RF: git-annex specific handling in to_filename + allow NIBABEL_REMOVE_BEFORE_TO_FILENAME env var

Author: yarikoptic

nibabel/filebasedimages.py

@@ -17,6 +17,13 @@
                               splitext_addext)
 from .openers import ImageOpener
 
+# OS-specific path
+_GIT_ANNEX_OBJECTS_PATH = os.path.join('.git', 'annex', 'objects')
+
+def _is_annex_symlink(path):
+    """Return True if file is a symlink to the git-annex objects"""
+    return os.path.islink(path) and _GIT_ANNEX_OBJECTS_PATH in os.path.realpath(path)
+
 
 class ImageFileError(Exception):
     pass
@@ -349,10 +356,11 @@ def to_filename(self, filename):
         None
         '''
         self.file_map = file_map = self.filespec_to_file_map(filename)
+        remove_env = os.environ.get('NIBABEL_REMOVE_BEFORE_TO_FILENAME', None)
         for _, fh in file_map.items():
             if not isinstance(fh, FileHolder):
                 continue
-            if os.path.exists(fh.filename):
+            if os.path.lexists(fh.filename) and (remove_env or _is_annex_symlink(fh.filename)):
                 # Remove previous file where new file would be saved
                 # Necessary e.g. for cases where file is a symlink pointing
                 # to some non-writable file (e.g. under git annex control)