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(Annotation.required_fields())
annot = Annotation()
annot.annotation_pipeline = "the annotation pipeline"
annot.checksums = {"md5": "72bdc024d83226ccc90fbd2177e78d56"}
annot.format = "gff3"
annot.format_doc = "the format url"
annot.orf_process = "the orf process"
annot.study = "prediabetes"
annot.size = 131313
print("Creating a temp file for example/testing purposes.")
temp_file = tempfile.NamedTemporaryFile(delete=False).name
print("Local file: %s" % temp_file)
annot.local_file = temp_file
