PsqlDosBackend.maintain: use ProfileAccessManager.lock(#5331)

The `maintain` method of the `PsqlDosBackend` is updated to acquire
exclusive access to a profile by calling `ProfileAccessManager.lock` if
a `full` maintenance is requested. The lock is requested before the call
to `get_unreferenced_keyset` method is called, even though technically
that operation doesn't need it, but it could be confusing to a user if
the maintenance starts working and only after a while refuses access.

The logic is moved from `aiida.storage.control` to the recently created
`PsqlDosBackend`. The same goes for the `get_repository_info` function.
The `verdi storage info` command is updated to now obtain this info from
the storage backend instead of the free functions.

aiida/cmdline/commands/cmd_storage.py

@@ -93,14 +93,16 @@ def storage_integrity():
 def storage_info(statistics):
     """Summarise the contents of the storage."""
     from aiida.cmdline.utils.common import get_database_summary
+    from aiida.manage.manager import get_manager
     from aiida.orm import QueryBuilder
-    from aiida.storage.control import get_repository_info
+
+    manager = get_manager()
+    storage = manager.get_profile_storage()
 
     with spinner():
-        data = {
-            'database': get_database_summary(QueryBuilder, statistics),
-            'repository': get_repository_info(statistics=statistics),
-        }
+        data = storage.get_info(statistics=statistics)
+        data.setdefault('database', {})
+        data['database']['summary'] = get_database_summary(QueryBuilder, statistics)
 
     echo.echo_dictionary(data, sort_keys=False, fmt='yaml')
 
@@ -117,27 +119,33 @@ def storage_info(statistics):
     help=
     'Run the maintenance in dry-run mode which will print actions that would be taken without actually executing them.'
 )
-def storage_maintain(full, dry_run):
+@click.pass_context
+def storage_maintain(ctx, full, dry_run):
     """Performs maintenance tasks on the repository."""
-    from aiida.storage.control import repository_maintain
+    from aiida.manage.manager import get_manager
+
+    manager = get_manager()
+    profile = ctx.obj.profile
+    storage = manager.get_profile_storage()
 
     if full:
         echo.echo_warning(
-            '\nIn order to safely perform the full maintenance operations on the internal storage, no other '
-            'process should be using the AiiDA profile being maintained. '
-            'This includes daemon workers, verdi shells, scripts with the profile loaded, etc). '
-            'Please make sure there is nothing like this currently running and that none is started until '
-            'these procedures conclude. '
-            'For performing maintanance operations that are safe to run while actively using AiiDA, just run '
-            '`verdi storage maintain`, without the `--full` flag.\n'
+            '\nIn order to safely perform the full maintenance operations on the internal storage, the profile '
+            f'{profile.name} needs to be locked. '
+            'This means that no other process will be able to access it and will fail instead. '
+            'Moreover, if any process is already using the profile, the locking attempt will fail and you will '
+            'have to either look for these processes and kill them or wait for them to stop by themselves. '
+            'Note that this includes verdi shells, daemon workers, scripts that manually load it, etc.\n'
+            'For performing maintenance operations that are safe to run while actively using AiiDA, just run '
+            '`verdi storage maintain` without the `--full` flag.\n'
         )
 
     else:
         echo.echo(
             '\nThis command will perform all maintenance operations on the internal storage that can be safely '
             'executed while still running AiiDA. '
             'However, not all operations that are required to fully optimize disk usage and future performance '
-            'can be done in this way. '
+            'can be done in this way.\n'
             'Whenever you find the time or opportunity, please consider running `verdi repository maintenance '
             '--full` for a more complete optimization.\n'
         )
@@ -146,5 +154,5 @@ def storage_maintain(full, dry_run):
         if not click.confirm('Are you sure you want continue in this mode?'):
             return
 
-    repository_maintain(full=full, dry_run=dry_run)
+    storage.maintain(full=full, dry_run=dry_run)
     echo.echo_success('Requested maintenance procedures finished.')

aiida/orm/implementation/storage_backend.py

@@ -243,3 +243,34 @@ def get_global_variable(self, key: str) -> Union[None, str, int, float]:
 
