add: do not delete stage files before add

dvc/repo/add.py

@@ -98,8 +98,11 @@ def add(  # noqa: C901
                 **kwargs,
             )
 
+            # remove existing stages that are to-be replaced with these
+            # new stages for the graph checks.
+            old_stages = set(repo.stages) - set(stages)
             try:
-                repo.check_modified_graph(stages)
+                repo.check_modified_graph(stages, list(old_stages))
             except OverlappingOutputPathsError as exc:
                 msg = (
                     "Cannot add '{out}', because it is overlapping with other "
@@ -233,7 +236,6 @@ def _create_stages(
     transfer=False,
     **kwargs,
 ):
-    from dvc.dvcfile import Dvcfile
     from dvc.stage import Stage, create_stage, restore_meta
 
     expanded_targets = glob_targets(targets, glob=glob)
@@ -259,12 +261,9 @@ def _create_stages(
             external=external,
         )
         restore_meta(stage)
-        Dvcfile(repo, stage.path).remove()
         if desc:
             stage.outs[0].desc = desc
 
-        repo._reset()  # pylint: disable=protected-access
-
         if not stage:
             if pbar is not None:
                 pbar.total -= 1

tests/func/test_add.py

@@ -24,7 +24,11 @@
 from dvc.hash_info import HashInfo
 from dvc.main import main
 from dvc.objects.db import ODBManager
-from dvc.output import OutputAlreadyTrackedError, OutputIsStageFileError
+from dvc.output import (
+    OutputAlreadyTrackedError,
+    OutputDoesNotExistError,
+    OutputIsStageFileError,
+)
 from dvc.stage import Stage
 from dvc.stage.exceptions import (
     StageExternalOutputsError,
@@ -1190,3 +1194,42 @@ def test_add_ignored(tmp_dir, scm, dvc):
     assert str(exc.value) == ("bad DVC file name '{}' is git-ignored.").format(
         os.path.join("dir", "subdir.dvc")
     )
+
+
+def test_add_on_not_existing_file_should_not_remove_stage_file(tmp_dir, dvc):
+    (stage,) = tmp_dir.dvc_gen("foo", "foo")
+    (tmp_dir / "foo").unlink()
+    dvcfile_contents = (tmp_dir / stage.path).read_text()
+
+    with pytest.raises(OutputDoesNotExistError):
+        dvc.add("foo")
+    assert (tmp_dir / "foo.dvc").exists()
+    assert (tmp_dir / stage.path).read_text() == dvcfile_contents
+
+
+@pytest.mark.parametrize(
+    "target",
+    [
+        "dvc.repo.Repo.check_modified_graph",
+        "dvc.stage.Stage.save",
+        "dvc.stage.Stage.commit",
+    ],
+)
+def test_add_does_not_remove_stage_file_on_failure(
+    tmp_dir, dvc, mocker, target
+):
+    (stage,) = tmp_dir.dvc_gen("foo", "foo")
+    tmp_dir.gen("foo", "foobar")  # update file
+    dvcfile_contents = (tmp_dir / stage.path).read_text()
+
+    exc_msg = f"raising error from mocked '{target}'"
+    mocker.patch(
+        target,
+        side_effect=DvcException(exc_msg),
+    )
+
+    with pytest.raises(DvcException) as exc_info:
+        dvc.add("foo")
+    assert str(exc_info.value) == exc_msg
+    assert (tmp_dir / "foo.dvc").exists()
+    assert (tmp_dir / stage.path).read_text() == dvcfile_contents