def run(parser, args):
args.tomlfile = args.toml
args.toml = toml.load(args.toml)
print(args)
# TODO: Move logging config to separate configuration file
# set up logging to file
logging.basicConfig(
level=logging.DEBUG,
format='%(levelname)s::%(asctime)s::%(name)s::%(message)s',
filename=args.log_file,
filemode='w')
# define a Handler that writes INFO messages or higher to the sys.stderr
console = logging.StreamHandler()
console.setLevel(logging.INFO)
# set a format which is simpler for console use
formatter = logging.Formatter('%(name)-15s: %(levelname)-8s %(message)s')
console.setFormatter(formatter)
# add the handler to the root logger
logging.getLogger('').addHandler(console)
# Start by logging sys.argv and the parameters used
logger = logging.getLogger("Manager")
logger.info(" ".join(sys.argv))
print_args(args, logger=logger)
logger.info("Initialising iterAlign.")
logger.info("Setting up FastQ monitoring.")
#### Check if a run is active - if not, wait.
args.simulation = True
connection = None
if args.watch is None:
args.simulation = False
logger.info("Creating rpc connection for device {}.".format(
args.device))
try:
connection, messageport = get_rpc_connection(args.device)
except ValueError as e:
print(e)
sys.exit(1)
send_message(connection, "Iteralign Connected to MinKNOW",
Severity.WARN)
logger.info("Loaded RPC")
while parse_message(connection.acquisition.current_status()
)['status'] != "PROCESSING":
time.sleep(1)
#### Check if we know where data is being written to , if not... wait
args.watch = parse_message(connection.acquisition.get_acquisition_info(
))['config_summary']['reads_directory']
else:
messageport = ""
event_handler = FastqHandler(args, logging, messageport, connection)
# This block handles the fastq
observer = Observer()
observer.schedule(event_handler, path=args.watch, recursive=True)
observer.daemon = True
try:
observer.start()
logger.info("FastQ Monitoring Running.")
while 1:
time.sleep(1)
except KeyboardInterrupt:
logger.info("Exiting - Will take a few seconds to clean up!")
observer.stop()
observer.join()
os._exit(0)
def run(parser, args):
# new code block: change the reference path within the args.toml file into the args.mindex path
d = toml.load(args.toml)
print(d["conditions"]["reference"])
args.tomlfile = args.toml
args.toml = toml.load(args.toml)
print(args)
# TODO: Move logging config to separate configuration file
# set up logging to file
logging.basicConfig(level=logging.DEBUG,
format='%(levelname)s::%(asctime)s::%(name)s::%(message)s',
filename=args.log_file,
filemode='w')
# define a Handler that writes INFO messages or higher to the sys.stderr
console = logging.StreamHandler()
console.setLevel(logging.INFO)
# set a format which is simpler for console use
formatter = logging.Formatter('%(name)-15s: %(levelname)-8s %(message)s')
console.setFormatter(formatter)
# add the handler to the root logger
logging.getLogger('').addHandler(console)
# Start by logging sys.argv and the parameters used
logger = logging.getLogger("Manager")
logger.info(" ".join(sys.argv))
print_args(args, logger=logger)
logger.info("Initialising iterAlign.")
logger.info("Setting up FastQ monitoring.")
#### Check if a run is active - if not, wait.
args.simulation = True
connection = None
#set default message severity level.
severity = 2
if args.watch is None:
args.simulation = False
logger.info("Creating rpc connection for device {}.".format(args.device))
try:
connection, messageport = get_rpc_connection(args.device)
except ValueError as e:
print(e)
sys.exit(1)
#send_message_port("Iteralign Connected to MinKNOW", args.host, messageport)
send_message(connection, "Iteralign Connected to MinKNOW.", Severity.WARN)
logger.info("Loaded RPC")
while parse_message(connection.acquisition.current_status())['status'] != "PROCESSING":
time.sleep(1)
### Check if we know where data is being written to , if not... wait
args.watch = parse_message(connection.acquisition.get_acquisition_info())['config_summary'][
'reads_directory']
else:
messageport = ""
event_handler = FastqHandler(args, logging, messageport, connection)
# This block handles the fastq
observer = Observer()
observer.schedule(event_handler, path=args.watch, recursive=True)
observer.daemon = True
try:
observer.start()
logger.info("FastQ Monitoring Running.")
while 1:
time.sleep(1)
except KeyboardInterrupt:
logger.info("Exiting - Will take a few seconds to clean up!")
observer.stop()
observer.join()
if args.keepfiles:
logging.info("The 'keepfiles' argument was set, files generated by classifier have been retained")
else:
if os.path.isdir(args.path):
for path, dirs, files in os.walk(args.path):
for f in files:
if f.startswith(args.prefix):
os.unlink(f)
logging.info("file removed: {}".format(f))
if os.path.isdir("./"):
for path, dirs, files in os.walk("./"):
for f in files:
if f.endswith(args.creport):
os.unlink(f)
logging.info("file removed: {}".format(f))
logging.info("All files generated by classifier have been removed.")
os._exit(0)
