Add fs_access for unknown URIs in relocateOutputs() _realpath(). (#1376)

Author: DailyDreaming

cwltool/job.py

@@ -409,7 +409,7 @@ def _execute(
                     )
                 else:
                     raise ValueError(
-                        "'lsiting' in self.generatefiles but no "
+                        "'listing' in self.generatefiles but no "
                         "generatemapper was setup."
                     )
 

cwltool/process.py

@@ -399,12 +399,13 @@ def _relocate(src: str, dst: str) -> None:
     def _realpath(
         ob: CWLObjectType,
     ) -> None:  # should be type Union[CWLFile, CWLDirectory]
-        if cast(str, ob["location"]).startswith("file:"):
-            ob["location"] = file_uri(
-                os.path.realpath(uri_file_path(cast(str, ob["location"])))
-            )
-        if cast(str, ob["location"]).startswith("/"):
-            ob["location"] = os.path.realpath(cast(str, ob["location"]))
+        location = cast(str, ob["location"])
+        if location.startswith("file:"):
+            ob["location"] = file_uri(os.path.realpath(uri_file_path(location)))
+        elif location.startswith("/"):
+            ob["location"] = os.path.realpath(location)
+        elif not location.startswith("_:") and ":" in location:
+            ob["location"] = file_uri(fs_access.realpath(location))
 
     outfiles = list(_collectDirEntries(outputObj))
     visit_class(outfiles, ("File", "Directory"), _realpath)