def init():
	#
	# requires: 
	#
	# effects: 
	# 1. Processes command line options
	# 2. Initializes global file descriptors/file names
	#
	# returns:
	#
 
    global diagFile, errorFile
 
    db.useOneConnection(1)
 
    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)
		
    # 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()))
    errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))

def init():
	#
	# requires: 
	#
	# effects: 
	# 1. Processes command line options
	# 2. Initializes global file descriptors/file names
	#
	# returns:
	#
 
    global diagFile, errorFile, diagFileName, errorFileName
 
    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)
		
    diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
    errorFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))

def exit(status, message = None):
	'''
	# requires: status, the numeric exit status (integer)
	#           message (string)
	#
	# effects:
	# Print message to stderr and exits
	#
	# returns:
	#
	'''
 
	if message is not None:
		sys.stderr.write('\n' + str(message) + '\n')
 
	try:
		inputFile.close()
		outputFile.close()
		diagFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
		errorFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
		diagFile.close()
		errorFile.close()
	except:
		pass

	db.useOneConnection()
	sys.exit(status)

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, outputFile, diagFile, errorFile, errorFileName, diagFileName
 
	db.useOneConnection(1)
        db.set_sqlUser(user)
        db.set_sqlPasswordFromFile(passwordFileName)
 
	diagFileName = inputFileName + '.diagnostics'
	errorFileName = inputFileName + '.error'
 	outputFileName = inputFileName + '.trans'

	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:
		outputFile = open(outputFileName, 'w')
	except:
		exit(1, 'Could not open file %s\n' % outputFileName)
		
	# 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' % (db.get_sqlServer()))
        diagFile.write('Database: %s\n' % (db.get_sqlDatabase()))
	diagFile.write('Input File: %s\n' % (inputFileName))
	diagFile.write('Output File: %s\n' % (outputFileName))

	errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))

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 diagFile, errorFile, inputFile, errorFileName, diagFileName
    global strainFile
 
    db.useOneConnection(1)
    db.set_sqlUser(user)
    db.set_sqlPasswordFromFile(passwordFileName)
 
    fdate = mgi_utils.date('%m%d%Y')	# current date
    head, tail = os.path.split(inputFileName) 
    diagFileName = tail + '.' + fdate + '.diagnostics'
    errorFileName = tail + '.' + fdate + '.error'

    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:
        inputFile = open(inputFileName, 'r')
    except:
        exit(1, 'Could not open file %s\n' % inputFileName)

    try:
        strainFile = open(strainFileName, 'w')
    except:
        exit(1, 'Could not open file %s\n' % strainFileName)

    # 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' % (db.get_sqlServer()))
    diagFile.write('Database: %s\n' % (db.get_sqlDatabase()))

    errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))

    return

def init():
    global bcpCommand
    global diagFile, errorFile, inputFile, errorFileName, diagFileName
    global markerFile, refFile, aliasFile
 
    db.useOneConnection(1)
    db.set_sqlUser(user)
    db.set_sqlPasswordFromFile(passwordFileName)
 
    bcpCommand = bcpCommand + db.get_sqlServer() + ' ' + db.get_sqlDatabase() + ' %s ' + currentDir + ' %s "\\t" "\\n" mgd'

    head, tail = os.path.split(inputFileName) 

    diagFileName = outputDir + '/' + tail + '.diagnostics'
    errorFileName = outputDir + '/' + tail + '.error'

    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:
        inputFile = open(inputFileName, 'r')
    except:
        exit(1, 'Could not open file %s\n' % inputFileName)

    try:
        markerFile = open(markerFileName, 'w')
    except:
        exit(1, 'Could not open file %s\n' % markerFileName)

    try:
        refFile = open(refFileName, 'w')
    except:
        exit(1, 'Could not open file %s\n' % refFileName)

    try:
        aliasFile = open(aliasFileName, 'w')
    except:
        exit(1, 'Could not open file %s\n' % aliasFileName)

    # Log all SQL
    db.set_sqlLogFunction(db.sqlLogAll)

    diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
    diagFile.write('Server: %s\n' % (db.get_sqlServer()))
    diagFile.write('Database: %s\n' % (db.get_sqlDatabase()))

    errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))

    return

def createExcluded():

    excludeNote = 'The source of the material used to create this cDNA probe was different than that used to create the GenBank sequence record.'

    print 'excluded begin...%s' % (mgi_utils.date())
    db.sql('''select _Probe_key INTO TEMPORARY TABLE excluded from PRB_Notes 
	where note like 'The source of the material used to create this cDNA probe was different%'
	''', None)
    db.sql('create index idx1 on excluded(_Probe_key)', None)
    print 'excluded end...%s' % (mgi_utils.date())

def init():
    '''
    # requires: 
    #
    # effects: 
    # 1. Processes command line options
    # 2. Initializes local DBMS parameters
    # 3. Initializes global file descriptors/file names
    #
    # returns:
    #
    '''

    global inputFile, outputFile, diagFile, errorFile
    global inputFileName, errorFileName, diagFileName, outputFileName

