From 2f2bdc38191632f30b2c0be4f3445190dc896d90 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Fri, 22 Oct 2021 11:24:22 +0200
Subject: [PATCH 1/5] =?UTF-8?q?=F0=9F=91=8C=20IMPROVE:=20Ensure=20`QueryBu?=
 =?UTF-8?q?ilder`=20is=20passed=20`Backend`=20(#5186)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This PR ensures core code always calls `QueryBuilder` with a specific
`Backend`, as opposed to assuming the loaded `Backend`. This will allow
for muliple backends to be used at the same time (for example export
archives), for features including graph traversal and visualisation.
---
 aiida/cmdline/utils/common.py                 |  8 +++--
 aiida/orm/implementation/django/comments.py   |  2 +-
 aiida/orm/implementation/django/logs.py       |  2 +-
 .../orm/implementation/sqlalchemy/comments.py |  2 +-
 aiida/orm/implementation/sqlalchemy/logs.py   |  2 +-
 aiida/orm/nodes/data/array/bands.py           |  4 +--
 aiida/orm/nodes/data/cif.py                   |  4 +--
 aiida/orm/nodes/data/code.py                  |  8 ++---
 aiida/orm/nodes/data/upf.py                   | 14 ++++-----
 aiida/orm/nodes/node.py                       |  8 ++---
 aiida/orm/querybuilder.py                     | 11 +++++--
 aiida/orm/utils/links.py                      |  8 ++---
 aiida/orm/utils/remote.py                     |  6 ++--
 aiida/tools/graph/age_entities.py             | 11 -------
 aiida/tools/graph/age_rules.py                |  7 +++--
 aiida/tools/graph/deletions.py                | 20 ++++++------
 aiida/tools/graph/graph_traversers.py         | 24 +++++++++-----
 aiida/tools/visualization/graph.py            | 31 +++++++++++++++----
 18 files changed, 101 insertions(+), 71 deletions(-)

diff --git a/aiida/cmdline/utils/common.py b/aiida/cmdline/utils/common.py
index 36fa393170..9c57980ab9 100644
--- a/aiida/cmdline/utils/common.py
+++ b/aiida/cmdline/utils/common.py
@@ -11,11 +11,15 @@
 import logging
 import os
 import sys
+from typing import TYPE_CHECKING
 
 from tabulate import tabulate
 
 from . import echo
 
+if TYPE_CHECKING:
+    from aiida.orm import WorkChainNode
+
 __all__ = ('is_verbose',)
 
 
@@ -306,7 +310,7 @@ def get_process_function_report(node):
     return '\n'.join(report)
 
 
-def get_workchain_report(node, levelname, indent_size=4, max_depth=None):
+def get_workchain_report(node: 'WorkChainNode', levelname, indent_size=4, max_depth=None):
     """
     Return a multi line string representation of the log messages and output of a given workchain
 
@@ -333,7 +337,7 @@ def get_subtree(uuid, level=0):
         Get a nested tree of work calculation nodes and their nesting level starting from this uuid.
         The result is a list of uuid of these nodes.
         """
-        builder = orm.QueryBuilder()
+        builder = orm.QueryBuilder(backend=node.backend)
         builder.append(cls=orm.WorkChainNode, filters={'uuid': uuid}, tag='workcalculation')
         builder.append(
             cls=orm.WorkChainNode,
diff --git a/aiida/orm/implementation/django/comments.py b/aiida/orm/implementation/django/comments.py
index be7fe71b9d..ab874b6b52 100644
--- a/aiida/orm/implementation/django/comments.py
+++ b/aiida/orm/implementation/django/comments.py
@@ -168,7 +168,7 @@ def delete_many(self, filters):
             raise exceptions.ValidationError('filters must not be empty')
 
         # Apply filter and delete found entities
-        builder = QueryBuilder().append(Comment, filters=filters, project='id').all()
+        builder = QueryBuilder(backend=self.backend).append(Comment, filters=filters, project='id').all()
         entities_to_delete = [_[0] for _ in builder]
         for entity in entities_to_delete:
             self.delete(entity)
diff --git a/aiida/orm/implementation/django/logs.py b/aiida/orm/implementation/django/logs.py
index 7b3b725c2c..4ddd8fe10f 100644
--- a/aiida/orm/implementation/django/logs.py
+++ b/aiida/orm/implementation/django/logs.py
@@ -144,7 +144,7 @@ def delete_many(self, filters):
             raise exceptions.ValidationError('filters must not be empty')
 
         # Apply filter and delete found entities
-        builder = QueryBuilder().append(Log, filters=filters, project='id')
+        builder = QueryBuilder(backend=self.backend).append(Log, filters=filters, project='id')
         entities_to_delete = builder.all(flat=True)
         for entity in entities_to_delete:
             self.delete(entity)
diff --git a/aiida/orm/implementation/sqlalchemy/comments.py b/aiida/orm/implementation/sqlalchemy/comments.py
index da100140dd..618aa021bf 100644
--- a/aiida/orm/implementation/sqlalchemy/comments.py
+++ b/aiida/orm/implementation/sqlalchemy/comments.py
@@ -171,7 +171,7 @@ def delete_many(self, filters):
             raise exceptions.ValidationError('filters must not be empty')
 
         # Apply filter and delete found entities
-        builder = QueryBuilder().append(Comment, filters=filters, project='id')
+        builder = QueryBuilder(backend=self.backend).append(Comment, filters=filters, project='id')
         entities_to_delete = builder.all(flat=True)
         for entity in entities_to_delete:
             self.delete(entity)
diff --git a/aiida/orm/implementation/sqlalchemy/logs.py b/aiida/orm/implementation/sqlalchemy/logs.py
index b4d75ad6ac..62a973171d 100644
--- a/aiida/orm/implementation/sqlalchemy/logs.py
+++ b/aiida/orm/implementation/sqlalchemy/logs.py
@@ -153,7 +153,7 @@ def delete_many(self, filters):
             raise exceptions.ValidationError('filter must not be empty')
 
         # Apply filter and delete found entities
-        builder = QueryBuilder().append(Log, filters=filters, project='id')
+        builder = QueryBuilder(backend=self.backend).append(Log, filters=filters, project='id')
         entities_to_delete = builder.all(flat=True)
         for entity in entities_to_delete:
             self.delete(entity)
diff --git a/aiida/orm/nodes/data/array/bands.py b/aiida/orm/nodes/data/array/bands.py
index 83484b0983..ec6adffeb3 100644
--- a/aiida/orm/nodes/data/array/bands.py
+++ b/aiida/orm/nodes/data/array/bands.py
@@ -1803,7 +1803,7 @@ def _prepare_json(self, main_file_name='', comments=True):  # pylint: disable=un
 MATPLOTLIB_FOOTER_TEMPLATE_EXPORTFILE_WITH_DPI = Template("""pl.savefig("$fname", format="$format", dpi=$dpi)""")
 
 
-def get_bands_and_parents_structure(args):
+def get_bands_and_parents_structure(args, backend=None):
     """Search for bands and return bands and the closest structure that is a parent of the instance.
 
     :returns:
@@ -1817,7 +1817,7 @@ def get_bands_and_parents_structure(args):
     from aiida import orm
     from aiida.common import timezone
 
-    q_build = orm.QueryBuilder()
+    q_build = orm.QueryBuilder(backend=backend)
     if args.all_users is False:
         q_build.append(orm.User, tag='creator', filters={'email': orm.User.objects.get_default().email})
     else:
diff --git a/aiida/orm/nodes/data/cif.py b/aiida/orm/nodes/data/cif.py
index 5b0696e103..f0278d0724 100644
--- a/aiida/orm/nodes/data/cif.py
+++ b/aiida/orm/nodes/data/cif.py
@@ -329,7 +329,7 @@ def read_cif(fileobj, index=-1, **kwargs):
         return struct_list[index]
 
     @classmethod
-    def from_md5(cls, md5):
+    def from_md5(cls, md5, backend=None):
         """
         Return a list of all CIF files that match a given MD5 hash.
 
@@ -337,7 +337,7 @@ def from_md5(cls, md5):
             otherwise the CIF file will not be found.
         """
         from aiida.orm.querybuilder import QueryBuilder
-        builder = QueryBuilder()
+        builder = QueryBuilder(backend=backend)
         builder.append(cls, filters={'attributes.md5': {'==': md5}})
         return builder.all(flat=True)
 
diff --git a/aiida/orm/nodes/data/code.py b/aiida/orm/nodes/data/code.py
index 9bd8787b13..c936e0ef16 100644
--- a/aiida/orm/nodes/data/code.py
+++ b/aiida/orm/nodes/data/code.py
@@ -151,7 +151,7 @@ def get_description(self):
         return f'{self.description}'
 
     @classmethod
-    def get_code_helper(cls, label, machinename=None):
+    def get_code_helper(cls, label, machinename=None, backend=None):
         """
         :param label: the code label identifying the code to load
         :param machinename: the machine name where code is setup
@@ -164,7 +164,7 @@ def get_code_helper(cls, label, machinename=None):
         from aiida.orm.computers import Computer
         from aiida.orm.querybuilder import QueryBuilder
 
-        query = QueryBuilder()
+        query = QueryBuilder(backend=backend)
         query.append(cls, filters={'label': label}, project='*', tag='code')
         if machinename:
             query.append(Computer, filters={'label': machinename}, with_node='code')
@@ -249,7 +249,7 @@ def get_from_string(cls, code_string):
             raise MultipleObjectsError(f'{code_string} could not be uniquely resolved')
 
     @classmethod
-    def list_for_plugin(cls, plugin, labels=True):
+    def list_for_plugin(cls, plugin, labels=True, backend=None):
         """
         Return a list of valid code strings for a given plugin.
 
