DESCRIPTION_PREFIXES = \
[ "A","B","C","D","E","F","G","H","I",
]
specificArgvList = \
[
]
for medRoute in ROUTE_LIST:
for descriptionPrefix in DESCRIPTION_PREFIXES:
specificArgv = [
"-r", medRoute, "-d", descriptionPrefix,
"results/queryResults.%s.%s.tab" % (descriptionPrefix, medRoute)
]
specificArgvList.append(specificArgv)
prog = ProgressDots(1, 1, "Processes", total=len(specificArgvList))
for specificArgv in specificArgvList:
key = "%.3d.%s" % (prog.getCounts(), str.join("_", specificArgv))
key = key.replace("/", "..")
# Don't want to use directory separator in temp log file name
argv = list(baseArgv)
argv.extend(specificArgv)
log.info("Starting: " + str.join(" ", argv))
logFile = stdOpen(LOG_FILE_TEMPLATE % key, "w")
# Blocking sub-process call if want serial processes.
#subprocess.call(argv, stderr=logFile);
# Non-blocking subprocess.Popen to spawn parallel processes
process = subprocess.Popen(argv, stderr=logFile)
log.info("Process ID: %s" % process.pid)
def syncTable(sourceConn,
targetConn,
syncTableName,
rowIDStrSet=None,
formatter=None):
if formatter is None:
idCol = DBUtil.defaultIDColumn(syncTableName)
idQuery = "select %s from %s" % (idCol, syncTableName)
# Collect all of the IDs known in the target database and store in memory for rapid lookup
print("Querying for IDs from Target Database", file=sys.stderr)
targetIdTable = DBUtil.execute(idQuery, conn=targetConn)
targetIdSet = set()
for row in targetIdTable:
targetId = row[0]
targetIdSet.add(targetId)
# Query data out of the source table, but do it by a cursor so we can stream through large data tables
print("Querying for Source Data", file=sys.stderr)
dataQuery = "select * from %s" % (syncTableName)
sourceCursor = sourceConn.cursor()
sourceCursor.execute(dataQuery)
colNames = DBUtil.columnNamesFromCursor(sourceCursor)
targetCursor = targetConn.cursor()
insertQuery = None
updateQuery = None
progress = ProgressDots()
row = sourceCursor.fetchone()
while row is not None:
dataModel = RowItemModel(row, colNames)
if rowIDStrSet is None or str(dataModel[idCol]) in rowIDStrSet:
if rowIDStrSet is not None:
print("Syncing record: %s" % dataModel[idCol],
file=sys.stderr)
if dataModel[idCol] not in targetIdSet:
# Row does not yet exist in target database, need to insert it
if insertQuery is None:
insertQuery = DBUtil.buildInsertQuery(
syncTableName, list(dataModel.keys()))
insertParams = list(dataModel.values())
targetCursor.execute(insertQuery, insertParams)
else:
# Row already exists in target database, just update values
if updateQuery is None:
updateQuery = DBUtil.buildUpdateQuery(
syncTableName, list(dataModel.keys()))
updateParams = []
updateParams.extend(list(dataModel.values()))
updateParams.append(dataModel[idCol])
targetCursor.execute(updateQuery, updateParams)
if progress.GetCounts() % progress.big == 0:
targetConn.commit()
row = sourceCursor.fetchone()
progress.Update()
progress.PrintStatus()
targetConn.commit()
else:
##Do something with thr formatter
##Set up the formatter
theFormatter = formatter(syncTableName,
targetConn,
includeColumnNames=True,
autoCommit=True)
#Call DB execute
res = DBUtil.execute("select * from %s" % syncTableName,
includeColumnNames=True,
conn=sourceConn,
formatter=theFormatter)
stopWords = set(stopWordFile.read().split())
countPerToken = dict()
conn = DBUtil.connection()
cursor = conn.cursor()
try:
query = \
"""select stride_pager_message_id, date_entered, messaging_id, name, message_text
from stride_pager_message
where message_text !~ 'covering for ID'
limit 100000
"""
cursor.execute(query)
prog = ProgressDots()
row = cursor.fetchone()
while row is not None:
