Revert "better handle symlinks in Directories (#1462)" (#1483)

This reverts commit 23acadf.

Author: mr-c

cwltool/process.py

@@ -356,28 +356,19 @@ def _relocate(src: str, dst: str) -> None:
             return
 
         # If the source is not contained in source_directories we're not allowed to delete it
-        real_src = fs_access.realpath(src)
+        src = fs_access.realpath(src)
         src_can_deleted = any(
-            os.path.commonprefix([p, real_src]) == p for p in source_directories
+            os.path.commonprefix([p, src]) == p for p in source_directories
         )
 
         _action = "move" if action == "move" and src_can_deleted else "copy"
 
         if _action == "move":
             _logger.debug("Moving %s to %s", src, dst)
-            if fs_access.isdir(src):
-                if fs_access.isdir(dst):
-                    if len(fs_access.listdir(dst)) > 0:
-                        # merge directories
-                        for dir_entry in scandir(src):
-                            _relocate(
-                                dir_entry.path, fs_access.join(dst, dir_entry.name)
-                            )
-                    else:
-                        os.rmdir(dst)
-                        shutil.move(src, dst)
-                else:
-                    shutil.move(src, dst)
+            if fs_access.isdir(src) and fs_access.isdir(dst):
+                # merge directories
+                for dir_entry in scandir(src):
+                    _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
             else:
                 shutil.move(src, dst)
 

tests/symlinks.cwl

@@ -6,7 +6,10 @@
 
 from .util import get_data, needs_docker
 
-from io import StringIO
+if sys.version_info[0] < 3:
+    from StringIO import StringIO
+else:
+    from io import StringIO
 
 
 @needs_docker
@@ -15,21 +18,6 @@ def test_for_910() -> None:
     assert main([get_data("tests/wf/910.cwl")]) == 0
 
 
-def test_symlinks_with_absolute_paths(tmp_path: Path) -> None:
-    """Confirm that absolute paths in Directory types don't cause problems."""
-    assert (
-        main(
-            [
-                "--debug",
-                f"--outdir={tmp_path}/result",
-                f"--tmpdir-prefix={tmp_path}/tmp",
-                get_data("tests/symlinks.cwl"),
-            ]
-        )
-        == 0
-    )
-
-
 @needs_docker
 def test_for_conflict_file_names(tmp_path: Path) -> None:
     stream = StringIO()