objects: use object IDs and references instead of naive objs in status/transfer (#6360)

* objects.status: use object IDs instead of naive objects

* objects.transfer: use object IDs instead of naive objects

* objects: add ReferenceHashFile

* odb: add ReferenceObjectDB

* repo: collect used object IDs instead of naive objs

* support basic/naive fs serialization

* objects.stage: stage file objects in addition to trees

* objects: remove save(), update transfer()

* output/dep: update for osave removal

* path_info: support both url and path attributes

* status/gc: use object IDs instead of naive objs

* diff: update staging usage

* commit: update staging usage

* tests: clean staging when needed

* tests: update for save/transfer/stage changes

* dvcfs: don't allow config serialization (repofs should be used instead)

* utils: return mtime as str, size as int

* tests: update unit tests for save/stage/transfer changes

* objects: use Repo.open when needed in ReferenceHashFile

* fix ls test staging

* objects.stage: don't skip hash check when loading from state

- individual hashes will still be loaded from state if they are still
  valid

* ReferenceHashFile: serialize repo fs paths relative to repo root

* preserve state when staging

* objects.tree: skip hash computation in digest() when we have already
loaded hash from state

* always check file existence in referencehashfile

* update repofs test since stage no longer allows nonexistent files

* odb: only protect on check() if hash was verified

* staging: use unique memfs namespace for staging per dest ODB

* tests: clean full staging namespace

* refodb: preserve repofs cache dir

* repodependency: stage imports to local ODB and strict check circular
imports

* fetch: fetch staging last

* staging: make dest odb mandatory and preserve state

* refodb: cache nonlocal fs's

* fix rebase errors

* repofs: support full instantiation from fs config

* repofs: preserve subrepo factory for erepos

* tests: clarify repofs dirty file behavior

dvc/checkout.py

@@ -35,7 +35,9 @@ def _changed(path_info, fs, obj, cache, state=None):
     actual = state.get(path_info, fs) if state else None
     if actual is None:
         try:
-            actual = stage(cache, path_info, fs, obj.hash_info.name).hash_info
+            actual = stage(
+                cache, path_info, fs, obj.hash_info.name, dry_run=True
+            )[1].hash_info
         except FileNotFoundError:
             logger.debug("'%s' doesn't exist.", path_info)
             return True
@@ -61,7 +63,9 @@ def _remove(path_info, fs, cache, force=False):
         fs.remove(path_info)
         return
 
-    current = stage(cache, path_info, fs, fs.PARAM_CHECKSUM).hash_info
+    current = stage(cache, path_info, fs, fs.PARAM_CHECKSUM, dry_run=True)[
+        1
+    ].hash_info
     try:
         obj = load(cache, current)
         check(cache, obj)

dvc/data_cloud.py

@@ -6,8 +6,8 @@ from typing import TYPE_CHECKING, Iterable, Optional
 from dvc.objects.db import get_index
 
 if TYPE_CHECKING:
+    from dvc.hash_info import HashInfo
     from dvc.objects.db.base import ObjectDB
-    from dvc.objects.file import HashFile
 
 logger = logging.getLogger(__name__)
 
@@ -64,7 +64,7 @@ class DataCloud:
 
     def push(
         self,
-        objs: Iterable["HashFile"],
+        objs: Iterable["HashInfo"],
         jobs: Optional[int] = None,
         remote: Optional[str] = None,
         odb: Optional["ObjectDB"] = None,
@@ -93,7 +93,7 @@ class DataCloud:
 
     def pull(
         self,
-        objs: Iterable["HashFile"],
+        objs: Iterable["HashInfo"],
         jobs: Optional[int] = None,
         remote: Optional[str] = None,
         odb: Optional["ObjectDB"] = None,
@@ -123,7 +123,7 @@ class DataCloud:
 
     def status(
         self,
-        objs: Iterable["HashFile"],
+        objs: Iterable["HashInfo"],
         jobs: Optional[int] = None,
         remote: Optional[str] = None,
         odb: Optional["ObjectDB"] = None,

dvc/dependency/repo.py

@@ -1,8 +1,8 @@
 import os
 from collections import defaultdict
+from copy import copy
 from typing import TYPE_CHECKING, Dict, Optional, Set, Tuple
 
-from funcy import first
 from voluptuous import Required
 
 from dvc.path_info import PathInfo
@@ -10,6 +10,7 @@ from dvc.path_info import PathInfo
 from .base import Dependency
 
 if TYPE_CHECKING:
+    from dvc.hash_info import HashInfo
     from dvc.objects.db.base import ObjectDB
     from dvc.objects.file import HashFile
 
@@ -91,23 +92,24 @@ class RepoDependency(Dependency):
 
     def get_used_objs(
         self, **kwargs
-    ) -> Dict[Optional["ObjectDB"], Set["HashFile"]]:
+    ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
         used, _ = self._get_used_and_obj(**kwargs)
         return used
 
     def _get_used_and_obj(
         self, obj_only=False, **kwargs
-    ) -> Tuple[Dict[Optional["ObjectDB"], Set["HashFile"]], "HashFile"]:
+    ) -> Tuple[Dict[Optional["ObjectDB"], Set["HashInfo"]], "HashFile"]:
         from dvc.config import NoRemoteError
         from dvc.exceptions import NoOutputOrStageError, PathMissingError
-        from dvc.objects.stage import get_staging, stage
+        from dvc.objects.stage import stage
+        from dvc.objects.tree import Tree
 
         local_odb = self.repo.odb.local
         locked = kwargs.pop("locked", True)
         with self._make_repo(
             locked=locked, cache_dir=local_odb.cache_dir
         ) as repo:
-            used_objs = defaultdict(set)
+            used_obj_ids = defaultdict(set)
             rev = repo.get_rev()
             if locked and self.def_repo.get(self.PARAM_REV_LOCK) is None:
                 self.def_repo[self.PARAM_REV_LOCK] = rev
@@ -115,7 +117,7 @@ class RepoDependency(Dependency):
             path_info = PathInfo(repo.root_dir) / str(self.def_path)
             if not obj_only:
                 try:
-                    for odb, objs in repo.used_objs(
+                    for odb, obj_ids in repo.used_objs(
                         [os.fspath(path_info)],
                         force=True,
                         jobs=kwargs.get("jobs"),
@@ -124,14 +126,14 @@ class RepoDependency(Dependency):
                         if odb is None:
                             odb = repo.cloud.get_remote_odb()
                             odb.read_only = True
-                        self._check_circular_import(objs)
-                        used_objs[odb].update(objs)
+                        self._check_circular_import(odb, obj_ids)
+                        used_obj_ids[odb].update(obj_ids)
                 except (NoRemoteError, NoOutputOrStageError):
                     pass
 
             try:
-                staged_obj = stage(
-                    None,
+                staging, staged_obj = stage(
+                    local_odb,
                     path_info,
                     repo.repo_fs,
                     local_odb.fs.PARAM_CHECKSUM,
@@ -140,27 +142,51 @@ class RepoDependency(Dependency):
                 raise PathMissingError(
                     self.def_path, self.def_repo[self.PARAM_URL]
                 ) from exc
-            staging = get_staging()
+            staging = copy(staging)
             staging.read_only = True
 
             self._staged_objs[rev] = staged_obj
-            used_objs[staging].add(staged_obj)
-            return used_objs, staged_obj
+            used_obj_ids[staging].add(staged_obj.hash_info)
+            if isinstance(staged_obj, Tree):
+                used_obj_ids[staging].update(
+                    entry.hash_info for _, entry in staged_obj
+                )
+            return used_obj_ids, staged_obj
 
-    def _check_circular_import(self, objs):
+    def _check_circular_import(self, odb, obj_ids):
         from dvc.exceptions import CircularImportError
         from dvc.fs.repo import RepoFileSystem
+        from dvc.objects.db.reference import ReferenceObjectDB
         from dvc.objects.tree import Tree
 
-        obj = first(objs)
-        if isinstance(obj, Tree):
-            _, obj = first(obj)
-        if not isinstance(obj.fs, RepoFileSystem):
+        if not isinstance(odb, ReferenceObjectDB):
             return
 
-        self_url = self.repo.url or self.repo.root_dir
-        if obj.fs.repo_url is not None and obj.fs.repo_url == self_url:
-            raise CircularImportError(self, obj.fs.repo_url, self_url)
+        def iter_objs():
+            for hash_info in obj_ids:
+                if hash_info.isdir:
+                    tree = Tree.load(odb, hash_info)
+                    yield from (odb.get(entry.hash_info) for _, entry in tree)
+                else:
+                    yield odb.get(hash_info)
+
+        checked_urls = set()
+        for obj in iter_objs():
+            if not isinstance(obj.fs, RepoFileSystem):
+                continue
+            if (
+                obj.fs.repo_url in checked_urls
+                or obj.fs.root_dir in checked_urls
+            ):
+                continue
+            self_url = self.repo.url or self.repo.root_dir
+            if (
+                obj.fs.repo_url is not None
+                and obj.fs.repo_url == self_url
+                or obj.fs.root_dir == self.repo.root_dir
+            ):
+                raise CircularImportError(self, obj.fs.repo_url, self_url)
+            checked_urls.update([obj.fs.repo_url, obj.fs.root_dir])
 
     def get_obj(self, filter_info=None, **kwargs):
         locked = kwargs.get("locked", True)

dvc/external_repo.py

@@ -42,14 +42,6 @@ def external_repo(
     config = _get_remote_config(url) if os.path.isdir(url) else {}
     config.update(cache_config)
 
-    def make_repo(path, **_kwargs):
-        _config = cache_config.copy()
-        if os.path.isdir(url):
-            rel = os.path.relpath(path, _kwargs["scm"].root_dir)
-            repo_path = os.path.join(url, rel)
-            _config.update(_get_remote_config(repo_path))
-        return Repo(path, config=_config, **_kwargs)
-
     root_dir = path if for_write else os.path.realpath(path)
     repo_kwargs = dict(
         root_dir=root_dir,
@@ -57,7 +49,7 @@ def external_repo(
         scm=None if for_write else Git(root_dir),
         rev=None if for_write else rev,
         config=config,
-        repo_factory=make_repo,
+        repo_factory=erepo_factory(url, cache_config),
         **kwargs,
     )
 
@@ -87,6 +79,18 @@ def external_repo(
             _remove(path)
 
 
+def erepo_factory(url, cache_config, *args, **kwargs):
+    def make_repo(path, **_kwargs):
+        _config = cache_config.copy()
+        if os.path.isdir(url):
+            rel = os.path.relpath(path, _kwargs["scm"].root_dir)
+            repo_path = os.path.join(url, rel)
+            _config.update(_get_remote_config(repo_path))
+        return Repo(path, config=_config, **_kwargs)
+
+    return make_repo
+
+
 CLONES: Dict[str, str] = {}
 CACHE_DIRS: Dict[str, str] = {}
 

dvc/fs/__init__.py

@@ -32,8 +32,9 @@ FS_MAP = {
 }
 
 
-def get_fs_cls(remote_conf):
-    scheme = urlparse(remote_conf["url"]).scheme
+def get_fs_cls(remote_conf, scheme=None):
+    if not scheme:
+        scheme = urlparse(remote_conf["url"]).scheme
     return FS_MAP.get(scheme, LocalFileSystem)
 
 

dvc/fs/base.py

@@ -59,6 +59,11 @@ class BaseFileSystem:
 
         self.jobs = kwargs.get("jobs") or self._JOBS
         self.hash_jobs = kwargs.get("checksum_jobs") or self.HASH_JOBS
+        self._config = kwargs
+
+    @property
+    def config(self):
+        return self._config
 
     @classmethod
     def _strip_protocol(cls, path: str):

dvc/fs/dvc.py

@@ -32,6 +32,10 @@ class DvcFileSystem(BaseFileSystem):  # pylint:disable=abstract-method
         super().__init__(**kwargs)
         self.repo = kwargs["repo"]
 
+    @property
+    def config(self):
+        raise NotImplementedError
+
     def _find_outs(self, path, *args, **kwargs):
         outs = self.repo.find_outs_by_path(path, *args, **kwargs)
 

dvc/fs/repo.py

@@ -35,14 +35,29 @@ class RepoFileSystem(BaseFileSystem):  # pylint:disable=abstract-method
 
     scheme = "local"
     PARAM_CHECKSUM = "md5"
+    PARAM_REPO_URL = "repo_url"
+    PARAM_REPO_ROOT = "repo_root"
+    PARAM_REV = "rev"
+    PARAM_CACHE_DIR = "cache_dir"
+    PARAM_CACHE_TYPES = "cache_types"
+    PARAM_SUBREPOS = "subrepos"
 
     def __init__(
-        self, repo=None, subrepos=False, repo_factory: RepoFactory = None
+        self,
+        repo: Optional["Repo"] = None,
+        subrepos=False,
+        repo_factory: RepoFactory = None,
+        **kwargs,
     ):
         super().__init__()
 
         from dvc.utils.collections import PathStringTrie
 
+        if repo is None:
+            repo, repo_factory = self._repo_from_fs_config(
+                subrepos=subrepos, **kwargs
+            )
+
         if not repo_factory:
             from dvc.repo import Repo
 
@@ -72,6 +87,67 @@ class RepoFileSystem(BaseFileSystem):  # pylint:disable=abstract-method
             return None
         return self._main_repo.url
 