@@ -260,7 +260,7 @@ def list_for_plugin(cls, plugin, labels=True):
           otherwise a list of integers with the code PKs.
         """
         from aiida.orm.querybuilder import QueryBuilder
-        query = QueryBuilder()
+        query = QueryBuilder(backend=backend)
         query.append(cls, filters={'attributes.input_plugin': {'==': plugin}})
         valid_codes = query.all(flat=True)
 
diff --git a/aiida/orm/nodes/data/upf.py b/aiida/orm/nodes/data/upf.py
index 1ad082dd37..b212327ba2 100644
--- a/aiida/orm/nodes/data/upf.py
+++ b/aiida/orm/nodes/data/upf.py
@@ -70,7 +70,7 @@ def get_pseudos_from_structure(structure, family_name):
     return pseudo_list
 
 
-def upload_upf_family(folder, group_label, group_description, stop_if_existing=True):
+def upload_upf_family(folder, group_label, group_description, stop_if_existing=True, backend=None):
     """Upload a set of UPF files in a given group.
 
     :param folder: a path containing all UPF files to be added.
@@ -120,7 +120,7 @@ def upload_upf_family(folder, group_label, group_description, stop_if_existing=T
 
     for filename in filenames:
         md5sum = md5_file(filename)
-        builder = orm.QueryBuilder()
+        builder = orm.QueryBuilder(backend=backend)
         builder.append(UpfData, filters={'attributes.md5': {'==': md5sum}})
         existing_upf = builder.first()
 
@@ -321,7 +321,7 @@ def store(self, *args, **kwargs):  # pylint: disable=signature-differs
         return super().store(*args, **kwargs)
 
     @classmethod
-    def from_md5(cls, md5):
+    def from_md5(cls, md5, backend=None):
         """Return a list of all `UpfData` that match the given md5 hash.
 
         .. note:: assumes hash of stored `UpfData` nodes is stored in the `md5` attribute
@@ -330,7 +330,7 @@ def from_md5(cls, md5):
         :return: list of existing `UpfData` nodes that have the same md5 hash
         """
         from aiida.orm.querybuilder import QueryBuilder
-        builder = QueryBuilder()
+        builder = QueryBuilder(backend=backend)
         builder.append(cls, filters={'attributes.md5': {'==': md5}})
         return builder.all(flat=True)
 
@@ -366,7 +366,7 @@ def get_upf_family_names(self):
         """Get the list of all upf family names to which the pseudo belongs."""
         from aiida.orm import QueryBuilder, UpfFamily
 
-        query = QueryBuilder()
+        query = QueryBuilder(backend=self.backend)
         query.append(UpfFamily, tag='group', project='label')
         query.append(UpfData, filters={'id': {'==': self.id}}, with_group='group')
         return query.all(flat=True)
@@ -448,7 +448,7 @@ def get_upf_group(cls, group_label):
         return UpfFamily.get(label=group_label)
 
     @classmethod
-    def get_upf_groups(cls, filter_elements=None, user=None):
+    def get_upf_groups(cls, filter_elements=None, user=None, backend=None):
         """Return all names of groups of type UpfFamily, possibly with some filters.
 
         :param filter_elements: A string or a list of strings.
@@ -460,7 +460,7 @@ def get_upf_groups(cls, filter_elements=None, user=None):
         """
         from aiida.orm import QueryBuilder, UpfFamily, User
 
-        builder = QueryBuilder()
+        builder = QueryBuilder(backend=backend)
         builder.append(UpfFamily, tag='group', project='*')
 
         if user:
diff --git a/aiida/orm/nodes/node.py b/aiida/orm/nodes/node.py
index 723705f109..c8694d2405 100644
--- a/aiida/orm/nodes/node.py
+++ b/aiida/orm/nodes/node.py
@@ -456,11 +456,11 @@ def validate_incoming(self, source: 'Node', link_type: LinkType, link_label: str
         """
         from aiida.orm.utils.links import validate_link
 
-        validate_link(source, self, link_type, link_label)
+        validate_link(source, self, link_type, link_label, backend=self.backend)
 
         # Check if the proposed link would introduce a cycle in the graph following ancestor/descendant rules
         if link_type in [LinkType.CREATE, LinkType.INPUT_CALC, LinkType.INPUT_WORK]:
-            builder = QueryBuilder().append(
+            builder = QueryBuilder(backend=self.backend).append(
                 Node, filters={'id': self.pk}, tag='parent').append(
                 Node, filters={'id': source.pk}, tag='child', with_ancestors='parent')  # yapf:disable
             if builder.count() > 0:
@@ -537,7 +537,7 @@ def get_stored_link_triples(
         if link_label_filter:
             edge_filters['label'] = {'like': link_label_filter}
 
-        builder = QueryBuilder()
+        builder = QueryBuilder(backend=self.backend)
         builder.append(Node, filters=node_filters, tag='main')
 
         node_project = ['uuid'] if only_uuid else ['*']
@@ -894,7 +894,7 @@ def _iter_all_same_nodes(self, allow_before_store=False) -> Iterator['Node']:
         if not node_hash or not self._cachable:
             return iter(())
 
-        builder = QueryBuilder()
+        builder = QueryBuilder(backend=self.backend)
         builder.append(self.__class__, filters={'extras._aiida_hash': node_hash}, project='*', subclassing=False)
         nodes_identical = (n[0] for n in builder.iterall())
 
diff --git a/aiida/orm/querybuilder.py b/aiida/orm/querybuilder.py
index 82444e5d55..d3c04ebc56 100644
--- a/aiida/orm/querybuilder.py
+++ b/aiida/orm/querybuilder.py
@@ -136,8 +136,8 @@ def __init__(
         :param distinct: Whether to return de-duplicated rows
 
         """
-        backend = backend or get_manager().get_backend()
-        self._impl: BackendQueryBuilder = backend.query()
+        self._backend = backend or get_manager().get_backend()
+        self._impl: BackendQueryBuilder = self._backend.query()
 
         # SERIALISABLE ATTRIBUTES
         # A list storing the path being traversed by the query
@@ -189,6 +189,11 @@ def __init__(
         if order_by:
             self.order_by(order_by)
 
+    @property
+    def backend(self) -> 'Backend':
+        """Return the backend used by the QueryBuilder."""
+        return self._backend
+
     def as_dict(self, copy: bool = True) -> QueryDictType:
         """Convert to a JSON serialisable dictionary representation of the query."""
         data: QueryDictType = {
@@ -225,7 +230,7 @@ def __str__(self) -> str:
 
     def __deepcopy__(self, memo) -> 'QueryBuilder':
         """Create deep copy of the instance."""
-        return type(self)(**self.as_dict())  # type: ignore
+        return type(self)(backend=self.backend, **self.as_dict())  # type: ignore
 
     def get_used_tags(self, vertices: bool = True, edges: bool = True) -> List[str]:
         """Returns a list of all the vertices that are being used.
diff --git a/aiida/orm/utils/links.py b/aiida/orm/utils/links.py
index 535ca0caa5..f79667777f 100644
--- a/aiida/orm/utils/links.py
+++ b/aiida/orm/utils/links.py
@@ -21,7 +21,7 @@
 LinkQuadruple = namedtuple('LinkQuadruple', ['source_id', 'target_id', 'link_type', 'link_label'])
 
 
-def link_triple_exists(source, target, link_type, link_label):
+def link_triple_exists(source, target, link_type, link_label, backend=None):
     """Return whether a link with the given type and label exists between the given source and target node.
 
     :param source: node from which the link is outgoing
@@ -42,7 +42,7 @@ def link_triple_exists(source, target, link_type, link_label):
 
     # Here we have two stored nodes, so we need to check if the same link already exists in the database.
     # Finding just a single match is sufficient so we can use the `limit` clause for efficiency
-    builder = QueryBuilder()
+    builder = QueryBuilder(backend=backend)
     builder.append(Node, filters={'id': source.id}, project=['id'])
     builder.append(Node, filters={'id': target.id}, edge_filters={'type': link_type.value, 'label': link_label})
     builder.limit(1)
@@ -50,7 +50,7 @@ def link_triple_exists(source, target, link_type, link_label):
     return builder.count() != 0
 
 
-def validate_link(source, target, link_type, link_label):
+def validate_link(source, target, link_type, link_label, backend=None):
     """
     Validate adding a link of the given type and label from a given node to ourself.
 