pagerText = row[-1]
tokens = pagerText.split()
for iToken, token in enumerate(tokens):
tokens[iToken] = token.strip("#?:!.,;").lower()
# Remove flanking punctuations. Case insensitive
for token in tokens:
if token not in stopWords and len(
token) > 1: # Skip stop words and single character words
if token not in countPerToken:
countPerToken[token] = 0
countPerToken[token] += 1
row = cursor.fetchone()
prog.update()
def queryPatientEpisodes(outputFile, extractor):
log.info(
"Select patient admissions with provider category of Tt Pamf Med (Primary) or Tt Med Univ (Primary)"
)
conn = DBUtil.connection()
cursor = conn.cursor()
try:
# # Clinical item category for admission diagnoses
# # ADMIT_DX_CATEGORY_ID = 2;
# admitDxCategoryId = DBUtil.execute("select clinical_item_category_id from clinical_item_category where description like '%%ADMIT_DX%%'", conn=conn)[0][0];
# # Look for items indicating suspected infection / sepsis
# ivAntibioticItemIds = loadIVAntibioticItemIds(extractor);
# bloodCultureItemIds = loadBloodCultureItemIds(extractor);
# respiratoryViralPanelItemIds = loadRespiratoryViralPanelItemIds(extractor);
# # Merge IV antibiotics and blood cultures, respiratory panels as items that suggest sepsis is suspected
# suspectSepsisItemIds = ivAntibioticItemIds.union(bloodCultureItemIds.union(respiratoryViralPanelItemIds));
# suspectSepsisItemIdsStr = str.join(',', [str(itemId) for itemId in suspectSepsisItemIds]); # Convert to comma-separated string via a str.join function on list contracture
# # Look for primary surgery teams to exclude
# excludeTeamCategory = "SurgerySpecialty";
# excludeTreatmentTeams = list();
# for row in extractor.loadMapData("TreatmentTeamGroups"):
# if row["team_category"] == excludeTeamCategory:
# excludeTreatmentTeams.append(row["treatment_team"]);
# query = SQLQuery();
# query.addSelect("clinical_item_id");
# query.addFrom("clinical_item");
# query.addWhereIn("description", excludeTreatmentTeams );
# excludeTeamItemIds = set();
# for row in DBUtil.execute(query, conn=conn):
# excludeTeamItemIds.add(row[0]);
# excludeTeamItemIdsStr = str.join(',', [str(itemId) for itemId in excludeTeamItemIds]); # Convert to comma-separated string via a str.join function on list contracture
# First pass query to get the list of patients and emergency department presentation times
cohortQuery = \
"""
select adt1.pat_anon_id, adt1.pat_enc_csn_anon_id, adt1.shifted_transf_in_dt_tm as edAdmitTime, adt2.shifted_transf_out_dt_tm as dischargeTime
from stride_adt as adt1, stride_adt as adt2
where
adt1.pat_anon_id in
(select patient_id from patient_item inner join clinical_item on patient_item.clinical_item_id = clinical_item.clinical_item_id where clinical_item.clinical_item_category_id = 161 AND clinical_item.description = '%s')
and adt1.pat_enc_csn_anon_id = adt2.pat_enc_csn_anon_id
""" % ("Tt Pamf Med (Primary)")
print >> sys.stderr, cohortQuery
cursor.execute(cohortQuery)
patientEpisodes = list()
patientEpisodeById = dict()
# Collect Build basic patient ID and
# ED presentation dates and Discharge date/time
prog = ProgressDots()
row = cursor.fetchone()
while row is not None:
(patientId, encounterId, edAdmitTime, dischargeTime) = row
#patientId = int(patientId);
patientEpisode = \
RowItemModel \
( { "patient_id":patientId,
"edAdmitTime":edAdmitTime,
"dischargeTime":dischargeTime,
"encounter_id":encounterId,
"payorTitle": None, # Default encounter data to null in case can't find it later
"bpSystolic": None,
"bpDiastolic": None,
"temperature": None,
"pulse": None,
"respirations": None,
}
)
patientEpisodes.append(patientEpisode)