+    @property
+    def config(self):
+        return {
+            self.PARAM_REPO_URL: self.repo_url,
+            self.PARAM_REPO_ROOT: self.root_dir,
+            self.PARAM_REV: getattr(self._main_repo.fs, "rev", None),
+            self.PARAM_CACHE_DIR: os.path.abspath(
+                self._main_repo.odb.local.cache_dir
+            ),
+            self.PARAM_CACHE_TYPES: self._main_repo.odb.local.cache_types,
+            self.PARAM_SUBREPOS: self._traverse_subrepos,
+        }
+
+    @classmethod
+    def _repo_from_fs_config(
+        cls, **config
+    ) -> Tuple["Repo", Optional["RepoFactory"]]:
+        from dvc.external_repo import erepo_factory, external_repo
+        from dvc.repo import Repo
+
+        url = config.get(cls.PARAM_REPO_URL)
+        root = config.get(cls.PARAM_REPO_ROOT)
+        assert url or root
+
+        def _open(*args, **kwargs):
+            # NOTE: if original repo was an erepo (and has a URL),
+            # we cannot use Repo.open() since it will skip erepo
+            # cache/remote setup for local URLs
+            if url is None:
+                return Repo.open(*args, **kwargs)
+            return external_repo(*args, **kwargs)
+
+        cache_dir = config.get(cls.PARAM_CACHE_DIR)
+        cache_config = (
+            {}
+            if not cache_dir
+            else {
+                "cache": {
+                    "dir": cache_dir,
+                    "type": config.get(cls.PARAM_CACHE_TYPES),
+                }
+            }
+        )
+        repo_kwargs: dict = {
+            "rev": config.get(cls.PARAM_REV),
+            "subrepos": config.get(cls.PARAM_SUBREPOS, False),
+            "uninitialized": True,
+        }
+        factory: Optional["RepoFactory"] = None
+        if url is None:
+            repo_kwargs["config"] = cache_config
+        else:
+            repo_kwargs["cache_dir"] = cache_dir
+            factory = erepo_factory(url, cache_config)
+
+        with _open(
+            url if url else root,
+            **repo_kwargs,
+        ) as repo:
+            return repo, factory
+
     def _get_repo(self, path: str) -> Optional["Repo"]:
         """Returns repo that the path falls in, using prefix.
 

dvc/hash_info.py

@@ -14,6 +14,7 @@ class HashInfo:
     value: Optional[str]
     size: Optional[int] = field(default=None, compare=False)
     nfiles: Optional[int] = field(default=None, compare=False)
+    obj_name: Optional[str] = field(default=None, compare=False)
 
     def __bool__(self):
         return bool(self.value)

dvc/objects/__init__.py

@@ -1,8 +1,5 @@
 import logging
-from concurrent.futures import ThreadPoolExecutor, as_completed
-from typing import TYPE_CHECKING, Optional
-
-from dvc.progress import Tqdm
+from typing import TYPE_CHECKING
 
 from .tree import Tree
 
@@ -15,50 +12,12 @@ if TYPE_CHECKING:
 logger = logging.getLogger(__name__)
 
 
-def save(
-    odb: "ObjectDB",
-    obj: "HashFile",
-    jobs: Optional[int] = None,
-    **kwargs,
-):
-    if isinstance(obj, Tree):
-        from .stage import get_staging
-
-        with ThreadPoolExecutor(max_workers=jobs) as executor:
-            for future in Tqdm(
-                as_completed(
-                    executor.submit(
-                        odb.add,
-                        entry.path_info,
-                        entry.fs,
-                        entry.hash_info,
-                        **kwargs,
-                    )
-                    for _, entry in obj
-                ),
-                desc="Saving files",
-                total=len(obj),
-                unit="file",
-            ):
-                future.result()
-
-            # if dir cache for this tree has already been staged, move the
-            # staged object when possible
-            staging = get_staging(odb)
-            if staging.exists(obj.hash_info):
-                obj = staging.get(obj.hash_info)
-                kwargs["move"] = True
-
-    assert obj.path_info and obj.fs and obj.hash_info
-    odb.add(obj.path_info, obj.fs, obj.hash_info, **kwargs)
-
-
-def check(odb: "ObjectDB", obj: "HashFile"):
+def check(odb: "ObjectDB", obj: "HashFile", **kwargs):
     if isinstance(obj, Tree):
         for _, entry in obj:
-            odb.check(entry.hash_info)
+            odb.check(entry.hash_info, **kwargs)
 
-    odb.check(obj.hash_info)
+    odb.check(obj.hash_info, **kwargs)
 
 
 def load(odb: "ObjectDB", hash_info: "HashInfo") -> "HashFile":

dvc/objects/db/base.py

@@ -13,7 +13,7 @@ from dvc.progress import Tqdm
 if TYPE_CHECKING:
     from dvc.fs.base import BaseFileSystem
     from dvc.hash_info import HashInfo
-    from dvc.types import AnyPath
+    from dvc.types import AnyPath, DvcPath
 
 logger = logging.getLogger(__name__)
 
@@ -76,7 +76,14 @@ class ObjectDB:
             hash_info,
         )
 
-    def _add_file(self, from_fs, from_info, to_info, move):
+    def _add_file(
+        self,
+        from_fs: "BaseFileSystem",
+        from_info: "AnyPath",
+        to_info: "DvcPath",
+        _hash_info: "HashInfo",
+        move: bool = False,
+    ):
         self.makedirs(to_info.parent)
         use_move = isinstance(from_fs, type(self.fs)) and move
         try:
@@ -131,8 +138,8 @@ class ObjectDB:
             pass
 
         cache_info = self.hash_to_path_info(hash_info.value)
-        # using our makedirs to create dirs with proper permissions
-        self._add_file(fs, path_info, cache_info, move)
+        self._add_file(fs, path_info, cache_info, hash_info, move)
+
         try:
             if verify:
                 self.check(hash_info, check_hash=True)
@@ -145,7 +152,7 @@ class ObjectDB:
         if callback:
             callback(1)
 
-    def hash_to_path_info(self, hash_):
+    def hash_to_path_info(self, hash_) -> "DvcPath":
         return self.path_info / hash_[0:2] / hash_[2:]
 
     # Override to return path as a string instead of PathInfo for clouds
@@ -199,9 +206,10 @@ class ObjectDB:
             self.fs.remove(obj.path_info)
             raise
 
-        # making cache file read-only so we don't need to check it
-        # next time
-        self.protect(obj.path_info)
+        if check_hash:
+            # making cache file read-only so we don't need to check it
+            # next time
+            self.protect(obj.path_info)
 
     def _list_paths(self, prefix=None, progress_callback=None):
         if prefix:
@@ -378,17 +386,20 @@ class ObjectDB:
     def _remove_unpacked_dir(self, hash_):
         pass
 
-    def gc(self, used, jobs=None):
+    def gc(self, used, jobs=None, cache_odb=None, shallow=True):
         from ..tree import Tree
 
         if self.read_only:
             raise ObjectDBPermissionError("Cannot gc read-only ODB")
+        if not cache_odb:
+            cache_odb = self
         used_hashes = set()
-        for obj in used:
-            used_hashes.add(obj.hash_info.value)
-            if isinstance(obj, Tree):
+        for hash_info in used:
+            used_hashes.add(hash_info.value)
+            if hash_info.isdir and not shallow:
+                tree = Tree.load(cache_odb, hash_info)
                 used_hashes.update(
-                    entry_obj.hash_info.value for _, entry_obj in obj
+                    entry_obj.hash_info.value for _, entry_obj in tree
                 )
 
         removed = False

dvc/objects/db/reference.py

@@ -0,0 +1,77 @@
+import io
+import logging
+import os
+from typing import TYPE_CHECKING, Dict
+
+from dvc.scheme import Schemes
+
+from ..errors import ObjectFormatError
+from ..reference import ReferenceHashFile
+from .base import ObjectDB
+
+if TYPE_CHECKING:
+    from dvc.fs.base import BaseFileSystem
+    from dvc.hash_info import HashInfo
+    from dvc.types import AnyPath, DvcPath
+
+logger = logging.getLogger(__name__)
+
+
+class ReferenceObjectDB(ObjectDB):
+    """Reference ODB.
+
+    File objects are stored as ReferenceHashFiles which reference paths outside
+    of the staging ODB fs. Tree objects are stored natively.
+    """
+
+    def __init__(self, *args, **kwargs):
+        super().__init__(*args, **kwargs)
+        self._fs_cache: Dict[tuple, "BaseFileSystem"] = {}
+
+    def get(self, hash_info: "HashInfo"):
+        if hash_info.isdir:
+            return super().get(hash_info)
+        path_info = self.hash_to_path(hash_info.value)
+        try:
+            with self.fs.open(path_info, "rb") as fobj:
+                ref_file = ReferenceHashFile.from_bytes(
+                    fobj.read(), fs_cache=self._fs_cache
+                )
+        except OSError:
+            raise FileNotFoundError
+        try:
+            ref_file.check(self, check_hash=False)
+        except ObjectFormatError:
+            self.fs.remove(path_info)
+            raise
+        return ref_file
+
+    def _add_file(
+        self,
+        from_fs: "BaseFileSystem",
+        from_info: "AnyPath",
+        to_info: "DvcPath",
+        hash_info: "HashInfo",
+        move: bool = False,
+    ):
+        self.makedirs(to_info.parent)
+        if hash_info.isdir:
+            return super()._add_file(
+                from_fs, from_info, to_info, hash_info, move
+            )
+        ref_file = ReferenceHashFile(from_info, from_fs, hash_info)
+        ref_fobj = io.BytesIO(ref_file.to_bytes())
+        ref_fobj.seek(0)
+        try:
+            self.fs.upload_fobj(ref_fobj, to_info)
+        except OSError as exc:
+            if isinstance(exc, FileExistsError) or (
+                os.name == "nt"
+                and exc.__context__
+                and isinstance(exc.__context__, FileExistsError)
+            ):
+                logger.debug("'%s' file already exists, skipping", to_info)
+            else:
+                raise
+        if from_fs.scheme != Schemes.LOCAL:
+            self._fs_cache[ReferenceHashFile.config_tuple(from_fs)] = from_fs

dvc/objects/file.py

@@ -8,7 +8,9 @@ from .errors import ObjectFormatError
 if TYPE_CHECKING:
     from dvc.fs.base import BaseFileSystem
     from dvc.hash_info import HashInfo
-    from dvc.types import DvcPath
+    from dvc.types import AnyPath
+
+    from .db.base import ObjectDB
 
 logger = logging.getLogger(__name__)
 
@@ -16,7 +18,7 @@ logger = logging.getLogger(__name__)
 class HashFile:
     def __init__(
         self,
-        path_info: Optional["DvcPath"],
+        path_info: Optional["AnyPath"],
         fs: Optional["BaseFileSystem"],
         hash_info: "HashInfo",
         name: Optional[str] = None,
@@ -57,10 +59,9 @@ class HashFile:
             )
         )
 
-    def check(self, odb, check_hash=True):
-        from .stage import get_file_hash
-
+    def check(self, odb: "ObjectDB", check_hash: bool = True):
         if not check_hash:
+            assert self.fs
             if not self.fs.exists(self.path_info):
                 raise FileNotFoundError(
                     errno.ENOENT, os.strerror(errno.ENOENT), self.path_info
@@ -68,6 +69,11 @@ class HashFile:
             else:
                 return None
 
+        self._check_hash(odb)
+
+    def _check_hash(self, odb):
+        from .stage import get_file_hash
+
         actual = get_file_hash(
             self.path_info, self.fs, self.hash_info.name, odb.state
         )

