def updateDatabase(cmds):
dbServer = os.environ['MGD_DBSERVER']
dbName = os.environ['MGD_DBNAME']
dbUser = os.environ['MGD_DBUSER']
dbPasswordFile = os.environ['MGD_DBPASSWORDFILE']
dbPassword = string.strip(open(dbPasswordFile, 'r').readline())
db.set_sqlLogin(dbUser, dbPassword, dbServer, dbName)
# process in batches of 100
total = len(cmds)
try:
db.useOneConnection(1)
while cmds:
print('Current running time (secs): %s' %
(time.time() - STARTTIME))
db.sql(cmds[:100], 'auto')
cmds = cmds[100:]
db.useOneConnection(0)
except:
bailout('Failed during database updates')
print('Processed %d updates to SEQ_Sequence._SequenceStatus_key' % total)
print('Total running time (secs): %s' % (time.time() - STARTTIME))
return
def init():
# Purpose: initialize file descriptors, create connection to
# the database and load lookups
# Returns: nothing
# Assumes: nothing
# Effects: gives SQL commands to the database
# Throws: nothing
global inFile, outFile, nextKey
print('%s' % mgi_utils.date())
print('Initializing')
db.useOneConnection(1)
db.set_sqlLogin(user, password, mgdServer, mgdDB)
results = db.sql(
'''select max(_Assoc_key) + 1 as nextKey from %s''' % table, 'auto')
nextKey = results[0]['nextKey']
if nextKey == None:
nextKey = 1001
inFilePath = os.environ['INFILE_NAME']
try:
inFile = open(inFilePath, 'r')
except:
exit('Could not open file for reading %s\n' % inFilePath)
outFilePath = '%s/%s.bcp' % (os.environ['OUTPUTDIR'], table)
try:
outFile = open(outFilePath, 'w')
except:
exit('Could not open file for writing %s\n' % outFilePath)
loadLookups()
def init():
# Purpose: initialize file descriptors, create connection to
# the database and load lookups
# Returns: nothing
# Assumes: nothing
# Effects: gives SQL commands to the database
# Throws: nothing
global inFile, outFile, nextKey
print '%s' % mgi_utils.date()
print 'Initializing'
db.useOneConnection(1)
db.set_sqlLogin(user, password, mgdServer, mgdDB)
results = db.sql('''select max(_Assoc_key) + 1 as nextKey from %s''' % table, 'auto')
nextKey = results[0]['nextKey']
if nextKey == None:
nextKey = 1001
inFilePath = os.environ['INFILE_NAME']
try:
inFile = open(inFilePath, 'r')
except:
exit('Could not open file for reading %s\n' % inFilePath)
outFilePath = '%s/%s.bcp' % (os.environ['OUTPUTDIR'], table)
try:
outFile = open(outFilePath, 'w')
except:
exit('Could not open file for writing %s\n' % outFilePath)
loadLookups()
def setupSql (server, # str. name of database server
database, # str. name of database
username, # str. user with full permissions on database
password # str. password for 'username'
):
# Purpose: initialize the 'db' module to use the desired database
# login information
# Returns: nothing
# Assumes: the parameters are all valid
# Effects: initializes the 'db' module with the given login info, and
# tells it to use one connection (rather than a separate
# connection for each db.sql() call)
# Throws: nothing
db.set_sqlLogin (username, password, server, database)
db.useOneConnection(1)
return
def parseCommandArgs(): """ Reads in command line args, prints usage if necessary if successful, inits db and returns assayKey """ try: optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:K:') except: showUsage() server = None database = None user = None password = None assayKey = None for opt in optlist: if opt[0] == '-S': server = opt[1] elif opt[0] == '-D': database = opt[1] elif opt[0] == '-U': user = opt[1] elif opt[0] == '-P': password = string.strip(open(opt[1], 'r').readline()) elif opt[0] == '-K': assayKey = string.atoi(opt[1]) else: showUsage() if server is None or \ database is None or \ user is None or \ password is None or \ assayKey is None: showUsage() db.set_sqlLogin(user, password, server, database) return assayKey
def readCommandLine():
"""
Read command line input
returns options
"""
parser = OptionParser(usage=USAGE)
parser.add_option("-S", dest="dbServer")
parser.add_option("-D", dest="dbName")
parser.add_option("-U", dest="dbUser")
parser.add_option("-P", dest="passwordFile")
parser.add_option("-K", dest="evidenceKey")
(options, args) = parser.parse_args()
if options.dbServer or options.dbName \
or options.dbUser or options.passwordFile:
if not options.dbServer:
parser.error('Need to specify -S dbServer')
if not options.dbName:
parser.error('Need to specify -D dbName')
if not options.dbUser:
parser.error('Need to specify -U dbUser')
if not options.passwordFile:
parser.error('Need to specify -P passwordFile')
password = password = open(options.passwordFile, 'r').readline().strip()
