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 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():
'''
# 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 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():
# Purpose: process command line options
# Returns: nothing
# Assumes: nothing
# Effects: initializes global variables
# exits if files cannot be opened
# Throws: nothing
global inputFile, diagFile, errorFile, errorFileName, diagFileName
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:
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)
# 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))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
return
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 initDB():
#
# requires:
#
# effects:
# 1. Initializes database options
# 2. Loads global dictionaries
#
# returns:
#
global primerDict, primer2Dict, markerDict, marker2Dict
db.useOneConnection(1)
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
# Set Log File Descriptor
db.set_sqlLogFD(diagFile)
# cache all MIT primers that have a UniSTS ID
db.sql('select p._Probe_key, p.name, stsID = a1.accID, mgiID = a2.accID ' + \
'into #primers ' + \
'from PRB_Probe p, ACC_Accession a1, ACC_Accession a2 ' + \
'where p._Probe_key = a1._Object_key ' + \
'and a1._MGIType_key = 3 ' + \
'and a1._LogicalDB_key = 80 ' + \
'and a1.preferred = 1 ' + \
'and p._Probe_key = a2._Object_key ' + \
'and a2._MGIType_key = 3 ' + \
'and a2._LogicalDB_key = 1 ' + \
'and a2.preferred = 1', None)
db.sql('create index idx1 on #primers(_Probe_key)', None)
results = db.sql('select * from #primers', 'auto')
for r in results:
primerDict[r['stsID']] = (r['name'], r['mgiID'])
# cache all MIT primers for J:34136
db.sql('select p._Probe_key, p.name into #primers2 ' + \
'from PRB_Probe p ' + \
'where p._SegmentType_key = 63473 ' + \
'and p.name like "d%mit%"', None)
db.sql('create index idx1 on #primers2(_Probe_key)', None)
results = db.sql('select a.accID, p.name from #primers2 p, ACC_Accession a ' + \
'where p._Probe_key = a._Object_key ' + \
'and a._MGIType_key = 3 ' + \
'and a._LogicalDB_key = 1 ' + \
'and a.prefixPart = "MGI:" ' + \
'and a.preferred = 1', 'auto')
for r in results:
primer2Dict[r['name']] = r['accID']
# cache all MIT primer/marker relationships using primers cached by UniSTS ID
results = db.sql('select a.accID, p.stsID, p.name, m.chromosome, m.symbol ' + \
'from #primers p, PRB_Marker pm, MRK_Marker m, ACC_Accession a ' + \
'where p._Probe_key = pm._Probe_key ' + \
'and pm._Marker_key = m._Marker_key ' + \
'and pm._Marker_key = a._Object_key ' + \
'and a._MGIType_key = 2 ' + \
'and a._LogicalDB_key = 1 ' + \
'and a.prefixPart = "MGI:" ' + \
'and a.preferred = 1', 'auto')
for r in results:
if not markerDict.has_key(r['name']):
markerDict[r['name']] = []
markerDict[r['name']].append(r)
# cache all MIT primer/marker relationships using primers cached by J:34136
results = db.sql('select a.accID, p.name, m.chromosome, m.symbol ' + \
'from #primers2 p, PRB_Marker pm, MRK_Marker m, ACC_Accession a ' + \
'where p._Probe_key = pm._Probe_key ' + \
'and pm._Marker_key = m._Marker_key ' + \
'and pm._Marker_key = a._Object_key ' + \
'and a._MGIType_key = 2 ' + \
'and a._LogicalDB_key = 1 ' + \
'and a.prefixPart = "MGI:" ' + \
'and a.preferred = 1', 'auto')
for r in results:
if not marker2Dict.has_key(r['name']):
marker2Dict[r['name']] = []
marker2Dict[r['name']].append(r)
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 refFileName, refFile
global mgiTypeKey
global refAssocKey, createdByKey
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'
refFileName = tail + '.MGI_Reference_Assoc.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:
refFile = open(refFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % refFileName)
# 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('Object Type: %s\n' % (mgiType))
diagFile.write('Input File: %s\n' % (inputFileName))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
mgiTypeKey = loadlib.verifyMGIType(mgiType, 0, errorFile)
createdByKey = loadlib.verifyUser(createdBy, 0, errorFile)
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 transTypeFile, transFile
global transTypeFileName, transFileName
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
# the default output file names are bases on 'inputFileName'
head, fileName = os.path.split(inputFileName)
# rename 'head'
head = outputFileDir
fdate = mgi_utils.date('%m%d%Y') # current date
diagFileName = head + '/' + fileName + '.' + fdate + '.diagnostics'
print diagFileName
errorFileName = head + '/' + fileName + '.' + fdate + '.error'
print errorFileName
transTypeFileName = head + '/' + fileName + '.' + fdate + '.MGI_TranslationType.bcp'
print transTypeFileName
transFileName = head + '/' + fileName + '.' + fdate + '.MGI_Translation.bcp'
print transFileName
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:
transTypeFile = open(transTypeFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % transTypeFileName)
try:
transFile = open(transFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % transFileName)
# 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))
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 inputFile, diagFile, errorFile, errorFileName, diagFileName
global transTypeFile, transFile
global transTypeFileName, transFileName
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
# the default output file names are bases on 'inputFileName'
head, fileName = os.path.split(inputFileName)
# rename 'head'
head = outputFileDir
fdate = mgi_utils.date('%m%d%Y') # current date
diagFileName = head + '/' + fileName + '.' + fdate + '.diagnostics'
print diagFileName
errorFileName = head + '/' + fileName + '.' + fdate + '.error'
print errorFileName
transTypeFileName = head + '/' + fileName + '.' + fdate + '.MGI_TranslationType.bcp'
print transTypeFileName
transFileName = head + '/' + fileName + '.' + fdate + '.MGI_Translation.bcp'
print transFileName
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:
transTypeFile = open(transTypeFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % transTypeFileName)
try:
transFile = open(transFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % transFileName)
# 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))
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 inputFile, diagFile, errorFile, errorFileName, diagFileName
global refFileName, refFile
global mgiTypeKey
global refAssocKey, createdByKey
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'
refFileName = tail + '.MGI_Reference_Assoc.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:
refFile = open(refFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % refFileName)
# 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('Object Type: %s\n' % (mgiType))
diagFile.write('Input File: %s\n' % (inputFileName))
errorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
mgiTypeKey = loadlib.verifyMGIType(mgiType, 0, errorFile)
createdByKey = loadlib.verifyUser(createdBy, 0, errorFile)