dvc/objects/reference.py

@@ -0,0 +1,135 @@
+import errno
+import logging
+import os
+import pickle
+from typing import TYPE_CHECKING, Optional, Tuple
+
+from .errors import ObjectFormatError
+from .file import HashFile
+
+if TYPE_CHECKING:
+    from dvc.fs.base import BaseFileSystem
+    from dvc.hash_info import HashInfo
+    from dvc.types import AnyPath
+
+    from .db.base import ObjectDB
+
+logger = logging.getLogger(__name__)
+
+
+class ReferenceHashFile(HashFile):
+    PARAM_PATH = "path"
+    PARAM_HASH = "hash"
+    PARAM_MTIME = "mtime"
+    PARAM_SIZE = "size"
+    PARAM_FS_CONFIG = "fs_config"
+
+    def __init__(
+        self,
+        path_info: "AnyPath",
+        fs: "BaseFileSystem",
+        hash_info: "HashInfo",
+        mtime: Optional[str] = None,
+        size: Optional[int] = None,
+        **kwargs,
+    ):
+        super().__init__(path_info, fs, hash_info, **kwargs)
+        cur_mtime, cur_size = self._get_mtime_and_size()
+        self.mtime = cur_mtime if mtime is None else mtime
+        self.hash_info.size = cur_size if size is None else size
+
+    def __str__(self):
+        return f"ref object {self.hash_info} -> {self.path_info}"
+
+    def check(self, odb: "ObjectDB", check_hash: bool = True):
+        assert self.fs
+        if not self.fs.exists(self.path_info):
+            raise FileNotFoundError(
+                errno.ENOENT, os.strerror(errno.ENOENT), self.path_info
+            )
+        if not (self.mtime, self.size) == self._get_mtime_and_size():
+            raise ObjectFormatError(f"{self} is changed")
+        if check_hash:
+            self._check_hash(odb)
+
+    def _get_mtime_and_size(self) -> Tuple[Optional[str], int]:
+        from dvc.utils.fs import get_mtime_and_size
+
+        assert self.fs
+        if hasattr(self.fs, "stat"):
+            try:
+                return get_mtime_and_size(self.path_info, self.fs)
+            except FileNotFoundError:
+                pass
+        return None, self.fs.getsize(self.path_info)
+
+    def to_bytes(self):
+        from dvc.fs.repo import RepoFileSystem
+        from dvc.path_info import PathInfo
+
+        # NOTE: dumping reference FS's this way is insecure, as the
+        # fully parsed remote FS config will include credentials
+        #
+        # ReferenceHashFiles should currently only be serialized in
+        # memory and not to disk
+        path_info = self.path_info
+        if isinstance(self.fs, RepoFileSystem):
+            path_info = PathInfo(path_info).relative_to(self.fs.root_dir)
+
+        dict_ = {
+            self.PARAM_PATH: path_info,
+            self.PARAM_HASH: self.hash_info,
+            self.PARAM_MTIME: self.mtime,
+            self.PARAM_SIZE: self.size,
+            self.PARAM_FS_CONFIG: self.config_tuple(self.fs),
+        }
+        try:
+            return pickle.dumps(dict_)
+        except pickle.PickleError as exc:
+            raise ObjectFormatError(f"Could not pickle {self}") from exc
+
+    @classmethod
+    def from_bytes(cls, data: bytes, fs_cache: Optional[dict] = None):
+        from dvc.fs import get_fs_cls
+        from dvc.fs.repo import RepoFileSystem
+
+        try:
+            dict_ = pickle.loads(data)
+        except pickle.PickleError as exc:
+            raise ObjectFormatError("ReferenceHashFile is corrupted") from exc
+
+        try:
+            path_info = dict_[cls.PARAM_PATH]
+            hash_info = dict_[cls.PARAM_HASH]
+        except KeyError as exc:
+            raise ObjectFormatError("ReferenceHashFile is corrupted") from exc
+
+        scheme, config_pairs = dict_.get(cls.PARAM_FS_CONFIG)
+        fs = fs_cache.get((scheme, config_pairs)) if fs_cache else None
+        if not fs:
+            config = dict(config_pairs)
+            if RepoFileSystem.PARAM_REPO_URL in config:
+                fs = RepoFileSystem(**config)
+                path_info = fs.root_dir / path_info
+            else:
+                fs_cls = get_fs_cls(config, scheme=path_info.scheme)
+                fs = fs_cls(**config)
+        return ReferenceHashFile(
+            path_info,
+            fs,
+            hash_info,
+            mtime=dict_.get(cls.PARAM_MTIME),
+            size=dict_.get(cls.PARAM_SIZE),
+        )
+
+    @staticmethod
+    def config_tuple(fs: "BaseFileSystem"):
+        return (
+            fs.scheme,
+            tuple(
+                (key, value)
+                for key, value in sorted(
+                    fs.config.items(), key=lambda item: item[0]
+                )
+            ),
+        )

dvc/objects/stage.py

@@ -1,6 +1,10 @@
+import hashlib
+import logging
+import os
+import pathlib
 from concurrent.futures import ThreadPoolExecutor
 from functools import partial
-from typing import TYPE_CHECKING, Optional
+from typing import TYPE_CHECKING, Dict, Tuple
 
 from dvc.exceptions import DvcIgnoreInCollectedDirError
 from dvc.hash_info import HashInfo
@@ -8,32 +12,34 @@ from dvc.ignore import DvcIgnore
 from dvc.progress import Tqdm
 from dvc.utils import file_md5
 
+from .db.reference import ReferenceObjectDB
 from .file import HashFile
 
 if TYPE_CHECKING:
     from dvc.fs.base import BaseFileSystem
-    from dvc.types import DvcPath
+    from dvc.types import AnyPath, DvcPath
 
     from .db.base import ObjectDB
 
-
-_STAGING_DIR = "staging"
-_STAGING_MEMFS_PATH = f"dvc-{_STAGING_DIR}"
+logger = logging.getLogger(__name__)
 
 
-def _upload_file(path_info, fs, odb):
+_STAGING_MEMFS_PATH = "dvc-staging"
+
+
+def _upload_file(path_info, fs, odb, upload_odb):
     from dvc.utils import tmp_fname
     from dvc.utils.stream import HashedStreamReader
 
-    tmp_info = odb.path_info / tmp_fname()
+    tmp_info = upload_odb.path_info / tmp_fname()
     with fs.open(path_info, mode="rb", chunk_size=fs.CHUNK_SIZE) as stream:
         stream = HashedStreamReader(stream)
-        odb.fs.upload_fobj(
+        upload_odb.fs.upload_fobj(
             stream, tmp_info, desc=path_info.name, size=fs.getsize(path_info)
         )
 
-    obj = HashFile(tmp_info, odb.fs, stream.hash_info)
-    return path_info, obj
+    odb.add(tmp_info, upload_odb.fs, stream.hash_info)
+    return path_info, odb.get(stream.hash_info)
 
 
 def _get_file_hash(path_info, fs, name):
@@ -71,15 +77,20 @@ def get_file_hash(path_info, fs, name, state=None):
     return hash_info
 
 
-def _get_file_obj(path_info, fs, name, odb=None, upload=False):
-    if upload:
-        assert odb and name == "md5"
-        return _upload_file(path_info, fs, odb)
-
+def _get_file_obj(
+    path_info, fs, name, odb=None, upload_odb=None, dry_run=False
+):
     state = odb.state if odb else None
-    obj = HashFile(
-        path_info, fs, get_file_hash(path_info, fs, name, state=state)
-    )
+    hash_info = get_file_hash(path_info, fs, name, state=state)
+    if upload_odb and not dry_run:
+        assert odb and name == "md5"
+        return _upload_file(path_info, fs, odb, upload_odb)
+
+    if dry_run:
+        obj = HashFile(path_info, fs, hash_info)
+    else:
+        odb.add(path_info, fs, hash_info, move=False)
+        obj = odb.get(hash_info)
     return path_info, obj
 
 
@@ -87,9 +98,9 @@ def _build_objects(
     path_info,
     fs,
     name,
-    odb=None,
-    upload=False,
     dvcignore=None,
+    jobs=None,
+    no_progress_bar=False,
     **kwargs,
 ):
     if dvcignore:
@@ -99,33 +110,24 @@ def _build_objects(
     with Tqdm(
         unit="md5",
         desc="Computing file/dir hashes (only done once)",
-        disable=kwargs.pop("no_progress_bar", False),
+        disable=no_progress_bar,
     ) as pbar:
         worker = pbar.wrap_fn(
             partial(
                 _get_file_obj,
                 fs=fs,
                 name=name,
-                odb=odb,
-                upload=upload,
+                **kwargs,
             )
         )
         with ThreadPoolExecutor(
-            max_workers=kwargs.pop("jobs", fs.hash_jobs)
+            max_workers=jobs if jobs is not None else fs.hash_jobs
         ) as executor:
             yield from executor.map(worker, walk_iterator)
 
 
-def _iter_objects(path_info, fs, name, upload=False, **kwargs):
-    if not upload and name in fs.DETAIL_FIELDS:
-        for details in fs.find(path_info, detail=True):
-            file_info = path_info.replace(path=details["name"])
-            hash_info = HashInfo(name, details[name], size=details.get("size"))
-            yield file_info, HashFile(file_info, fs, hash_info)
-
-        return None
-
-    yield from _build_objects(path_info, fs, name, upload=upload, **kwargs)
+def _iter_objects(path_info, fs, name, **kwargs):
+    yield from _build_objects(path_info, fs, name, **kwargs)
 
 
 def _build_tree(path_info, fs, name, **kwargs):
@@ -145,14 +147,13 @@ def _build_tree(path_info, fs, name, **kwargs):
         # Yes, this is a BUG, as long as we permit "/" in
         # filenames on Windows and "\" on Unix
         tree.add(file_info.relative_to(path_info).parts, obj)
-    tree.digest()
     return tree
 
 
-def _get_tree_obj(path_info, fs, name, odb=None, **kwargs):
+def _get_tree_obj(path_info, fs, fs_info, name, odb=None, **kwargs):
     from .tree import Tree
 
-    value = fs.info(path_info).get(name)
+    value = fs_info.get(name)
     if odb and value:
         hash_info = HashInfo(name, value)
         try:
@@ -168,40 +169,59 @@ def _get_tree_obj(path_info, fs, name, odb=None, **kwargs):
             pass
 
     tree = _build_tree(path_info, fs, name, odb=odb, **kwargs)
+    state = odb.state if odb and odb.state else None
+    hash_info = None
+    if state:
+        hash_info = state.get(  # pylint: disable=assignment-from-none
+            path_info, fs
+        )
+    tree.digest(hash_info=hash_info)
+    odb.add(tree.path_info, tree.fs, tree.hash_info, move=True)
+    raw = odb.get(tree.hash_info)
+    # cleanup unneeded memfs tmpfile and return tree based on the
+    # ODB fs/path
+    if odb.fs != tree.fs:
+        tree.fs.remove(tree.path_info)
+    tree.fs = raw.fs
+    tree.path_info = raw.path_info
     return tree
 
 
-def get_staging(odb: Optional["ObjectDB"] = None) -> "ObjectDB":
+_url_cache: Dict[str, str] = {}
+
+
+def _make_staging_url(path_info: "AnyPath"):
+    from dvc.path_info import CloudURLInfo
+    from dvc.scheme import Schemes
+
+    url = CloudURLInfo(f"{Schemes.MEMORY}://{_STAGING_MEMFS_PATH}")
+    if path_info:
+        if isinstance(path_info, (str, pathlib.PurePath)):
+            path = os.path.abspath(path_info)
+        else:
+            path = str(path_info)
+        if path not in _url_cache:
+            _url_cache[path] = hashlib.sha256(path.encode("utf-8")).hexdigest()
+        url /= _url_cache[path]
+    return url
+
+
+def _get_staging(odb: "ObjectDB") -> "ObjectDB":
     """Return an ODB that can be used for staging objects.
 
-    If odb.fs is local, .dvc/tmp/staging will be returned. Otherwise
-    the the global (temporary) memfs ODB will be returned.
+    Staging will be a reference ODB stored in the the global memfs.
     """
 
     from dvc.fs.memory import MemoryFileSystem
-    from dvc.path_info import CloudURLInfo, PathInfo
-    from dvc.scheme import Schemes
 
-    from .db import get_odb
-
-    if odb and odb.fs.scheme == Schemes.LOCAL and odb.tmp_dir:
-        fs = odb.fs
-        path_info: "DvcPath" = PathInfo(odb.tmp_dir) / _STAGING_DIR
-        config = odb.config
-    else:
-        fs = MemoryFileSystem()
-        path_info = CloudURLInfo(f"{Schemes.MEMORY}://{_STAGING_MEMFS_PATH}")
-        config = {}
-    return get_odb(fs, path_info, **config)
-
-
-def is_memfs_staging(odb: "ObjectDB"):
-    staging = get_staging()
-    return odb.fs == staging.fs and odb.path_info == staging.path_info
+    fs = MemoryFileSystem()
+    path_info = _make_staging_url(odb.path_info)
+    state = odb.state
+    return ReferenceObjectDB(fs, path_info, state=state)
 
 
 def _load_from_state(odb, staging, path_info, fs, name):
-    from . import load
+    from . import check, load
     from .errors import ObjectFormatError
     from .tree import Tree
 
@@ -212,6 +232,7 @@ def _load_from_state(odb, staging, path_info, fs, name):
             if odb_.exists(hash_info):
                 try:
                     obj = load(odb_, hash_info)
+                    check(odb_, obj, check_hash=False)
                     if isinstance(obj, Tree):
                         obj.hash_info.nfiles = len(obj)
                         for key, entry in obj:
@@ -222,8 +243,8 @@ def _load_from_state(odb, staging, path_info, fs, name):
                         obj.path_info = path_info
                     assert obj.hash_info.name == name
                     obj.hash_info.size = hash_info.size
-                    return obj
-                except ObjectFormatError:
+                    return odb_, obj
+                except (ObjectFormatError, FileNotFoundError):
                     pass
     raise FileNotFoundError
 
@@ -248,17 +269,31 @@ def _stage_external_tree_info(odb, tree, name):
 
 
 def stage(
-    odb: Optional["ObjectDB"],
+    odb: "ObjectDB",
     path_info: "DvcPath",
     fs: "BaseFileSystem",
     name: str,
     upload: bool = False,
+    dry_run: bool = False,
     **kwargs,
-) -> "HashFile":
+) -> Tuple["ObjectDB", "HashFile"]:
+    """Stage (prepare) objects from the given path for addition to an ODB.
+
+    Returns at tuple of (staging_odb, object) where addition to the ODB can
+    be completed by transferring the object from staging to the dest ODB.
+
+    If dry_run is True, object hashes will be computed and returned, but file
+    objects themselves will not be added to the staging ODB (i.e. the resulting
+    file objects cannot transferred from staging to another ODB).
+
+    If upload is True, files will be uploaded to a temporary path on the dest
+    ODB filesystem, and staged objects will reference the uploaded path rather
+    than the original source path.
+    """
     assert path_info and path_info.scheme == fs.scheme
 
     details = fs.info(path_info)
-    staging = get_staging(odb)
+    staging = _get_staging(odb)
     if odb:
         try:
             return _load_from_state(odb, staging, path_info, fs, name)
@@ -267,26 +302,29 @@ def stage(
 
     if details["type"] == "directory":
         obj = _get_tree_obj(
-            path_info, fs, name, odb=odb, upload=upload, **kwargs
+            path_info,
+            fs,
+            details,
+            name,
+            odb=staging,
+            upload_odb=odb if upload else None,
+            dry_run=dry_run,
+            **kwargs,
         )
-        if name == "md5":
-            if odb and odb.exists(obj.hash_info):
-                raw = odb.get(obj.hash_info)
-            else:
-                staging.add(obj.path_info, obj.fs, obj.hash_info)
-                raw = staging.get(obj.hash_info)
-            # cleanup unneeded memfs tmpfile and return obj based on staging
-            # ODB fs/path
-            if obj.fs != raw.fs:
-                obj.fs.remove(obj.path_info)
-            obj.fs = raw.fs
-            obj.path_info = raw.path_info
-        else:
+        logger.debug("staged tree '%s'", obj)
+        if name != "md5":
             obj = _stage_external_tree_info(odb, obj, name)
     else:
-        _, obj = _get_file_obj(path_info, fs, name, odb=odb, upload=upload)
+        _, obj = _get_file_obj(
+            path_info,
+            fs,
+            name,
+            odb=staging,
+            upload_odb=odb if upload else None,
+            dry_run=dry_run,
+        )
 
     if odb and odb.state and obj.hash_info:
         odb.state.save(path_info, fs, obj.hash_info)
 
