better handle symlinks in Directories

cwltool/process.py

@@ -356,19 +356,28 @@ def _relocate(src: str, dst: str) -> None:
             return
 
         # If the source is not contained in source_directories we're not allowed to delete it
-        src = fs_access.realpath(src)
+        real_src = fs_access.realpath(src)
         src_can_deleted = any(
-            os.path.commonprefix([p, src]) == p for p in source_directories
+            os.path.commonprefix([p, real_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) and fs_access.isdir(dst):
-                # merge directories
-                for dir_entry in scandir(src):
-                    _relocate(dir_entry.path, fs_access.join(dst, dir_entry.name))
+            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)
             else:
                 shutil.move(src, dst)
 

tests/symlinks.cwl

@@ -0,0 +1,14 @@
+#!/usr/bin/env cwl-runner
+cwlVersion: v1.0
+class: CommandLineTool
+inputs: []
+baseCommand: [ bash, -c ]
+arguments:
+# - "mkdir foo; echo 42 > foo/bar; ln -s bar foo/baz"
+ - "mkdir foo; echo 42 > foo/bar; ln -s $PWD/foo/bar foo/baz"
+# - "mkdir foo; ln -s $PWD/foo/bar foo/baz ; echo 42 > foo/bar"
+outputs:
+  result:
+    type: Directory
+    outputBinding:
+      glob: foo

tests/test_relocate.py

@@ -6,10 +6,7 @@
 
 from .util import get_data, needs_docker
 
-if sys.version_info[0] < 3:
-    from StringIO import StringIO
-else:
-    from io import StringIO
+from io import StringIO
 
 
 @needs_docker
@@ -18,6 +15,21 @@ 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()