def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {"format": LOG_FORMAT, "datefmt": LOG_DATEFMT, "level": log_level}
if args.logfile:
kwargs["filename"] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
with nested(open(args.input_file), open(args.output_file, "w")) as (f, fo):
reader = csv.DictReader(f, delimiter="\t")
writer = csv.DictWriter(fo, reader.fieldnames, delimiter="\t", lineterminator=os.linesep)
writer.writeheader()
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
vid_mapper = VidMapper(host, user, passwd, logger, args.study)
counter = Counter()
for r in reader:
counter["input_lines"] += 1
try:
vid_mapper.map_vid(r)
except ValueError:
counter["skipped_lines"] += 1
continue
else:
counter["output_lines"] += 1
writer.writerow(r)
for k, v in counter.iteritems():
logger.info("%s: %d" % (k, v))
def __init__(self, **kwargs):
omero_host = vlu.ome_host()
omero_user = vlu.ome_user()
omero_passwd = vlu.ome_passwd()
self.kb = KB(driver='omero')(omero_host, omero_user, omero_passwd)
super(UniverseApplication, self).__init__(**kwargs)
self.config.omero_default_host = kwargs.get('omero_default_host')
self.config.omero_default_user = kwargs.get('omero_default_user')
self.config.omero_default_passwd = kwargs.get('omero_default_passwd')
self.config.vl_loglevel = kwargs.get('vl_loglevel', 'INFO')
self.config.vl_import_enabled_users = kwargs.get('vl_import_enabled_users')
def main(argv=None):
app = App()
parser = app.make_parser()
args = parser.parse_args(argv)
loglevel = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': loglevel}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
def main(argv):
parser = make_parser()
args = parser.parse_args(argv)
log_level = getattr(logging, args.loglevel)
kwargs = {'format': LOG_FORMAT, 'datefmt': LOG_DATEFMT, 'level': log_level}
if args.logfile:
kwargs['filename'] = args.logfile
logging.basicConfig(**kwargs)
logger = logging.getLogger()
with nested(open(args.input_file), open(args.output_file, "w")) as (f, fo):
reader = csv.DictReader(f, delimiter="\t")
writer = csv.DictWriter(fo,
reader.fieldnames,
delimiter="\t",
lineterminator=os.linesep)
writer.writeheader()
try:
host = args.host or vlu.ome_host()
user = args.user or vlu.ome_user()
passwd = args.passwd or vlu.ome_passwd()
except ValueError, ve:
logger.critical(ve)
sys.exit(ve)
vid_mapper = VidMapper(host, user, passwd, logger, args.study)
counter = Counter()
for r in reader:
counter["input_lines"] += 1
try:
vid_mapper.map_vid(r)
except ValueError:
counter["skipped_lines"] += 1
continue
else:
counter["output_lines"] += 1
writer.writerow(r)
for k, v in counter.iteritems():
logger.info("%s: %d" % (k, v))