    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:
	outputFile = open(outputFileName, 'w')
    except:
	exit(1, 'Could not open file %s\n' % outputFileName)
	    
    # Log all SQL 
    db.set_sqlLogFunction(db.sqlLogAll)

    # Set Log File Descriptor
    db.set_commandLogFile(diagFileName)

    # Set Log File Descriptor
    diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
    diagFile.write('Server: %s\n' % (db.get_sqlServer()))
    diagFile.write('Database: %s\n' % (db.get_sqlDatabase()))
    diagFile.write('Input File: %s\n' % (inputFileName))
    errorFile.write('\nStart file: %s\n\n' % (mgi_utils.date()))

def init():
    global inFile, provider, bcpFilePath, bcpFile

    print '%s' % mgi_utils.date()
    print 'Initializing'

    inFile = sys.stdin
    if len(sys.argv) != 2:
            print Usage
            sys.exit(1)

    provider = sys.argv[1]
    try:
        bcpFilePath = os.environ['BCP_FILE_PATH']
        bcpFile = open(bcpFilePath, 'w')
    except:
        'Could not open file for writing %s\n' % bcpFilePath
        sys.exit(1)

    if provider == 'ensembl':
        loadEnsemblRawBioTypeByGMIDLookup()

    elif provider == 'ncbi':
        loadNCBIRawBioTypeByGMIDLookup()

    else:
        'Provider not recognized: %s' % provider
        sys.exit(1)
    loadSequenceKeyLookup()
    loadMarkerTypeKeyLookup()

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 run():
    # Purpose: iterate through the input file, resolving to keys
    #  and writing to a bcp file
    # Returns: nothing
    # Assumes: inFile and outFile are valid file descriptors
    # Effects: writes to the file system
    # Throws: nothing

    global nextKey
    print '%s' % mgi_utils.date()
    print 'Creating bcp file'
    for line in inFile.readlines():
        (seqId1, qualifier, seqId2) = string.split(line, TAB)
	seqId1 = string.strip(seqId1)
	qualifier = string.strip(qualifier)
	seqId2 = string.strip(seqId2)
        if seq1Lookup.has_key(seqId1):
	    seqKey1 = seq1Lookup[seqId1]
	else:
	    print 'SeqId1 %s is not in the database' % seqId1
	    continue
	if qualLookup.has_key(qualifier):
	    qualKey = qualLookup[qualifier]
	else:
	    print 'Qualifier %s is not in the database' % qualifier
	    continue 
 	if seq2Lookup.has_key(seqId2):
	    seqKey2 = seq2Lookup[seqId2]
	else:
            print 'SeqId2 %s is not in the database' % seqId2
	    continue
	outFile.write('%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s%s' % \
	    (nextKey, TAB, seqKey1, TAB, qualKey, TAB, seqKey2, \
		TAB, CREATEDBY_KEY, TAB, CREATEDBY_KEY, TAB, cdate, TAB, cdate, CRT))
	nextKey = nextKey + 1

def exit(
    status,          # numeric exit status (integer)
    message = None   # exit message (string)
    ):

    # Purpose:
    # Returns: nothing
    # Assumes: nothing
    # Effects: nothing
    # Throws: nothing

    if message is not None:
        sys.stderr.write('\n' + str(message) + '\n')
 
    try:
        diagFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
        diagFile.close()
    except:
        pass

    try:
        reportlib.finish_nonps(reportFile)
    except:
	pass

    db.useOneConnection(0)
    sys.exit(status)

def exit(status, message = None):
	'''
	# requires: status, the numeric exit status (integer)
	#           message (string)
	#
	# effects:
	# Print message to stderr and exits
	#
	# returns:
	#
	'''
 
	if message is not None:
		sys.stderr.write('\n' + str(message) + '\n')
 
	try:
                diagFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
		diagFile.close()
		accFile.close()
		accrefFile.close()
		markerFile.close()
	except:
		pass

	sys.exit(status)

def exit(
    status,          # numeric exit status (integer)
    message = None   # exit message (string)
    ):

    if message is not None:
        sys.stderr.write('\n' + str(message) + '\n')
 
    try:
        diagFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
        errorFile.write('\n\nEnd Date/Time: %s\n' % (mgi_utils.date()))
        diagFile.close()
        errorFile.close()
    except:
        pass

    db.useOneConnection(0)
    sys.exit(status)

def deleteByUser():
    # Purpose: delete records created by current load
    # Returns: nothing
    # Assumes: a connection has been made to the database
    # Effects: deletes records from a database
    # Throws: nothing

    print '%s' % mgi_utils.date()
    print 'Deleting records for this user'
    db.sql('''delete from %s where _CreatedBy_key = %s''' % (table, CREATEDBY_KEY), None)
    db.commit()

def createBCP():

	outBCP = open('%s/%s.bcp' % (datadir, table), 'w')

