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():
global fpB6BcpFile, fpMgpBcpFile, sourceLookup, nextAssocKey
try:
fpB6BcpFile = open(b6BcpFile, 'w')
except:
'Could not open file for writing %s\n' % b6BcpFile
sys.exit(1)
if B6_ONLY == 'false':
try:
fpMgpBcpFile = open(mgpBcpFile, 'w')
except:
'Could not open file for writing %s\n' % mgpBcpFile
sys.exit(1)
loadSourceLookup()
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
db.useOneConnection(1)
#
# get next _Assoc_key
#
results = db.sql(''' select nextval('seq_source_assoc_seq') as nextAssocKey ''', 'auto')
nextAssocKey = results[0]['nextAssocKey']
return 0
def initialize():
global mgi_to_uniprotFile
global uniprotFile
global markerIPFile
global markerIPRef
global annotEvidence, annotEditor, annotDate
#
# initialize caches
#
db.useOneConnection(1)
db.set_sqlLogFunction(db.sqlLogAll)
mgi_to_uniprotFile = os.getenv('MGI_UNIPROT_LOAD_FILE')
uniprotFile = os.getenv('UNIPROT_ACC_ASSOC_FILE')
markerIPFile = os.getenv('MARKER_IP_ASSOC_FILE')
markerIPRef = os.environ['MARKER_IP_ANNOT_REF']
annotEvidence = os.environ['ANNOT_EVIDENCECODE']
annotEditor = os.environ['ANNOT_EDITOR']
annotDate = os.environ['ANNOT_DATE']
rc = 0
#
# Make sure the required environment variables are set.
#
if not mgi_to_uniprotFile:
print 'Environment variable not set: MGI_UNIPROT_LOAD_FILE'
rc = 1
if not uniprotFile:
print 'Environment variable not set: UNIPROT_ACC_ASSOC'
rc = 1
if not markerIPFile:
print 'Environment variable not set: MARKER_IP_ASSOC_FILE'
rc = 1
if not markerIPRef:
print 'Environment variable not set: MARKER_IP_ANNOT_REF'
rc = 1
if not annotEvidence:
print 'Environment variable not set: ANNOT_EVIDENCECODE'
rc = 1
if not annotEditor:
print 'Environment variable not set: ANNOT_EDITOR'
rc = 1
if not annotDate:
print 'Environment variable not set: ANNOT_DATE'
rc = 1
return rc
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():
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 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 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 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():
# 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, 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 initialize():
global inputFileName, outputFileName, inputFile, outputFile
db.useOneConnection(1)
db.set_sqlLogFunction(db.sqlLogAll)
inputFileName = os.getenv('INFILE_1_0')
outputFileName = os.getenv('OUTPUT_1_0_PROTEINCODING')
#
# Make sure the required environment variables are set.
#
if not inputFileName:
print 'Environment variable not set: INFILE_1_0'
return 1
#
# Make sure the required environment variables are set.
#
if not outputFileName:
print 'Environment variable not set: OUTPUT_1_0_PROTEINCODING'
return 1
#
# Open the input file
#
try:
inputFile = open(inputFileName, 'r')
except:
print 'Cannot open file: ' + inputFileName
return 1
#
# Open the output file
#
try:
outputFile = open(outputFileName, 'w')
except:
print 'Cannot open file: ' + outputFileName
return 1
return 0
def init():
global fpB6AnnotFile, fpMgpAnnotFile
try:
fpB6AnnotFile = open(b6AnnotFile, 'w')
except:
'Could not open file for writing %s\n' % b6AnnotFile
sys.exit(1)
try:
fpMgpAnnotFile = open(mgpAnnotFile, 'w')
except:
'Could not open file for writing %s\n' % mgpAnnotFile
sys.exit(1)
loadFeatureTypeLookup()
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
db.useOneConnection(1)
return 0
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 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 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 initialize():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global alleleFile, mutationFile, mutantFile, refFile
global accFile, accRefFile, noteFile, annotFile
global newAlleleFile
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'
newAlleleFileName = outputDir + '/' + tail + '.new'
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:
newAlleleFile = open(newAlleleFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % newAlleleFileName)
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
alleleFile = open(alleleFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % alleleFileName)
