def create_parser(description):
cli = BaseCLI(description, None, 1, hostname_required=True)
cli.remove_options(['--config-file'])
cli.parser.add_argument('config_file',
help='project-specific config file')
cli.parser.add_argument('--catalog-id', type=int, default=1)
cli.parser.add_argument(
'--scratch-directory',
help='directory for temporary storage of downloaded files')
return (cli)
def main():
logger = logging.getLogger(__name__)
logger.setLevel("WARNING")
cli = BaseCLI(__name__,
"Create a sitemap from a table specified on the command line or a set of tables from a config file",
__version__, hostname_required=True)
cli.remove_options(["--credential-file", "--token", "--oauth2-token"])
cli.parser.add_argument("--catalog", default=1, metavar="<1>", help="Catalog number")
cli.parser.add_argument("-p", "--priority", type=float,
help="A floating-point number between 0.0 and 1.0 indicating the table's priority")
cli.parser.add_argument("-s", "--schema", help="the name of the schema of the (single) table to include")
cli.parser.add_argument("-t", "--table", help="the name of the (single) table to include")
args = cli.parse_cli()
if args.priority is not None:
if args.priority < 0 or args.priority > 1:
logger.error("priority should be a floating-point number between 0 and 1")
sys.exit(1)
if not ((args.schema and args.table) or args.config_file):
logger.error("must specify either a schema and table or a config file")
sys.exit(1)
sb = SitemapBuilder("https", args.host, args.catalog)
if args.schema and args.table:
sb.add_table_spec(args.schema, args.table, priority=args.priority)
if args.config_file:
rows = json.load(open(args.config_file))
for row in rows:
if row.get("schema") is None or row.get("table") is None:
logger.warning("malformed entry in {f}: schema or table is missing. Skipping".format(f=args.config_file))
next
if row.get("priority") is None:
priority = args.priority
else:
try:
priority = float(row.get("priority"))
if priority < 0 or priority > 1:
logger.warning("bad priority '{p}' - should be a floating-point number between 0 and 1. Ignoring".format(p=priority))
priority = args.priority
except ValueError:
logger.warning("malformed priority '{p}' - should be a floating-point number between 0 and 1. Ignoring".format(p=row.get("priority")))
priority = args.priority
sb.add_table_spec(row["schema"], row["table"], priority=priority)
sb.write_sitemap(sys.stdout)
return 0
"Input_Bag": args.inputBagRID,
"Notes": args.notes,
"Execution_Status": args.status,
"Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
}
entities = run_table.insert([run_data])
rid = entities[0]["RID"]
else:
run_data = {
"RID": args.update,
"Replicate": args.repRID,
"Workflow": args.workflowRID,
"Reference_Genome": args.referenceRID,
"Input_Bag": args.inputBagRID,
"Notes": args.notes,
"Execution_Status": args.status,
"Execution_Status_Detail": args.statusDetail.replace('\\n','\n')
}
entities = run_table.update([run_data])
rid = args.update
print(rid)
if __name__ == '__main__':
args = get_args()
cli = BaseCLI("Custom RNASeq query", None, 1)
cli.remove_options(["--config-file"])
host = args.host
credentials = {"cookie": args.cookie}
main(host, 2, credentials)
