diff options
| -rwxr-xr-x | scripts/maintenance/QTL_Reaper_v6.py | 29 |
1 files changed, 28 insertions, 1 deletions
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py index 3f202285..477af973 100755 --- a/scripts/maintenance/QTL_Reaper_v6.py +++ b/scripts/maintenance/QTL_Reaper_v6.py @@ -3,6 +3,7 @@ #!/usr/bin/python import reaper import MySQLdb +import contextlib from argparse import ArgumentParser @@ -100,7 +101,31 @@ def run_qtl_reaper(cursor, genotypeDir, ProbeSetFreezeIds): print(ProbeSetFreezeIds) - cursor.close() + +@contextlib.contextmanager +def dbconnection(db, user, passwd, host, port): + """Connect to the database in a contextmanager.""" + conn = MySQLdb.Connect(db=db, user=user, passwd=passwd, host=host, port=port) + try: + yield conn + except MySQLdb.Error as _err: + conn.rollback() + finally: + conn.commit() + conn.close() + + +def read_db_config(path): + with open(path, "r") as infile: + lines = tuple(line.strip() for line in infile.readlines()) + return { + "user": lines[0], + "passwd": lines[1], + "host": lines[2], + "port": int(lines[3] or "3306"), + "db": lines[4] + } + def main(): parser = ArgumentParser(prog="QTLReaper", description="Python-2 QTLReaper.") @@ -116,6 +141,8 @@ def main(): nargs="*", help="The ProbeSetFreezeIds to act on.") args = parser.parse_args() + with dbconnection(**read_db_config(args.db_config_file)) as conn: + run_qtl_reaper(conn.cursor(), args.genotype_dir, args.ProbeSetFreezeIds) if __name__ == "__main__": main() |