Fixes to calc step

preprocessor/preprocessor/steps/calc.py

@@ -4,29 +4,36 @@ import subprocess
 from typing import List
 from glob import glob
 import shutil
+import logging
+
 from osgeo import gdal, osr
 
 from ..util import replace_ext
 
 
+logger = logging.getLogger(__name__)
+
+
 def calc_step(source_dir: os.PathLike, target_dir: os.PathLike, formulas: List[dict]):
     for i, item in enumerate(formulas):
         # get first filename as a base
-        filename = next(glob(join(source_dir, item['inputs']['glob'])))
+        filename = glob(join(source_dir, list(item['inputs'].values())[0]['glob']))
         target_filename = join(
             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)
+            logger.warn('Calc output filename %s already exists' % target_filename)
 
         calc_formula(source_dir, item['inputs'], target_filename, item['formula'], item.get('data_type', 'Float32'))
 
     # take all original files with from the last step
     for filename in glob('%s/*' % source_dir):
-        shutil.copy(filename, join(target_dir, basename(filename)))
+        target_filename = join(target_dir, basename(filename))
+        if isfile(target_filename):
+            logger.warn('Calc output filename %s already exists' % target_filename)
+        shutil.copy(filename, target_filename)
 
 
 def calc_formula(source_dir: os.PathLike, inputs: List[dict], target_filename: os.PathLike, formula: str, data_type: str="Float32", nodata_value: float=None):
@@ -39,10 +46,10 @@ def calc_formula(source_dir: os.PathLike, inputs: List[dict], target_filename: o
 
     for name, locator in inputs:
         # select first
-        filename = next(glob(join(source_dir, locator['glob'])))
+        filename = glob(join(source_dir, locator['glob']))[0]
         cmd.extend([
             "-%s" % name, filename,
-            "-%s_band=%d" % locator.get('band', 1),
+            "--%s_band=%d" % locator.get('band', 1),
         ])
 
     if nodata_value is not None: