fixup! db: Implement basic import/export of data

Simplify argparse argument checking
nextstrain · Jan 3, 2023 · bc3f5c5 · bc3f5c5
1 parent 6e6e20d
commit bc3f5c5
Show file tree

Hide file tree

Showing 2 changed files with 14 additions and 10 deletions.
diff --git a/augur/db/export/__init__.py b/augur/db/export/__init__.py
@@ -9,7 +9,7 @@
 
 def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("export", help=first_line(__doc__))
-    parser.add_argument('--db', required=True, help="SQLite3 database file to export from.")
+    parser.add_argument('--db', help="SQLite3 database file to export from.")
     parser.add_argument('--output-metadata', help="Metadata file to output.")
     parser.add_argument('--output-sequences', help="Metadata file to output.")
     parser.add_argument('--metadata-table', default=DEFAULT_IMPORTED_METADATA_TABLE, help="Table name in database that contains metadata.")
@@ -20,12 +20,14 @@ def register_parser(parent_subparsers):
 def run(args):
     validate_args(args)
 
-    if args.db:
-        export_sqlite3(args.db,
-            args.metadata_table, args.sequences_table,
-            args.output_metadata, args.output_sequences)
+    export_sqlite3(args.db,
+        args.metadata_table, args.sequences_table,
+        args.output_metadata, args.output_sequences)
 
 
 def validate_args(args):
+    if not args.db:
+        raise AugurError("Must provide a database filepath.")
+
     if not any((args.output_metadata, args.output_sequences)):
         raise AugurError("Must choose to output metadata and/or sequences.")
diff --git a/augur/db/import_/__init__.py b/augur/db/import_/__init__.py
@@ -11,7 +11,7 @@ def register_parser(parent_subparsers):
     parser = parent_subparsers.add_parser("import", help=first_line(__doc__))
     parser.add_argument('--metadata', '-m', help="Metadata file to import into the database.")
     parser.add_argument('--sequences', '-s', help="Sequences file (FASTA) to import into the database.")
-    parser.add_argument('--output-db', required=True, help="Destination SQLite3 database file.")
+    parser.add_argument('--output-db', help="Destination SQLite3 database file.")
     parser.add_argument('--metadata-table', default=DEFAULT_IMPORTED_METADATA_TABLE, help="Table name to store metadata in.")
     parser.add_argument('--sequences-table', default=DEFAULT_IMPORTED_SEQUENCES_TABLE, help="Table name to store sequences in.")
     parser.add_argument('--skip-strain-indexing', action='store_true', help="""
@@ -23,12 +23,14 @@ def register_parser(parent_subparsers):
 def run(args):
     validate_args(args)
 
-    if args.output_db:
-        import_sqlite3(args.metadata, args.metadata_table,
-            args.sequences, args.sequences_table,
-            args.output_db, args.skip_strain_indexing)
+    import_sqlite3(args.metadata, args.metadata_table,
+        args.sequences, args.sequences_table,
+        args.output_db, args.skip_strain_indexing)
 
 
 def validate_args(args):
+    if not args.output_db:
+        raise AugurError("Must provide a database filepath.")
+
     if not any((args.metadata, args.sequences)):
         raise AugurError("Must provide metadata and/or sequences.")