Deal with normalized paths when importing from a WDL JSON file

src/toil/wdl/wdltoil.py

@@ -57,7 +57,7 @@
  from typing import NotRequired
 from mypy_extensions import Arg, DefaultArg
 from urllib.error import HTTPError
-from urllib.parse import quote, unquote, urljoin, urlsplit
+from urllib.parse import quote, unquote, urljoin, urlsplit, urlparse
 from functools import partial
 
 import WDL.Error
@@ -1318,7 +1318,11 @@ def _virtualize_filename(self, filename: str) -> str:
  else:
  # Otherwise this is a local file and we want to fake it as a Toil file store file
  # Make it an absolute path
- if self.execution_dir is not None:
+ parsed = urlparse(filename)
+ if parsed.scheme == "file":
+ # conversion was already done by normalize_uri
+ abs_filename = unquote(parsed.path)
+ elif self.execution_dir is not None:
  # To support relative paths from execution directory, join the execution dir and filename
  # If filename is already an abs path, join() will not do anything
  abs_filename = os.path.join(self.execution_dir, filename)