@@ -153,7 +153,7 @@ def validate_link(source, target, link_type, link_label):
     if outdegree == 'unique_triple' or indegree == 'unique_triple':
         # For a `unique_triple` degree we just have to check if an identical triple already exist, either in the cache
         # or stored, in which case, the new proposed link is a duplicate and thus illegal
-        duplicate_link_triple = link_triple_exists(source, target, link_type, link_label)
+        duplicate_link_triple = link_triple_exists(source, target, link_type, link_label, backend)
 
     # If the outdegree is `unique` there cannot already be any other outgoing link of that type
     if outdegree == 'unique' and source.get_outgoing(link_type=link_type, only_uuid=True).all():
diff --git a/aiida/orm/utils/remote.py b/aiida/orm/utils/remote.py
index 71f3e339d3..deb40ab874 100644
--- a/aiida/orm/utils/remote.py
+++ b/aiida/orm/utils/remote.py
@@ -37,13 +37,13 @@ def clean_remote(transport, path):
         pass
 
 
-def get_calcjob_remote_paths(pks=None, past_days=None, older_than=None, computers=None, user=None):
+def get_calcjob_remote_paths(pks=None, past_days=None, older_than=None, computers=None, user=None, backend=None):
     """
     Return a mapping of computer uuids to a list of remote paths, for a given set of calcjobs. The set of
     calcjobs will be determined by a query with filters based on the pks, past_days, older_than,
     computers and user arguments.
 
-    :param pks: onlu include calcjobs with a pk in this list
+    :param pks: only include calcjobs with a pk in this list
     :param past_days: only include calcjobs created since past_days
     :param older_than: only include calcjobs older than
     :param computers: only include calcjobs that were ran on these computers
@@ -74,7 +74,7 @@ def get_calcjob_remote_paths(pks=None, past_days=None, older_than=None, computer
     if pks:
         filters_calc['id'] = {'in': pks}
 
-    query = orm.QueryBuilder()
+    query = orm.QueryBuilder(backend=backend)
     query.append(CalcJobNode, tag='calc', project=['attributes.remote_workdir'], filters=filters_calc)
     query.append(orm.Computer, with_node='calc', tag='computer', project=['*'], filters=filters_computer)
     query.append(orm.User, with_node='calc', filters={'email': user.email})
diff --git a/aiida/tools/graph/age_entities.py b/aiida/tools/graph/age_entities.py
index a729d58ee7..de5fcec0d1 100644
--- a/aiida/tools/graph/age_entities.py
+++ b/aiida/tools/graph/age_entities.py
@@ -225,17 +225,6 @@ def aiida_cls(self):
         """Class of nodes contained in the entity set (node or group)"""
         return self._aiida_cls
 
-    def get_entities(self):
-        """Iterator that returns the AiiDA entities"""
-        for entity, in orm.QueryBuilder().append(
-            self._aiida_cls, project='*', filters={
-                self._identifier: {
-                    'in': self.keyset
-                }
-            }
-        ).iterall():
-            yield entity
-
 
 class DirectedEdgeSet(AbstractSetContainer):
     """Extension of AbstractSetContainer
diff --git a/aiida/tools/graph/age_rules.py b/aiida/tools/graph/age_rules.py
index f768d8d07a..973d334909 100644
--- a/aiida/tools/graph/age_rules.py
+++ b/aiida/tools/graph/age_rules.py
@@ -11,6 +11,7 @@
 
 from abc import ABCMeta, abstractmethod
 from collections import defaultdict
+from copy import deepcopy
 
 import numpy as np
 
@@ -65,7 +66,7 @@ class QueryRule(Operation, metaclass=ABCMeta):
     found in the last iteration of the query (ReplaceRule).
     """
 
-    def __init__(self, querybuilder, max_iterations=1, track_edges=False):
+    def __init__(self, querybuilder: orm.QueryBuilder, max_iterations=1, track_edges=False):
         """Initialization method
 
         :param querybuilder: an instance of the QueryBuilder class from which to take the
@@ -107,7 +108,7 @@ def get_spec_from_path(query_dict, idx):
         for pathspec in query_dict['path']:
             if not pathspec['entity_type']:
                 pathspec['entity_type'] = 'node.Node.'
-        self._qbtemplate = orm.QueryBuilder(**query_dict)
+        self._qbtemplate = deepcopy(querybuilder)
         query_dict = self._qbtemplate.as_dict()
         self._first_tag = query_dict['path'][0]['tag']
         self._last_tag = query_dict['path'][-1]['tag']
@@ -163,7 +164,7 @@ def _init_run(self, operational_set):
 
         # Copying qbtemplate so there's no problem if it is used again in a later run:
         query_dict = self._qbtemplate.as_dict()
-        self._querybuilder = orm.QueryBuilder.from_dict(query_dict)
+        self._querybuilder = deepcopy(self._qbtemplate)
 
         self._entity_to_identifier = operational_set[self._entity_to].identifier
 
diff --git a/aiida/tools/graph/deletions.py b/aiida/tools/graph/deletions.py
index d14d9c7dd5..61e0454f1d 100644
--- a/aiida/tools/graph/deletions.py
+++ b/aiida/tools/graph/deletions.py
@@ -71,17 +71,18 @@ def _missing_callback(_pks: Iterable[int]):
         for _pk in _pks:
             DELETE_LOGGER.warning(f'warning: node with pk<{_pk}> does not exist, skipping')
 
-    pks_set_to_delete = get_nodes_delete(pks, get_links=False, missing_callback=_missing_callback,
-                                         **traversal_rules)['nodes']
+    pks_set_to_delete = get_nodes_delete(
+        pks, get_links=False, missing_callback=_missing_callback, backend=backend, **traversal_rules
+    )['nodes']
 
     DELETE_LOGGER.report('%s Node(s) marked for deletion', len(pks_set_to_delete))
 
     if pks_set_to_delete and DELETE_LOGGER.level == logging.DEBUG:
-        builder = QueryBuilder().append(
-            Node, filters={'id': {
-                'in': pks_set_to_delete
-            }}, project=('uuid', 'id', 'node_type', 'label')
-        )
+        builder = QueryBuilder(
+            backend=backend
+        ).append(Node, filters={'id': {
+            'in': pks_set_to_delete
+        }}, project=('uuid', 'id', 'node_type', 'label'))
         DELETE_LOGGER.debug('Node(s) to delete:')
         for uuid, pk, type_string, label in builder.iterall():
             try:
@@ -113,6 +114,7 @@ def _missing_callback(_pks: Iterable[int]):
 def delete_group_nodes(
     pks: Iterable[int],
     dry_run: Union[bool, Callable[[Set[int]], bool]] = True,
+    backend=None,
     **traversal_rules: bool
 ) -> Tuple[Set[int], bool]:
     """Delete nodes contained in a list of groups (not the groups themselves!).
@@ -149,7 +151,7 @@ def delete_group_nodes(
     :returns: (node pks to delete, whether they were deleted)
 
     """
-    group_node_query = QueryBuilder().append(
+    group_node_query = QueryBuilder(backend=backend).append(
         Group,
         filters={
             'id': {
@@ -160,4 +162,4 @@ def delete_group_nodes(
     ).append(Node, project='id', with_group='groups')
     group_node_query.distinct()
     node_pks = group_node_query.all(flat=True)
-    return delete_nodes(node_pks, dry_run=dry_run, **traversal_rules)
+    return delete_nodes(node_pks, dry_run=dry_run, backend=backend, **traversal_rules)
diff --git a/aiida/tools/graph/graph_traversers.py b/aiida/tools/graph/graph_traversers.py
index 6468ead76e..8f9f0c0f6d 100644
--- a/aiida/tools/graph/graph_traversers.py
+++ b/aiida/tools/graph/graph_traversers.py
@@ -9,7 +9,7 @@
 ###########################################################################
 """Module for functions to traverse AiiDA graphs."""
 import sys
-from typing import Any, Callable, Dict, Iterable, List, Mapping, Optional, Set, cast
+from typing import TYPE_CHECKING, Any, Callable, Dict, Iterable, List, Mapping, Optional, Set, cast
 
 from numpy import inf
 
@@ -20,6 +20,9 @@
 from aiida.tools.graph.age_entities import Basket
 from aiida.tools.graph.age_rules import RuleSaveWalkers, RuleSequence, RuleSetWalkers, UpdateRule
 
+if TYPE_CHECKING:
+    from aiida.orm.implementation import Backend
+
 if sys.version_info >= (3, 8):
     from typing import TypedDict
 