if patientEpisode["encounter_id"] not in patientEpisodeById:
patientEpisodeById[
patientEpisode["encounter_id"]] = patientEpisode
prog.update()
row = cursor.fetchone()
prog.printStatus()
# Second query phase to link to encounter information (e.g., insurance, admitting vital signs)
encounterIds = columnFromModelList(patientEpisodes, "encounter_id")
query = SQLQuery()
query.addSelect("pat_id")
query.addSelect("pat_enc_csn_id")
query.addSelect("title")
query.addSelect("bp_systolic")
query.addSelect("bp_diastolic")
query.addSelect("temperature")
query.addSelect("pulse")
query.addSelect("respirations")
query.addFrom("stride_patient_encounter")
query.addWhereIn("pat_enc_csn_id", encounterIds)
cursor.execute(str(query), query.params)
row = cursor.fetchone()
while row is not None:
(patientId, encounterId, payorTitle, bpSystolic, bpDiastolic,
temperature, pulse, respirations) = row
if encounterId in patientEpisodeById:
patientEpisode = patientEpisodeById[encounterId]
if patientEpisode["payorTitle"] is None:
patientEpisode["payorTitle"] = set()
# Single encounters may have multiple payors to track
patientEpisode["payorTitle"].add(payorTitle)
patientEpisode["bpSystolic"] = bpSystolic
patientEpisode["bpDiastolic"] = bpDiastolic
patientEpisode["temperature"] = temperature
patientEpisode["pulse"] = pulse
patientEpisode["respirations"] = respirations
row = cursor.fetchone()
# Drop results as tab-delimited text output
formatter = TextResultsFormatter(outputFile)
formatter.formatResultDicts(patientEpisodes, addHeaderRow=True)
return patientEpisodes
finally:
cursor.close()
conn.close()
def queryPatientEpisodes(outputFile, extractor):
log.info(
"Select patient admissions with possible/probable sepsis within 24 hours of admission (long query >60 min?)..."
)
conn = DBUtil.connection()
cursor = conn.cursor()
try:
# Clinical item category for admission diagnoses
# ADMIT_DX_CATEGORY_ID = 2;
admitDxCategoryId = DBUtil.execute(
"select clinical_item_category_id from clinical_item_category where description like '%%ADMIT_DX%%'",
conn=conn)[0][0]
# Look for items indicating suspected infection / sepsis
ivAntibioticItemIds = loadIVAntibioticItemIds(extractor)
bloodCultureItemIds = loadBloodCultureItemIds(extractor)
respiratoryViralPanelItemIds = loadRespiratoryViralPanelItemIds(
extractor)
# Merge IV antibiotics and blood cultures, respiratory panels as items that suggest sepsis is suspected
suspectSepsisItemIds = ivAntibioticItemIds.union(
bloodCultureItemIds.union(respiratoryViralPanelItemIds))
suspectSepsisItemIdsStr = str.join(
',', [str(itemId) for itemId in suspectSepsisItemIds])
# Convert to comma-separated string via a str.join function on list contracture
# Look for primary surgery teams to exclude
excludeTeamCategory = "SurgerySpecialty"
excludeTreatmentTeams = list()
for row in extractor.loadMapData("TreatmentTeamGroups"):
if row["team_category"] == excludeTeamCategory:
excludeTreatmentTeams.append(row["treatment_team"])
query = SQLQuery()
query.addSelect("clinical_item_id")
query.addFrom("clinical_item")
query.addWhereIn("description", excludeTreatmentTeams)
excludeTeamItemIds = set()
for row in DBUtil.execute(query, conn=conn):
excludeTeamItemIds.add(row[0])
excludeTeamItemIdsStr = str.join(
',', [str(itemId) for itemId in excludeTeamItemIds])
# Convert to comma-separated string via a str.join function on list contracture
# First pass query to get the list of patients and emergency department presentation times
cohortQuery = \
"""
-- Pick out date(s) when admitted through emergency department and matching discharge time
