Updated module imports

src/autobigs/cli/info.py

@@ -0,0 +1,46 @@
+from argparse import ArgumentParser, Namespace
+import asyncio
+from autobigs.engine.data.remote.databases.bigsdb import BIGSdbIndex
+
+def setup_parser(parser: ArgumentParser):
+    parser.description = "Fetches the latest BIGSdb MLST database definitions."
+    parser.add_argument(
+        "--retrieve-bigsdbs", "-l",
+        action="store_true",
+        dest="list_dbs",
+        required=False,
+        default=False,
+        help="Lists all known BIGSdb MLST databases (fetched from known APIs and cached)."
+    )
+
+    parser.add_argument(
+        "--retrieve-bigsdb-schemas", "-lschemas",
+        nargs="+",
+        action="extend",
+        dest="list_bigsdb_schemas",
+        required=False,
+        default=[],
+        type=str,
+        help="Lists the known schema IDs for a given BIGSdb sequence definition database name. The name, and then the ID of the schema is given."
+    )
+
+    parser.set_defaults(run=run_asynchronously)
+    return parser
+
+async def run(args: Namespace):
+    async with BIGSdbIndex() as bigsdb_index:
+        if args.list_dbs:
+            known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
+            print("\n".join(known_seqdef_dbs.keys()))
+
+        for bigsdb_schema_name in args.list_bigsdb_schemas:
+            schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
+            for schema_desc, schema_id in schemas.items():
+                print(f"{schema_desc}: {schema_id}")
+
+        if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
+            print("Nothing to do. Try specifying \"-l\".")
+
+def run_asynchronously(args: Namespace):
+    asyncio.run(run(args))
+