@@ -35,6 +38,7 @@ def get_nodes_delete(
     starting_pks: Iterable[int],
     get_links: bool = False,
     missing_callback: Optional[Callable[[Iterable[int]], None]] = None,
+    backend: Optional['Backend'] = None,
     **traversal_rules: bool
 ) -> TraverseGraphOutput:
     """
@@ -59,9 +63,10 @@ def get_nodes_delete(
     traverse_output = traverse_graph(
         starting_pks,
         get_links=get_links,
+        backend=backend,
         links_forward=traverse_links['forward'],
         links_backward=traverse_links['backward'],
-        missing_callback=missing_callback
+        missing_callback=missing_callback,
     )
 
     function_output = {
@@ -74,7 +79,10 @@ def get_nodes_delete(
 
 
 def get_nodes_export(
-    starting_pks: Iterable[int], get_links: bool = False, **traversal_rules: bool
+    starting_pks: Iterable[int],
+    get_links: bool = False,
+    backend: Optional['Backend'] = None,
+    **traversal_rules: bool
 ) -> TraverseGraphOutput:
     """
     This function will return the set of all nodes that can be connected
@@ -99,6 +107,7 @@ def get_nodes_export(
     traverse_output = traverse_graph(
         starting_pks,
         get_links=get_links,
+        backend=backend,
         links_forward=traverse_links['forward'],
         links_backward=traverse_links['backward']
     )
@@ -186,7 +195,8 @@ def traverse_graph(
     get_links: bool = False,
     links_forward: Iterable[LinkType] = (),
     links_backward: Iterable[LinkType] = (),
-    missing_callback: Optional[Callable[[Iterable[int]], None]] = None
+    missing_callback: Optional[Callable[[Iterable[int]], None]] = None,
+    backend: Optional['Backend'] = None
 ) -> TraverseGraphOutput:
     """
     This function will return the set of all nodes that can be connected
@@ -239,7 +249,7 @@ def traverse_graph(
             return {'nodes': set(), 'links': set()}
         return {'nodes': set(), 'links': None}
 
-    query_nodes = orm.QueryBuilder()
+    query_nodes = orm.QueryBuilder(backend=backend)
     query_nodes.append(orm.Node, project=['id'], filters={'id': {'in': operational_set}})
     existing_pks = set(query_nodes.all(flat=True))
     missing_pks = operational_set.difference(existing_pks)
@@ -266,7 +276,7 @@ def traverse_graph(
         rules += [RuleSaveWalkers(stash)]
 
     if links_forward:
-        query_outgoing = orm.QueryBuilder()
+        query_outgoing = orm.QueryBuilder(backend=backend)
         query_outgoing.append(orm.Node, tag='sources')
         query_outgoing.append(orm.Node, edge_filters=filters_forwards, with_incoming='sources')
         rule_outgoing = UpdateRule(query_outgoing, max_iterations=1, track_edges=get_links)
@@ -276,7 +286,7 @@ def traverse_graph(
         rules += [RuleSetWalkers(stash)]
 
     if links_backward:
-        query_incoming = orm.QueryBuilder()
+        query_incoming = orm.QueryBuilder(backend=backend)
         query_incoming.append(orm.Node, tag='sources')
         query_incoming.append(orm.Node, edge_filters=filters_backwards, with_outgoing='sources')
         rule_incoming = UpdateRule(query_incoming, max_iterations=1, track_edges=get_links)
diff --git a/aiida/tools/visualization/graph.py b/aiida/tools/visualization/graph.py
index 2793ce9ce0..b864ad28bb 100644
--- a/aiida/tools/visualization/graph.py
+++ b/aiida/tools/visualization/graph.py
@@ -10,17 +10,21 @@
 """ provides functionality to create graphs of the AiiDa data providence,
 *via* graphviz.
 """
-
 import os
 from types import MappingProxyType  # pylint: disable=no-name-in-module,useless-suppression
+from typing import TYPE_CHECKING, Optional
 
 from graphviz import Digraph
 
 from aiida import orm
 from aiida.common import LinkType
+from aiida.manage.manager import get_manager
 from aiida.orm.utils.links import LinkPair
 from aiida.tools.graph.graph_traversers import traverse_graph
 
+if TYPE_CHECKING:
+    from aiida.orm.implementation import Backend
+
 __all__ = ('Graph', 'default_link_styles', 'default_node_styles', 'pstate_node_styles', 'default_node_sublabels')
 
 
@@ -359,7 +363,8 @@ def __init__(
         link_style_fn=None,
         node_style_fn=None,
         node_sublabel_fn=None,
-        node_id_type='pk'
+        node_id_type='pk',
+        backend: Optional['Backend'] = None
     ):
         """a class to create graphviz graphs of the AiiDA node provenance
 
@@ -398,10 +403,16 @@ def __init__(
         self._node_styles = node_style_fn or default_node_styles
         self._node_sublabels = node_sublabel_fn or default_node_sublabels
         self._node_id_type = node_id_type
+        self._backend = backend or get_manager().get_backend()
 
         self._ignore_node_style = _OVERRIDE_STYLES_DICT['ignore_node']
         self._origin_node_style = _OVERRIDE_STYLES_DICT['origin_node']
 
+    @property
+    def backend(self) -> 'Backend':
+        """The backend used to create the graph"""
+        return self._backend
+
     @property
     def graphviz(self):
         """return a copy of the graphviz.Digraph"""
@@ -539,10 +550,11 @@ def add_incoming(self, node, link_types=(), annotate_links=None, return_pks=True
             (node_pk,),
             max_iterations=1,
             get_links=True,
+            backend=self.backend,
             links_backward=valid_link_types,
         )
 
-        traversed_nodes = orm.QueryBuilder().append(
+        traversed_nodes = orm.QueryBuilder(backend=self.backend).append(
             orm.Node,
             filters={'id': {
                 'in': traversed_graph['nodes']
@@ -595,10 +607,11 @@ def add_outgoing(self, node, link_types=(), annotate_links=None, return_pks=True
             (node_pk,),
             max_iterations=1,
             get_links=True,
+            backend=self.backend,
             links_forward=valid_link_types,
         )
 
-        traversed_nodes = orm.QueryBuilder().append(
+        traversed_nodes = orm.QueryBuilder(backend=self.backend).append(
             orm.Node,
             filters={'id': {
                 'in': traversed_graph['nodes']
@@ -664,6 +677,7 @@ def recurse_descendants(
             (origin_pk,),
             max_iterations=depth,
             get_links=True,
+            backend=self.backend,
             links_forward=valid_link_types,
         )
 
@@ -674,13 +688,14 @@ def recurse_descendants(
                 traversed_graph['nodes'],
                 max_iterations=1,
                 get_links=True,
+                backend=self.backend,
                 links_backward=[LinkType.INPUT_WORK, LinkType.INPUT_CALC]
             )
             traversed_graph['nodes'] = traversed_graph['nodes'].union(traversed_outputs['nodes'])
             traversed_graph['links'] = traversed_graph['links'].union(traversed_outputs['links'])
 
         # Do one central query for all nodes in the Graph and generate a {id: Node} dictionary
-        traversed_nodes = orm.QueryBuilder().append(
+        traversed_nodes = orm.QueryBuilder(backend=self.backend).append(
             orm.Node,
             filters={'id': {
                 'in': traversed_graph['nodes']
@@ -755,6 +770,7 @@ def recurse_ancestors(
             (origin_pk,),
             max_iterations=depth,
             get_links=True,
+            backend=self.backend,
             links_backward=valid_link_types,
         )
 
@@ -765,13 +781,14 @@ def recurse_ancestors(
                 traversed_graph['nodes'],
                 max_iterations=1,
                 get_links=True,
+                backend=self.backend,
                 links_forward=[LinkType.CREATE, LinkType.RETURN]
             )
             traversed_graph['nodes'] = traversed_graph['nodes'].union(traversed_outputs['nodes'])
             traversed_graph['links'] = traversed_graph['links'].union(traversed_outputs['links'])
 
         # Do one central query for all nodes in the Graph and generate a {id: Node} dictionary
-        traversed_nodes = orm.QueryBuilder().append(
+        traversed_nodes = orm.QueryBuilder(backend=self.backend).append(
             orm.Node,
             filters={'id': {
                 'in': traversed_graph['nodes']
@@ -842,6 +859,7 @@ def add_origin_to_targets(
         self.add_node(origin_node, style_override=dict(origin_style))
 
         query = orm.QueryBuilder(
+            backend=self.backend,
             **{
                 'path': [{
                     'cls': origin_node.__class__,
@@ -902,6 +920,7 @@ def add_origins_to_targets(
             origin_filters = {}
 
         query = orm.QueryBuilder(
+            backend=self.backend,
             **{'path': [{
                 'cls': origin_cls,
                 'filters': origin_filters,

From a80812c30ebb0de12f0429954508f9ceb6120d34 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Sat, 23 Oct 2021 09:14:24 +0200
Subject: [PATCH 2/5] =?UTF-8?q?=E2=99=BB=EF=B8=8F=20REFACTOR:=20Delegate?=
 =?UTF-8?q?=20`RepositoryBackend`=20control=20to=20the=20`Backend`=20(#516?=
 =?UTF-8?q?9)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

This commit moves `Profile.get_repository() -> Repository`,
to `Backend.get_repository() -> BackendRepository`.

The original delegation,
(1) did not allow different backends to implement different repository classes, and
(2) made it impossible to implement/instantiate a `Backend` that was not directly dependent on the currently loaded `Profile`.

