Raising error when a file would be overridden

preprocessor/preprocessor/steps/calc.py

 import os
-from os.path import basename, dirname, join
-from math import ceil, floor
-import logging
-import uuid
-import os
+from os.path import basename, dirname, join, isfile
 import subprocess
 from typing import List
 from glob import glob
@@ -21,6 +17,10 @@ def calc_step(source_dir: os.PathLike, target_dir: os.PathLike, formulas: List[d
             target_dir,
             replace_ext(basename(filename), item.get('output_postfix', '_proc%d' % i) + '.tif', False)
         )
+        # fail if a file would be overridden
+        # TODO: maybe just log an error
+        if isfile(target_filename):
+            raise Exception('Calc output filename %s already exists' % target_filename)
 
         calc_formula(source_dir, item['inputs'], target_filename, item['formula'], item.get('data_type', 'Float32'))
 

preprocessor/preprocessor/steps/output.py

@@ -19,7 +19,7 @@ def output_step(source_dir: os.PathLike, target_dir: os.PathLike, options: dict=
 
     # warp each individual file
     warped_files = []
-    for filename in glob(join(source_dir, '*')):
+    for filename in glob(join(source_dir, '*.tif')):
         target_filename = join(target_dir, replace_ext(basename(filename), extension))
         gdal.Warp(target_filename, filename, options=gdal.WarpOptions(
             **options