try:
mutationFile = open(mutationFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % mutationFileName)
try:
mutantFile = open(mutantFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % mutantFileName)
try:
refFile = open(refFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % refFileName)
try:
accFile = open(accFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accFileName)
try:
accRefFile = open(accRefFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accRefFileName)
try:
noteFile = open(noteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteFileName)
try:
annotFile = open(annotFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % annotFileName)
# 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()))
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
def init():
global diagFile, errorFile, errorFileName, diagFileName
global outResultStFile, outResultFile, outResultImageFile
global inResultsFile, inStructureFile
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
diagFileName = 'resultsload.diagnostics'
errorFileName = 'resultsload.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)
# Input Files
try:
inResultsFile = open(inResultsFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inResultsFileName)
try:
inStructureFile = open(inStructureFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inStructureFileName)
# Output Files
try:
outResultStFile = open(outResultStFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outResultStFileName)
try:
outResultFile = open(outResultFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outResultFileName)
try:
outResultImageFile = open(outResultImageFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outResultImageFileName)
# 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 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 diagFileName, errorFileName, synFileName
global inputFile, diagFile, errorFile, synFile
global mgiTypeKey, createdByKey, referenceKey
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
head, tail = os.path.split(inputFileName)
diagFileName = logDir + '/' + tail + '.diagnostics'
errorFileName = logDir + '/' + tail + '.error'
synFileName = 'MGI_Synonym.bcp'
print inputFileName
print logDir
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:
synFile = open(outputDir + '/' + synFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % synFileName)
# 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()))
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)
# if reference is J:0, then no reference is given
if jnum == 'J:0':
referenceKey = ''
else:
referenceKey = loadlib.verifyReference(jnum, 0, errorFile)
# exit if we can't resolve mgiType, createdBy or jnum
if mgiTypeKey == 0 or \
createdByKey == 0 or \
referenceKey == 0:
exit(1)
if mode == 'reload':
print 'mode is: %s, deleting synonyms' % mode
sys.stdout.flush()
db.sql('delete from MGI_Synonym ' + \
'where _MGIType_key = %d ' % (mgiTypeKey) + \
'and _CreatedBy_key = %d ' % (createdByKey), None)
def initialize():
global mgi_to_uniprotFile
global mgi_to_markertypeFile
global uniprotFile
global ec2goFile, goECFile
global ip2goFile, goIPFile
global spkw2goFile, goSPKWFile
global goECRef, goIPRef, goSPKWRef
global annotEvidence, annotEditor, annotDate, annotNote, annotNotePrefix
#
# initialize caches
#
db.useOneConnection(1)
db.set_sqlLogFunction(db.sqlLogAll)
mgi_to_uniprotFile = os.getenv('MGI_UNIPROT_LOAD_FILE')
mgi_to_markertypeFile = os.getenv('MGI_ACC_ASSOC_FILE')
uniprotFile = os.getenv('UNIPROT_ACC_ASSOC_FILE')
ec2goFile = os.getenv('EC2GOFILE')
goECFile = os.getenv('GO_EC_ASSOC_FILE')
goECRef = os.environ['GO_EC_ANNOT_REF']
ip2goFile = os.getenv('IP2GOFILE')
goIPFile = os.getenv('GO_IP_ASSOC_FILE')
goIPRef = os.environ['GO_IP_ANNOT_REF']
spkw2goFile = os.getenv('SPKW2GOFILE')
goSPKWFile = os.getenv('GO_SPKW_ASSOC_FILE')
goSPKWRef = os.environ['GO_SPKW_ANNOT_REF']
annotEvidence = os.environ['ANNOT_EVIDENCECODE']
annotEditor = os.environ['ANNOT_EDITOR']
annotDate = os.environ['ANNOT_DATE']
annotNote = os.environ['ANNOT_NOTE']
annotNotePrefix = os.environ['ANNOT_NOTEPREFIX']
