# 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()

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()

# 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) + \

# requires:

#

# effects:

# Verifies the processing mode is valid. If it is not valid,

# the program is aborted.

# Sets globals based on processing mode.

# Deletes data based on processing mode.

#

# returns:

# nothing

#

global bcpon

if mode == 'preview':

bcpon = 0

elif mode != 'load' and mode != 'reload':

# requires:

# synType - the Synonym Type

# lineNum - the line number of the record from the input file

#

# effects:

# verifies that:

# the Synonym Type exists

# writes to the error file if the Synonym Type is invalid

#

# returns:

# 0 if the Synonym Type is invalid

# Synonym Type Key if the Synonym Type is valid

#

synTypeKey = 0

if synTypeDict.has_key(synType):

synTypeKey = synTypeDict[synType]

else:

errorFile.write('Invalid Synonym Type (%d) %s\n' % (lineNum, synType))

synTypeKey = 0

# requires:

#

# effects:

# Sets the global primary keys values needed for the load

#

# returns:

# nothing

#

global synKey

results = db.sql(' select nextval(mgi_synonym_seq') as maxKey ', 'auto')

# requires:

#

# effects:

# loads global dictionaries for quicker lookup

#

# returns:

# nothing

global synTypeDict, synDict

# create synonym type lookup

results = db.sql('select _SynonymType_key, synonymType from MGI_SynonymType ' + \

'where _MGIType_key = %s' % (mgiTypeKey), 'auto')

for r in results:

synTypeDict[r['synonymType']] = r['_SynonymType_key']

# create existing synonym lookup for all MGI accessioned objects

results = db.sql('''select a.accid as mgiID, s.synonym

from MRK_Marker m, ACC_Accession a, MGI_Synonym s

where m._Organism_key = 1

and m._Marker_key = a._Object_key

and a._LogicalDB_key = 1

and a._MGIType_key = 2

and a.prefixPart = 'MGI:'

and a.preferred = 1

and a._MGIType_key = s._MGIType_key

and a._Object_key = s._Object_key

''', 'auto')

for r in results:

mgiID = r['mgiID']

synonym = r['synonym']

if mgiID not in synDict.keys():

synDict[mgiID] = [synonym]

else:

# requires:

#

# effects:

# Reads input file

# Verifies and Processes each line in the input file

#

# returns:

# nothing

#

global synKey

mgiIdsWithSynonyms = synDict.keys()

lineNum = 0

# For each line in the input file

for line in inputFile.readlines():

error = 0

lineNum = lineNum + 1

# Split the line into tokens

tokens = string.split(line[:-1], '\t')

try:

accID = tokens[0]

synonym = tokens[1]

synType = tokens[2]

except:

exit(1, 'Invalid Line (%d): %s\n' % (lineNum, line))

objectKey = loadlib.verifyObject(accID, mgiTypeKey, None, lineNum, errorFile)

if accID in mgiIdsWithSynonyms:

if synonym in synDict[accID]:

errorFile.write('Duplicate synonym: %s for %s\n' % (synonym, accID))

continue

synTypeKey = verifySynonymType(synType, lineNum)

if len(synonym) == 0:

errorFile.write('Invalid Synonym:Empty (%d) %s\n' % (lineNum, synonym))

if objectKey == 0 or \

synTypeKey == 0 or \

len(synonym) == 0:

# set error flag to true

error = 1

# if errors, continue to next record

if error:

continue

# if no errors, process

synFile.write('%d|%d|%d|%d|%s|%s|%s|%s|%s|%s\n' \

% (synKey, objectKey, mgiTypeKey, synTypeKey, referenceKey, synonym, createdByKey, createdByKey, loaddate, loaddate))

# requires:

#

# effects:

# BCPs the data into the database

#

# returns:

# nothing

#

synFile.close()

if not bcpon:

print 'Skipping BCP. Mode: %s' % mode

sys.stdout.flush()

return

print 'Executing BCP'

sys.stdout.flush()

db.commit()

bcp1 = bcpCommand % ('MGI_Synonym', synFileName)

diagFile.write('%s\n' % bcp1)

os.system(bcp1)

db.commit()

db.sql(''' select setval('mgi_synonym_seq', (select max(_Synonym_key) from MGI_Synonym)) ''', None)