def getNumberOfEvents(dbname, tablename):
db = utils.MySQLConnect(dbname)
cur = db.cursor()
cur.execute("""select COUNT( distinct EventID) from %s""" % tablename)
for row in cur.fetchall():
nbEvents = str(row[0])
#print "number of Events is %s" %nbEvents
return nbEvents
def getListOfEvents(dbname, tablename):
listEvents = []
db = utils.MySQLConnect(dbname)
cur = db.cursor()
cur.execute("""select distinct EventID from %s order by EventID""" %
tablename)
for row in cur.fetchall():
listEvents.append(str(row[0]))
return listEvents
def getlistAEROIDSinMapping(dbname, tablename):
listAERO_IDs = []
db = utils.MySQLConnect(dbname)
cur = db.cursor()
cur.execute("""SELECT distinct AERO_ID FROM %s order by AERO_ID""" %
tablename)
for row in cur.fetchall():
#AERO_term = URIRef("http://purl.obolibrary.org/obo/"+row[0])
listAERO_IDs.append(row[0])
return listAERO_IDs
def getListMappedAEROIDs(dbname, tablename):
a = {}
db = utils.MySQLConnect(dbname)
cur = db.cursor()
#get all the Meddra IDs in the mapping
cur.execute("""select distinct AERO_ID, llt1_code from %s""" % tablename)
for row in cur.fetchall():
mappedAEROID = str(row[0])
mappedMedDRATermID = str(row[1])
a[mappedMedDRATermID] = mappedAEROID
return a
def getMedDRANamesforeachEventID(dbname, table, EventID):
listMedDRANames = []
###print "event ID is", EventID
db = utils.MySQLConnect(dbname)
cur = db.cursor()
#get the rows from the mysql table
cur.execute('set profiling = 1')
try:
cur.execute("""SELECT EventID, llt1_code, llt1_name, llt2_code, llt2_name, llt3_code, llt3_name, llt4_code, llt4_name, llt5_code, llt5_name FROM %s WHERE EventID=%%s""" % table, (EventID))
except Exception:
cur.execute('show profiles')
for row in cur3:
print(row)
#browse result
for row in cur.fetchall():
listMedDRANames.append(str(row[2]))
listMedDRANames.append(str(row[4]))
listMedDRANames.append(str(row[6]))
listMedDRANames.append(str(row[8]))
listMedDRANames.append(str(row[10]))
return listMedDRANames