-    return obj
+    return staging, obj

dvc/objects/status.py

@@ -2,6 +2,7 @@ import logging
 from typing import TYPE_CHECKING, Dict, Iterable, NamedTuple, Optional, Set
 
 from dvc.hash_info import HashInfo
+from dvc.scheme import Schemes
 
 from .tree import Tree
 
@@ -14,23 +15,21 @@ logger = logging.getLogger(__name__)
 
 
 class StatusResult(NamedTuple):
-    exists: Set["HashFile"]
-    missing: Set["HashFile"]
+    exists: Set["HashInfo"]
+    missing: Set["HashInfo"]
 
 
 class CompareStatusResult(NamedTuple):
-    ok: Set["HashFile"]
-    missing: Set["HashFile"]
-    new: Set["HashFile"]
-    deleted: Set["HashFile"]
+    ok: Set["HashInfo"]
+    missing: Set["HashInfo"]
+    new: Set["HashInfo"]
+    deleted: Set["HashInfo"]
 
 
-def _indexed_dir_hashes(odb, index, hash_infos, name, cache_odb):
-    from . import load
-
+def _indexed_dir_hashes(odb, index, dir_objs, name, cache_odb):
     # Validate our index by verifying all indexed .dir hashes
     # still exist on the remote
-    dir_hashes = {hash_info.value for hash_info in hash_infos}
+    dir_hashes = set(dir_objs.keys())
     indexed_dirs = set(index.dir_hashes())
     indexed_dir_exists = set()
     if indexed_dirs:
@@ -51,10 +50,12 @@ def _indexed_dir_hashes(odb, index, hash_infos, name, cache_odb):
     # If .dir hash exists in the ODB, assume directory contents
     # also exists
     for dir_hash in dir_exists:
-        try:
-            tree = load(cache_odb, HashInfo(name, dir_hash))
-        except FileNotFoundError:
-            continue
+        tree = dir_objs.get(dir_hash)
+        if not tree:
+            try:
+                tree = Tree.load(cache_odb, HashInfo(name, dir_hash))
+            except FileNotFoundError:
+                continue
         file_hashes = [entry.hash_info.value for _, entry in tree]
         if dir_hash not in index:
             logger.debug(
@@ -67,21 +68,13 @@ def _indexed_dir_hashes(odb, index, hash_infos, name, cache_odb):
         yield tree.hash_info.value
 
 
-def _status_staging(objs: Iterable["HashFile"]) -> "StatusResult":
-    exists: Set["HashFile"] = set()
-    for obj in objs:
-        if isinstance(obj, Tree):
-            exists.update(entry for _, entry in obj)
-        exists.add(obj)
-    return StatusResult(exists, set())
-
-
 def status(
     odb: "ObjectDB",
-    objs: Iterable["HashFile"],
+    obj_ids: Iterable["HashInfo"],
     name: Optional[str] = None,
     index: Optional["ObjectDBIndexBase"] = None,
     cache_odb: Optional["ObjectDB"] = None,
+    shallow: bool = True,
     **kwargs,
 ) -> "StatusResult":
     """Return status of whether or not the specified objects exist odb.
@@ -93,39 +86,41 @@ def status(
         exists: objs that exist in odb
         missing: objs that do not exist in ODB
     """
-    from .stage import is_memfs_staging
-
     logger.debug("Preparing to collect status from '%s'", odb.path_info)
     if not name:
         name = odb.fs.PARAM_CHECKSUM
 
-    if is_memfs_staging(odb):
-        # assume memfs staged objects already exist
-        return _status_staging(objs)
+    if cache_odb is None:
+        cache_odb = odb
 
-    hash_objs: Dict[str, "HashFile"] = {}
-    hashes: Set[str] = set()
-    dir_infos: Set["HashInfo"] = set()
-    exists: Set[str] = set()
-    for obj in objs:
-        assert obj.hash_info and obj.hash_info.value
-        if isinstance(obj, Tree):
-            for _, entry in obj:
-                assert entry.hash_info and entry.hash_info.value
-                hash_objs[entry.hash_info.value] = entry
-                hashes.add(entry.hash_info.value)
+    hash_infos: Dict[str, "HashInfo"] = {}
+    dir_objs: Dict[str, Optional["HashFile"]] = {}
+    for hash_info in obj_ids:
+        assert hash_info.value
+        if hash_info.isdir:
+            if shallow:
+                tree = None
+            else:
+                tree = Tree.load(cache_odb, hash_info)
+                for _, entry in tree:
+                    assert entry.hash_info and entry.hash_info.value
+                    hash_infos[entry.hash_info.value] = entry.hash_info
             if index:
-                dir_infos.add(obj.hash_info)
-        hashes.add(obj.hash_info.value)
-        hash_objs[obj.hash_info.value] = obj
+                dir_objs[hash_info.value] = tree
+        hash_infos[hash_info.value] = hash_info
+
+    if odb.fs.scheme == Schemes.MEMORY:
+        # assume memfs staged objects already exist
+        return StatusResult(set(hash_infos.values()), set())
+
+    hashes: Set[str] = set(hash_infos.keys())
+    exists: Set[str] = set()
 
     logger.debug("Collecting status from '%s'", odb.path_info)
     if index and hashes:
-        if dir_infos:
-            if cache_odb is None:
-                cache_odb = odb
+        if dir_objs:
             exists = hashes.intersection(
-                _indexed_dir_hashes(odb, index, dir_infos, name, cache_odb)
+                _indexed_dir_hashes(odb, index, dir_objs, name, cache_odb)
             )
             hashes.difference_update(exists)
         if hashes:
@@ -137,15 +132,15 @@ def status(
             odb.hashes_exist(hashes, name=str(odb.path_info), **kwargs)
         )
     return StatusResult(
-        {hash_objs[hash_] for hash_ in exists},
-        {hash_objs[hash_] for hash_ in (hashes - exists)},
+        {hash_infos[hash_] for hash_ in exists},
+        {hash_infos[hash_] for hash_ in (hashes - exists)},
     )
 
 
 def compare_status(
     src: "ObjectDB",
     dest: "ObjectDB",
-    objs: Iterable["HashFile"],
+    obj_ids: Iterable["HashInfo"],
     log_missing: bool = True,
     check_deleted: bool = True,
     src_index: Optional["ObjectDBIndexBase"] = None,
@@ -160,11 +155,17 @@ def compare_status(
         new: hashes that only exist in src
         deleted: hashes that only exist in dest
     """
-    dest_exists, dest_missing = status(dest, objs, index=dest_index, **kwargs)
+    if "cache_odb" not in kwargs:
+        kwargs["cache_odb"] = src
+    dest_exists, dest_missing = status(
+        dest, obj_ids, index=dest_index, **kwargs
+    )
     # for transfer operations we can skip src status check when all objects
     # already exist in dest
     if dest_missing or check_deleted:
-        src_exists, src_missing = status(src, objs, index=src_index, **kwargs)
+        src_exists, src_missing = status(
+            src, obj_ids, index=src_index, **kwargs
+        )
     else:
         src_exists = dest_exists
         src_missing = set()
@@ -176,7 +177,8 @@ def compare_status(
     )
     if log_missing and result.missing:
         missing_desc = "\n".join(
-            f"name: {obj.name}, {obj.hash_info}" for obj in result.missing
+            f"name: {hash_info.obj_name}, {hash_info}"
+            for hash_info in result.missing
         )
         logger.warning(
             "Some of the cache files do not exist neither locally "

dvc/objects/transfer.py

@@ -4,14 +4,15 @@ import logging
 from concurrent import futures
 from concurrent.futures import ThreadPoolExecutor
 from functools import partial, wraps
-from typing import TYPE_CHECKING, Iterable, Optional, Set
+from typing import TYPE_CHECKING, Callable, Iterable, Optional
+
+from funcy import split
 
 from dvc.progress import Tqdm
 
-from .file import HashFile
-from .tree import Tree
-
 if TYPE_CHECKING:
+    from dvc.hash_info import HashInfo
+
     from .db.base import ObjectDB
     from .db.index import ObjectDBIndexBase
 
@@ -20,9 +21,9 @@ logger = logging.getLogger(__name__)
 
 def _log_exceptions(func):
     @wraps(func)
-    def wrapper(odb, obj, *args, **kwargs):
+    def wrapper(path_info, *args, **kwargs):
         try:
-            func(odb, obj, *args, **kwargs)
+            func(path_info, *args, **kwargs)
             return 0
         except Exception as exc:  # pylint: disable=broad-except
             # NOTE: this means we ran out of file descriptors and there is no
@@ -31,23 +32,17 @@ def _log_exceptions(func):
             if isinstance(exc, OSError) and exc.errno == errno.EMFILE:
                 raise
 
-            logger.exception(
-                "failed to transfer '%s' to '%s'",
-                obj.path_info,
-                odb.get(obj.hash_info).path_info,
-            )
+            logger.exception("failed to transfer '%s'", path_info)
             return 1
 
     return wrapper
 
 
-def _transfer(src, dest, dir_objs, file_objs, missing, jobs, verify, **kwargs):
-    from . import save
-    from .stage import is_memfs_staging
-
-    is_staged = is_memfs_staging(src)
-    func = _log_exceptions(save)
-    total = len(dir_objs) + len(file_objs)
+def _transfer(
+    src, dest, dir_ids, file_ids, missing_ids, jobs, verify, move, **kwargs
+):
+    func = _log_exceptions(dest.add)
+    total = len(dir_ids) + len(file_ids)
     if total == 0:
         return 0
     with Tqdm(total=total, unit="file", desc="Transferring") as pbar:
@@ -59,37 +54,43 @@ def _transfer(src, dest, dir_objs, file_objs, missing, jobs, verify, **kwargs):
                 jobs,
                 func,
                 src,
-                dest,
-                is_staged,
                 verify,
+                move,
             )
-            processor.save_func = func
+            processor.add_func = func
             _do_transfer(
                 src,
                 dest,
-                dir_objs,
-                file_objs,
-                {obj.hash_info for obj in missing},
+                dir_ids,
+                file_ids,
+                missing_ids,
                 processor,
+                verify=verify,
+                move=move,
                 **kwargs,
             )
     return total
 
 
-def _create_tasks(executor, jobs, func, src, dest, is_staged, verify, objs):
+def _create_tasks(executor, jobs, func, src, verify, move, obj_ids):
     fails = 0
-    obj_iter = iter(objs)
+    hash_iter = iter(obj_ids)
+
+    def submit(hash_info):
+        obj = src.get(hash_info)
+        return executor.submit(
+            func,
+            obj.path_info,
+            obj.fs,
+            obj.hash_info,
+            verify=verify,
+            move=move,
+        )
 
     def create_taskset(amount):
         return {
-            executor.submit(
-                func,
-                dest,
-                _raw_obj(src, obj, is_staged),
-                move=False,
-                verify=verify,
-            )
-            for obj in itertools.islice(obj_iter, amount)
+            submit(hash_info)
+            for hash_info in itertools.islice(hash_iter, amount)
         }
 
     tasks = create_taskset(jobs * 5)
@@ -100,39 +101,46 @@ def _create_tasks(executor, jobs, func, src, dest, is_staged, verify, objs):
     return fails
 
 
-def _raw_obj(odb, obj, is_staged=False):
-    if is_staged:
-        return HashFile(obj.path_info, obj.fs, obj.hash_info)
-    return odb.get(obj.hash_info)
-
-
 def _do_transfer(
-    src,
-    dest,
-    dir_objs,
-    file_objs,
-    missing_hashes,
-    processor,
+    src: "ObjectDB",
+    dest: "ObjectDB",
+    dir_ids: Iterable["HashInfo"],
+    file_ids: Iterable["HashInfo"],
+    missing_ids: Iterable["HashInfo"],
+    processor: Callable,
     src_index: Optional["ObjectDBIndexBase"] = None,
     dest_index: Optional["ObjectDBIndexBase"] = None,
+    cache_odb: Optional["ObjectDB"] = None,
     **kwargs,
 ):
     from dvc.exceptions import FileTransferError
+    from dvc.objects.errors import ObjectFormatError
 
     total_fails = 0
     succeeded_dir_objs = []
-    all_file_objs = set(file_objs)
+    all_file_ids = set(file_ids)
 
