def testRequiredFields(self):
required = ViralSeqSet.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a tuple.")
self.assertTrue(len(required) > 0,
"required_fields() did not return empty value.")
def testRequiredFields(self):
""" Test the required_fields() method. """
required = ViralSeqSet.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a tuple.")
self.assertTrue(
len(required) > 0, "required_fields() did not return empty value.")
def set_logging():
root = logging.getLogger()
root.setLevel(logging.DEBUG)
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
set_logging()
session = iHMPSession(username, password)
print("Required fields: ")
print(ViralSeqSet.required_fields())
vss = ViralSeqSet()
vss.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56" }
vss.study = "prediabetes"
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
# Optional properties
vss.comment = "test viral_seq_set comment"
vss.format = "gff3"
vss.format_doc = "the format url"
vss.local_file = temp_file
root = logging.getLogger()
root.setLevel(logging.DEBUG)
ch = logging.StreamHandler(sys.stdout)
ch.setLevel(logging.DEBUG)
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
set_logging()
session = iHMPSession(username, password)
print("Required fields: ")
print(ViralSeqSet.required_fields())
vss = ViralSeqSet()
vss.checksums = {"md5": "72bdc024d83226ccc90fbd2177e78d56"}
vss.study = "prediabetes"
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
# Optional properties
vss.comment = "test viral_seq_set comment"
vss.format = "gff3"
vss.format_doc = "the format url"
vss.local_file = temp_file