select adt1.pat_anon_id, adt1.pat_enc_csn_anon_id, adt1.shifted_transf_in_dt_tm as edAdmitTime, adt2.shifted_transf_out_dt_tm as dischargeTime
from stride_adt as adt1, stride_adt as adt2
where
-- Admission event
adt1.department_in = 'EMERGENCY DEPARTMENT' and
adt1.event_in = 'Admission' and
adt1.pat_anon_id in
( -- Select any patient with any suspected sepsis related order (i.e., IV antibiotics or blood cultures)
-- select patient_id
-- from patient_item as pi
-- where pi.clinical_item_id in (%s)
-- except
-- -- Exclude any patient who has been on a primary surgery team
-- select patient_id
-- from patient_item
-- where clinical_item_id in (%s)
-12434586418575,-12432455207729,-12428492282572,-12428492282572,-12424048595257,-12414081679705
) and
adt1.pat_enc_csn_anon_id = adt2.pat_enc_csn_anon_id and
-- Discharge event
adt2.event_out = 'Discharge'
order by adt1.shifted_transf_in_dt_tm
""" % (suspectSepsisItemIdsStr, excludeTeamItemIdsStr)
print >> sys.stderr, cohortQuery
cursor.execute(cohortQuery)
patientEpisodes = list()
patientEpisodeById = dict()
# Collect Build basic patient ID and
# ED presentation dates and Discharge date/time
prog = ProgressDots()
row = cursor.fetchone()
while row is not None:
(patientId, encounterId, edAdmitTime, dischargeTime) = row
#patientId = int(patientId);
patientEpisode = \
RowItemModel \
( { "patient_id":patientId,
"edAdmitTime":edAdmitTime,
"dischargeTime":dischargeTime,
"encounter_id":encounterId,
"payorTitle": None, # Default encounter data to null in case can't find it later
"bpSystolic": None,
"bpDiastolic": None,
"temperature": None,
"pulse": None,
"respirations": None,
}
)
patientEpisodes.append(patientEpisode)
if patientEpisode["encounter_id"] not in patientEpisodeById:
patientEpisodeById[
patientEpisode["encounter_id"]] = patientEpisode
prog.update()
row = cursor.fetchone()
prog.printStatus()
# Second query phase to link to encounter information (e.g., insurance, admitting vital signs)
encounterIds = columnFromModelList(patientEpisodes, "encounter_id")
query = SQLQuery()
query.addSelect("pat_id")
query.addSelect("pat_enc_csn_id")
query.addSelect("title")
query.addSelect("bp_systolic")
query.addSelect("bp_diastolic")
query.addSelect("temperature")
query.addSelect("pulse")
query.addSelect("respirations")
query.addFrom("stride_patient_encounter")
query.addWhereIn("pat_enc_csn_id", encounterIds)
cursor.execute(str(query), query.params)
row = cursor.fetchone()
while row is not None:
(patientId, encounterId, payorTitle, bpSystolic, bpDiastolic,
temperature, pulse, respirations) = row
if encounterId in patientEpisodeById:
patientEpisode = patientEpisodeById[encounterId]
if patientEpisode["payorTitle"] is None:
patientEpisode["payorTitle"] = set()
# Single encounters may have multiple payors to track
patientEpisode["payorTitle"].add(payorTitle)
patientEpisode["bpSystolic"] = bpSystolic
patientEpisode["bpDiastolic"] = bpDiastolic
patientEpisode["temperature"] = temperature
patientEpisode["pulse"] = pulse
patientEpisode["respirations"] = respirations
row = cursor.fetchone()
# Drop results as tab-delimited text output
formatter = TextResultsFormatter(outputFile)
formatter.formatResultDicts(patientEpisodes, addHeaderRow=True)
return patientEpisodes
finally:
cursor.close()
conn.close()
from medinfo.db import DBUtil;
from medinfo.db.Model import SQLQuery;
from medinfo.common.Util import ProgressDots;
from medinfo.common.Util import log;
conn = DBUtil.connection();
try:
results = DBUtil.execute("select clinical_item_id from clinical_item where clinical_item_category_id = 161",conn=conn);
clinicalItemIds = tuple([row[0] for row in results]);