	print 'sequences1 begin...%s' % (mgi_utils.date())
	db.sql('''select s._Object_key as sequenceKey, p._Object_key as probeKey, p._Accession_key 
		INTO TEMPORARY TABLE sequences1 
		from ACC_Accession s, ACC_Accession p 
		where s._MGIType_key = 19 
		and lower(s.accID) = lower(p.accID) 
		and p._MGIType_key = 3 
		and s._LogicalDB_key = p._LogicalDB_key
		''', None)
	db.sql('create index idx2 on sequences1 (sequenceKey)', None)
	db.sql('create index idx3 on sequences1 (probeKey)', None)
	db.sql('create index idx4 on sequences1 (_Accession_key)', None)
	print 'sequences1 end...%s' % (mgi_utils.date())

	print 'deletion begin...%s' % (mgi_utils.date())
	db.sql('delete from sequences1 using excluded e where sequences1.probeKey = e._Probe_key', None)
	print 'deletion end...%s' % (mgi_utils.date())
	db.commit()

	print 'sequences2 begin...%s' % (mgi_utils.date())
	db.sql('''select s.sequenceKey, s.probeKey, ar._Refs_key as refskey, 
			ar._ModifiedBy_key as userKey, ar.modification_date as mdate 
		INTO TEMPORARY TABLE sequences2 
		from sequences1 s, ACC_AccessionReference ar 
		where s._Accession_key = ar._Accession_key
		''', None)
	db.sql('create index idx5 on sequences2 (sequenceKey, probeKey, refsKey, userKey, mdate)', None)
	db.sql('create index idx6 on sequences2 (userKey)', None)
	db.sql('create index idx7 on sequences2 (mdate)', None)
	print 'sequences2 end...%s' % (mgi_utils.date())

	print 'final begin...%s' % (mgi_utils.date())
	results = db.sql('''select distinct sequenceKey, probeKey, refsKey, 
		max(userKey) as userKey, max(mdate) as mdate 
		from sequences2 
		group by sequenceKey, probeKey, refsKey
		''', 'auto')
	print 'final end...%s' % (mgi_utils.date())

	for r in results:
		outBCP.write(mgi_utils.prvalue(r['sequenceKey']) + DL + \
		       	mgi_utils.prvalue(r['probeKey']) + DL + \
		       	mgi_utils.prvalue(r['refsKey']) + DL + \
			r['mdate'] + DL + \
        		mgi_utils.prvalue(r['userKey']) + DL + mgi_utils.prvalue(r['userKey']) + DL + \
			loaddate + DL + loaddate + NL)
	outBCP.close()

def priority2():

	# allele names

        print 'processing priority 2...%s' % mgi_utils.date()

	cmd = '''select distinct a._Allele_key, a.name as label 
		 from ALL_Allele a where a.isWildType = 0 
	      '''

	if alleleKey is not None:
		cmd = cmd + 'and a._Allele_key = %s\n' % alleleKey

	writeRecord(db.sql(cmd, 'auto'), 1, 2, 'AN', 'allele name')

def init():
    global diagFile, errorFile, inputFile, errorFileName, diagFileName
 
    db.useOneConnection(1)
    db.set_sqlUser(user)
    db.set_sqlPasswordFromFile(passwordFileName)
 
    head, tail = os.path.split(inputFileName) 

    diagFileName = outputDir + '/' + tail + '.diagnostics'
    errorFileName = outputDir + '/' + tail + '.error'

    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:
        inputFile = open(inputFileName, 'r')
    except:
        exit(1, 'Could not open file %s\n' % inputFileName)

    # Log all SQL
    db.set_sqlLogFunction(db.sqlLogAll)

    diagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
    diagFile.write('Server: %s\n' % (db.get_sqlServer()))
    diagFile.write('Database: %s\n' % (db.get_sqlDatabase()))

    errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))

    return

def priority3():

	# synonyms

        print 'processing priority 3...%s' % mgi_utils.date()

	cmd = '''select distinct s._Object_key as _Allele_key, s.synonym as label
		from MGI_SynonymType st, MGI_Synonym s 
		where st._MGIType_key = 11 
		and st._SynonymType_key = s._SynonymType_key 
		'''

	if alleleKey is not None:
		cmd = cmd + 'and s._Object_key = %s\n' % alleleKey

	writeRecord(db.sql(cmd, 'auto'), 1, 3, 'AY', 'synonym')

def writeRecord(results, labelStatusKey, priority, labelType, labelTypeName):

    for r in results:

	if labelTypeName is None:
	    labelTypeName = r['labelTypeName']

        outBCP.write(mgi_utils.prvalue(r['_Allele_key']) + COLDL + \
        	mgi_utils.prvalue(labelStatusKey) + COLDL + \
        	mgi_utils.prvalue(priority) + COLDL + \
        	mgi_utils.prvalue(r['label']) + COLDL + \
        	mgi_utils.prvalue(labelType) + COLDL + \
        	mgi_utils.prvalue(labelTypeName) + COLDL + \
        	loaddate + COLDL + \
        	loaddate + LINEDL)

    print 'processed (%d) records...%s' % (len(results), mgi_utils.date())