-    for dir_obj in dir_objs:
-        bound_file_objs = set()
-        directory_hashes = {entry.hash_info for _, entry in dir_obj}
+    for dir_hash in dir_ids:
+        from .tree import Tree
 
-        for file_obj in all_file_objs.copy():
-            if file_obj.hash_info in directory_hashes:
-                bound_file_objs.add(file_obj)
-                all_file_objs.remove(file_obj)
+        bound_file_ids = set()
+        dir_obj: Optional["Tree"] = None
+        for odb in (cache_odb, src):
+            if odb is not None:
+                try:
+                    dir_obj = Tree.load(odb, dir_hash)
+                    break
+                except (FileNotFoundError, ObjectFormatError):
+                    pass
+        assert dir_obj
+        entry_ids = {entry.hash_info for _, entry in dir_obj}
 
-        dir_fails = processor(bound_file_objs)
+        for file_hash in all_file_ids.copy():
+            if file_hash in entry_ids:
+                bound_file_ids.add(file_hash)
+                all_file_ids.remove(file_hash)
+
+        dir_fails = processor(bound_file_ids)
         if dir_fails:
             logger.debug(
                 "failed to upload full contents of '%s', "
@@ -145,7 +153,7 @@ def _do_transfer(
                 dest.get(dir_obj.hash_info).path_info,
             )
             total_fails += dir_fails + 1
-        elif directory_hashes.intersection(missing_hashes):
+        elif entry_ids.intersection(missing_ids):
             # if for some reason a file contained in this dir is
             # missing both locally and in the remote, we want to
             # push whatever file content we have, but should not
@@ -156,15 +164,19 @@ def _do_transfer(
                 dir_obj.name,
             )
         else:
-            is_dir_failed = processor.save_func(
-                dest, src.get(dir_obj.hash_info), move=False
+            raw_obj = src.get(dir_obj.hash_info)
+            is_dir_failed = processor.add_func(  # type: ignore[attr-defined]
+                raw_obj.path_info,
+                raw_obj.fs,
+                raw_obj.hash_info,
+                **kwargs,
             )
             total_fails += is_dir_failed
             if not is_dir_failed:
                 succeeded_dir_objs.append(dir_obj)
 
     # insert the rest
-    total_fails += processor(all_file_objs)
+    total_fails += processor(all_file_ids)
     if total_fails:
         if src_index:
             src_index.clear()
@@ -179,15 +191,17 @@ def _do_transfer(
                 dir_obj.hash_info,
                 len(file_hashes),
             )
+            assert dir_obj.hash_info and dir_obj.hash_info.value
             dest_index.update([dir_obj.hash_info.value], file_hashes)
 
 
 def transfer(
     src: "ObjectDB",
     dest: "ObjectDB",
-    objs: Iterable["HashFile"],
+    obj_ids: Iterable["HashInfo"],
     jobs: Optional[int] = None,
     verify: bool = False,
+    move: bool = False,
     **kwargs,
 ) -> int:
     """Transfer (copy) the specified objects from one ODB to another.
@@ -201,27 +215,25 @@ def transfer(
         src.path_info,
         dest.path_info,
     )
-    status = compare_status(src, dest, objs, check_deleted=False, **kwargs)
+    if src == dest:
+        return 0
+
+    status = compare_status(src, dest, obj_ids, check_deleted=False, **kwargs)
     if not status.new:
         return 0
 
-    files: Set["HashFile"] = set()
-    dirs: Set["HashFile"] = set()
-    for obj in status.new:
-        if isinstance(obj, Tree):
-            dirs.add(obj)
-        else:
-            files.add(obj)
+    dir_ids, file_ids = split(lambda hash_info: hash_info.isdir, status.new)
     if jobs is None:
         jobs = dest.fs.jobs
 
     return _transfer(
         src,
         dest,
-        dirs,
-        files,
+        set(dir_ids),
+        set(file_ids),
         status.missing,
         jobs,
         verify,
+        move,
         **kwargs,
     )

dvc/objects/tree.py

@@ -1,7 +1,7 @@
 import json
 import logging
 import posixpath
-from typing import Dict, Optional, Tuple
+from typing import TYPE_CHECKING, Dict, Optional, Tuple
 
 from funcy import cached_property
 
@@ -9,6 +9,9 @@ from .errors import ObjectFormatError
 from .file import HashFile
 from .stage import get_file_hash
 
+if TYPE_CHECKING:
+    from dvc.hash_info import HashInfo
+
 logger = logging.getLogger(__name__)
 
 
@@ -29,7 +32,7 @@ class Tree(HashFile):
         self.__dict__.pop("trie", None)
         self._dict[key] = obj
 
-    def digest(self):
+    def digest(self, hash_info: Optional["HashInfo"] = None):
         from dvc.fs.memory import MemoryFileSystem
         from dvc.path_info import CloudURLInfo
         from dvc.utils import tmp_fname
@@ -40,8 +43,12 @@ class Tree(HashFile):
             fobj.write(self.as_bytes())
         self.fs = memfs
         self.path_info = path_info
-        self.hash_info = get_file_hash(path_info, memfs, "md5")
-        self.hash_info.value += ".dir"
+        if hash_info:
+            self.hash_info = hash_info
+        else:
+            self.hash_info = get_file_hash(path_info, memfs, "md5")
+            assert self.hash_info.value
+            self.hash_info.value += ".dir"
         try:
             self.hash_info.size = sum(obj.size for _, obj in self)
         except TypeError:

dvc/output.py

@@ -25,16 +25,15 @@ from .fs.s3 import S3FileSystem
 from .hash_info import HashInfo
 from .istextfile import istextfile
 from .objects import Tree
-from .objects import save as osave
 from .objects.errors import ObjectFormatError
 from .objects.stage import stage as ostage
+from .objects.transfer import transfer as otransfer
 from .scheme import Schemes
 from .utils import relpath
 from .utils.fs import path_isin
 
 if TYPE_CHECKING:
     from .objects.db.base import ObjectDB
-    from .objects.file import HashFile
 
 logger = logging.getLogger(__name__)
 
@@ -404,21 +403,21 @@ class Output:
         return self.odb.hash_to_path_info(self.hash_info.value).url
 
     def get_hash(self):
-        if not self.use_cache:
-            return ostage(
-                self.repo.odb.local,
-                self.path_info,
-                self.fs,
-                self.fs.PARAM_CHECKSUM,
-                dvcignore=self.dvcignore,
-            ).hash_info
-        return ostage(
-            self.odb,
+        if self.use_cache:
+            odb = self.odb
+            name = self.odb.fs.PARAM_CHECKSUM
+        else:
+            odb = self.repo.odb.local
+            name = self.fs.PARAM_CHECKSUM
+        _, obj = ostage(
+            odb,
             self.path_info,
             self.fs,
-            self.odb.fs.PARAM_CHECKSUM,
+            name,
             dvcignore=self.dvcignore,
-        ).hash_info
+            dry_run=not self.use_cache,
+        )
+        return obj.hash_info
 
     @property
     def is_dir_checksum(self):
@@ -545,7 +544,7 @@ class Output:
             logger.debug("Output '%s' didn't change. Skipping saving.", self)
             return
 
-        self.obj = ostage(
+        _, self.obj = ostage(
             self.odb,
             self.path_info,
             self.fs,
@@ -574,14 +573,20 @@ class Output:
             if granular:
                 obj = self._commit_granular_dir(filter_info)
             else:
-                obj = ostage(
+                staging, obj = ostage(
                     self.odb,
                     filter_info or self.path_info,
                     self.fs,
                     self.odb.fs.PARAM_CHECKSUM,
                     dvcignore=self.dvcignore,
                 )
-                osave(self.odb, obj)
+                otransfer(
+                    staging,
+                    self.odb,
+                    {obj.hash_info},
+                    shallow=False,
+                    move=True,
+                )
             checkout(
                 filter_info or self.path_info,
                 self.fs,
@@ -595,7 +600,7 @@ class Output:
 
     def _commit_granular_dir(self, filter_info):
         prefix = filter_info.relative_to(self.path_info).parts
-        save_obj = ostage(
+        staging, save_obj = ostage(
             self.odb,
             self.path_info,
             self.fs,
@@ -604,7 +609,13 @@ class Output:
         )
         save_obj = save_obj.filter(prefix)
         checkout_obj = save_obj.get(prefix)
-        osave(self.odb, save_obj)
+        otransfer(
+            staging,
+            self.odb,
+            {save_obj.hash_info} | {entry.hash_info for _, entry in save_obj},
+            shallow=True,
+            move=True,
+        )
         return checkout_obj
 
     def dumpd(self):
@@ -786,7 +797,7 @@ class Output:
 
         upload = not (update and from_fs.isdir(from_info))
         jobs = jobs or min((from_fs.jobs, odb.fs.jobs))
-        obj = ostage(
+        staging, obj = ostage(
             odb,
             from_info,
             from_fs,
@@ -795,7 +806,14 @@ class Output:
             jobs=jobs,
             no_progress_bar=no_progress_bar,
         )
-        osave(odb, obj, jobs=jobs, move=upload)
+        otransfer(
+            staging,
+            odb,
+            {obj.hash_info},
+            jobs=jobs,
+            move=upload,
+            shallow=False,
+        )
 
         self.hash_info = obj.hash_info
         return obj
@@ -825,7 +843,7 @@ class Output:
         try:
             objects.check(self.odb, obj)
         except FileNotFoundError:
-            self.repo.cloud.pull([obj], **kwargs)
+            self.repo.cloud.pull([obj.hash_info], **kwargs)
 
         if self.obj:
             return self.obj
@@ -839,8 +857,8 @@ class Output:
 
     def collect_used_dir_cache(
         self, remote=None, force=False, jobs=None, filter_info=None
-    ) -> Dict[Optional["ObjectDB"], Set["HashFile"]]:
-        """Fetch dir cache and return used objects for this out."""
+    ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
+        """Fetch dir cache and return used object IDs for this out."""
 
         try:
             self.get_dir_cache(jobs=jobs, remote=remote)
@@ -866,13 +884,12 @@ class Output:
         if filter_info and filter_info != self.path_info:
             prefix = filter_info.relative_to(self.path_info).parts
             obj = obj.filter(prefix)
-        self._set_obj_names(obj)
-        return {None: {obj}}
+        return {None: set(self._named_obj_ids(obj))}
 
     def get_used_objs(
         self, **kwargs
-    ) -> Dict[Optional["ObjectDB"], Set["HashFile"]]:
-        """Return filtered set of used objects for this out."""
+    ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
+        """Return filtered set of used object IDs for this out."""
 
         if not self.use_cache:
             return {}
@@ -905,19 +922,21 @@ class Output:
         obj = self.get_obj(filter_info=kwargs.get("filter_info"))
         if not obj:
             obj = self.odb.get(self.hash_info)
-        self._set_obj_names(obj)
 
-        return {None: {obj}}
+        return {None: set(self._named_obj_ids(obj))}
 
-    def _set_obj_names(self, obj):
-        obj.name = str(self)
+    def _named_obj_ids(self, obj):
+        name = str(self)
+        obj.hash_info.obj_name = name
+        yield obj.hash_info
         if isinstance(obj, Tree):
             for key, entry_obj in obj:
-                entry_obj.name = self.fs.sep.join([obj.name, *key])
+                entry_obj.hash_info.obj_name = self.fs.sep.join([name, *key])
+                yield entry_obj.hash_info
 
     def get_used_external(
         self, **kwargs
-    ) -> Dict[Optional["ObjectDB"], Set["HashFile"]]:
+    ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
         if not self.use_cache or not self.stage.is_repo_import:
             return {}
 

dvc/path_info.py

@@ -64,6 +64,8 @@ class PathInfo(pathlib.PurePath, _BasePath):
 
     url = fspath
 
+    path = fspath
+
     def relpath(self, other):
         return self.__class__(relpath(self, other))
 

dvc/repo/diff.py

@@ -134,8 +134,12 @@ def _output_paths(repo, repo_fs, targets):
     def _to_checksum(output):
         if on_working_fs:
             return ostage(
-                repo.odb.local, output.path_info, repo.odb.local.fs, "md5"
-            ).hash_info.value
+                repo.odb.local,
+                output.path_info,
+                repo.odb.local.fs,
+                "md5",
+                dry_run=True,
+            )[1].hash_info.value
         return output.hash_info.value
 
     for stage in repo.stages:

dvc/repo/fetch.py

@@ -1,9 +1,8 @@
 import logging
 
-from dvc.config import NoRemoteError
 from dvc.exceptions import DownloadError, FileTransferError
+from dvc.scheme import Schemes
 
-from ..scheme import Schemes
 from . import locked
 
 logger = logging.getLogger(__name__)
@@ -60,10 +59,13 @@ def fetch(
     except DownloadError as exc:
         failed += exc.amount
 
-    for odb, objs in used.items():
+    for odb, obj_ids in sorted(
+        used.items(),
+        key=lambda item: item[0] and item[0].fs.scheme == Schemes.MEMORY,
+    ):
         d, f = _fetch(
             self,
-            objs,
+            obj_ids,
             jobs=jobs,
             remote=remote,
             odb=odb,
@@ -77,14 +79,11 @@ def fetch(
     return downloaded
 