rc = 0
#
# Make sure the required environment variables are set.
#
if not mgi_to_uniprotFile:
print 'Environment variable not set: MGI_UNIPROT_LOAD_FILE'
rc = 1
if not uniprotFile:
print 'Environment variable not set: UNIPROT_ACC_ASSOC'
rc = 1
if not mgi_to_markertypeFile:
print 'Environment variable not set: MGI_ACC_ASSOC_FILE'
rc = 1
if not ec2goFile:
print 'Environment variable not set: EC2GOFILE'
rc = 1
if not goECFile:
print 'Environment variable not set: GO_EC_ASSOC_FILE'
rc = 1
if not goECRef:
print 'Environment variable not set: GO_EC_ANNOTREF'
rc = 1
if not ip2goFile:
print 'Environment variable not set: IP2GOFILE'
rc = 1
if not goIPFile:
print 'Environment variable not set: GO_IP_ASSOC_FILE'
rc = 1
if not goIPRef:
print 'Environment variable not set: GO_IP_ANNOTREF'
rc = 1
if not goSPKWFile:
print 'Environment variable not set: GO_SPKW_ASSOC_FILE'
rc = 1
if not goSPKWRef:
print 'Environment variable not set: GO_SPKW_ANNOTREF'
rc = 1
if not annotEvidence:
print 'Environment variable not set: ANNOT_EVIDENCECODE'
rc = 1
if not annotEditor:
print 'Environment variable not set: ANNOT_EDITOR'
rc = 1
if not annotDate:
print 'Environment variable not set: ANNOT_DATE'
rc = 1
if not annotNote:
print 'Environment variable not set: ANNOT_NOTE'
rc = 1
if not annotNotePrefix:
print 'Environment variable not set: ANNOT_NOTEPREFIX'
rc = 1
return rc
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 diagFileName, errorFileName, synFileName
global inputFile, diagFile, errorFile, synFile
global mgiTypeKey, createdByKey, referenceKey
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
head, tail = os.path.split(inputFileName)
diagFileName = logDir + '/' + tail + '.diagnostics'
errorFileName = logDir + '/' + tail + '.error'
synFileName = 'MGI_Synonym.bcp'
print inputFileName
print logDir
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:
synFile = open(outputDir + '/' + synFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % synFileName)
# 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()))
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)
# if reference is J:0, then no reference is given
if jnum == 'J:0':
referenceKey = ''
else:
referenceKey = loadlib.verifyReference(jnum, 0, errorFile)
# exit if we can't resolve mgiType, createdBy or jnum
if mgiTypeKey == 0 or \
createdByKey == 0 or \
referenceKey == 0:
exit(1)
if mode == 'reload':
print 'mode is: %s, deleting synonyms' % mode
sys.stdout.flush()
db.sql('delete from MGI_Synonym ' + \
'where _MGIType_key = %d ' % (mgiTypeKey) + \
'and _CreatedBy_key = %d ' % (createdByKey), None)
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():
global diagFile, errorFile, errorFileName, diagFileName
global outAccFile, outPrepFile, outAssayFile, outAssayNoteFile
global outGelLaneFile, outGelLaneStFile, outGelRowFile, outGelBandFile
global inPrimerFile, inPrepFile, inAssayFile, inGelLaneFile, inGelBandFile
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
fdate = mgi_utils.date('%m%d%Y') # current date
diagFileName = sys.argv[0] + '.' + fdate + '.diagnostics'
errorFileName = sys.argv[0] + '.' + 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)
# Input Files
try:
inPrepFile = open(inPrepFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inPrepFileName)
try:
inAssayFile = open(inAssayFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inAssayFileName)
try:
inGelLaneFile = open(inGelLaneFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inGelLaneFileName)
try:
inGelBandFile = open(inGelBandFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inGelBandFileName)
# Output Files
try:
outPrepFile = open(outPrepFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outPrepFileName)
try:
outAssayFile = open(outAssayFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outAssayFileName)
try:
outAssayNoteFile = open(outAssayNoteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outAssayNoteFileName)
try:
outGelLaneFile = open(outGelLaneFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outGelLaneFileName)
try:
outGelLaneStFile = open(outGelLaneStFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outGelLaneStFileName)
try:
outGelRowFile = open(outGelRowFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outGelRowFileName)
try:
outGelBandFile = open(outGelBandFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outGelBandFileName)
try:
outAccFile = open(outAccFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % outAccFileName)
# 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 init(outputfile,
title = None,
outputdir = None,
printHeading = 'JAX',
isHTML = 0,
fileExt = None,
sqlOneConnection = 1,
sqlLogging = 1):
'''
# requires: outputfile, the name of the output file (string)
# title, the title of the report (string)
# outputdir, the directory in which to place the output file (string);
# the default is the current working directory
# printHeading, set to Header Type if the header is to be printed (default is JAX)
# isHTML, set to 1 if the output file is HTML format, 0 otherwise
# (default is 0)
# fileExt, the file extension of the output file (e.g. ".rpt", ".tab")
#
# effects:
# 1. Opens the output file under $HOME/mgireport directory for writing
# 2. Initializes the output file with the title of the report, if given
#
# returns:
# The file descriptor which was initialized
#
'''