# set the server and database settings
db.set_sqlLogin(options.dbUser, password, options.dbServer, options.dbName)
else:
# using default database options
pass
return options
user = opt[1]
elif opt[0] == '-P':
password = string.strip(open(opt[1], 'r').readline())
elif opt[0] == '-K':
objectKey = opt[1]
else:
showUsage()
if server is None or \
database is None or \
user is None or \
password is None or \
objectKey is None:
showUsage()
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
userKey = loadlib.verifyUser(user, 0, None)
# call functions based on the way the program is invoked
scriptName = os.path.basename(sys.argv[0])
# all of these invocations will only affect a certain subset of data
if scriptName == 'allelecombination.py':
processAll()
elif scriptName == 'allelecombinationByAllele.py':
processByAllele(objectKey)
def init():
'''
# requires:
#
# effects:
# 1. Processes command line options
# 2. Initializes local DBMS parameters
# 3. Initializes global file descriptors/file names
#
# returns:
#
'''
global inputFile, diagFile, errorFile, errorFileName, diagFileName
global passwordFileName
global noteFile, noteFileName, noteChunkFile, noteChunkFileName, sqlFile, sqlFileName
global mode
global noteTypeName
global objectTypeKey, createdByKey
global mgiObjects
try:
optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:M:I:O:T:')
except:
showUsage()
#
# Set server, database, user, passwords depending on options
# specified by user.
#
server = None
database = None
user = None
password = None
for opt in optlist:
if opt[0] == '-S':
server = opt[1]
elif opt[0] == '-D':
database = opt[1]
elif opt[0] == '-U':
user = opt[1]
elif opt[0] == '-P':
passwordFileName = opt[1]
elif opt[0] == '-M':
mode = opt[1]
elif opt[0] == '-I':
inputFileName = opt[1]
elif opt[0] == '-O':
objectType = opt[1]
elif opt[0] == '-T':
noteTypeName = re.sub('"', '', opt[1])
else:
showUsage()
# Initialize db.py DBMS parameters
password = string.strip(open(passwordFileName, 'r').readline())
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
head, tail = os.path.split(inputFileName)
diagFileName = tail + '.diagnostics'
errorFileName = tail + '.error'
noteFileName = tail + '.' + noteTable + '.bcp'
noteChunkFileName = tail + '.' + noteChunkTable + '.bcp'
sqlFileName = tail + '.sql'
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
diagFile = open(diagFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % diagFileName)
try:
errorFile = open(errorFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % errorFileName)
try:
noteFile = open(noteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteFileName)
try:
noteChunkFile = open(noteChunkFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteChunkFileName)
try:
sqlFile = open(sqlFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % sqlFileName)
# Set Log File Descriptor
try:
db.set_sqlLogFD(diagFile)
except:
pass
diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
diagFile.write('Server: %s\n' % (server))
diagFile.write('Database: %s\n' % (database))
diagFile.write('User: %s\n' % (user))
diagFile.write('Input File: %s\n' % (inputFileName))
diagFile.write('Object Type: %s\n' % (objectType))
diagFile.write('Note Type: %s\n' % (noteTypeName))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
objectTypeKey = accessionlib.get_MGIType_key(objectType)
createdByKey = loadlib.verifyUser(db.get_sqlUser(), 0, errorFile)
results = db.sql('''
select accID, _Object_key from ACC_Accession
where _MGIType_key = %s
and _LogicalDB_key = 1
and prefixPart = 'MGI:'
and preferred = 1
''' % (objectTypeKey), 'auto')
for r in results:
mgiObjects[r['accID']] = r['_Object_key']
def loadLookup():
global seqsToToggleList
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
cmds = []
# get eucomm mutant cell lines (MCLs)
cmds.append('''select c._CellLine_key
into temporary table eucommCL
from ALL_CellLine c, ALL_CellLine_Derivation d
where d._Creator_key = 4856374
and d._Derivation_key = c._Derivation_key''')
cmds.append('create index idx_1 on eucommCL(_CellLine_key)')
# get sequences associated with eucomm MCLs (via the allele)
cmds.append('''select t._CellLine_key, saa._Sequence_key
into temporary table eucommSeq
from eucommCL t, ALL_Allele_CellLine aac, SEQ_Allele_Assoc saa
where t._CellLine_key = aac._MutantCellLine_key
and aac._Allele_key = saa._Allele_key''')
cmds.append('create index idx_2 on eucommSeq(_Sequence_key)')
# filter for just the upstream vector end and get the seqID
cmds.append('''select t.*, a.accID
into temporary table eucommUpstSeq
from eucommSeq t, SEQ_GeneTrap sgt, ACC_Accession a