         :raises: `KeyError` if the setting does not exist
         """
+
+    @abc.abstractmethod
+    def maintain(self, full: bool = False, dry_run: bool = False, **kwargs) -> None:
+        """Perform maintenance tasks on the storage.
+
+        If `full == True`, then this method may attempt to block the profile associated with the
+        storage to guarantee the safety of its procedures. This will not only prevent any other
+        subsequent process from accessing that profile, but will also first check if there is
+        already any process using it and raise if that is the case. The user will have to manually
+        stop any processes that is currently accessing the profile themselves or wait for it to
+        finish on its own.
+
+        :param full:
+            flag to perform operations that require to stop using the profile to be maintained.
+
+        :param dry_run:
+            flag to only print the actions that would be taken without actually executing them.
+
+        """
+
+    @abc.abstractmethod
+    def get_info(self, statistics: bool = False) -> dict:
+        """Return general information on the storage.
+
+        :param statistics:
+            flag to request more detailed information about the content of the storage.
+
+        :returns:
+            a nested dict with the relevant information.
+
+        """

aiida/repository/backend/disk_object_store.py

@@ -7,13 +7,16 @@
 from disk_objectstore import Container
 
 from aiida.common.lang import type_check
+from aiida.storage.log import STORAGE_LOGGER
 
 from .abstract import AbstractRepositoryBackend
 
 __all__ = ('DiskObjectStoreRepositoryBackend',)
 
 BYTES_TO_MB = 1 / 1024**2
 
+logger = STORAGE_LOGGER.getChild('disk_object_store')
+
 
 class DiskObjectStoreRepositoryBackend(AbstractRepositoryBackend):
     """Implementation of the ``AbstractRepositoryBackend`` using the ``disk-object-store`` as the backend.
@@ -156,10 +159,6 @@ def maintain( # type: ignore[override] # pylint: disable=arguments-differ,too-ma
         :param do_vacuum:flag for forcing the vacuuming of the internal database when cleaning the repository.
         :return:a dictionary with information on the operations performed.
         """
-        from aiida.storage.control import MAINTAIN_LOGGER
-
-        logger = MAINTAIN_LOGGER.getChild('disk_object_store')
-
         if live and (do_repack or clean_storage or do_vacuum):
             overrides = {'do_repack': do_repack, 'clean_storage': clean_storage, 'do_vacuum': do_vacuum}
             keys = ', '.join([key for key, override in overrides if override is True])  # type: ignore

aiida/storage/__init__.py

@@ -14,10 +14,8 @@
 # yapf: disable
 # pylint: disable=wildcard-import
 
-from .control import *
 
 __all__ = (
-    'MAINTAIN_LOGGER',
 )
 
 # yapf: enable

aiida/storage/log.py

@@ -0,0 +1,14 @@
+# -*- coding: utf-8 -*-
+###########################################################################
+# Copyright (c), The AiiDA team. All rights reserved.                     #
+# This file is part of the AiiDA code.                                    #
+#                                                                         #
+# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
+# For further information on the license, see the LICENSE.txt file        #
+# For further information please visit http://www.aiida.net               #
+###########################################################################
+"""Initialize the storage logger."""
+
+from aiida.common.log import AIIDA_LOGGER
+
+STORAGE_LOGGER = AIIDA_LOGGER.getChild('storage')

aiida/storage/psql_dos/backend.py

@@ -11,7 +11,7 @@
 # pylint: disable=missing-function-docstring
 from contextlib import contextmanager, nullcontext
 import functools
-from typing import TYPE_CHECKING, Iterator, List, Optional, Sequence, Union
+from typing import TYPE_CHECKING, Iterator, List, Optional, Sequence, Set, Union
 
 from disk_objectstore import Container
 from sqlalchemy import table
@@ -22,6 +22,7 @@
 from aiida.orm import User
 from aiida.orm.entities import EntityTypes
 from aiida.orm.implementation import BackendEntity, StorageBackend
+from aiida.storage.log import STORAGE_LOGGER
 from aiida.storage.psql_dos.migrator import REPOSITORY_UUID_KEY, PsqlDostoreMigrator
 from aiida.storage.psql_dos.models import base
 