suffix = ''
if fileExt != None:
suffix = fileExt
if isHTML:
suffix = suffix + '.html'
elif isHTML:
suffix = suffix + '.html'
else:
suffix = '.rpt'
outputfile = os.path.splitext(outputfile)
if outputdir is None:
outputdir = os.getcwd()
filename = outputdir + '/' + outputfile[0] + suffix
fp = open(filename, 'w')
if isHTML:
fp.write("<HTML>")
fp.write("<BODY>")
fp.write("<PRE>")
# see finish_nonps for closing of these markups
if printHeading is not None:
header(fp, printHeading)
if title is not None:
fp.write(str.center(title, column_width) + 2 * CRT)
if sqlOneConnection:
db.useOneConnection(1)
if sqlLogging:
db.set_sqlLogFunction(db.sqlLogAll)
return fp
def init():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global strainFile, markerFile, accFile, annotFile
global noteFile, noteChunkFile
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)
try:
markerFile = open(markerFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % markerFileName)
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)
try:
noteChunkFile = open(noteChunkFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteChunkFileName)
try:
annotFile = open(annotFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % annotFileName)
# 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 init():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global outSetFile, outMemberFile
global setKey, setMemberKey, createdByKey, mgiTypeKey, useSetKey
global DEBUG
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
diagFileName = '%s/setload.diagnostics' % (outputDir)
errorFileName = '%s/setload.error' % (outputDir)
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)
# Output Files
try:
fullPathSetFile = '%s/%s' % (outputDir, outSetFileName)
outSetFile = open(fullPathSetFile, 'w')
except:
exit(1, 'Could not open file %s\n' % fullPathSetFile)
try:
fullPathMemberFile = '%s/%s' % (outputDir, outMemberFileName)
outMemberFile = open(fullPathMemberFile, 'w')
except:
exit(1, 'Could not open file %s\n' % fullPathMemberFile)
# 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()))
if mode == 'preview':
DEBUG = 1
bcpon = 0
elif mode != 'load':
exit(1, 'Invalid Processing Mode: %s\n' % (mode))
results = db.sql('select max(_Set_key) + 1 as maxKey from MGI_Set', 'auto')
setKey = results[0]['maxKey']
createdByKey = loadlib.verifyUser(createdBy, 0, errorFile)
mgiTypeKey = loadlib.verifyMGIType(setType, 0, errorFile)
#
# use existing MGI_Set, or create a new one
#
results = db.sql(
'select _Set_key from MGI_Set where _MGIType_key = %s and name = \'%s\''
% (mgiTypeKey, setName), 'auto')
if len(results) > 0:
for r in results:
setKey = r['_Set_key']
# delete/reload
db.sql('delete from MGI_SetMember where _Set_key = %s' % (setKey),
None)
else:
outSetFile.write(str(setKey) + TAB + \
str(mgiTypeKey) + TAB + \
str(setName) + TAB + \
'1' + TAB + \
str(createdByKey) + TAB + str(createdByKey) + TAB + \
loaddate + TAB + loaddate + CRT)
results = db.sql(
'select max(_SetMember_key) + 1 as maxKey from MGI_SetMember', 'auto')
setMemberKey = results[0]['maxKey']
return
def initialize():
# Purpose: open file descriptors; write timestamps to log files
# Returns: 1 if error, else 0
# Assumes: Nothing
# Effects: Sets global variables, exits if a file can't be opened,
# creates files in the file system
global fpDiagFile, fpErrorFile, fpInputFile, errorFileName, diagFileName
global fpAlleleFile, fpMutationFile, fpRefFile
global fpAccFile, fpNoteFile, fpAnnotFile
global fpNewAlleleRptFile
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:
fpDiagFile = open(diagFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % diagFileName)
try:
fpErrorFile = open(errorFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % errorFileName)
try:
fpNewAlleleRptFile = open(newAlleleRptFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % newAlleleRptFileName)
try:
fpInputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
fpAlleleFile = open(alleleFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % alleleFileName)
try:
fpMutationFile = open(mutationFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % mutationFileName)
try:
fpRefFile = open(refFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % refFileName)
try:
fpAccFile = open(accFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accFileName)
try:
fpNoteFile = open(noteFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % noteFileName)
try:
fpAnnotFile = open(annotFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % annotFileName)
# Log all SQL
db.set_sqlLogFunction(db.sqlLogAll)
fpDiagFile.write('Start Date/Time: %s\n' % (mgi_utils.date()))
fpDiagFile.write('Server: %s\n' % (db.get_sqlServer()))
