def test_ForwardDbFpSupplier(self):
# Additional tests to complete code coverage
conn = DbConnect(RDConfig.RDTestDatabase, 'simple_combined')
self.assertRaises(ValueError, DbFpSupplier.ForwardDbFpSupplier, conn.GetData(),
fpColName='typo')
suppl = DbFpSupplier.ForwardDbFpSupplier(conn.GetData(), fpColName='AutoFragmentFp')
self.assertIn('ID', suppl.GetColumnNames())
def GetFingerprints(details):
""" returns an iterable sequence of fingerprints
each fingerprint will have a _fieldsFromDb member whose first entry is
the id.
"""
if details.dbName and details.tableName:
try:
conn = DbConnect(details.dbName, details.tableName)
if hasattr(details, 'dbUser'):
conn.user = details.dbUser
if hasattr(details, 'dbPassword'):
conn.password = details.dbPassword
except:
import traceback
FingerprintMols.error(
'Error: Problems establishing connection to database: %s|%s\n'
% (details.dbName, details.tableName))
traceback.print_exc()
cmd = _ConstructSQL(details, extraFields=details.fpColName)
curs = conn.GetCursor()
#curs.execute(cmd)
#print 'CURSOR:',curs,curs.closed
if _dataSeq:
suppl = _dataSeq(curs,
cmd,
depickle=not details.noPickle,
klass=DataStructs.ExplicitBitVect)
_dataSeq._conn = conn
else:
suppl = DbFpSupplier.ForwardDbFpSupplier(
data, fpColName=details.fpColName)
elif details.inFileName:
conn = None
try:
inF = open(details.inFileName, 'r')
except IOError:
import traceback
FingerprintMols.error('Error: Problems reading from file %s\n' %
(details.inFileName))
traceback.print_exc()
supple = []
done = 0
while not done:
try:
id, fp = cPickle.load(inF)
except:
done = 1
else:
fp._fieldsFromDb = [id]
suppl.append(fp)
else:
suppl = None
return suppl
def GetFingerprints(details):
""" returns an iterable sequence of fingerprints
each fingerprint will have a _fieldsFromDb member whose first entry is
the id.
"""
if details.dbName and details.tableName:
conn: DbConnect = _ConnectToDatabase(details)
cmd = _ConstructSQL(details, extraFields=details.fpColName)
curs = conn.GetCursor()
# curs.execute(cmd)
# print 'CURSOR:',curs,curs.closed
if _dataSeq:
suppl = _dataSeq(curs, cmd, depickle=not details.noPickle, klass=DataStructs.ExplicitBitVect)
_dataSeq._conn = conn
return suppl
return DbFpSupplier.ForwardDbFpSupplier(data, fpColName=details.fpColName)
if details.inFileName:
try:
inF = open(details.inFileName, 'r')
except IOError:
import traceback
FingerprintMols.error(f'Error: Problems reading from file {details.inFileName}\n')
traceback.print_exc()
suppl = []
done = 0
while not done:
try:
ID, fp = pickle.load(inF)
except Exception:
done = 1
else:
fp._fieldsFromDb = [ID]
suppl.append(fp)
return suppl
return None