 
-def _fetch(repo, objs, **kwargs):
+def _fetch(repo, obj_ids, **kwargs):
     downloaded = 0
     failed = 0
     try:
-        downloaded += repo.cloud.pull(objs, **kwargs)
-    except NoRemoteError:
-        if any(obj.fs.scheme == Schemes.LOCAL for obj in objs):
-            raise
+        downloaded += repo.cloud.pull(obj_ids, **kwargs)
     except FileTransferError as exc:
         failed += exc.amount
     return downloaded, failed

dvc/repo/gc.py

@@ -1,14 +1,9 @@
 import logging
-from typing import TYPE_CHECKING, Set
 
 from dvc.exceptions import InvalidArgumentError
 
-from ..scheme import Schemes
 from . import locked
 
-if TYPE_CHECKING:
-    from dvc.objects.file import HashFile
-
 logger = logging.getLogger(__name__)
 
 
@@ -50,20 +45,19 @@ def gc(
     from contextlib import ExitStack
 
     from dvc.objects.db import get_index
-    from dvc.objects.stage import get_staging
     from dvc.repo import Repo
 
     if not repos:
         repos = []
     all_repos = [Repo(path) for path in repos]
 
-    used_objs: Set["HashFile"] = set()
+    used_obj_ids = set()
     with ExitStack() as stack:
         for repo in all_repos:
             stack.enter_context(repo.lock)
 
         for repo in all_repos + [self]:
-            for objs in repo.used_objs(
+            for obj_ids in repo.used_objs(
                 all_branches=all_branches,
                 with_deps=with_deps,
                 all_tags=all_tags,
@@ -73,28 +67,21 @@ def gc(
                 force=force,
                 jobs=jobs,
             ).values():
-                used_objs.update(objs)
+                used_obj_ids.update(obj_ids)
 
     for scheme, odb in self.odb.by_scheme():
         if not odb:
             continue
 
-        removed = odb.gc(
-            {obj for obj in used_objs if obj.fs.scheme == scheme},
-            jobs=jobs,
-        )
+        removed = odb.gc(used_obj_ids, jobs=jobs)
         if not removed:
             logger.info(f"No unused '{scheme}' cache to remove.")
-    get_staging(self.odb.local).gc(set(), jobs=jobs)
 
     if not cloud:
         return
 
     odb = self.cloud.get_remote_odb(remote, "gc -c")
-    removed = odb.gc(
-        {obj for obj in used_objs if obj.fs.scheme == Schemes.LOCAL},
-        jobs=jobs,
-    )
+    removed = odb.gc(used_obj_ids)
     if removed:
         get_index(odb).clear()
     else:

dvc/repo/push.py

@@ -41,11 +41,11 @@ def push(
     )
 
     pushed = len(used_run_cache)
-    for odb, objs in used.items():
+    for odb, obj_ids in used.items():
         if odb and odb.read_only:
             continue
         try:
-            pushed += self.cloud.push(objs, jobs, remote=remote, odb=odb)
+            pushed += self.cloud.push(obj_ids, jobs, remote=remote, odb=odb)
         except FileTransferError as exc:
             raise UploadError(exc.amount)
     return pushed

dvc/repo/status.py

@@ -89,16 +89,16 @@ def _cloud_status(
     )
 
     ret = {}
-    for odb, objs in used.items():
+    for odb, obj_ids in used.items():
         if odb is not None:
             # ignore imported objects
             continue
         status_info = self.cloud.status(
-            objs, jobs, remote=remote, log_missing=False
+            obj_ids, jobs, remote=remote, log_missing=False
         )
         for status_ in ("deleted", "new", "missing"):
-            for obj in getattr(status_info, status_, []):
-                ret[obj.name] = status_
+            for hash_info in getattr(status_info, status_, []):
+                ret[hash_info.obj_name] = status_
 
     return ret
 

dvc/stage/__init__.py

@@ -36,8 +36,8 @@ from .utils import (
 
 if TYPE_CHECKING:
     from dvc.dvcfile import DVCFile
+    from dvc.hash_info import HashInfo
     from dvc.objects.db.base import ObjectDB
-    from dvc.objects.file import HashFile
 
 logger = logging.getLogger(__name__)
 # Disallow all punctuation characters except hyphen and underscore
@@ -639,8 +639,8 @@ class Stage(params.StageParams):
 
     def get_used_objs(
         self, *args, **kwargs
-    ) -> Dict[Optional["ObjectDB"], Set["HashFile"]]:
-        """Return set of objects used by this stage."""
+    ) -> Dict[Optional["ObjectDB"], Set["HashInfo"]]:
+        """Return set of object IDs used by this stage."""
         used_objs = defaultdict(set)
         for out in self.filter_outs(kwargs.get("filter_info")):
             for odb, objs in out.get_used_objs(*args, **kwargs).items():

dvc/state.py

@@ -89,10 +89,14 @@ class State(StateBase):  # pylint: disable=too-many-instance-attributes
         inode = get_inode(path_info)
 
         logger.debug(
-            "state save (%s, %s, %s) %s", inode, mtime, size, hash_info.value
+            "state save (%s, %s, %s) %s",
+            inode,
+            mtime,
+            str(size),
+            hash_info.value,
         )
 
-        self.md5s[inode] = (mtime, size, hash_info.value)
+        self.md5s[inode] = (mtime, str(size), hash_info.value)
 
     def get(self, path_info, fs):
         """Gets the hash for the specified path info. Hash will be
@@ -122,10 +126,10 @@ class State(StateBase):  # pylint: disable=too-many-instance-attributes
 
         value = self.md5s.get(inode)
 
-        if not value or value[0] != mtime or value[1] != size:
+        if not value or value[0] != mtime or value[1] != str(size):
             return None
 
-        return HashInfo("md5", value[2], size=int(size))
+        return HashInfo("md5", value[2], size=size)
 
     def save_link(self, path_info, fs):
         """Adds the specified path to the list of links created by dvc. This

dvc/utils/fs.py

@@ -65,9 +65,7 @@ def get_mtime_and_size(path, fs, dvcignore=None):
         mtime = base_stat.st_mtime
         mtime = int(nanotime.timestamp(mtime))
 
-    # State of files handled by dvc is stored in db as TEXT.
-    # We cast results to string for later comparisons with stored values.
-    return str(mtime), str(size)
+    return str(mtime), size
 
 
 class BasePathNotInCheckedPathException(DvcException):

tests/func/objects/db/test_index.py

@@ -4,6 +4,7 @@ from dvc.exceptions import DownloadError, UploadError
 from dvc.fs.local import LocalFileSystem
 from dvc.objects.db import get_index
 from dvc.utils.fs import remove
+from tests.utils import clean_staging
 
 
 @pytest.fixture
@@ -16,6 +17,7 @@ def test_indexed_on_status(tmp_dir, dvc, index):
     foo = tmp_dir.dvc_gen({"foo": "foo content"})[0].outs[0]
     bar = tmp_dir.dvc_gen({"bar": {"baz": "baz content"}})[0].outs[0]
     baz_hash = bar.obj.trie.get(("baz",)).hash_info
+    clean_staging()
     dvc.push()
     index.clear()
 
@@ -29,6 +31,7 @@ def test_indexed_on_push(tmp_dir, dvc, index):
     foo = tmp_dir.dvc_gen({"foo": "foo content"})[0].outs[0]
     bar = tmp_dir.dvc_gen({"bar": {"baz": "baz content"}})[0].outs[0]
     baz_hash = bar.obj.trie.get(("baz",)).hash_info
+    clean_staging()
 
     dvc.push()
     assert {bar.hash_info.value, baz_hash.value} == set(index.hashes())

tests/func/test_commit.py

@@ -7,6 +7,7 @@ from dvc.dvcfile import PIPELINE_FILE
 from dvc.output import OutputDoesNotExistError
 from dvc.stage.exceptions import StageCommitError
 from dvc.utils.serialize import dump_yaml, load_yaml
+from tests.utils import clean_staging
 
 
 def test_commit_recursive(tmp_dir, dvc):
@@ -53,6 +54,8 @@ def test_commit_with_deps(tmp_dir, dvc, run_copy, run_kw):
     assert foo_stage.outs[0].changed_cache()
     assert stage.outs[0].changed_cache()
 
+    clean_staging()
+
     dvc.commit(stage.path, with_deps=True)
     assert not foo_stage.outs[0].changed_cache()
     assert not stage.outs[0].changed_cache()
@@ -66,6 +69,8 @@ def test_commit_changed_md5(tmp_dir, dvc):
     stage_file_content["md5"] = "1111111111"
     dump_yaml(stage.path, stage_file_content)
 
+    clean_staging()
+
     with pytest.raises(StageCommitError):
         dvc.commit(stage.path)
 
@@ -78,6 +83,8 @@ def test_commit_no_exec(tmp_dir, dvc):
     stage = dvc.run(
         name="my", cmd="mycmd", deps=["dep"], outs=["out"], no_exec=True
     )
+    clean_staging()
+
     assert dvc.status(stage.path)
     dvc.commit(stage.path, force=True)
     assert dvc.status(stage.path) == {}
@@ -90,6 +97,7 @@ def test_commit_granular_output(tmp_dir, dvc):
         outs=["foo", "bar"],
         no_commit=True,
     )
+    clean_staging()
 
     cache = tmp_dir / ".dvc" / "cache"
     assert not list(cache.glob("*/*"))
@@ -103,6 +111,7 @@ def test_commit_granular_output(tmp_dir, dvc):
 def test_commit_granular_output_file(tmp_dir, dvc):
     tmp_dir.gen("foo", "foo")
     dvc.add("foo", no_commit=True)
+    clean_staging()
     dvc.commit("foo")
     assert dvc.status() == {}
 
@@ -118,13 +127,12 @@ def test_commit_granular_output_dir(tmp_dir, dvc):
         }
     )
     dvc.add("data", no_commit=True)
+    clean_staging()
     dvc.commit("data")
     assert dvc.status() == {}
 
 
 def test_commit_granular_dir(tmp_dir, dvc):
-    from dvc.objects.stage import _STAGING_DIR
-
     tmp_dir.gen(
         {
             "data": {
@@ -135,21 +143,18 @@ def test_commit_granular_dir(tmp_dir, dvc):
         }
     )
     dvc.add("data", no_commit=True)
+    clean_staging()
 
     cache = tmp_dir / ".dvc" / "cache"
-    staging = tmp_dir / ".dvc" / "tmp" / _STAGING_DIR
 
     assert set(cache.glob("*/*")) == set()
-    assert set(staging.glob("*/*")) == {
-        staging / "1a" / "ca2c799df82929bbdd976557975546.dir"
-    }
 
     dvc.commit(os.path.join("data", "foo"))
     assert set(cache.glob("*/*")) == {
         cache / "1a" / "ca2c799df82929bbdd976557975546.dir",
         cache / "ac" / "bd18db4cc2f85cedef654fccc4a4d8",
     }
-    assert set(staging.glob("*/*")) == set()
+    clean_staging()
 
     dvc.commit(os.path.join("data", "subdir"))
     assert set(cache.glob("*/*")) == {
@@ -158,7 +163,7 @@ def test_commit_granular_dir(tmp_dir, dvc):
         cache / "4c" / "e8d2a2cf314a52fa7f315ca37ca445",
         cache / "68" / "dde2c3c4e7953c2290f176bbdc9a54",
     }
-    assert set(staging.glob("*/*")) == set()
+    clean_staging()
 
     dvc.commit(os.path.join("data"))
     assert set(cache.glob("*/*")) == {
@@ -168,13 +173,13 @@ def test_commit_granular_dir(tmp_dir, dvc):
         cache / "68" / "dde2c3c4e7953c2290f176bbdc9a54",
         cache / "37" / "b51d194a7513e45b56f6524f2d51f2",
     }
-    assert set(staging.glob("*/*")) == set()
 
 
 def test_commit_no_exec_missing_dep(tmp_dir, dvc):
     stage = dvc.run(
         name="my", cmd="mycmd", deps=["dep"], outs=["out"], no_exec=True
     )
+    clean_staging()
     assert dvc.status(stage.path)
 
     with pytest.raises(DependencyDoesNotExistError):
@@ -183,6 +188,7 @@ def test_commit_no_exec_missing_dep(tmp_dir, dvc):
 
 def test_commit_no_exec_missing_out(tmp_dir, dvc):
     stage = dvc.run(name="my", cmd="mycmd", outs=["out"], no_exec=True)
+    clean_staging()
     assert dvc.status(stage.path)
 
     with pytest.raises(OutputDoesNotExistError):
@@ -192,6 +198,7 @@ def test_commit_no_exec_missing_out(tmp_dir, dvc):
 def test_commit_pipeline_stage(tmp_dir, dvc, run_copy):
     tmp_dir.gen("foo", "foo")
     stage = run_copy("foo", "bar", no_commit=True, name="copy-foo-bar")
+    clean_staging()
     assert dvc.status(stage.addressing)
     assert dvc.commit(stage.addressing, force=True) == [stage]
     assert not dvc.status(stage.addressing)
@@ -205,6 +212,7 @@ def test_commit_pipeline_stage(tmp_dir, dvc, run_copy):
 def test_imported_entries_unchanged(tmp_dir, dvc, erepo_dir):
     with erepo_dir.chdir():
         erepo_dir.dvc_gen("file", "file content", "initial commit")
+    clean_staging()
 
     stage = dvc.imp(os.fspath(erepo_dir), "file")
 

tests/func/test_data_cloud.py

@@ -50,7 +50,7 @@ def test_cloud(tmp_dir, dvc, remote):  # pylint:disable=unused-argument
     out = stage.outs[0]
     cache = out.cache_path
     foo_hash = out.hash_info
-    foo_objs = out.get_used_objs().get(None, set())
+    foo_hashes = out.get_used_objs().get(None, set())
 
