Merge pull request mmcdermott#224 from mmcdermott/mimic-premeds-minor…

…-fixes Minor fixes in MIMIC_example
VectorInstitute · Nov 12, 2024 · 553250e · 553250e
2 parents f38901d + 069b2b9
commit 553250e
Showing 1 changed file with 3 additions and 3 deletions.
diff --git a/MIMIC-IV_Example/pre_MEDS.py b/MIMIC-IV_Example/pre_MEDS.py
@@ -229,7 +229,7 @@ def main(cfg: DictConfig):
         )
         exit(0)
 
-    all_fps = list(input_dir.glob("**/*.*"))
+    all_fps = list(input_dir.rglob("*/*.*"))
 
     dfs_to_load = {}
     seen_fps = {}
@@ -299,9 +299,9 @@ def main(cfg: DictConfig):
 
         logger.info(f"Loading {str(df_to_load_fp.resolve())} for manipulating other dataframes...")
         if df_to_load_fp.suffix in [".csv.gz"]:
-            df = read_fn(df_to_load_fp, columns=cols)
+            df = df_to_load_read_fn(df_to_load_fp, columns=cols)
         else:
-            df = read_fn(df_to_load_fp)
+            df = df_to_load_read_fn(df_to_load_fp)
         logger.info(f"  Loaded in {datetime.now() - st}")
 
         for fp in fps: