ch.setLevel(logging.DEBUG) formatter = logging.Formatter('%(asctime)s - %(name)s - %(levelname)s - %(message)s') ch.setFormatter(formatter) root.addHandler(ch) 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 # Optional properties annot.comment = "hello world" annot.date = "2011-11-11" annot.sop = "the SOP" annot.annotation_source = "the annotation source"
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 # Optional properties annot.comment = "hello world" annot.date = "2011-11-11" annot.sop = "the SOP" annot.annotation_source = "the annotation source"