     (stage_dir,) = tmp_dir.dvc_gen(
         {
@@ -63,7 +63,6 @@ def test_cloud(tmp_dir, dvc, remote):  # pylint:disable=unused-argument
     )
     out_dir = stage_dir.outs[0]
     cache_dir = out_dir.cache_path
-    dir_objs = {out_dir.obj}
     dir_hash = out_dir.hash_info
     dir_hashes = {dir_hash} | {
         entry_obj.hash_info for _, entry_obj in out_dir.obj
@@ -72,23 +71,23 @@ def test_cloud(tmp_dir, dvc, remote):  # pylint:disable=unused-argument
     def _check_status(status, **kwargs):
         for key in ("ok", "missing", "new", "deleted"):
             expected = kwargs.get(key, set())
-            assert expected == {obj.hash_info for obj in getattr(status, key)}
+            assert expected == set(getattr(status, key))
 
     # Check status
-    status = dvc.cloud.status(foo_objs)
+    status = dvc.cloud.status(foo_hashes)
     _check_status(status, new={foo_hash})
 
-    status_dir = dvc.cloud.status(dir_objs)
+    status_dir = dvc.cloud.status(dir_hashes)
     _check_status(status_dir, new=dir_hashes)
 
     # Move cache and check status
     # See issue https://github.com/iterative/dvc/issues/4383 for details
     backup_dir = dvc.odb.local.cache_dir + ".backup"
     move(dvc.odb.local.cache_dir, backup_dir)
-    status = dvc.cloud.status(foo_objs)
+    status = dvc.cloud.status(foo_hashes)
     _check_status(status, missing={foo_hash})
 
-    status_dir = dvc.cloud.status(dir_objs)
+    status_dir = dvc.cloud.status(dir_hashes)
     _check_status(status_dir, missing=dir_hashes)
 
     # Restore original cache:
@@ -96,42 +95,42 @@ def test_cloud(tmp_dir, dvc, remote):  # pylint:disable=unused-argument
     move(backup_dir, dvc.odb.local.cache_dir)
 
     # Push and check status
-    dvc.cloud.push(foo_objs)
+    dvc.cloud.push(foo_hashes)
     assert os.path.exists(cache)
     assert os.path.isfile(cache)
 
-    dvc.cloud.push(dir_objs)
+    dvc.cloud.push(dir_hashes)
     assert os.path.isfile(cache_dir)
 
-    status = dvc.cloud.status(foo_objs)
+    status = dvc.cloud.status(foo_hashes)
     _check_status(status, ok={foo_hash})
 
-    status_dir = dvc.cloud.status(dir_objs)
+    status_dir = dvc.cloud.status(dir_hashes)
     _check_status(status_dir, ok=dir_hashes)
 
     # Remove and check status
     remove(dvc.odb.local.cache_dir)
 
-    status = dvc.cloud.status(foo_objs)
+    status = dvc.cloud.status(foo_hashes)
     _check_status(status, deleted={foo_hash})
 
-    status_dir = dvc.cloud.status(dir_objs)
+    status_dir = dvc.cloud.status(dir_hashes)
     _check_status(status_dir, deleted=dir_hashes)
 
     # Pull and check status
-    dvc.cloud.pull(foo_objs)
+    dvc.cloud.pull(foo_hashes)
     assert os.path.exists(cache)
     assert os.path.isfile(cache)
     with open(cache) as fd:
         assert fd.read() == "foo"
 
-    dvc.cloud.pull(dir_objs)
+    dvc.cloud.pull(dir_hashes)
     assert os.path.isfile(cache_dir)
 
-    status = dvc.cloud.status(foo_objs)
+    status = dvc.cloud.status(foo_hashes)
     _check_status(status, ok={foo_hash})
 
-    status_dir = dvc.cloud.status(dir_objs)
+    status_dir = dvc.cloud.status(dir_hashes)
     _check_status(status_dir, ok=dir_hashes)
 
 
@@ -242,10 +241,13 @@ def test_hash_recalculation(mocker, dvc, tmp_dir, local_remote):
 
 
 def test_missing_cache(tmp_dir, dvc, local_remote, caplog):
+    from tests.utils import clean_staging
+
     tmp_dir.dvc_gen({"foo": "foo", "bar": "bar"})
 
     # purge cache
     remove(dvc.odb.local.cache_dir)
+    clean_staging()
 
     header = (
         "Some of the cache files do not exist "
@@ -355,6 +357,8 @@ def test_pull_external_dvc_imports(tmp_dir, dvc, scm, erepo_dir):
 
 
 def clean(outs, dvc=None):
+    from tests.utils import clean_staging
+
     if dvc:
         outs = outs + [dvc.odb.local.cache_dir]
     for path in outs:
@@ -363,6 +367,7 @@ def clean(outs, dvc=None):
     if dvc:
         os.makedirs(dvc.odb.local.cache_dir, exist_ok=True)
         clean_repos()
+        clean_staging()
 
 
 def recurse_list_dir(d):

tests/func/test_external_repo.py

@@ -3,13 +3,14 @@ from unittest.mock import ANY, patch
 
 from dvc.external_repo import CLONES, external_repo
 from dvc.fs.local import LocalFileSystem
-from dvc.objects import save
 from dvc.objects.stage import stage
+from dvc.objects.transfer import transfer
 from dvc.path_info import PathInfo
 from dvc.scm.git import Git
 from dvc.utils import relpath
 from dvc.utils.fs import makedirs, remove
 from tests.unit.fs.test_repo import make_subrepo
+from tests.utils import clean_staging
 
 
 def test_external_repo(erepo_dir):
@@ -198,16 +199,23 @@ def test_subrepos_are_ignored(tmp_dir, erepo_dir):
         # clear cache to test saving to cache
         cache_dir = tmp_dir / repo.odb.local.cache_dir
         remove(cache_dir)
+        clean_staging()
         makedirs(cache_dir)
 
-        obj = stage(
+        staging, obj = stage(
             repo.odb.local,
             PathInfo(repo.root_dir) / "dir",
             repo.repo_fs,
             "md5",
             dvcignore=repo.dvcignore,
         )
-        save(repo.odb.local, obj)
+        transfer(
+            staging,
+            repo.odb.local,
+            {obj.hash_info},
+            shallow=False,
+            move=True,
+        )
         assert set(cache_dir.glob("??/*")) == {
             cache_dir / "e1" / "d9e8eae5374860ae025ec84cfd85c7.dir",
             cache_dir / "37" / "b51d194a7513e45b56f6524f2d51f2",

tests/func/test_import.py

@@ -13,6 +13,7 @@ from dvc.stage.exceptions import StagePathNotFoundError
 from dvc.system import System
 from dvc.utils.fs import makedirs, remove
 from tests.unit.fs.test_repo import make_subrepo
+from tests.utils import clean_staging
 
 
 def test_import(tmp_dir, scm, dvc, erepo_dir):
@@ -290,6 +291,8 @@ def test_push_wildcard_from_bare_git_repo(
     dvc_repo = make_tmp_dir("dvc-repo", scm=True, dvc=True)
     with dvc_repo.chdir():
         dvc_repo.dvc.imp(os.fspath(tmp_dir), "dirextra")
+        clean_staging()
+
         with pytest.raises(PathMissingError):
             dvc_repo.dvc.imp(os.fspath(tmp_dir), "dir123")
 
@@ -593,6 +596,7 @@ def test_circular_import(tmp_dir, dvc, scm, erepo_dir):
     dvc.imp(os.fspath(erepo_dir), "dir", "dir_imported")
     scm.add("dir_imported.dvc")
     scm.commit("import")
+    clean_staging()
 
     with erepo_dir.chdir():
         with pytest.raises(CircularImportError):

tests/func/test_ls.py

@@ -512,6 +512,7 @@ def test_ls_target(erepo_dir, use_scm):
 )
 def test_subrepo(dvc_top_level, erepo):
     from tests.func.test_get import make_subrepo
+    from tests.utils import clean_staging
 
     dvc_files = {"foo.txt": "foo.txt", "dvc_dir": {"lorem": "lorem"}}
     scm_files = {"bar.txt": "bar.txt", "scm_dir": {"ipsum": "ipsum"}}
@@ -523,6 +524,7 @@ def test_subrepo(dvc_top_level, erepo):
             repo.scm_gen(scm_files, commit=f"scm track for top {repo}")
             if hasattr(repo, "dvc"):
                 repo.dvc_gen(dvc_files, commit=f"dvc track for {repo}")
+        clean_staging()
 
     def _list_files(repo, path=None):
         return set(map(itemgetter("path"), Repo.ls(os.fspath(repo), path)))

tests/func/test_remote.py

@@ -157,18 +157,16 @@ def test_dir_hash_should_be_key_order_agnostic(tmp_dir, dvc):
     )
     tree.digest()
     with patch("dvc.objects.stage._get_tree_obj", return_value=tree):
-        hash1 = stage(
-            dvc.odb.local, path_info, dvc.odb.local.fs, "md5"
-        ).hash_info
+        _, obj = stage(dvc.odb.local, path_info, dvc.odb.local.fs, "md5")
+        hash1 = obj.hash_info
 
     tree = Tree.from_list(
         [{"md5": "1", "relpath": "1"}, {"md5": "2", "relpath": "2"}]
     )
     tree.digest()
     with patch("dvc.objects.stage._get_tree_obj", return_value=tree):
-        hash2 = stage(
-            dvc.odb.local, path_info, dvc.odb.local.fs, "md5"
-        ).hash_info
+        _, obj = stage(dvc.odb.local, path_info, dvc.odb.local.fs, "md5")
+        hash2 = obj.hash_info
 
     assert hash1 == hash2
 

tests/func/test_run_single_stage.py

@@ -900,10 +900,13 @@ class TestShouldNotCheckoutUponCorruptedLocalHardlinkCache(TestDvc):
         self.dvc = DvcRepo(".")
 
     def test(self):
+        from tests.utils import clean_staging
+
         cmd = f"python {self.CODE} {self.FOO} {self.BAR}"
         stage = self.dvc.run(
             deps=[self.FOO], outs=[self.BAR], cmd=cmd, single_stage=True
         )
+        clean_staging()
 
         os.chmod(self.BAR, 0o644)
         with open(self.BAR, "w") as fd:

tests/unit/fs/test_dvc.py

@@ -243,15 +243,15 @@ def test_get_hash_granular(tmp_dir, dvc):
     fs = DvcFileSystem(repo=dvc)
     subdir = PathInfo(tmp_dir) / "dir" / "subdir"
     assert fs.info(subdir).get("md5") is None
-    assert stage(dvc.odb.local, subdir, fs, "md5").hash_info == HashInfo(
+    _, obj = stage(dvc.odb.local, subdir, fs, "md5", dry_run=True)
+    assert obj.hash_info == HashInfo(
         "md5", "af314506f1622d107e0ed3f14ec1a3b5.dir"
     )
     assert (
         fs.info(subdir / "data")["md5"] == "8d777f385d3dfec8815d20f7496026dc"
     )
-    assert stage(
-        dvc.odb.local, subdir / "data", fs, "md5"
-    ).hash_info == HashInfo("md5", "8d777f385d3dfec8815d20f7496026dc")
+    _, obj = stage(dvc.odb.local, subdir / "data", fs, "md5", dry_run=True)
+    assert obj.hash_info == HashInfo("md5", "8d777f385d3dfec8815d20f7496026dc")
 
 
 def test_get_hash_dirty_file(tmp_dir, dvc):
@@ -261,9 +261,10 @@ def test_get_hash_dirty_file(tmp_dir, dvc):
     fs = DvcFileSystem(repo=dvc)
     expected = "8c7dd922ad47494fc02c388e12c00eac"
     assert fs.info(PathInfo(tmp_dir) / "file").get("md5") == expected
-    assert stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5"
-    ).hash_info == HashInfo("md5", expected)
+    _, obj = stage(
+        dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5", dry_run=True
+    )
+    assert obj.hash_info == HashInfo("md5", expected)
 
 
 def test_get_hash_dirty_dir(tmp_dir, dvc):
@@ -273,6 +274,7 @@ def test_get_hash_dirty_dir(tmp_dir, dvc):
     fs = DvcFileSystem(repo=dvc)
     expected = "5ea40360f5b4ec688df672a4db9c17d1.dir"
     assert fs.info(PathInfo(tmp_dir) / "dir").get("md5") == expected
-    assert stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5"
-    ).hash_info == HashInfo("md5", expected)
+    _, obj = stage(
+        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5", dry_run=True
+    )
+    assert obj.hash_info == HashInfo("md5", expected)

tests/unit/fs/test_repo.py

@@ -8,6 +8,7 @@ from dvc.fs.repo import RepoFileSystem
 from dvc.hash_info import HashInfo
 from dvc.objects.stage import stage
 from dvc.path_info import PathInfo
+from tests.utils import clean_staging
 
 
 def test_exists(tmp_dir, dvc):
@@ -512,9 +513,8 @@ def test_get_hash_cached_file(tmp_dir, dvc, mocker):
     fs = RepoFileSystem(repo=dvc)
     expected = "acbd18db4cc2f85cedef654fccc4a4d8"
     assert fs.info(PathInfo(tmp_dir) / "foo").get("md5") is None
-    assert stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "foo", fs, "md5"
-    ).hash_info == HashInfo("md5", expected)
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "foo", fs, "md5")
+    assert obj.hash_info == HashInfo("md5", expected)
     (tmp_dir / "foo").unlink()
     assert fs.info(PathInfo(tmp_dir) / "foo")["md5"] == expected
 
