validate_main.py

from .sraparse import SRAParseObjSet, SRAParseObj,  XMLValidator
from .utils import cmn, json2, logger
from . import io_adaptor
from . import utils


class ValidatorTemplate:
	def __init__(self, objtype):
		self.nObj = 0
		self.validated = list()
		self.objtype = objtype
		self.objset = self.objtype + '_SET'
		self.validator_log = dict()
		self.versioned_xml = list()
		self.validated = list()


def main(args, versioned_xml, validated, nObjs, validator, xml_validator):
	validated_xml_file = cmn.writel(args['-out'], versioned_xml)
	print ('written:' + validated_xml_file)
	print ('validated:', len(validated))
	print ('failed:', nObjs - len(validated))
	if validated:
		validated_xml_set = SRAParseObjSet.from_file(validated_xml_file)
		if not (validated_xml_set.is_valid__xml(xml_validator) or args.has("-skip-updated-xml-validation")):
			utils.sanity_check_fail('__xml_validation_failed__')
		logger('ok\n')
	else:
		logger('..no valid objects found\n')

	errlog = { e : v.errorlog  for e, v in validator.items()}
	semanticlog = { e : v.semanticlog  for e, v in validator.items()}


	errlog = io_adaptor.format_errlog(errlog)
	collected = io_adaptor.collectreports({"versioning":errlog, "semantic_rules": semanticlog}) 

	if args.has('-jsonlog'):
		print(json2.dumpf(args['-jsonlog'] + '.err.json', errlog))
		print(json2.dumpf(args['-jsonlog'] + '.sem.json', semanticlog))
		print(json2.dumpf(args['-jsonlog'] + '.raw.json', collected))
		better_errors = io_adaptor.better_errors(collected)
		print(json2.dumpf(args['-jsonlog'], better_errors))
	else:
		better_errors = io_adaptor.better_errors(collected)
		json2.pp(better_errors)
	
	return better_errors