fpDiagFile.write('Database: %s\n' % (db.get_sqlDatabase()))
fpErrorFile.write('Start Date/Time: %s\n\n' % (mgi_utils.date()))
return 0
def init():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global outSetFile, outMemberFile
global setKey, setMemberKey, createdByKey, mgiTypeKey, useSetKey
global DEBUG
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
diagFileName = '%s/setload.diagnostics' % (outputDir)
errorFileName = '%s/setload.error' % (outputDir)
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)
# Output Files
try:
fullPathSetFile = '%s/%s' % (outputDir, outSetFileName)
outSetFile = open(fullPathSetFile, 'w')
except:
exit(1, 'Could not open file %s\n' % fullPathSetFile)
try:
fullPathMemberFile = '%s/%s' % (outputDir, outMemberFileName)
outMemberFile = open(fullPathMemberFile, 'w')
except:
exit(1, 'Could not open file %s\n' % fullPathMemberFile)
# 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()))
if mode == 'preview':
DEBUG = 1
bcpon = 0
elif mode != 'load':
exit(1, 'Invalid Processing Mode: %s\n' % (mode))
results = db.sql('select max(_Set_key) + 1 as maxKey from MGI_Set', 'auto')
setKey = results[0]['maxKey']
createdByKey = loadlib.verifyUser(createdBy, 0, errorFile)
mgiTypeKey = loadlib.verifyMGIType(setType, 0, errorFile)
#
# use existing MGI_Set, or create a new one
#
results = db.sql('select _Set_key from MGI_Set where _MGIType_key = %s and name = \'%s\''
% (mgiTypeKey, setName), 'auto')
if len(results) > 0:
for r in results:
setKey = r['_Set_key']
# delete/reload
db.sql('delete from MGI_SetMember where _Set_key = %s' % (setKey), None)
else:
outSetFile.write(str(setKey) + TAB + \
str(mgiTypeKey) + TAB + \
str(setName) + TAB + \
'1' + TAB + \
str(createdByKey) + TAB + str(createdByKey) + TAB + \
loaddate + TAB + loaddate + CRT)
results = db.sql('select max(_SetMember_key) + 1 as maxKey from MGI_SetMember', 'auto')
setMemberKey = results[0]['maxKey']
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 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 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()))
def initialize():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global alleleFile, mutationFile, mutantFile, refFile
global accFile, accRefFile, noteFile, noteChunkFile, annotFile
global newAlleleFile
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'
newAlleleFileName = outputDir + '/' + tail + '.new'
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:
newAlleleFile = open(newAlleleFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % newAlleleFileName)
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
try:
alleleFile = open(alleleFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % alleleFileName)
try:
mutationFile = open(mutationFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % mutationFileName)
try:
mutantFile = open(mutantFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % mutantFileName)
try:
refFile = open(refFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % refFileName)
try:
accFile = open(accFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accFileName)
try:
accRefFile = open(accRefFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % accRefFileName)
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:
annotFile = open(annotFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % annotFileName)
# 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()))
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)
import loadlib
#
# from configuration file
#
user = os.environ['MGD_DBUSER']
passwordFileName = os.environ['MGD_DBPASSWORDFILE']
loaddate = loadlib.loaddate
modifiedBy = os.environ['MODIFIEDBY']
modifiedByKey = None
newMkrType = os.environ['NEWMKRTYPE']
newMkrTypeKey = None
db.useOneConnection(1)
db.set_sqlUser(user)
db.set_sqlPasswordFromFile(passwordFileName)
db.set_sqlLogFunction(db.sqlLogAll)
inputFileName = os.environ['NOMENDATAFILE']
inputFile = None # file descriptor
updateList = [] # list of marker keys to update
mgiToMrkKeyDict = {} # {mgiID:markerKey, ...}
try:
inputFile = open(inputFileName, 'r')
except:
exit(1, 'Could not open file %s\n' % inputFileName)
#
# get keys for NEWMKRTYPE and MODIFIEDBY
#
results = db.sql('''select _Marker_Type_key from MRK_Types where name = '%s' ''' % newMkrType, 'auto')
if len(results) == 0:
exit (1, 'Invalid marker type %s\n' % newMkrType)
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 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():
global diagFile, errorFile, inputFile, errorFileName, diagFileName
global strainFile, markerFile, accFile, annotFile
global noteFile
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', encoding="latin-1")
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)
try:
markerFile = open(markerFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % markerFileName)
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)
try:
annotFile = open(annotFileName, 'w')
except:
exit(1, 'Could not open file %s\n' % annotFileName)
# 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
