Move file virtualization in toil-wdl-runner to task boundaries

src/toil/common.py

@@ -1121,6 +1121,9 @@ def _setupAutoDeployment(
             logger.debug('Injecting user script %s into batch system.', userScriptResource)
             self._batchSystem.setUserScript(userScriptResource)
 
+    def url_exists(self, src_uri: str) -> bool:
+        return self._jobStore.url_exists(self.normalize_uri(src_uri))
+
     # Importing a file with a shared file name returns None, but without one it
     # returns a file ID. Explain this to MyPy.
 

src/toil/jobStores/googleJobStore.py

@@ -383,7 +383,7 @@ def _get_blob_from_url(cls, url, exists=False):
 
         if exists:
             if not blob.exists():
-                raise NoSuchFileException
+                raise NoSuchFileException(fileName)
             # sync with cloud so info like size is available
             blob.reload()
         return blob

src/toil/test/wdl/wdltoil_test.py

@@ -6,7 +6,7 @@
 import subprocess
 import unittest
 from uuid import uuid4
-from typing import Optional
+from typing import Optional, Union
 
 from unittest.mock import patch
 from typing import Any, Dict, List, Set
@@ -49,11 +49,10 @@ def tearDown(self) -> None:
 WDL_CONFORMANCE_TEST_COMMIT = "2d617b703a33791f75f30a9db43c3740a499cd89"
 # These tests are known to require things not implemented by
 # Toil and will not be run in CI.
-WDL_CONFORMANCE_TESTS_UNSUPPORTED_BY_TOIL= [
+WDL_CONFORMANCE_TESTS_UNSUPPORTED_BY_TOIL = [
     16, # Basic object test (deprecated and removed in 1.1); MiniWDL and toil-wdl-runner do not support Objects, so this will fail if ran by them
     21, # Parser: expression placeholders in strings in conditional expressions in 1.0, Cromwell style; Fails with MiniWDL and toil-wdl-runner
     64, # Legacy test for as_map_as_input; It looks like MiniWDL does not have the function as_map()
-    72, # Symlink passthrough; see <https://github.com/DataBiosphere/toil/issues/5031>
     77, # Test that array cannot coerce to a string. WDL 1.1 does not allow compound types to coerce into a string. This should return a TypeError.
 ]