Repository: iterative/dvc

Issue:
`data status --not-in-remote`: fails when empty cache while tracking file and directory since dvc 3.61.0
# Bug Report

## `data status --not-in-remote`: fails when empty cache while tracking file and directory

## Description

The dvc data status started to fail with the "failed to load directory" exception on our CI since the dvc 3.61.0. It only fails under certain conditions:
- The cache is cleared
- There is at least single dvc tracked file in repo
- There is at least single dvc tracked dir in the repo

### Reproduce

```console
# setup env
11022  mkdir local-remote
11023  mkdir dvc-repo
11024  cd dvc-repo
11025  git init
11026  dvc init 
11027  dvc remote add -d local-remote ../local-remote

# exists 0
11028  dvc data status --not-in-remote 

# track foo dir with bar file
11029  mkdir foo
11030  echo "Hi" > foo/bar
11032  dvc add foo

# exits 1 foo not in remote
11033  dvc data status --not-in-remote

# track changes using git 
11034  git add .
11035  git commit -m "Track files"

# remove cache dir
11044  rm -r -f .dvc/cache/

# reports data not in cache and remote correctly as expected 
11045  dvc data status --not-in-remote

# add and track file
echo "Hi" > myfile.txt
dvc add myfile.txt 

# fails with exception
dvc data status --not-in-remote

# does not fail with exception after removal
rm -r -f myfile.txt.dvc
dvc data status --not-in-remote
```

```console
╰─❯ dvc data status --not-in-remote 
ERROR: unexpected error - failed to load directory ('foo',): [Errno 2] No such file or directory: '/mnt/local-remote/files/md5/00/6898527324190cf40bd8a2d720d0e8.dir'                                                                                                                  
                                                                                                                                                                                                                                                                                       
Having any troubles? Hit us up at https://dvc.org/support, we are always happy to help!
```

### Expected

```console
╰─❯ dvc data status --not-in-remote 
Not in cache:                                                                                                                                                                                                                                                                          
  (use "dvc fetch <file>..." to download files)                                                                                                                                                                                                                                        
        foo/

Not in remote:
  (use "dvc push <file>..." to upload files)
        foo/
```

### Environment information

**Output of `dvc doctor`:**

```console
╰─❯ dvc doctor 
DVC version: 3.61.0 (pip)
-------------------------
Platform: Python 3.12.8 on Linux-5.15.0-140-generic-x86_64-with-glibc2.35
Subprojects:
        dvc_data = 3.16.10
        dvc_objects = 5.1.1
        dvc_render = 1.0.2
        dvc_task = 0.40.2
        scmrepo = 3.4.0
Supports:
        http (aiohttp = 3.12.14, aiohttp-retry = 2.9.1),
        https (aiohttp = 3.12.14, aiohttp-retry = 2.9.1),
        s3 (s3fs = 2025.3.0, boto3 = 1.38.27)
Config:
        Global: /root/.config/dvc
        System: /etc/xdg/dvc
Cache types: reflink, hardlink, symlink
Cache directory: overlay on overlay
Caches: local
Remotes: local
Workspace directory: overlay on overlay
Repo: dvc, git
Repo.site_cache_dir: /var/tmp/dvc/repo/25af5712cc579ad2f985713085f12c26
```

**Additional Information (if any):**

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Discussion:
Hi, I'm also having issues with this command, see: https://github.com/iterative/dvc/issues/2036#issuecomment-3127697575
> Hi, I'm also having issues with this command, see: [#2036 (comment)](https://github.com/iterative/dvc/issues/2036#issuecomment-3127697575)

Please open a new issue with details. This issue is unrelated to the issue you are having. 



Patch:
diff --git a/dvc/repo/data.py b/dvc/repo/data.py
index 4a731be053..dc5f2b4b53 100644
--- a/dvc/repo/data.py
+++ b/dvc/repo/data.py
@@ -7,6 +7,7 @@
 from dvc.fs.callbacks import DEFAULT_CALLBACK, Callback, TqdmCallback
 from dvc.log import logger
 from dvc.ui import ui
+from dvc_data.index import DataIndexDirError
 
 if TYPE_CHECKING:
     from dvc.repo import Repo
@@ -328,10 +329,21 @@ def _get_entries_not_in_remote(
     from dvc.repo.worktree import worktree_view
     from dvc_data.index import StorageKeyError
 
+    entries: dict[DataIndexKey, DataIndexEntry] = {}
+
+    def _onerror(entry, exc):
+        if not isinstance(exc, DataIndexDirError):
+            raise exc
+        # We don't have the contents of this dir file, so we will only check this key.
+        entries[entry.key] = entry
+
     # View into the index, with only pushable entries
     index = worktree_view(repo.index, push=True)
     data_index = index.data["repo"]
 
