Deal with normalized paths when importing from a WDL JSON file (#5121)

* Deal with already absolute'd paths from Toil.normalize in a JSON file import * Run filename through unquote before running urlparse * Update src/toil/wdl/wdltoil.py Co-authored-by: Adam Novak <[email protected]> --------- Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com> Co-authored-by: Adam Novak <[email protected]>
DataBiosphere · Oct 24, 2024 · e98eb4b · e98eb4b
1 parent 5beff7c
commit e98eb4b
Showing 1 changed file with 6 additions and 2 deletions.
diff --git a/src/toil/wdl/wdltoil.py b/src/toil/wdl/wdltoil.py
@@ -44,7 +44,7 @@
 
 from functools import partial
 from urllib.error import HTTPError
-from urllib.parse import quote, unquote, urljoin, urlsplit
+from urllib.parse import quote, unquote, urljoin, urlsplit, urlparse
 
 import WDL.Error
 import WDL.runtime.config
@@ -1520,7 +1520,11 @@ 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)