where t._Sequence_key = sgt._Sequence_key
and sgt._VectorEnd_key = 3983010
and sgt._Sequence_key = a._Object_key
and a._MGIType_key = 19
and a._LogicalDB_key = 9
and a.preferred = 1''')
# get tigem MCLs
cmds.append('''select c._CellLine_key
into temporary table tigemCL
from ALL_CellLine c, ALL_CellLine_Derivation d
where d._Creator_key = 3982963
and d._Derivation_key = c._Derivation_key''')
cmds.append('create index idx_3 on tigemCL(_CellLine_key)')
# get sequences associated with tigem MCLs (via allele)
cmds.append('''select t._CellLine_key, saa._Sequence_key
into temporary table tigemSeq
from tigemCL t, ALL_Allele_CellLine aac, SEQ_Allele_Assoc saa
where t._CellLine_key = aac._MutantCellLine_key
and aac._Allele_key = saa._Allele_key''')
cmds.append('create index idx_4 on tigemSeq(_Sequence_key)')
# get the seqID
cmds.append('''select t.*, a.accID
into temporary table tigemAccid
from tigemSeq t, ACC_Accession a
where t._Sequence_key = a._Object_key
and a._MGIType_key = 19
and a._LogicalDB_key = 9
and a.preferred = 1''')
# union the eucomm and tigem sets
cmds.append('''select t.accID
into temporary table allSets
from eucommUpstSeq t
union
select te.accID
from tigemAccid te''')
# load the lookup list
cmds.append('select distinct * from allSets')
results = db.sql(cmds, 'auto')
for r in results[11]:
seqID = r['accID']
seqsToToggleList.append(seqID)
def processArgs ():
# Purpose: process the command-line arguments to get us ready for
# real processing, including doing error-checking of the parms
# Returns: tuple with seven items -- list of strings (input lines),
# string (vocab name), integer (vocab key), string (J#),
# integer (reference key), integer (logical db key), string
# (logical db name)
# Assumes: the user account specified will have write privileges
# Modifies: reads from the file system, queries the database
# Throws: propagates SystemExit from bailout() if errors occur
if len(sys.argv) < 9:
bailout ('Too few command-line arguments')
elif len(sys.argv) > 9:
bailout ('Too many command-line arguments')
[ file, vocab, jnum, ldb, user, pwd, server, dbname ] = sys.argv[1:]
# see if we can read the input file, exit if not
try:
fp = open (file, 'r')
inputLines = map (string.strip, fp.readlines())
fp.close()
except:
bailout ('Cannot read input file: %s' % file)
# see if we can read the password file, exit if not
try:
fp = open (pwd, 'r')
password = fp.readline().strip()
fp.close()
except:
bailout ('Cannot read password file: %s' % pwd)
# see if we can log in to the database, exit if not
db.set_sqlLogin (user, password, server, dbname)
try:
db.sql ('SELECT COUNT(1) FROM MGI_dbInfo', 'auto')
except:
bailout ('Database login failed')
# try to look up the key for the given vocabulary name
results = db.sql ('''SELECT _Vocab_key, _Refs_key, _LogicalDB_key
FROM VOC_Vocab
WHERE name = '%s' ''' % vocab, 'auto')
if not results:
vocabKey = None
dbRefsKey = None
dbLdbKey = None
else:
vocabKey = results[0]['_Vocab_key']
dbRefsKey = results[0]['_Refs_key']
dbLdbKey = results[0]['_LogicalDB_key']
# try to look up the key for the given J#
results = db.sql ('''SELECT _Object_key
FROM ACC_Accession
WHERE _MGIType_key = 1 -- reference
AND _LogicalDB_key = 1 -- MGI
AND accID = '%s' ''' % jnum, 'auto')
if not results:
bailout ('Unknown reference ID: %s' % jnum)
refsKey = results[0]['_Object_key']
if dbRefsKey and (dbRefsKey != refsKey):
bailout ('Mismatching _Refs_key: %s has %d, vocab has %d' % \
(jnum, refsKey, dbRefsKey))
# confirm that ldb is a valid logical database key
try:
ldbKey = int(ldb)
except:
bailout ('Invalid _LogicalDB_key: %s not an integer' % ldb)
results = db.sql ('''SELECT name
FROM ACC_LogicalDB
WHERE _LogicalDB_key = %d''' % ldbKey, 'auto')
if not results:
bailout ('Unknown _LogicalDB_key: %d' % ldbKey)
ldbName = results[0]['name']
if dbLdbKey and (dbLdbKey != ldbKey):
bailout ('Mismatching _LogicalDB_key: vocab has %d, not %d' \
% (dbLdbKey, ldbKey))
return inputLines, vocab, vocabKey, jnum, refsKey, ldbKey, ldbName
def init():
'''
# requires:
#
# effects:
# 1. Processes command line options
# 2. Initializes local DBMS parameters
# 3. Initializes global file descriptors/file names
# 4. Initializes global keys
#
# returns:
#
'''
global inputFile, diagFile, errorFile, errorFileName, diagFileName
global passwordFileName, noteFileName
global exptFile, exptMarkerFile, accFile, noteFile
global inputFileName, exptFileName, exptMarkerFileName, accFileName
global mode, exptType
try:
optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:M:I:R:E:C:')
except:
showUsage()