Additionally, the commit improves the docstring of the `Backend`,
and fixes a minor issue, that `verdi profile delete` left an empty repository folder for that profile.
---
 .../db/migrations/0047_migrate_repository.py  |  4 +-
 .../1feaea71bd5a_migrate_repository.py        |  4 +-
 aiida/backends/testbase.py                    |  2 +-
 aiida/cmdline/commands/cmd_setup.py           |  2 +-
 aiida/cmdline/commands/cmd_status.py          |  2 +-
 aiida/manage/configuration/config.py          |  5 ++-
 aiida/manage/configuration/profile.py         | 10 -----
 aiida/manage/manager.py                       | 24 ++++++------
 aiida/orm/implementation/backends.py          | 16 +++++++-
 aiida/orm/implementation/sql/backends.py      | 20 ++++++++--
 aiida/orm/nodes/node.py                       |  6 +--
 aiida/orm/nodes/repository.py                 |  3 +-
 aiida/repository/repository.py                | 39 ++++++++++---------
 aiida/tools/importexport/dbexport/main.py     |  5 +--
 .../importexport/dbimport/backends/common.py  |  5 +--
 docs/source/nitpick-exceptions                |  2 +
 tests/cmdline/commands/test_setup.py          |  4 +-
 tests/orm/data/test_array.py                  |  2 +-
 tests/repository/test_repository.py           | 28 ++-----------
 tests/tools/importexport/test_repository.py   |  2 +-
 20 files changed, 95 insertions(+), 90 deletions(-)

diff --git a/aiida/backends/djsite/db/migrations/0047_migrate_repository.py b/aiida/backends/djsite/db/migrations/0047_migrate_repository.py
index 14b11695be..32c5dbd7ee 100644
--- a/aiida/backends/djsite/db/migrations/0047_migrate_repository.py
+++ b/aiida/backends/djsite/db/migrations/0047_migrate_repository.py
@@ -35,10 +35,12 @@ def migrate_repository(apps, schema_editor):
     from aiida.common import exceptions
     from aiida.common.progress_reporter import get_progress_reporter, set_progress_bar_tqdm, set_progress_reporter
     from aiida.manage.configuration import get_profile
+    from aiida.manage.manager import get_manager
 
     DbNode = apps.get_model('db', 'DbNode')
 
     profile = get_profile()
+    backend = get_manager().get_backend()
     node_count = DbNode.objects.count()
     missing_node_uuids = []
     missing_repo_folder = []
@@ -107,7 +109,7 @@ def migrate_repository(apps, schema_editor):
     # Store the UUID of the repository container in the `DbSetting` table. Note that for new databases, the profile
     # setup will already have stored the UUID and so it should be skipped, or an exception for a duplicate key will be
     # raised. This migration step is only necessary for existing databases that are migrated.
-    container_id = profile.get_repository().uuid
+    container_id = backend.get_repository().uuid
     with schema_editor.connection.cursor() as cursor:
         cursor.execute(
             f"""
diff --git a/aiida/backends/sqlalchemy/migrations/versions/1feaea71bd5a_migrate_repository.py b/aiida/backends/sqlalchemy/migrations/versions/1feaea71bd5a_migrate_repository.py
index ab234d022d..cc33aac2ca 100644
--- a/aiida/backends/sqlalchemy/migrations/versions/1feaea71bd5a_migrate_repository.py
+++ b/aiida/backends/sqlalchemy/migrations/versions/1feaea71bd5a_migrate_repository.py
@@ -35,6 +35,7 @@ def upgrade():
     from aiida.common import exceptions
     from aiida.common.progress_reporter import get_progress_reporter, set_progress_bar_tqdm, set_progress_reporter
     from aiida.manage.configuration import get_profile
+    from aiida.manage.manager import get_manager
 
     connection = op.get_bind()
 
@@ -46,6 +47,7 @@ def upgrade():
     )
 
     profile = get_profile()
+    backend = get_manager().get_backend()
     node_count = connection.execute(select(func.count()).select_from(DbNode)).scalar()
     missing_repo_folder = []
     shard_count = 256
@@ -106,7 +108,7 @@ def upgrade():
     # Store the UUID of the repository container in the `DbSetting` table. Note that for new databases, the profile
     # setup will already have stored the UUID and so it should be skipped, or an exception for a duplicate key will be
     # raised. This migration step is only necessary for existing databases that are migrated.
-    container_id = profile.get_repository().uuid
+    container_id = backend.get_repository().uuid
     statement = text(
         f"""
         INSERT INTO db_dbsetting (key, val, description)
diff --git a/aiida/backends/testbase.py b/aiida/backends/testbase.py
index f6307df575..8fd5bc5a51 100644
--- a/aiida/backends/testbase.py
+++ b/aiida/backends/testbase.py
@@ -142,7 +142,7 @@ def initialise_repository(cls):
         """Initialise the repository"""
         from aiida.manage.configuration import get_profile
         profile = get_profile()
-        repository = profile.get_repository()
+        repository = cls.backend.get_repository()
         repository.initialise(clear=True, **profile.defaults['repository'])
 
     @classmethod
diff --git a/aiida/cmdline/commands/cmd_setup.py b/aiida/cmdline/commands/cmd_setup.py
index 28f52ef8ad..63b58c0baf 100644
--- a/aiida/cmdline/commands/cmd_setup.py
+++ b/aiida/cmdline/commands/cmd_setup.py
@@ -94,7 +94,7 @@ def setup(
     # with that UUID and we have to make sure that the provided repository corresponds to it.
     backend_manager = manager.get_backend_manager()
     repository_uuid_database = backend_manager.get_repository_uuid()
-    repository_uuid_profile = profile.get_repository().uuid
+    repository_uuid_profile = backend.get_repository().uuid
 
     if repository_uuid_database != repository_uuid_profile:
         echo.echo_critical(
diff --git a/aiida/cmdline/commands/cmd_status.py b/aiida/cmdline/commands/cmd_status.py
index 0117c15f14..1180c7cd0c 100644
--- a/aiida/cmdline/commands/cmd_status.py
+++ b/aiida/cmdline/commands/cmd_status.py
@@ -85,7 +85,7 @@ def verdi_status(print_traceback, no_rmq):
 
     # Getting the repository
     try:
-        repository = profile.get_repository()
+        repository = manager.get_backend().get_repository()
     except Exception as exc:
         message = 'Error with repository folder'
         print_status(ServiceStatus.ERROR, 'repository', message, exception=exc, print_traceback=print_traceback)
diff --git a/aiida/manage/configuration/config.py b/aiida/manage/configuration/config.py
index 5d6de33c90..efba5cecce 100644
--- a/aiida/manage/configuration/config.py
+++ b/aiida/manage/configuration/config.py
@@ -361,8 +361,9 @@ def delete_profile(
         profile = self.get_profile(name)
 
         if include_repository:
-            repository = profile.get_repository()
-            repository.delete()
+            folder = profile.repository_path
+            if folder.exists():
+                shutil.rmtree(folder)
 
         if include_database:
             postgres = Postgres.from_profile(profile)
diff --git a/aiida/manage/configuration/profile.py b/aiida/manage/configuration/profile.py
index 1dee9e8c89..cfa2673a98 100644
--- a/aiida/manage/configuration/profile.py
+++ b/aiida/manage/configuration/profile.py
@@ -128,16 +128,6 @@ def __init__(self, name, attributes, from_config=False):
         # Currently, whether a profile is a test profile is solely determined by its name starting with 'test_'
         self._test_profile = bool(self.name.startswith('test_'))
 
-    def get_repository(self) -> 'Repository':
-        """Return the repository configured for this profile."""
-        from disk_objectstore import Container
-
-        from aiida.repository import Repository
-        from aiida.repository.backend import DiskObjectStoreRepositoryBackend
-        container = Container(self.repository_path / 'container')
-        backend = DiskObjectStoreRepositoryBackend(container=container)
-        return Repository(backend=backend)
-
     @property
     def uuid(self):
         """Return the profile uuid.
diff --git a/aiida/manage/manager.py b/aiida/manage/manager.py
index 51a9cd79f7..cc79e13729 100644
--- a/aiida/manage/manager.py
+++ b/aiida/manage/manager.py
@@ -132,11 +132,23 @@ def _load_backend(self, schema_check: bool = True, repository_check: bool = True
             backend_manager.load_backend_environment(profile, validate_schema=schema_check)
             configuration.BACKEND_UUID = profile.uuid
 
+        backend_type = profile.database_backend
+
+        # Can only import the backend classes after the backend has been loaded
+        if backend_type == BACKEND_DJANGO:
+            from aiida.orm.implementation.django.backend import DjangoBackend
+            self._backend = DjangoBackend()
+        elif backend_type == BACKEND_SQLA:
+            from aiida.orm.implementation.sqlalchemy.backend import SqlaBackend
+            self._backend = SqlaBackend()
+        else:
+            raise ValueError(f'unknown database backend type: {backend_type}')
+
         # Perform the check on the repository compatibility. Since this is new functionality and the stability is not
         # yet known, we issue a warning in the case the repo and database are incompatible. In the future this might
         # then become an exception once we have verified that it is working reliably.
         if repository_check and not profile.is_test_profile:
-            repository_uuid_config = profile.get_repository().uuid
+            repository_uuid_config = self._backend.get_repository().uuid
             repository_uuid_database = backend_manager.get_repository_uuid()
 
             from aiida.cmdline.utils import echo
@@ -149,16 +161,6 @@ def _load_backend(self, schema_check: bool = True, repository_check: bool = True
                     'Please make sure that the configuration of your profile is correct.\n'
                 )
 
