:copyright: © 2019 by the Choppy team.
:license: AGPL, see LICENSE.md for more details.
"""
from __future__ import unicode_literals
import logging
import json
import os
import subprocess
import csv
import sys
from choppy import exit_code
from choppy.config import get_global_config
global_config = get_global_config()
module_logger = logging.getLogger(__name__)
class Validator:
"""Module to validate JSON inputs.
"""
def __init__(self, wdl, json):
self.wdl = os.path.abspath(wdl)
self.json = os.path.abspath(json)
womtool_path = global_config.get('general', 'womtool_path')
if not womtool_path:
raise Exception('You need to tell choppy-pipe where womtool is.')
self.wdl_tool = os.path.abspath(womtool_path)
self.logger = logging.getLogger('choppy.validator.Validator')
def parse_args():
"""parses and sets up the command line argument system above
with config file parsing."""
global parser, global_config, loglevel
early_parser = argparse.ArgumentParser(
description=__doc__,
formatter_class=argparse.ArgumentDefaultsHelpFormatter,
add_help=False)
early_parser.add_argument('--config',
'-c',
type=os.path.exists,
action='store',
help='change default configuration location')
group = early_parser.add_mutually_exclusive_group()
group.add_argument('--debug',
action='store_true',
default=False,
help="Debug mode.")
group.add_argument('-q',
'--quite',
action='store_true',
default=False,
help="Only display key message.")
group.add_argument('-v',
'--verbose',
action='count',
default=0,
help='Increase output verbosity')
args, remainder_argv = early_parser.parse_known_args()
if args.debug:
loglevel = logging.DEBUG
elif args.verbose:
verbose = args.verbose
# Configure logger for requested verbosity.
if verbose >= 3:
loglevel = logging.SPAM
elif verbose >= 2:
loglevel = logging.DEBUG
elif verbose >= 1:
loglevel = logging.VERBOSE
elif args.quite:
loglevel = logging.ERROR
set_logger('root', loglevel)
# Override config file defaults if explicitly requested
if args.config:
init_config(config_file=args.config)
global_config = get_global_config()
else:
init_config()
global_config = get_global_config()
if not (args.debug or args.verbose or args.quite):
loglevel = global_config.get_loglevel('server', 'log_level')
parser.add_argument('--handler',
action='store',
default='stream',
choices=('stream', 'file'),
help="Log handler, stream or file?")
server = parser.add_argument_group()
server.add_argument('-S',
'--server',
action='store',
default="localhost",
type=str,
choices=global_config.servers,
help='Choose a cromwell server from {}'.format(
global_config.servers))
server.add_argument('-f',
'--framework',
action='store',
default='flask',
choices=['bjoern', 'gevent', 'flask'],
help='Run server with framework.')
server.add_argument('-s',
'--swagger',
action='store_true',
default=False,
help="Enable swagger documentation.")
server.set_defaults(func=call_server)
argcomplete.autocomplete(parser)
args = parser.parse_args(remainder_argv)
return args