#
# Set server, database, user, passwords depending on options
# specified by user.
#
server = ''
database = ''
user = ''
password = ''
inputFileName = ''
jnum = ''
createdBy = ''
for opt in optlist:
if opt[0] == '-S':
server = opt[1]
elif opt[0] == '-D':
database = opt[1]
elif opt[0] == '-U':
user = opt[1]
elif opt[0] == '-P':
passwordFileName = opt[1]
elif opt[0] == '-M':
mode = opt[1]
elif opt[0] == '-I':
inputFileName = opt[1]
elif opt[0] == '-E':
exptType = re.sub('"', '', opt[1])
else:
showUsage()
# User must specify Server, Database, User and Password
password = string.strip(open(passwordFileName, 'r').readline())
if server == '' or \
database == '' or \
user == '' or \
password == '' or \
mode == '' or \
inputFileName == '' or \
exptType == '':
showUsage()
# Initialize db.py DBMS parameters
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
diagFileName = 'mappingload.diag'
errorFileName = 'mappingload.error'
exptFileName = 'MLD_Expts.mapping.bcp'
exptMarkerFileName = 'MLD_Expt_Marker.mapping.bcp'
accFileName = 'ACC_Accession.mapping.bcp'
noteFileName = 'MLD_Notes.mapping.bcp'
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
diagFile = open(diagFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % diagFileName)
try:
errorFile = open(errorFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % errorFileName)
try:
exptFile = open(exptFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % exptFileName)
try:
exptMarkerFile = open(exptMarkerFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % exptMarkerFileName)
try:
accFile = open(accFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accFileName)
try:
noteFile = open(noteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteFileName)
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
# Set Log File Descriptor
db.set_commandLogFile(diagFileName)
diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
diagFile.write('Server: %s\n' % (server))
diagFile.write('Database: %s\n' % (database))
diagFile.write('User: %s\n' % (user))
diagFile.write('Input File: %s\n' % (inputFileName))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
def init():
# Purpose: process command line options
# Returns: nothing
# Assumes: nothing
# Effects: initializes global variables
# calls showUsage() if usage error
# exits if files cannot be opened
# Throws: nothing
global diagFile, reportFile, reportFileName, diagFileName, passwordFileName
global mode
try:
optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:')
except:
showUsage()
