From 578643e865ce69c68c38f60868d18178b5e973f8 Mon Sep 17 00:00:00 2001
From: Matt Garber <matthew.garber@childrens.harvard.edu>
Date: Tue, 24 Oct 2023 09:12:45 -0400
Subject: [PATCH] study parser cleanup

---
 cumulus_library/cli_parser.py   |  6 +++---
 cumulus_library/study_parser.py | 12 ++++--------
 2 files changed, 7 insertions(+), 11 deletions(-)

diff --git a/cumulus_library/cli_parser.py b/cumulus_library/cli_parser.py
index e5f4bfd0..f25005aa 100644
--- a/cumulus_library/cli_parser.py
+++ b/cumulus_library/cli_parser.py
@@ -16,7 +16,7 @@ def add_table_builder_argument(parser: argparse.ArgumentParser) -> None:
     """Adds --builder arg to a subparser"""
     parser.add_argument(
         "--builder",
-        help=(argparse.SUPPRESS),
+        help=argparse.SUPPRESS,
     )
 
 
@@ -129,7 +129,7 @@ def get_parser() -> argparse.ArgumentParser:
     clean.add_argument(
         "--prefix",
         action="store_true",
-        help=(argparse.SUPPRESS),
+        help=argparse.SUPPRESS,
     )
 
     build = actions.add_parser(
@@ -145,7 +145,7 @@ def get_parser() -> argparse.ArgumentParser:
     build.add_argument(
         "--continue",
         dest="continue_from",
-        help=(argparse.SUPPRESS),
+        help=argparse.SUPPRESS,
     )
 
     export = actions.add_parser(
diff --git a/cumulus_library/study_parser.py b/cumulus_library/study_parser.py
index 2a6a7361..6fab3e05 100644
--- a/cumulus_library/study_parser.py
+++ b/cumulus_library/study_parser.py
@@ -94,15 +94,11 @@ def get_sql_file_list(self, continue_from: str = None) -> Optional[StrList]:
         sql_config = self._study_config.get("sql_config", {})
         sql_files = sql_config.get("file_names", [])
         if continue_from:
-            match_found = False
-            for file in sql_files:
-                print(continue_from.replace(".sql", ""))
-                print(file.replace(".sql", ""))
+            for pos, file in enumerate(sql_files):
                 if continue_from.replace(".sql", "") == file.replace(".sql", ""):
-                    sql_files = sql_files[sql_files.index(file) :]
-                    match_found = True
+                    sql_files = sql_files[pos:]
                     break
-            if not match_found:
+            else:
                 sys.exit(f"No tables matching '{continue_from}' found")
         return sql_files
 
@@ -206,7 +202,7 @@ def clean_study(
             print("The following views/tables were selected by prefix:")
             for view_table in view_table_list:
                 print(f"  {view_table[0]}")
-            confirm = input("Remove these tables? (Y/N)")
+            confirm = input("Remove these tables? (y/N)")
             if confirm.lower() not in ("y", "yes"):
                 sys.exit("Table cleaning aborted")
         with get_progress_bar(disable=verbose) as progress: