handle unsupported file operations

cwltool/job.py

@@ -711,10 +711,17 @@ def create_file_and_add_volume(
             file_literal.write(contents)
         if not host_outdir_tgt:
             self.append_volume(runtime, new_file, volume.target, writable=writable)
-        if writable:
-            ensure_writable(host_outdir_tgt or new_file)
-        else:
-            ensure_non_writable(host_outdir_tgt or new_file)
+        try:
+            if writable:
+                ensure_writable(host_outdir_tgt or new_file)
+            else:
+                ensure_non_writable(host_outdir_tgt or new_file)
+        except PermissionError as err:
+            _logger.warning(
+                "Encountered permission error trying to modify "
+                f"{host_outdir_tgt or new_file}:\n{err}"
+                "\nProceeding with caution."
+            )
         return host_outdir_tgt or new_file
 
     def add_volumes(

cwltool/process.py

@@ -373,7 +373,14 @@ def _relocate(src: str, dst: str) -> None:
                 for dir_entry in scandir(src):
                     _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
             else:
-                shutil.move(src, dst)
+                try:
+                    shutil.move(src, dst)
+                except (PermissionError, OSError, shutil.Error):
+                    # handle filesystems that don't support mode/attr changes
+                    try:
+                        shutil.move(src, dst, copy_function=shutil.copyfile)
+                    except:
+                        pass
 
         elif _action == "copy":
             _logger.debug("Copying %s to %s", src, dst)
@@ -384,7 +391,17 @@ def _relocate(src: str, dst: str) -> None:
                     os.unlink(dst)
                 shutil.copytree(src, dst)
             else:
-                shutil.copy2(src, dst)
+                try:
+                    shutil.copy2(src, dst)
+                except (PermissionError, OSError, shutil.Error):
+                    # handle filesystems that don't support mode/attr changes
+                    if os.path.isdir(dst):
+                        shutil.copyfile(src, os.path.join(dst, os.path.basename(src)))
+                    else:
+                        try:
+                            shutil.copyfile(src, dst)
+                        except:
+                            pass
 
     def _realpath(
         ob: CWLObjectType,