+    orig_data_index_onerror = data_index.onerror
+    data_index.onerror = _onerror
+
     view = filter_index(data_index, filter_keys=filter_keys)  # type: ignore[arg-type]
 
     missing_entries = []
@@ -340,7 +352,6 @@ def _get_entries_not_in_remote(
 
     n = 0
     with TqdmCallback(size=n, desc="Checking remote", unit="entry") as cb:
-        entries: dict[DataIndexKey, DataIndexEntry] = {}
         for key, entry in view.iteritems(shallow=not granular):
             if not (entry and entry.hash_info):
                 continue
@@ -368,6 +379,7 @@ def _get_entries_not_in_remote(
                 pass
             finally:
                 cb.relative_update()
+    data_index.onerror = orig_data_index_onerror
     return missing_entries
 
 
diff --git a/dvc/repo/fetch.py b/dvc/repo/fetch.py
index 3eafb01a2d..d4f64e1d80 100644
--- a/dvc/repo/fetch.py
+++ b/dvc/repo/fetch.py
@@ -10,6 +10,7 @@
 
 if TYPE_CHECKING:
     from dvc.output import Output
+    from dvc.repo import Repo
     from dvc.stage import Stage
 
 logger = logger.getChild(__name__)
@@ -24,7 +25,7 @@ def _onerror(entry, exc):
 
 
 def _collect_indexes(  # noqa: PLR0913
-    repo,
+    repo: "Repo",
     targets=None,
     remote=None,
     all_branches=False,
@@ -94,7 +95,7 @@ def outs_filter(out: "Output") -> bool:
 
 @locked
 def fetch(  # noqa: PLR0913
-    self,
+    self: "Repo",
     targets=None,
     jobs=None,
     remote=None,


Test patch:
diff --git a/tests/func/test_data_status.py b/tests/func/test_data_status.py
index fa3f2777a2..f45c53a8d1 100644
--- a/tests/func/test_data_status.py
+++ b/tests/func/test_data_status.py
@@ -918,3 +918,49 @@ def test_compat_legacy_new_cache_types(M, tmp_dir, dvc, scm):
         "committed": {"added": M.unordered("foo", "bar")},
         "git": M.dict(),
     }
+
+
+def test_missing_cache_remote_check(M, tmp_dir, dvc, scm, local_remote):
+    tmp_dir.dvc_gen({"dir": {"foo": "foo", "bar": "bar"}})
+    tmp_dir.dvc_gen("foobar", "foobar")
+    remove(dvc.cache.repo.path)
+
+    assert dvc.data_status(untracked_files="all", not_in_remote=True) == {
+        **EMPTY_STATUS,
+        "untracked": M.unordered("foobar.dvc", "dir.dvc", ".gitignore"),
+        "committed": {"added": M.unordered("foobar", join("dir", ""))},
+        "not_in_cache": M.unordered("foobar", join("dir", "")),
+        "git": M.dict(),
+        "not_in_remote": M.unordered("foobar", join("dir", "")),
+    }
+
+    assert dvc.data_status(
+        granular=True, untracked_files="all", not_in_remote=True
+    ) == {
+        **EMPTY_STATUS,
+        "untracked": M.unordered("foobar.dvc", "dir.dvc", ".gitignore"),
+        "committed": {"added": M.unordered("foobar", join("dir", ""))},
+        "uncommitted": {"unknown": M.unordered(join("dir", "foo"), join("dir", "bar"))},
+        "not_in_cache": M.unordered("foobar", join("dir", "")),
+        "git": M.dict(),
+        "not_in_remote": M.unordered("foobar", join("dir", "")),
+    }
+
+    assert dvc.data_status(["dir"], untracked_files="all", not_in_remote=True) == {
+        **EMPTY_STATUS,
+        "committed": {"added": [join("dir", "")]},
+        "not_in_cache": [join("dir", "")],
+        "git": M.dict(),
+        "not_in_remote": [join("dir", "")],
+    }
+
+    assert dvc.data_status(
+        ["dir"], untracked_files="all", not_in_remote=True, granular=True
+    ) == {
+        **EMPTY_STATUS,
+        "committed": {"added": [join("dir", "")]},
+        "uncommitted": {"unknown": M.unordered(join("dir", "foo"), join("dir", "bar"))},
+        "not_in_cache": [join("dir", "")],
+        "git": M.dict(),
+        "not_in_remote": [join("dir", "")],
+    }