-        backend_type = profile.database_backend
-
-        # Can only import the backend classes after the backend has been loaded
-        if backend_type == BACKEND_DJANGO:
-            from aiida.orm.implementation.django.backend import DjangoBackend
-            self._backend = DjangoBackend()
-        elif backend_type == BACKEND_SQLA:
-            from aiida.orm.implementation.sqlalchemy.backend import SqlaBackend
-            self._backend = SqlaBackend()
-
         # Reconfigure the logging with `with_orm=True` to make sure that profile specific logging configuration options
         # are taken into account and the `DbLogHandler` is configured.
         configure_logging(with_orm=True)
diff --git a/aiida/orm/implementation/backends.py b/aiida/orm/implementation/backends.py
index b1273661d9..c1ffb8b0b1 100644
--- a/aiida/orm/implementation/backends.py
+++ b/aiida/orm/implementation/backends.py
@@ -25,6 +25,7 @@
         BackendQueryBuilder,
         BackendUserCollection,
     )
+    from aiida.repository.backend.abstract import AbstractRepositoryBackend
 
 __all__ = ('Backend',)
 
@@ -32,7 +33,16 @@
 
 
 class Backend(abc.ABC):
-    """The public interface that defines a backend factory that creates backend specific concrete objects."""
+    """Abstraction for a backend to read/write persistent data for a profile's provenance graph.
+
+    AiiDA splits data storage into two sources:
+
+    - Searchable data, which is stored in the database and can be queried using the QueryBuilder
+    - Non-searchable data, which is stored in the repository and can be loaded using the RepositoryBackend
+
+    The two sources are inter-linked by the ``Node.repository_metadata``.
+    Once stored, the leaf values of this dictionary must be valid pointers to object keys in the repository.
+    """
 
     @abc.abstractmethod
     def migrate(self) -> None:
@@ -135,3 +145,7 @@ def delete_nodes_and_connections(self, pks_to_delete: Sequence[int]):
 
         :raises: ``AssertionError`` if a transaction is not active
         """
+
+    @abc.abstractmethod
+    def get_repository(self) -> 'AbstractRepositoryBackend':
+        """Return the object repository configured for this backend."""
diff --git a/aiida/orm/implementation/sql/backends.py b/aiida/orm/implementation/sql/backends.py
index 1423ce5d22..fb8b9321e7 100644
--- a/aiida/orm/implementation/sql/backends.py
+++ b/aiida/orm/implementation/sql/backends.py
@@ -9,17 +9,20 @@
 ###########################################################################
 """Generic backend related objects"""
 import abc
-import typing
+from typing import TYPE_CHECKING, Generic, TypeVar
 
 from .. import backends, entities
 
+if TYPE_CHECKING:
+    from aiida.repository.backend import DiskObjectStoreRepositoryBackend
+
 __all__ = ('SqlBackend',)
 
 # The template type for the base sqlalchemy/django ORM model type
-ModelType = typing.TypeVar('ModelType')  # pylint: disable=invalid-name
+ModelType = TypeVar('ModelType')  # pylint: disable=invalid-name
 
 
-class SqlBackend(typing.Generic[ModelType], backends.Backend):
+class SqlBackend(Generic[ModelType], backends.Backend):
     """
     A class for SQL based backends.  Assumptions are that:
         * there is an ORM
@@ -29,6 +32,17 @@ class SqlBackend(typing.Generic[ModelType], backends.Backend):
     if any of these assumptions do not fit then just implement a backend from :class:`aiida.orm.implementation.Backend`
     """
 
+    def get_repository(self) -> 'DiskObjectStoreRepositoryBackend':
+        from disk_objectstore import Container
+
+        from aiida.manage.manager import get_manager
+        from aiida.repository.backend import DiskObjectStoreRepositoryBackend
+
+        profile = get_manager().get_profile()
+        assert profile is not None, 'profile not loaded'
+        container = Container(profile.repository_path / 'container')
+        return DiskObjectStoreRepositoryBackend(container=container)
+
     @abc.abstractmethod
     def get_backend_entity(self, model: ModelType) -> entities.BackendEntity:
         """
diff --git a/aiida/orm/nodes/node.py b/aiida/orm/nodes/node.py
index c8694d2405..3d7f083d53 100644
--- a/aiida/orm/nodes/node.py
+++ b/aiida/orm/nodes/node.py
@@ -709,13 +709,13 @@ def _store(self, with_transaction: bool = True, clean: bool = True) -> 'Node':
         :param with_transaction: if False, do not use a transaction because the caller will already have opened one.
         :param clean: boolean, if True, will clean the attributes and extras before attempting to store
         """
+        from aiida.repository import Repository
         from aiida.repository.backend import SandboxRepositoryBackend
 
         # Only if the backend repository is a sandbox do we have to clone its contents to the permanent repository.
         if isinstance(self._repository.backend, SandboxRepositoryBackend):
-            profile = get_manager().get_profile()
-            assert profile is not None, 'profile not loaded'
-            repository = profile.get_repository()
+            repository_backend = self.backend.get_repository()
+            repository = Repository(backend=repository_backend)
             repository.clone(self._repository)
             # Swap the sandbox repository for the new permanent repository instance which should delete the sandbox
             self._repository_instance = repository
diff --git a/aiida/orm/nodes/repository.py b/aiida/orm/nodes/repository.py
index 11ee76401c..f8608299fb 100644
--- a/aiida/orm/nodes/repository.py
+++ b/aiida/orm/nodes/repository.py
@@ -50,8 +50,7 @@ def _repository(self) -> Repository:
         """
         if self._repository_instance is None:
             if self.is_stored:
-                from aiida.manage.manager import get_manager
-                backend = get_manager().get_profile().get_repository().backend
+                backend = self.backend.get_repository()
                 serialized = self.repository_metadata
                 self._repository_instance = Repository.from_serialized(backend=backend, serialized=serialized)
             else:
diff --git a/aiida/repository/repository.py b/aiida/repository/repository.py
index 4c2a94b067..12392b6d3d 100644
--- a/aiida/repository/repository.py
+++ b/aiida/repository/repository.py
@@ -51,19 +51,12 @@ def __str__(self) -> str:
 
     @property
     def uuid(self) -> Optional[str]:
-        """Return the unique identifier of the repository or ``None`` if it doesn't have one."""
+        """Return the unique identifier of the repository backend or ``None`` if it doesn't have one."""
         return self.backend.uuid
 
-    def initialise(self, **kwargs: Any) -> None:
-        """Initialise the repository if it hasn't already been initialised.
-
-        :param kwargs: keyword argument that will be passed to the ``initialise`` call of the backend.
-        """
-        self.backend.initialise(**kwargs)
-
     @property
     def is_initialised(self) -> bool:
-        """Return whether the repository has been initialised."""
+        """Return whether the repository backend has been initialised."""
         return self.backend.is_initialised
 
     @classmethod
@@ -417,16 +410,6 @@ def delete_object(self, path: FilePath, hard_delete: bool = False) -> None:
         directory = self.get_directory(path.parent)
         directory.objects.pop(path.name)
 
-    def delete(self) -> None:
-        """Delete the repository.
-
-        .. important:: This will not just delete the contents of the repository but also the repository itself and all
-            of its assets. For example, if the repository is stored inside a folder on disk, the folder may be deleted.
-
-        """
-        self.backend.erase()
-        self.reset()
-
     def erase(self) -> None:
         """Delete all objects from the repository.
 
@@ -510,3 +493,21 @@ def copy_tree(self, target: Union[str, pathlib.Path], path: FilePath = None) ->
 
                 with self.open(root / filename) as handle:
                     filepath.write_bytes(handle.read())
+
+    # these methods are not actually used in aiida-core, but are here for completeness
+
+    def initialise(self, **kwargs: Any) -> None:
+        """Initialise the repository if it hasn't already been initialised.
+
+        :param kwargs: keyword argument that will be passed to the ``initialise`` call of the backend.
+        """
+        self.backend.initialise(**kwargs)
+
+    def delete(self) -> None:
+        """Delete the repository.
+
+        .. important:: This will not just delete the contents of the repository but also the repository itself and all
+            of its assets. For example, if the repository is stored inside a folder on disk, the folder may be deleted.
+        """
+        self.backend.erase()
+        self.reset()
diff --git a/aiida/tools/importexport/dbexport/main.py b/aiida/tools/importexport/dbexport/main.py
index 83fbb502d6..5ddd78ff5d 100644
--- a/aiida/tools/importexport/dbexport/main.py
+++ b/aiida/tools/importexport/dbexport/main.py
@@ -572,9 +572,8 @@ def _write_node_repositories(
             container_export = Container(dirpath)
             container_export.init_container()
 
-            profile = get_manager().get_profile()
-            assert profile is not None, 'profile not loaded'
-            container_profile = profile.get_repository().backend.container
+            backend = get_manager().get_backend()
+            container_profile = backend.get_repository().container
 