log.info("Deleting for %s Clinical Items" % len(clinicalItemIds) );
query = SQLQuery();
query.addSelect("patient_item_id");
query.addFrom("patient_item");
query.addWhereIn("clinical_item_id", clinicalItemIds );
prog = ProgressDots();
prog.total = DBUtil.execute(query.totalQuery(), conn=conn)[0][0];
# Go ahead and load full result set into memory, so don't have potential concurrency issues with deleting items as traversing them
results = DBUtil.execute(query, conn=conn );
for row in results:
patientItemId = row[0];
DBUtil.execute("delete from patient_item where patient_item_id = %s", (patientItemId,), conn=conn);
prog.update();
prog.printStatus();
finally:
conn.close();
"""Helped script for parallel process debugging. Just takes one parameter, sleeps for that many seconds, then completes"""
import sys
from medinfo.common.Util import ProgressDots
import time
duration = int(sys.argv[1])
progress = ProgressDots()
for i in xrange(duration):
progress.update()
progress.printStatus()
def __call__(self, analysisQuery, conn=None):
"""Go through the validation file to assess order set usage amongst test cases
"""
extConn = True
if conn is None:
conn = self.connFactory.connection()
extConn = False
try:
conn = DBUtil.connection()
preparer = PreparePatientItems()
progress = ProgressDots(50, 1, "Patients")
for patientItemData in preparer.loadPatientItemData(analysisQuery):
patientId = patientItemData["patient_id"]
analysisResults = \
self.analyzePatientItems \
( patientItemData,
analysisQuery,
analysisQuery.baseRecQuery,
patientId,
analysisQuery.recommender,
conn=conn
)
if analysisResults is not None:
(queryItemCountById, verifyItemCountById,
recommendedItemIds, recommendedData,
orderSetItemData) = analysisResults
# Unpack results
# Start aggregating and calculating result stats
resultsStatData = self.calculateResultStats(
patientItemData, queryItemCountById,
verifyItemCountById, recommendedItemIds,
self.supportRecommender.patientCountByItemId,
analysisQuery.baseRecQuery, recommendedData)
resultsStatData["usedOrderSetIds"] = orderSetItemData[
"allUsedOrderSetIds"]
resultsStatData["numUsedOrderSets"] = len(
orderSetItemData["allUsedOrderSetIds"])
resultsStatData["numUsedOrderSetItems"] = len(
orderSetItemData["allUsedOrderSetItemIds"])
resultsStatData["numAvailableOrderSetItems"] = len(
orderSetItemData["allAvailableOrderSetItemIds"])
resultsStatData["numRecommendableUsedOrderSetItems"] = len(
orderSetItemData["recommendableUsedOrderSetItemIds"])
resultsStatData[
"numRecommendableAvailableOrderSetItems"] = len(
orderSetItemData[
"recommendableAvailableOrderSetItemIds"])
resultsStatData["numRecommendableQueryItems"] = len(
orderSetItemData["recommendableQueryItemIds"])
resultsStatData["numRecommendableVerifyItems"] = len(
orderSetItemData["recommendableVerifyItemIds"])
resultsStatData["numRecommendableQueryVerifyItems"] = len(
orderSetItemData["recommendableQueryItemIds"]
| orderSetItemData["recommendableVerifyItemIds"])
# Union of two sets
resultsStatData["orderSetItemUsageRate"] = 0.0
if resultsStatData["numAvailableOrderSetItems"] > 0:
resultsStatData["orderSetItemUsageRate"] = float(
resultsStatData["numUsedOrderSetItems"]
) / resultsStatData["numAvailableOrderSetItems"]
resultsStatData[
"recommendableQueryVerifyItemFromOrderSetRate"] = 0.0
if resultsStatData["numRecommendableQueryVerifyItems"] > 0:
resultsStatData[
"recommendableQueryVerifyItemFromOrderSetRate"] = float(
resultsStatData[
"numRecommendableUsedOrderSetItems"]
) / resultsStatData[
"numRecommendableQueryVerifyItems"]
yield resultsStatData
progress.Update()
# progress.PrintStatus();
finally:
if not extConn:
conn.close()