@@ -346,3 +347,60 @@ def get_global_variable(self, key: str) -> Union[None, str, int, float]:
             if setting is None:
                 raise KeyError(f'No setting found with key {key}')
             return setting.val
+
+    def maintain(self, full: bool = False, dry_run: bool = False, **kwargs) -> None:
+        from aiida.manage.profile_access import ProfileAccessManager
+
+        repository = self.get_repository()
+
+        if full:
+            maintenance_context = ProfileAccessManager(self._profile).lock
+        else:
+            maintenance_context = nullcontext
+
+        with maintenance_context():
+            unreferenced_objects = self.get_unreferenced_keyset()
+            STORAGE_LOGGER.info(f'Deleting {len(unreferenced_objects)} unreferenced objects ...')
+            if not dry_run:
+                repository.delete_objects(list(unreferenced_objects))
+
+            STORAGE_LOGGER.info('Starting repository-specific operations ...')
+            repository.maintain(live=not full, dry_run=dry_run, **kwargs)
+
+    def get_unreferenced_keyset(self, check_consistency: bool = True) -> Set[str]:
+        """Returns the keyset of objects that exist in the repository but are not tracked by AiiDA.
+
+        This should be all the soft-deleted files.
+
+        :param check_consistency:
+            toggle for a check that raises if there are references in the database with no actual object in the
+            underlying repository.
+
+        :return:
+            a set with all the objects in the underlying repository that are not referenced in the database.
+        """
+        from aiida import orm
+
+        STORAGE_LOGGER.info('Obtaining unreferenced object keys ...')
+
+        repository = self.get_repository()
+
+        keyset_repository = set(repository.list_objects())
+        keyset_database = set(orm.Node.objects(self).iter_repo_keys())
+
+        if check_consistency:
+            keyset_missing = keyset_database - keyset_repository
+            if len(keyset_missing) > 0:
+                raise RuntimeError(
+                    'There are objects referenced in the database that are not present in the repository. Aborting!'
+                )
+
+        return keyset_repository - keyset_database
+
+    def get_info(self, statistics: bool = False) -> dict:
+        repository = self.get_repository()
+        output_dict = {
+            'database': {},
+            'repository': repository.get_info(statistics),
+        }
+        return output_dict

aiida/tools/archive/implementations/sqlite/backend.py

@@ -376,6 +376,12 @@ def get_global_variable(self, key: str):
     def set_global_variable(self, key: str, value, description: Optional[str] = None, overwrite=True) -> None:
         raise ReadOnlyError()
 
+    def maintain(self, full: bool = False, dry_run: bool = False, **kwargs) -> None:
+        raise NotImplementedError
+
+    def get_info(self, statistics: bool = False) -> dict:
+        raise NotImplementedError
+
 
 def create_backend_cls(base_class, model_cls):
     """Create an archive backend class for the given model class."""

tests/cmdline/commands/test_storage.py

@@ -118,15 +118,24 @@ def tests_storage_maintain_logging(run_cli_command, monkeypatch, caplog):
     """Test all the information and cases of the storage maintain command."""
     import logging
 
-    from aiida.storage import control
+    from aiida.manage import get_manager
+    storage = get_manager().get_profile_storage()
+
+    def mock_maintain(*args, **kwargs):
+        """Mocks for `maintain` method of `storage`, logging the inputs passed."""
+        log_message = ''
 
-    def mock_maintain(**kwargs):
-        logmsg = 'Provided kwargs:\n'
+        log_message += 'Provided args:\n'
+        for arg in args:
+            log_message += f' > {arg}\n'
+
+        log_message += 'Provided kwargs:\n'
         for key, val in kwargs.items():
-            logmsg += f' > {key}: {val}\n'
-        logging.info(logmsg)
+            log_message += f' > {key}: {val}\n'
+
+        logging.info(log_message)
 
-    monkeypatch.setattr(control, 'repository_maintain', mock_maintain)
+    monkeypatch.setattr(storage, 'maintain', mock_maintain)
 
     with caplog.at_level(logging.INFO):
         _ = run_cli_command(cmd_storage.storage_maintain, user_input='Y')

tests/repository/backend/test_disk_object_store.py

@@ -281,7 +281,7 @@ def test_maintain_logging(caplog, populated_repository, do_vacuum):
     list_of_logmsg = []
     for record in caplog.records:
         assert record.levelname == 'REPORT'
-        assert record.name == 'aiida.maintain.disk_object_store'
+        assert record.name.endswith('.disk_object_store')
         list_of_logmsg.append(record.msg)
 
     assert 'packing' in list_of_logmsg[0].lower()