"--structure_type", action="store", dest="structure_type", required=True, help="Type of structure (astral, pdb, denovo, other)", ) parser.add_argument( "--mammoth_table", action="store", dest="table_destination", default="default", help="The StructureMammoth table in hpf database to store mammoth results, default=StructureMammoth, 1186=yeast experiment", ) args = parser.parse_args() record = ( session.query(MammothRun) .filter(MammothRun.supergroup_key == args.supergroup_key) .filter(MammothRun.version == args.version) .filter(MammothRun.group_key1 == args.group_key1) .filter(MammothRun.group_key2 == args.group_key2) .filter(MammothRun.status == "running") .first() ) store_scores(args.results_file, record, args.structure_type, args.version, args.table_destination) record.status = "complete" record.comment = "Mammoth run successful, imported results using store_scores.py" session.flush()
help="The version of the MCM run. Simply an arbitrary integer to allow for keeping track of multiple MCM runs, if desired") parser.add_argument("--supergroup_key", action="store", type=int, dest="supergroup_key", required=True, help="The supergroup of the mammoth run. ") parser.add_argument("--results_dir", action="store", dest="results_dir", required=True, help="The mammoth results directory") parser.add_argument("--structure_type", action="store", dest="structure_type", required=True, help="Type of structure (astral, pdb, denovo, other)") parser.add_argument("--mammoth_table", action="store", dest="table_destination", default="default", help="The StructureMammoth table in hpf database to store mammoth results, default=StructureMammoth, 1186=yeast experiment") args = parser.parse_args() records = session.query(MammothRun).filter(MammothRun.supergroup_key==args.supergroup_key)\ .filter(MammothRun.version==args.version)\ .filter(MammothRun.status=='notuploaded')\ .all() for mammoth_record in records: results_file = os.path.join(args.results_dir,"mammoth_sg_{0}_g_{1}_{2}.results".format(mammoth_record.supergroup_key, mammoth_record.group_key1, mammoth_record.group_key2)) print "loading: " + results_file ret = store_scores(results_file, mammoth_record, args.structure_type, args.version, args.table_destination) mammoth_record.status = 'complete' mammoth_record.comment = "Mammoth run successful, imported results using store_scores.py" session.flush()