@@ -526,15 +526,17 @@ def test_get_hash_cached_dir(tmp_dir, dvc, mocker):
     fs = RepoFileSystem(repo=dvc)
     expected = "8761c4e9acad696bee718615e23e22db.dir"
     assert fs.info(PathInfo(tmp_dir) / "dir").get("md5") is None
-    assert stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5"
-    ).hash_info == HashInfo("md5", "8761c4e9acad696bee718615e23e22db.dir")
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5")
+    assert obj.hash_info == HashInfo(
+        "md5", "8761c4e9acad696bee718615e23e22db.dir"
+    )
 
     shutil.rmtree(tmp_dir / "dir")
     assert fs.info(PathInfo(tmp_dir) / "dir")["md5"] == expected
-    assert stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5"
-    ).hash_info == HashInfo("md5", "8761c4e9acad696bee718615e23e22db.dir")
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5")
+    assert obj.hash_info == HashInfo(
+        "md5", "8761c4e9acad696bee718615e23e22db.dir"
+    )
 
 
 def test_get_hash_cached_granular(tmp_dir, dvc, mocker):
@@ -544,13 +546,13 @@ def test_get_hash_cached_granular(tmp_dir, dvc, mocker):
     fs = RepoFileSystem(repo=dvc)
     subdir = PathInfo(tmp_dir) / "dir" / "subdir"
     assert fs.info(subdir).get("md5") is None
-    assert stage(dvc.odb.local, subdir, fs, "md5").hash_info == HashInfo(
+    _, obj = stage(dvc.odb.local, subdir, fs, "md5")
+    assert obj.hash_info == HashInfo(
         "md5", "af314506f1622d107e0ed3f14ec1a3b5.dir"
     )
     assert fs.info(subdir / "data").get("md5") is None
-    assert stage(
-        dvc.odb.local, subdir / "data", fs, "md5"
-    ).hash_info == HashInfo("md5", "8d777f385d3dfec8815d20f7496026dc")
+    _, obj = stage(dvc.odb.local, subdir / "data", fs, "md5")
+    assert obj.hash_info == HashInfo("md5", "8d777f385d3dfec8815d20f7496026dc")
     (tmp_dir / "dir" / "subdir" / "data").unlink()
     assert (
         fs.info(subdir / "data")["md5"] == "8d777f385d3dfec8815d20f7496026dc"
@@ -568,50 +570,66 @@ def test_get_hash_mixed_dir(tmp_dir, scm, dvc):
         ]
     )
     tmp_dir.scm.commit("add dir")
+    clean_staging()
 
     fs = RepoFileSystem(repo=dvc)
-    actual = stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5"
-    ).hash_info
-    expected = HashInfo("md5", "e1d9e8eae5374860ae025ec84cfd85c7.dir")
-    assert actual == expected
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5")
+    assert obj.hash_info == HashInfo(
+        "md5", "e1d9e8eae5374860ae025ec84cfd85c7.dir"
+    )
 
 
 def test_get_hash_dirty_file(tmp_dir, dvc):
-    tmp_dir.dvc_gen("file", "file")
-    (tmp_dir / "file").write_text("something")
+    from dvc.objects import check
+    from dvc.objects.errors import ObjectFormatError
+    from dvc.objects.stage import get_file_hash
 
+    tmp_dir.dvc_gen("file", "file")
+    file_hash_info = HashInfo("md5", "8c7dd922ad47494fc02c388e12c00eac")
+
+    (tmp_dir / "file").write_text("something")
+    something_hash_info = HashInfo("md5", "437b930db84b8079c2dd804a71936b5f")
+
+    clean_staging()
+
+    # file is modified in workspace
+    # get_file_hash(file) should return workspace hash, not DVC cached hash
     fs = RepoFileSystem(repo=dvc)
     assert fs.info(PathInfo(tmp_dir) / "file").get("md5") is None
-    actual = stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5"
-    ).hash_info
-    expected = HashInfo("md5", "437b930db84b8079c2dd804a71936b5f")
-    assert actual == expected
+    staging, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5")
+    assert obj.hash_info == something_hash_info
+    check(staging, obj)
 
+    # file is removed in workspace
+    # any staged object referring to modified workspace obj is now invalid
     (tmp_dir / "file").unlink()
-    assert (
-        fs.info(PathInfo(tmp_dir) / "file")["md5"]
-        == "8c7dd922ad47494fc02c388e12c00eac"
+    with pytest.raises(ObjectFormatError):
+        check(staging, obj)
+
+    # get_file_hash(file) should return DVC cached hash
+    assert fs.info(PathInfo(tmp_dir) / "file")["md5"] == file_hash_info.value
+    hash_info = get_file_hash(
+        PathInfo(tmp_dir) / "file", fs, "md5", state=dvc.state
     )
-    actual = stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5"
-    ).hash_info
-    expected = HashInfo("md5", "8c7dd922ad47494fc02c388e12c00eac")
-    assert actual == expected
+    assert hash_info == file_hash_info
+
+    # tmp_dir/file can be staged even though it is missing in workspace since
+    # repofs will use the DVC cached hash (and refer to the local cache object)
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "file", fs, "md5")
+    assert obj.hash_info == file_hash_info
 
 
 def test_get_hash_dirty_dir(tmp_dir, dvc):
     tmp_dir.dvc_gen({"dir": {"foo": "foo", "bar": "bar"}})
     (tmp_dir / "dir" / "baz").write_text("baz")
+    clean_staging()
 
     fs = RepoFileSystem(repo=dvc)
-    actual = stage(
-        dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5"
-    ).hash_info
-    expected = HashInfo("md5", "ba75a2162ca9c29acecb7957105a0bc2.dir")
-    assert actual == expected
-    assert actual.nfiles == 3
+    _, obj = stage(dvc.odb.local, PathInfo(tmp_dir) / "dir", fs, "md5")
+    assert obj.hash_info == HashInfo(
+        "md5", "ba75a2162ca9c29acecb7957105a0bc2.dir"
+    )
+    assert obj.hash_info.nfiles == 3
 
 
 @pytest.mark.parametrize("traverse_subrepos", [True, False])

tests/unit/objects/db/test_local.py

@@ -6,7 +6,6 @@ import pytest
 from dvc.fs.local import LocalFileSystem
 from dvc.hash_info import HashInfo
 from dvc.objects.db.local import LocalObjectDB
-from dvc.objects.file import HashFile
 from dvc.path_info import PathInfo
 
 
@@ -18,21 +17,17 @@ def test_status_download_optimization(mocker, dvc):
     from dvc.objects.status import compare_status
 
     odb = LocalObjectDB(LocalFileSystem(), PathInfo("."))
-    objs = {
-        HashFile(
-            None, odb.fs, HashInfo("md5", "acbd18db4cc2f85cedef654fccc4a4d8")
-        ),
-        HashFile(
-            None, odb.fs, HashInfo("md5", "37b51d194a7513e45b56f6524f2d51f2")
-        ),
+    obj_ids = {
+        HashInfo("md5", "acbd18db4cc2f85cedef654fccc4a4d8"),
+        HashInfo("md5", "37b51d194a7513e45b56f6524f2d51f2"),
     }
 
-    local_exists = [obj.hash_info.value for obj in objs]
+    local_exists = [hash_info.value for hash_info in obj_ids]
     mocker.patch.object(odb, "hashes_exist", return_value=local_exists)
 
     src_odb = mocker.Mock()
 
-    compare_status(src_odb, odb, objs, check_deleted=False)
+    compare_status(src_odb, odb, obj_ids, check_deleted=False)
     assert src_odb.hashes_exist.call_count == 0
 
 
@@ -91,28 +86,24 @@ def test_set_exec_ignore_errors(tmp_dir, dvc, mocker, err):
 
 
 def test_staging_file(tmp_dir, dvc):
-    from dvc.objects import check, save
-    from dvc.objects.stage import get_staging, stage
+    from dvc.objects import check
+    from dvc.objects.stage import stage
+    from dvc.objects.transfer import transfer
 
     tmp_dir.gen("foo", "foo")
     fs = LocalFileSystem()
 
     local_odb = dvc.odb.local
-    staging_odb = get_staging(local_odb)
-    obj = stage(local_odb, tmp_dir / "foo", fs, "md5")
+    staging_odb, obj = stage(local_odb, tmp_dir / "foo", fs, "md5")
 
-    for odb in (local_odb, staging_odb):
-        path_info = odb.hash_to_path_info(obj.hash_info.value)
-        assert not odb.fs.exists(path_info)
+    assert not local_odb.exists(obj.hash_info)
+    assert staging_odb.exists(obj.hash_info)
 
-    # check for file after staging should fail since files are not added on
-    # stage()
     with pytest.raises(FileNotFoundError):
         check(local_odb, obj)
-    with pytest.raises(FileNotFoundError):
-        check(staging_odb, obj)
+    check(staging_odb, obj)
 
-    save(local_odb, obj)
+    transfer(staging_odb, local_odb, {obj.hash_info}, move=True)
     check(local_odb, obj)
     with pytest.raises(FileNotFoundError):
         check(staging_odb, obj)
@@ -122,35 +113,27 @@ def test_staging_file(tmp_dir, dvc):
 
 
 def test_staging_dir(tmp_dir, dvc):
-    from dvc.objects import check, save
-    from dvc.objects.stage import get_staging, stage
+    from dvc.objects import check
+    from dvc.objects.stage import stage
+    from dvc.objects.transfer import transfer
 
     tmp_dir.gen({"dir": {"foo": "foo", "bar": "bar"}})
     fs = LocalFileSystem()
     local_odb = dvc.odb.local
-    staging_odb = get_staging(local_odb)
 
-    obj = stage(local_odb, tmp_dir / "dir", fs, "md5")
+    staging_odb, obj = stage(local_odb, tmp_dir / "dir", fs, "md5")
 
-    path_info = local_odb.hash_to_path_info(obj.hash_info.value)
-    assert not local_odb.fs.exists(path_info)
-    path_info = staging_odb.hash_to_path_info(obj.hash_info.value)
-    assert staging_odb.fs.exists(path_info)
+    assert not local_odb.exists(obj.hash_info)
+    assert staging_odb.exists(obj.hash_info)
 
-    # check for raw object after staging should pass only when using the
-    # staging odb
-    raw = HashFile(obj.path_info, obj.fs, obj.hash_info)
     with pytest.raises(FileNotFoundError):
-        check(local_odb, raw)
-    check(staging_odb, raw)
+        check(local_odb, obj)
+    check(staging_odb, obj)
 
-    # checking the entire tree should fail since individual file entries are
-    # not added on stage()
+    transfer(staging_odb, local_odb, {obj.hash_info}, shallow=False, move=True)
+    check(local_odb, obj)
     with pytest.raises(FileNotFoundError):
         check(staging_odb, obj)
 
-    save(local_odb, obj)
-    check(local_odb, obj)
-
     path_info = local_odb.hash_to_path_info(obj.hash_info.value)
     assert fs.exists(path_info)

tests/unit/repo/test_repo.py

@@ -45,8 +45,6 @@ def test_find_outs_by_path_does_graph_checks(tmp_dir, dvc):
     [os.path.join("dir", "subdir", "file"), os.path.join("dir", "subdir")],
 )
 def test_used_objs(tmp_dir, dvc, path):
-    from dvc.objects.tree import Tree
-
     tmp_dir.dvc_gen({"dir": {"subdir": {"file": "file"}, "other": "other"}})
 
     expected = {
@@ -55,11 +53,8 @@ def test_used_objs(tmp_dir, dvc, path):
     }
 
     used = set()
-    for _, objs in dvc.used_objs([path]).items():
-        for obj in objs:
-            used.add(obj.hash_info)
-            if isinstance(obj, Tree):
-                used.update(entry_obj.hash_info for _, entry_obj in obj)
+    for _, obj_ids in dvc.used_objs([path]).items():
+        used.update(obj_ids)
 
     assert used == expected
 

tests/unit/utils/test_fs.py

@@ -38,11 +38,11 @@ class TestMtimeAndSize(TestDir):
         )
 
         self.assertIs(type(file_time), str)
-        self.assertIs(type(file_size), str)
-        self.assertEqual(file_size, str(actual_file_size))
+        self.assertIs(type(file_size), int)
+        self.assertEqual(file_size, actual_file_size)
         self.assertIs(type(dir_time), str)
-        self.assertIs(type(dir_size), str)
-        self.assertEqual(dir_size, str(actual_dir_size))
+        self.assertIs(type(dir_size), int)
+        self.assertEqual(dir_size, actual_dir_size)
 
 
 class TestContainsLink(TestCase):

tests/utils/__init__.py

@@ -42,3 +42,15 @@ def dump_sv(stream, metrics, delimiter=",", header=True):
         writer = csv.writer(stream)
         for d in metrics:
             writer.writerow(list(d.values()))
+
+
+def clean_staging():
+    from dvc.fs.memory import MemoryFileSystem
+    from dvc.objects.stage import _STAGING_MEMFS_PATH
+
+    try:
+        MemoryFileSystem().fs.rm(
+            f"memory://{_STAGING_MEMFS_PATH}", recursive=True
+        )
+    except FileNotFoundError:
+        pass