             # This should be done more effectively, starting by not having to load the node. Either the repository
             # metadata should be collected earlier when the nodes themselves are already exported or a single separate
diff --git a/aiida/tools/importexport/dbimport/backends/common.py b/aiida/tools/importexport/dbimport/backends/common.py
index 97b09101c8..5a5620be4f 100644
--- a/aiida/tools/importexport/dbimport/backends/common.py
+++ b/aiida/tools/importexport/dbimport/backends/common.py
@@ -43,9 +43,8 @@ def _copy_node_repositories(*, repository_metadatas: List[Dict], reader: Archive
     if not container_export.is_initialised:
         container_export.init_container()
 
-    profile = get_manager().get_profile()
-    assert profile is not None, 'profile not loaded'
-    container_profile = profile.get_repository().backend.container
+    backend = get_manager().get_backend()
+    container_profile = backend.get_repository().container
 
     def collect_hashkeys(objects, hashkeys):
         for obj in objects.values():
diff --git a/docs/source/nitpick-exceptions b/docs/source/nitpick-exceptions
index d7bfb15798..bb2f466230 100644
--- a/docs/source/nitpick-exceptions
+++ b/docs/source/nitpick-exceptions
@@ -45,6 +45,7 @@ py:class aiida.tools.importexport.dbexport.ArchiveData
 py:class aiida.tools.groups.paths.WalkNodeResult
 py:meth aiida.orm.groups.GroupCollection.delete
 
+py:class AbstractRepositoryBackend
 py:class Backend
 py:class BackendEntity
 py:class BackendEntityType
@@ -58,6 +59,7 @@ py:class CollectionType
 py:class Computer
 py:class Data
 py:class DbImporter
+py:class DiskObjectStoreRepositoryBackend
 py:class EntityType
 py:class EntityTypes
 py:class ExitCode
diff --git a/tests/cmdline/commands/test_setup.py b/tests/cmdline/commands/test_setup.py
index d23853c815..1121fc413b 100644
--- a/tests/cmdline/commands/test_setup.py
+++ b/tests/cmdline/commands/test_setup.py
@@ -80,7 +80,7 @@ def test_quicksetup(self):
         # Check that the repository UUID was stored in the database
         manager = get_manager()
         backend_manager = manager.get_backend_manager()
-        self.assertEqual(backend_manager.get_repository_uuid(), profile.get_repository().uuid)
+        self.assertEqual(backend_manager.get_repository_uuid(), self.backend.get_repository().uuid)
 
     def test_quicksetup_from_config_file(self):
         """Test `verdi quicksetup` from configuration file."""
@@ -167,4 +167,4 @@ def test_setup(self):
         # Check that the repository UUID was stored in the database
         manager = get_manager()
         backend_manager = manager.get_backend_manager()
-        self.assertEqual(backend_manager.get_repository_uuid(), profile.get_repository().uuid)
+        self.assertEqual(backend_manager.get_repository_uuid(), self.backend.get_repository().uuid)
diff --git a/tests/orm/data/test_array.py b/tests/orm/data/test_array.py
index 20d9ce1b98..a77c393fde 100644
--- a/tests/orm/data/test_array.py
+++ b/tests/orm/data/test_array.py
@@ -31,7 +31,7 @@ def test_read_stored():
     assert numpy.array_equal(loaded.get_array('array'), array)
 
     # Now pack all the files in the repository
-    container = get_manager().get_profile().get_repository().backend.container
+    container = get_manager().get_backend().get_repository().container
     container.pack_all_loose()
 
     loaded = load_node(node.uuid)
diff --git a/tests/repository/test_repository.py b/tests/repository/test_repository.py
index 0400e623d8..e2033623e9 100644
--- a/tests/repository/test_repository.py
+++ b/tests/repository/test_repository.py
@@ -37,8 +37,8 @@ def repository(request, tmp_path_factory) -> Repository:
 
     """
     with request.param(tmp_path_factory.mktemp('container')) as backend:
+        backend.initialise()
         repository = Repository(backend=backend)
-        repository.initialise()
         yield repository
 
 
@@ -78,12 +78,12 @@ def test_uuid(repository_uninitialised):
 
     if isinstance(repository.backend, SandboxRepositoryBackend):
         assert repository.uuid is None
-        repository.initialise()
+        repository.backend.initialise()
         assert repository.uuid is None
 
     if isinstance(repository.backend, DiskObjectStoreRepositoryBackend):
         assert repository.uuid is None
-        repository.initialise()
+        repository.backend.initialise()
         assert isinstance(repository.uuid, str)
 
 
@@ -92,7 +92,7 @@ def test_initialise(repository_uninitialised):
     repository = repository_uninitialised
 
     assert not repository.is_initialised
-    repository.initialise()
+    repository.backend.initialise()
     assert repository.is_initialised
 
 
@@ -508,26 +508,6 @@ def test_delete_object_hard(repository, generate_directory):
     assert not repository.backend.has_object(key)
 
 
-def test_delete(repository, generate_directory):
-    """Test the ``Repository.delete`` method."""
-    directory = generate_directory({
-        'file_a': b'content_a',
-        'relative': {
-            'file_b': b'content_b',
-        }
-    })
-
-    repository.put_object_from_tree(str(directory))
-
-    assert repository.has_object('file_a')
-    assert repository.has_object('relative/file_b')
-
-    repository.delete()
-
-    assert repository.is_empty()
-    assert not repository.is_initialised
-
-
 def test_erase(repository, generate_directory):
     """Test the ``Repository.erase`` method."""
     directory = generate_directory({
diff --git a/tests/tools/importexport/test_repository.py b/tests/tools/importexport/test_repository.py
index fc2d2a8358..2d8c6ddfa5 100644
--- a/tests/tools/importexport/test_repository.py
+++ b/tests/tools/importexport/test_repository.py
@@ -32,7 +32,7 @@ def test_export_repository(aiida_profile, tmp_path):
     export([node], filename=filepath)
 
     aiida_profile.reset_db()
-    container = get_manager().get_profile().get_repository().backend.container
+    container = get_manager().get_backend().get_repository().container
     container.init_container(clear=True)
     import_data(filepath, silent=True)
 

From 6e272a3f715e60f63129c072d192eeea2e44b771 Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Sun, 24 Oct 2021 21:34:09 +0200
Subject: [PATCH 3/5] =?UTF-8?q?=F0=9F=91=8C=20IMPROVE:=20Add=20`AuthInfo`?=
 =?UTF-8?q?=20joins=20to=20`QueryBuilder`=20(#5195)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Allow for `with_user` and `with_computer` when querying `AuthInfo`
---
 aiida/orm/computers.py                        |   4 +-
 aiida/orm/implementation/querybuilder.py      |   2 +-
 .../sqlalchemy/querybuilder/joiner.py         | 377 ++++++++++--------
 tests/orm/test_querybuilder.py                |  20 +
 4 files changed, 225 insertions(+), 178 deletions(-)

diff --git a/aiida/orm/computers.py b/aiida/orm/computers.py
index 4c77d96f41..ffeba6ad8f 100644
--- a/aiida/orm/computers.py
+++ b/aiida/orm/computers.py
@@ -84,7 +84,7 @@ def objects(cls) -> ComputerCollection:  # pylint: disable=no-self-argument
     def __init__(  # pylint: disable=too-many-arguments
         self,
         label: str = None,
-        hostname: str = None,
+        hostname: str = '',
         description: str = '',
         transport_type: str = '',
         scheduler_type: str = '',
@@ -137,7 +137,7 @@ def _hostname_validator(cls, hostname: str) -> None:
         """
         Validates the hostname.
         """
-        if not hostname.strip():
+        if not (hostname or hostname.strip()):
             raise exceptions.ValidationError('No hostname specified')
 
     @classmethod
diff --git a/aiida/orm/implementation/querybuilder.py b/aiida/orm/implementation/querybuilder.py
index 6e2c0de340..cb55bdc0b1 100644
--- a/aiida/orm/implementation/querybuilder.py
+++ b/aiida/orm/implementation/querybuilder.py
@@ -41,7 +41,7 @@ class EntityTypes(Enum):
 
 
 EntityRelationships: Dict[str, Set[str]] = {
-    'authinfo': set(),
+    'authinfo': {'with_computer', 'with_user'},
     'comment': {'with_node', 'with_user'},
     'computer': {'with_node'},
     'group': {'with_node', 'with_user'},
diff --git a/aiida/orm/implementation/sqlalchemy/querybuilder/joiner.py b/aiida/orm/implementation/sqlalchemy/querybuilder/joiner.py
index 08dd41ee58..b0e407fcb8 100644
--- a/aiida/orm/implementation/sqlalchemy/querybuilder/joiner.py
+++ b/aiida/orm/implementation/sqlalchemy/querybuilder/joiner.py
@@ -33,6 +33,10 @@ class _EntityMapper(Protocol):
 
