Merge pull request #758 from effigies/enh/samefile

ENH: Allow DerivativesDataSink to handle output==input

Author: effigies

niworkflows/interfaces/bids.py

@@ -25,6 +25,7 @@
 from json import dumps, loads
 from pathlib import Path
 import shutil
+import os
 from pkg_resources import resource_filename as _pkgres
 import re
 
@@ -627,6 +628,19 @@ def _run_interface(self, runtime):
             self._results["out_file"].append(str(out_file))
             self._results["compression"].append(str(dest_file).endswith(".gz"))
 
+            # An odd but possible case is that an input file is in the location of
+            # the output and we have made no changes to it.
+            # The primary use case is pre-computed derivatives where the output
+            # directory will be filled in.
+            # From a provenance perspective, I would rather inputs and outputs be
+            # cleanly separated, but that is better handled by warnings at the CLI
+            # level than a crash in a datasink.
+            try:
+                if os.path.samefile(orig_file, out_file):
+                    continue
+            except FileNotFoundError:
+                pass
+
             # Set data and header iff changes need to be made. If these are
             # still None when it's time to write, just copy.
             new_data, new_header = None, None