def testRequiredFields(self):
required = WgsAssembledSeqSet.required_fields()
self.assertEqual(type(required), tuple,
"required_fields() returns a tuple.")
self.assertTrue(len(required) > 0,
"required_field() did not return empty value.")
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("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
print("Required fields: ")
print(WgsAssembledSeqSet.required_fields())
seq_set = WgsAssembledSeqSet()
seq_set.assembler = "the assembler"
seq_set.assembly_name = "name for the assembly"
seq_set.comment = "test comment. Hello world!"
seq_set.checksums = { "md5": "72bdc024d83226ccc90fbd2177e78d56"}
seq_set.format = "fasta"
seq_set.format_doc = "the format doc"
seq_set.sequence_type = "nucleotide"
seq_set.size = 5000
seq_set.study = "prediabetes"
seq_set.links = { "computed_from": [ "b9af32d3ab623bcfbdce2ea3a502c015" ] }
# Optional properties
formatter = logging.Formatter(
'%(asctime)s - %(name)s - %(levelname)s - %(message)s')
ch.setFormatter(formatter)
root.addHandler(ch)
set_logging()
session = iHMPSession(username, password)
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
print("Required fields: ")
print(WgsAssembledSeqSet.required_fields())
seq_set = WgsAssembledSeqSet()
seq_set.assembler = "the assembler"
seq_set.assembly_name = "name for the assembly"
seq_set.comment = "test comment. Hello world!"
seq_set.checksums = {"md5": "72bdc024d83226ccc90fbd2177e78d56"}
seq_set.format = "fasta"
seq_set.format_doc = "the format doc"
seq_set.sequence_type = "nucleotide"
seq_set.size = 5000
seq_set.study = "prediabetes"
seq_set.links = {"computed_from": ["b9af32d3ab623bcfbdce2ea3a502c015"]}
# Optional properties