#
# Set server, database, user, passwords depending on options
# specified by user.
#
server = ''
database = ''
user = ''
password = ''
for opt in optlist:
if opt[0] == '-S':
server = opt[1]
elif opt[0] == '-D':
database = opt[1]
elif opt[0] == '-U':
user = opt[1]
elif opt[0] == '-P':
passwordFileName = opt[1]
else:
showUsage()
# User must specify Server, Database, User and Password
password = string.strip(open(passwordFileName, 'r').readline())
if server == '' or \
database == '' or \
user == '' or \
password == '':
showUsage()
# Initialize db.py DBMS parameters
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
head, tail = os.path.split(sys.argv[0])
diagFileName = os.environ['RUNTIME_DIR'] + '/' + tail + '.diagnostics'
reportFileName = tail + '.rpt'
try:
diagFile = open(diagFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % diagFileName)
try:
reportFile = reportlib.init(reportFileName, 'Deleted: Marker Annotations To Obsolete Terms', outputdir = os.environ['RUNTIME_DIR'])
except:
exit(1, 'Could not open file %s\n' % reportFileName)
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
# Set Log File Descriptor
#db.set_sqlLogFD(diagFile)
diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
diagFile.write('Server: %s\n' % (server))
diagFile.write('Database: %s\n' % (database))
diagFile.write('User: %s\n' % (user))
return
# - Added FILETYPE
#
import sys
import os
import db
#
# Main
#
server = os.environ['RADAR_DBSERVER']
database = os.environ['RADAR_DBNAME']
user = os.environ['RADAR_DBUSER']
passwordFileName = os.environ['RADAR_DBPASSWORDFILE']
password = str.strip(open(passwordFileName, 'r').readline())
jobStreamKey = os.environ['JOBSTREAMKEY']
fileName = os.environ['FILENAME']
fileType = os.environ['FILETYPE']
# Initialize db.py DBMS parameters
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
# Log the processed file
db.sql(
"select * from APP_logProcessedFile( %s, '%s', '%s')" %
(jobStreamKey, fileName, fileType), None)
db.commit()
db.useOneConnection(0)
def main():
global userKey
try:
optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:K:')
except:
showUsage()
server = None
database = None
user = None
password = None
objectKey = None
for opt in optlist:
if opt[0] == '-S':
server = opt[1]
elif opt[0] == '-D':
database = opt[1]
elif opt[0] == '-U':
user = opt[1]
elif opt[0] == '-P':
password = string.strip(open(opt[1], 'r').readline())
elif opt[0] == '-K':
objectKey = opt[1]
else:
showUsage()
if server is None or \
database is None or \
user is None or \
password is None or \
objectKey is None:
showUsage()
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
userKey = loadlib.verifyUser(user, 0, None)
# call functions based on the way the program is invoked
scriptName = os.path.basename(sys.argv[0])
# initialize the cre-system lookups
initCreSystems()
# all of these invocations will only affect a certain subset of data
if scriptName == 'allelecrecache.py':
processAll()
elif scriptName == 'allelecrecacheByAllele.py':
processByAllele(objectKey)
elif scriptName == 'allelecrecacheByAssay.py':
processByAssay(objectKey)
db.commit()
db.useOneConnection(0)
return
def init():
'''
# requires:
#
# effects:
# 1. Processes command line options
# 2. Initializes local DBMS parameters
# 3. Initializes global file descriptors/file names
# 4. Initializes global keys
#
# returns:
#
'''
global inputFile, diagFile, errorFile, errorFileName, diagFileName
global passwordFileName, noteFileName
global exptFile, exptMarkerFile, accFile, noteFile
global inputFileName, exptFileName, exptMarkerFileName, accFileName
global mode, exptType
try:
optlist, args = getopt.getopt(sys.argv[1:], 'S:D:U:P:M:I:R:E:C:')
except:
showUsage()
#
# Set server, database, user, passwords depending on options
# specified by user.
#
server = ''
database = ''
user = ''
password = ''
inputFileName = ''
jnum = ''
createdBy = ''
for opt in optlist:
if opt[0] == '-S':
server = opt[1]
elif opt[0] == '-D':
database = opt[1]
elif opt[0] == '-U':
user = opt[1]
elif opt[0] == '-P':
passwordFileName = opt[1]
elif opt[0] == '-M':
mode = opt[1]
elif opt[0] == '-I':
inputFileName = opt[1]
elif opt[0] == '-E':
exptType = re.sub('"', '', opt[1])
else:
showUsage()
# User must specify Server, Database, User and Password
password = str.strip(open(passwordFileName, 'r').readline())
if server == '' or \
database == '' or \
user == '' or \
password == '' or \
mode == '' or \
inputFileName == '' or \
exptType == '':
showUsage()
# Initialize db.py DBMS parameters
db.set_sqlLogin(user, password, server, database)
db.useOneConnection(1)
diagFileName = 'mappingload.diag'
errorFileName = 'mappingload.error'
exptFileName = 'MLD_Expts.mapping.bcp'
exptMarkerFileName = 'MLD_Expt_Marker.mapping.bcp'
accFileName = 'ACC_Accession.mapping.bcp'
noteFileName = 'MLD_Notes.mapping.bcp'
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
diagFile = open(diagFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % diagFileName)
try:
errorFile = open(errorFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % errorFileName)
try:
exptFile = open(exptFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % exptFileName)
try:
exptMarkerFile = open(exptMarkerFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % exptMarkerFileName)
try:
accFile = open(accFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accFileName)
try:
noteFile = open(noteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteFileName)
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
# Set Log File Descriptor
db.set_commandLogFile(diagFileName)
diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
diagFile.write('Server: %s\n' % (server))
diagFile.write('Database: %s\n' % (database))
diagFile.write('User: %s\n' % (user))
diagFile.write('Input File: %s\n' % (inputFileName))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
