main.py

from .config  import Config
from .utils import cmn, json2, logger

from . import validate_sample
from . import validate_experiment
from . import prevalidate

from . import sraparse
import os

def main(args):
	if args.has('-prevalidate') or args.has('-gendoc'):
		return prevalidate.main(args)


	base = os.path.dirname(os.path.realpath(__file__))

	if not args.has('-config'):
		if not args.has('-dev'):
			args.add_key('-config',  "{0}/config.json".format(base))
		else:
			args.add_key('-config',  "{0}/config-dev.json".format(base))  


	logger(str([args.keys, args.args()]) + '\n')

	if not args.has('-out'):
		logger('#__noOutFileGiven___\n')
		return

	if not args.has('-dbg') and (cmn.fexists(args['-out']) and not args.has('-overwrite-outfile')):
		logger('#__outfile:{0} exists\n'.format(args['-out']))
		return

	#try:
	if True:
		if args.has('-extract'):
			#import sraparse
			return sraparse.SRAParseObjSet.extract_attributes_to_json(args.args(), args['-out'])
		elif args.has("-test-sample"):
			testargs = ["./examples/samples.xml", "-config:{0}".format(args['-config']), "-out:./examples/samples.versioned.xml"]
			validate_sample.main(Config(testargs))
		elif args.has("-sample"):
			return validate_sample.main(args)
		elif args.has("-experiment"):
			return validate_experiment.main(args) 
		else:
			raise NotImplementedError("#__unknownArguments__")
	else:
	#except Exception as err:
		logger('#__unexpected__\n')
		logger(str(err.message) + '\n')
	


if __name__ == '__main__':
	main(Config.sys())