ydeng/autoBIGS.cli
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Fixed --csv output being blank when listing dbs
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Harrison Deng 2025-03-07 16:08:25 +00:00
parent 8e1b30ae7d
commit 09cc9787fd
1 changed files with 13 additions and 12 deletions
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src/autobigs/cli/info.py
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@ -53,18 +53,19 @@ async def run(args: Namespace):
writer.writerows(sorted_seqdef_dbs) writer.writerows(sorted_seqdef_dbs)
print("\nDatabase output written to {0}".format(args.csv_output)) print("\nDatabase output written to {0}".format(args.csv_output))
csv_scheme_rows = [] if args.list_bigsdb_schemes:
for bigsdb_scheme_name in args.list_bigsdb_schemes: csv_scheme_rows = []
schemes = await bigsdb_index.get_schemes_for_seqdefdb(bigsdb_scheme_name) for bigsdb_scheme_name in args.list_bigsdb_schemes:
csv_scheme_rows.extend([(name, id, bigsdb_scheme_name) for name, id in sorted(schemes.items())]) schemes = await bigsdb_index.get_schemes_for_seqdefdb(bigsdb_scheme_name)
print("The following are the known schemes for \"{0}\", and their associated IDs:".format(bigsdb_scheme_name)) csv_scheme_rows.extend([(name, id, bigsdb_scheme_name) for name, id in sorted(schemes.items())])
print("\n".join(["{0}: {1}".format(name, id) for name, id, database in csv_scheme_rows])) print("The following are the known schemes for \"{0}\", and their associated IDs:".format(bigsdb_scheme_name))
if args.csv_output: print("\n".join(["{0}: {1}".format(name, id) for name, id, database in csv_scheme_rows]))
with open(args.csv_output, "w") as csv_out_handle: if args.csv_output:
writer = csv.writer(csv_out_handle) with open(args.csv_output, "w") as csv_out_handle:
writer.writerow(("Name", "ID", "Database Name")) writer = csv.writer(csv_out_handle)
writer.writerows(csv_scheme_rows) writer.writerow(("Name", "ID", "Database Name"))
print("\nscheme list output written to {0}".format(args.csv_output)) writer.writerows(csv_scheme_rows)
print("\nscheme list output written to {0}".format(args.csv_output))
def run_asynchronously(args: Namespace): def run_asynchronously(args: Namespace):
asyncio.run(run(args)) asyncio.run(run(args))