClause();
for row in extractor.loadMapData("IVAntibiotics.Names"):
query.addWhere("description ~* '%s'" % row["name"] );
query.closeWhereOrClause();
ivAntibioticItemIds = set();
for row in DBUtil.execute(query):
ivAntibioticItemIds.add(row[0]);
return ivAntibioticItemIds;
def loadPatientInfo(self, patientIds=None, relativeTime=None, conn=None):
"""Load basic information about the specified patients.
Report patient state at given time, or default to time zero
"""
if relativeTime is None:
relativeTime = 0
# Just look for time zero default then
extConn = True
if conn is None:
conn = self.connFactory.connection()
extConn = False
try:
query = SQLQuery()
query.addSelect("sp.sim_patient_id")
query.addSelect("sp.name")
query.addSelect("sp.age_years")
query.addSelect("sp.gender")
query.addSelect("s.sim_state_id")
query.addSelect("s.name as state_name")
query.addSelect("s.description as state_description")
query.addSelect("sps.relative_time_start")
query.addSelect("sps.relative_time_end")
query.addFrom("sim_patient as sp")
query.addFrom("sim_patient_state as sps")
query.addFrom("sim_state as s")
query.addWhere("sp.sim_patient_id = sps.sim_patient_id")
query.addWhere("sps.sim_state_id = s.sim_state_id")
if patientIds is not None:
query.addWhereIn("sp.sim_patient_id", patientIds)
# Look for the state that matches the given relative time offset
query.addWhereOp("sps.relative_time_start", "<=", relativeTime)
query.openWhereOrClause()
query.addWhere("sps.relative_time_end is null")
query.addWhereOp("sps.relative_time_end", ">", relativeTime)
query.closeWhereOrClause()
query.addOrderBy("sp.name")
dataTable = DBUtil.execute(query,
includeColumnNames=True,
conn=conn)
dataModels = modelListFromTable(dataTable)
if len(dataModels) > 0:
# Secondary query to build lookup table of possible state transition options from patient current states
subQuery = SQLQuery()
subQuery.addSelect("pre_state_id")
subQuery.addSelect("post_state_id")
subQuery.addSelect("clinical_item_id")
subQuery.addSelect("time_trigger")
subQuery.addFrom("sim_state_transition as sst")
subQuery.addWhereIn(
"pre_state_id",
columnFromModelList(dataModels, "sim_state_id"))
subResults = DBUtil.execute(subQuery, conn=conn)
# For each pre-state, track which clinical items or times trigger which post-states
postStateIdByItemIdByPreStateId = dict()
postStateIdTimeTriggerByPreStateId = dict()
for preStateId, postStateId, itemId, timeTrigger in subResults:
if preStateId not in postStateIdByItemIdByPreStateId:
postStateIdByItemIdByPreStateId[preStateId] = dict()
postStateIdByItemIdByPreStateId[preStateId][
itemId] = postStateId
if timeTrigger is not None:
postStateIdTimeTriggerByPreStateId[preStateId] = (
postStateId, timeTrigger)
# Record in patient result models for retrieval
for i, dataModel in enumerate(dataModels):
patientId = dataModel["sim_patient_id"]
stateId = dataModel["sim_state_id"]
dataModel["postStateIdByItemId"] = dict()
if stateId in postStateIdByItemIdByPreStateId:
dataModel[
"postStateIdByItemId"] = postStateIdByItemIdByPreStateId[
stateId]
dataModel["postStateIdTimeTriggerByPreStateId"] = dict()
if stateId in postStateIdTimeTriggerByPreStateId:
dataModel[
"postStateIdTimeTrigger"] = postStateIdTimeTriggerByPreStateId[
stateId]
if dataModel[
"relative_time_end"] is None and "postStateIdTimeTrigger" in dataModel:
# Check that we haven't passed (and should thus trigger) a time-based state transition
(postStateId,
timeTrigger) = dataModel["postStateIdTimeTrigger"]
preStateTime = dataModel["relative_time_start"]
postStateTriggerTime = (preStateTime + timeTrigger)
if postStateTriggerTime <= relativeTime: # Trigger state transition just by time elapsed
#print >> sys.stderr, relativeTime, preStateTime, stateId, postStateTriggerTime, postStateId
self.recordStateTransition(patientId,
stateId,
postStateId,
postStateTriggerTime,
conn=conn)
# State change which can yield new triggers, so recursively reload.
# Small risk of infinite recusion if timeTriggers are zero. Otherwise, should converge as each recursion will update the preState relativeTimeStart
dataModels[i] = self.loadPatientInfo([patientId],
relativeTime,
conn=conn)[0]
return dataModels
finally:
if not extConn:
conn.close()