def call_validate(args):
"""
Calls the Validator to validate input json. Exits with feedback to user regarding errors in json or reports no
errors found.
:param args: validation subparser arguments.
:return:
"""
logger.info("Validation requested.")
validator = Validator(wdl=args.wdl, json=args.json)
result = validator.validate_json()
if len(result) != 0:
e = "{} input file contains the following errors:\n{}".format(args.json, "\n".join(result))
# This will also print to stdout so no need for a print statement
logger.critical(e)
sys.exit(1)
else:
s = 'No errors found in {}'.format(args.wdl)
print(s)
logger.info(s)
class ValidatorUnitTests(unittest.TestCase):
"""
This test class tests good inputs only. A separate one for bad inputs is below.
"""
@classmethod
def setUpClass(self):
resources = c.resource_dir
self.logger = logging.getLogger('test_validator')
hdlr = logging.FileHandler(
os.path.join(c.log_dir, 'test_validator.log'))
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
hdlr.setFormatter(formatter)
self.logger.addHandler(hdlr)
self.logger.setLevel(logging.INFO)
self.wdl = os.path.join(resources, 'test.wdl')
self.json = os.path.join(resources, 'test.json')
self.validator = Validator(wdl=self.wdl, json=self.json)
self.logger.info('Starting Validator tests...')
self.wdl_args = self.validator.get_wdl_args()
self.json_args = self.validator.get_json()
def test_validate_gs_url(self):
sb = SingleBucket("broad-cil-devel-bucket")
foo = open("validation_test.txt", "w")
foo.write("test")
foo.close()
sb.upload_file("validation_test.txt", "validation_test.txt")
result = self.validator.validate_gs_url(
"gs://broad-cil-devel-bucket/broad-file-inputs/validation_test.txt"
)
self.assertTrue(result)
def test_get_wdl_args(self):
self.assertIsInstance(self.wdl_args, dict)
def test_get_json(self):
self.logger.info("Testing get_json...")
self.assertIsInstance(self.json_args, dict)
def test_validate_param_json(self):
self.logger.info("Testing validate_param_json...")
for k, v in self.json_args.items():
if not self.validator.validate_param(k, self.wdl_args):
print(k, v)
self.assertIs(self.validator.validate_param(k, self.wdl_args),
True)
def test_validate_string(self):
self.logger.info("Testing validate_string...")
self.assertIs(self.validator.validate_string('foo'), True)
self.assertIs(self.validator.validate_string(0), False)
self.assertIs(self.validator.validate_string(1.0), False)
self.assertIs(self.validator.validate_string(True), False)
def test_validate_boolean(self):
self.logger.info("Testing validate_boolean...")
self.assertIs(self.validator.validate_boolean('foo'), False)
self.assertIs(self.validator.validate_boolean(0), False)
self.assertIs(self.validator.validate_boolean(1.0), False)
self.assertIs(self.validator.validate_boolean(True), True)
def test_validate_int(self):
self.logger.info("Testing validate_int...")
self.assertIs(self.validator.validate_int('foo'), False)
self.assertIs(self.validator.validate_int(0), True)
self.assertIs(self.validator.validate_int(1.0), False)
self.assertIs(self.validator.validate_int(True), True)
def test_validate_float(self):
self.logger.info("Testing validate_float...")
self.assertIs(self.validator.validate_float('foo'), False)
self.assertIs(self.validator.validate_float(0), False)
self.assertIs(self.validator.validate_float(1.0), True)
self.assertIs(self.validator.validate_float(True), False)
def test_validate_file(self):
self.assertIs(self.validator.validate_file(self.wdl), True)
self.assertIs(self.validator.validate_file('notexists.txt'), False)
def test_validate_samples_array(self):
samples_array = [['S1', self.wdl], ['S2', self.json],
['S3', 'not_exists.txt']]
result = self.validator.validate_samples_array(samples_array)
self.assertEqual(1, len(result))
def test_validate_json(self):
self.validator.validate_json()
@classmethod
def tearDownClass(self):
self.logger.info("Test done!")