Changing CSV argument to --csv or -o

pyproject.toml

@@ -6,7 +6,7 @@ build-backend = "setuptools.build_meta"
 name = "autoBIGS.cli"
 dynamic = ["version"]
 readme = "README.md"
-license = {file = "LICENSE"}
+license = {text = "GPL-3.0-or-later"}
 dependencies = [
     "autoBIGS-engine==0.12.*"
 ]
@@ -14,8 +14,8 @@ requires-python = ">=3.12"
 description = "A CLI tool to rapidly fetch fetch MLST profiles given sequences for various diseases."
 
 [project.urls]
-Repository = "https://github.com/RealYHD/autoBIGS.cli"
+Repository = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli"
-Issues = "https://github.com/RealYHD/autoBIGS.cli/issues"
+Issues = "https://github.com/Syph-and-VPD-Lab/autoBIGS.cli/issues"
 
 
 [project.scripts]

src/autobigs/cli/info.py

@@ -27,7 +27,7 @@ def setup_parser(parser: ArgumentParser):
     )
 
     parser.add_argument(
-        "--csv-prefix", "-o",
+        "--csv", "-o",
         dest="csv_output",
         required=False,
         default=None,
@@ -39,18 +39,21 @@ def setup_parser(parser: ArgumentParser):
 
 async def run(args: Namespace):
     async with BIGSdbIndex() as bigsdb_index:
+        if args.list_dbs and len(args.list_bigsdb_schemas) > 0:
+            print("Cannot specify both database listing and schema listing, please choose one!")
+            exit(1)
+
         if args.list_dbs:
             known_seqdef_dbs = await bigsdb_index.get_known_seqdef_dbs(force=False)
             sorted_seqdef_dbs = [(name, source) for name, source in sorted(known_seqdef_dbs.items())]
             print("The following are all known BIGS database names, and their source (sorted alphabetically):")
             print("\n".join(["{0}: {1}".format(name, source) for name, source in sorted_seqdef_dbs]))
             if args.csv_output:
-                dbs_csv_path = path.splitext(args.csv_output)[0] + "_" + "dbs.csv"
+                with open(args.csv_output, "w") as csv_out_handle:
-                with open(dbs_csv_path, "w") as csv_out_handle:
                     writer = csv.writer(csv_out_handle)
                     writer.writerow(("BIGSdb Names", "Source"))
                     writer.writerows(sorted_seqdef_dbs)
-                    print("\nDatabase output written to {0}".format(dbs_csv_path))
+                    print("\nDatabase output written to {0}".format(args.csv_output))
 
         for bigsdb_schema_name in args.list_bigsdb_schemas:
             schemas = await bigsdb_index.get_schemas_for_seqdefdb(bigsdb_schema_name)
@@ -58,14 +61,15 @@ async def run(args: Namespace):
             print("The following are the known schemas for \"{0}\", and their associated IDs:".format(bigsdb_schema_name))
             print("\n".join(["{0}: {1}".format(name, id) for name, id in sorted_schemas]))
             if args.csv_output:
-                schema_csv_path = path.splitext(args.csv_output)[0] + "_" + "schemas.csv"
+                with open(args.csv_output, "w") as csv_out_handle:
-                with open(schema_csv_path, "w") as csv_out_handle:
                     writer = csv.writer(csv_out_handle)
                     writer.writerow(("Name", "ID"))
                     writer.writerows(sorted_schemas)
-                    print("\nSchema list output written to {0}".format(schema_csv_path))
+                    print("\nSchema list output written to {0}".format(args.csv_output))
+
         if not (args.list_dbs or len(args.list_bigsdb_schemas) > 0):
             print("Nothing to do. Try specifying \"-l\" for a list of known databases, or \"-h\" for more information.")
+            exit(1)
 
 def run_asynchronously(args: Namespace):
     asyncio.run(run(args))