class ConnectionManager:
"""Context Management Protocol for Database access.
Implementation for accessing Oracle Databases."""
def __init__(self, config: tuple) -> None:
"""config should contain the following Infromation:
(username, password, connection_info)"""
self.config = config
pass
def __enter__(self) -> Cursor:
"""Returns a cursor for the interaction with the db"""
try:
self.connection = Connection(*self.config)
self.cursor = self.connection.cursor()
return self.cursor
except ProgrammingError as e:
raise CMProgrammingError(e)
except InterfaceError as e:
raise CMInterfaceError(e)
except Error as e:
raise CMError(e)
except Exception as e:
raise CMError(e)
pass
def __exit__(self, exc_type, exc_val, exc_tb) -> None:
"""Commits the buffered interactions and closes the cursor and the connection"""
self.connection.commit()
self.cursor.close()
self.connection.close()
if exc_type:
raise exc_type(exc_val)
pass
def cancel(self, connection):
connection_name = connection.name
oracle_connection = connection.handle
logger.info("Cancelling query '{}' ".format(connection_name))
try:
Connection.close(oracle_connection)
except Exception as e:
logger.error('Error closing connection for cancel request')
raise Exception(str(e))
logger.info("Canceled query '{}'".format(connection_name))
def _check_matches(con: cx_Oracle.Connection):
"""
Check there are not errors in imported matches
:param con: Oracle connection object
"""
cur = con.cursor()
# Matches outside of the protein
logger.info("checking out-of-bound matches")
cur.execute("""
SELECT M.PROTEIN_AC, M.METHOD_AC, M.POS_TO, P.LEN
FROM INTERPRO.MATCH_NEW M
INNER JOIN INTERPRO.PROTEIN P
ON M.PROTEIN_AC = P.PROTEIN_AC
WHERE M.POS_TO > P.LEN
""")
cnt = 0
for row in cur:
logger.critical("out-of-bound: {}\t{}\t{}\t{}".format(*row))
cnt += 1
if cnt:
cur.close()
con.close()
raise RuntimeError(f"{cnt} out-of-bound matches")
# Matches with invalid start/end positions
logger.info("checking invalid matches")
cur.execute("""
SELECT PROTEIN_AC, METHOD_AC, POS_FROM, POS_TO
FROM INTERPRO.MATCH_NEW
WHERE POS_FROM < 1 OR POS_FROM > POS_TO
""")
cnt = 0
for row in cur:
logger.critical("invalid: {}\t{}\t{}\t{}".format(*row))
cnt += 1
if cnt:
cur.close()
con.close()
raise RuntimeError(f"{cnt} invalid matches")
cur.close()
def close_connection(conn_db: cx_Oracle.Connection):
"""Close the connection
parameters:
*) conn_db : connection object
"""
conn_db.close()
from cx_Oracle import Connection
import time
import sys
while True:
time.sleep(0.2)
try:
c = Connection("cx_Oracle/dev@localhost")
c.close()
sys.stdout.write(".")
sys.stdout.flush()
except Exception, e:
print e
sys.stdout.write("x")
sys.stdout.flush()