     # pylint: disable=invalid-name
 
+    @property
+    def AuthInfo(self) -> Type[Model]:
+        ...
+
     @property
     def Node(self) -> Type[Model]:
         ...
@@ -97,41 +101,213 @@ def _entity_join_map(self) -> Dict[str, Dict[str, JoinFuncType]]:
         and the second defines the relationship with respect to a given tag.
         """
         mapping = {
-            'node': {
-                'with_log': self._join_log_node,
-                'with_comment': self._join_comment_node,
-                'with_incoming': self._join_outputs,
-                'with_outgoing': self._join_inputs,
-                'with_descendants': self._join_ancestors_recursive,
-                'with_ancestors': self._join_descendants_recursive,
-                'with_computer': self._join_to_computer_used,
-                'with_user': self._join_created_by,
-                'with_group': self._join_group_members,
+            'authinfo': {
+                'with_computer': self._join_computer_authinfo,
+                'with_user': self._join_user_authinfo,
             },
-            'computer': {
-                'with_node': self._join_computer,
+            'comment': {
+                'with_node': self._join_node_comment,
+                'with_user': self._join_user_comment,
             },
-            'user': {
-                'with_comment': self._join_comment_user,
-                'with_node': self._join_creator_of,
-                'with_group': self._join_group_user,
+            'computer': {
+                'with_node': self._join_node_computer,
             },
             'group': {
-                'with_node': self._join_groups,
+                'with_node': self._join_node_group,
                 'with_user': self._join_user_group,
             },
-            'comment': {
-                'with_node': self._join_node_comment,
-                'with_user': self._join_user_comment,
-            },
             'log': {
                 'with_node': self._join_node_log,
-            }
+            },
+            'node': {
+                'with_log': self._join_log_node,
+                'with_comment': self._join_comment_node,
+                'with_incoming': self._join_node_outputs,
+                'with_outgoing': self._join_node_inputs,
+                'with_descendants': self._join_node_ancestors_recursive,
+                'with_ancestors': self._join_node_descendants_recursive,
+                'with_computer': self._join_computer_node,
+                'with_user': self._join_user_node,
+                'with_group': self._join_group_node,
+            },
+            'user': {
+                'with_comment': self._join_comment_user,
+                'with_node': self._join_node_user,
+                'with_group': self._join_group_user,
+            },
         }
 
         return mapping  # type: ignore
 
-    def _join_outputs(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+    def _join_computer_authinfo(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: the aliased user you want to join to
+        :param entity_to_join: the (aliased) node or group in the DB to join with
+        """
+        _check_dbentities((joined_entity, self._entities.Computer), (entity_to_join, self._entities.AuthInfo),
+                          'with_computer')
+        new_query = query.join(entity_to_join, entity_to_join.dbcomputer_id == joined_entity.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_user_authinfo(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: the aliased user you want to join to
+        :param entity_to_join: the (aliased) node or group in the DB to join with
+        """
+        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.AuthInfo), 'with_user')
+        new_query = query.join(entity_to_join, entity_to_join.aiidauser_id == joined_entity.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_group_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity:
+            The (aliased) ORMclass that is
+            a group in the database
+        :param entity_to_join:
+            The (aliased) ORMClass that is a node and member of the group
+
+        **joined_entity** and **entity_to_join**
+        are joined via the table_groups_nodes table.
+        from **joined_entity** as group to **enitity_to_join** as node.
+        (**enitity_to_join** is *with_group* **joined_entity**)
+        """
+        _check_dbentities((joined_entity, self._entities.Group), (entity_to_join, self._entities.Node), 'with_group')
+        aliased_group_nodes = aliased(self._entities.table_groups_nodes)
+        new_query = query.join(aliased_group_nodes, aliased_group_nodes.c.dbgroup_id == joined_entity.id).join(
+            entity_to_join, entity_to_join.id == aliased_group_nodes.c.dbnode_id, isouter=isouterjoin
+        )
+        return JoinReturn(new_query, aliased_group_nodes)
+
+    def _join_node_group(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: The (aliased) node in the database
+        :param entity_to_join: The (aliased) Group
+
+        **joined_entity** and **entity_to_join** are
+        joined via the table_groups_nodes table.
+        from **joined_entity** as node to **enitity_to_join** as group.
+        (**enitity_to_join** is a group *with_node* **joined_entity**)
+        """
+        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Group), 'with_node')
+        aliased_group_nodes = aliased(self._entities.table_groups_nodes)
+        new_query = query.join(aliased_group_nodes, aliased_group_nodes.c.dbnode_id == joined_entity.id).join(
+            entity_to_join, entity_to_join.id == aliased_group_nodes.c.dbgroup_id, isouter=isouterjoin
+        )
+        return JoinReturn(new_query, aliased_group_nodes)
+
+    def _join_node_user(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: the aliased node
+        :param entity_to_join: the aliased user to join to that node
+        """
+        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.User), 'with_node')
+        new_query = query.join(entity_to_join, entity_to_join.id == joined_entity.user_id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_user_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: the aliased user you want to join to
+        :param entity_to_join: the (aliased) node or group in the DB to join with
+        """
+        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Node), 'with_user')
+        new_query = query.join(entity_to_join, entity_to_join.user_id == joined_entity.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_computer_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: the (aliased) computer entity
+        :param entity_to_join: the (aliased) node entity
+
+        """
+        _check_dbentities((joined_entity, self._entities.Computer), (entity_to_join, self._entities.Node),
+                          'with_computer')
+        new_query = query.join(entity_to_join, entity_to_join.dbcomputer_id == joined_entity.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_node_computer(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An entity that can use a computer (eg a node)
+        :param entity_to_join: aliased dbcomputer entity
+        """
+        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Computer), 'with_node')
+        new_query = query.join(entity_to_join, joined_entity.dbcomputer_id == entity_to_join.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_group_user(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased dbgroup
+        :param entity_to_join: aliased dbuser
+        """
+        _check_dbentities((joined_entity, self._entities.Group), (entity_to_join, self._entities.User), 'with_group')
+        new_query = query.join(entity_to_join, joined_entity.user_id == entity_to_join.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_user_group(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased user
+        :param entity_to_join: aliased group
+        """
+        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Group), 'with_user')
+        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.user_id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_node_comment(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased node
+        :param entity_to_join: aliased comment
+        """
+        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Comment), 'with_node')
+        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.dbnode_id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_comment_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased comment
+        :param entity_to_join: aliased node
+        """
+        _check_dbentities((joined_entity, self._entities.Comment), (entity_to_join, self._entities.Node),
+                          'with_comment')
+        new_query = query.join(entity_to_join, joined_entity.dbnode_id == entity_to_join.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_node_log(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased node
+        :param entity_to_join: aliased log
+        """
+        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Log), 'with_node')
+        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.dbnode_id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_log_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased log
+        :param entity_to_join: aliased node
+        """
+        _check_dbentities((joined_entity, self._entities.Log), (entity_to_join, self._entities.Node), 'with_log')
+        new_query = query.join(entity_to_join, joined_entity.dbnode_id == entity_to_join.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_user_comment(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased user
+        :param entity_to_join: aliased comment
+        """
+        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Comment), 'with_user')
+        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.user_id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_comment_user(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+        """
+        :param joined_entity: An aliased comment
+        :param entity_to_join: aliased user
+        """
+        _check_dbentities((joined_entity, self._entities.Comment), (entity_to_join, self._entities.User),
+                          'with_comment')
+        new_query = query.join(entity_to_join, joined_entity.user_id == entity_to_join.id, isouter=isouterjoin)
+        return JoinReturn(new_query)
+
+    def _join_node_outputs(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
         """
         :param joined_entity: The (aliased) ORMclass that is an input
         :param entity_to_join: The (aliased) ORMClass that is an output.
@@ -147,7 +323,7 @@ def _join_outputs(self, query: Query, joined_entity, entity_to_join, isouterjoin
                                ).join(entity_to_join, aliased_edge.output_id == entity_to_join.id, isouter=isouterjoin)
         return JoinReturn(new_query, aliased_edge)
 
-    def _join_inputs(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
+    def _join_node_inputs(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
         """
         :param joined_entity: The (aliased) ORMclass that is an output
         :param entity_to_join: The (aliased) ORMClass that is an input.
@@ -166,7 +342,7 @@ def _join_inputs(self, query: Query, joined_entity, entity_to_join, isouterjoin:
         ).join(entity_to_join, aliased_edge.input_id == entity_to_join.id, isouter=isouterjoin)
         return JoinReturn(new_query, aliased_edge)
 
-    def _join_descendants_recursive(
+    def _join_node_descendants_recursive(
         self,
         query: Query,
         joined_entity,
@@ -231,7 +407,7 @@ def _join_descendants_recursive(
         )
         return JoinReturn(new_query, descendants_recursive.c)
 
-    def _join_ancestors_recursive(
+    def _join_node_ancestors_recursive(
         self,
         query: Query,
         joined_entity,
@@ -297,155 +473,6 @@ def _join_ancestors_recursive(
         )
         return JoinReturn(new_query, ancestors_recursive.c)
 
-    def _join_group_members(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity:
-            The (aliased) ORMclass that is
-            a group in the database
-        :param entity_to_join:
-            The (aliased) ORMClass that is a node and member of the group
-
-        **joined_entity** and **entity_to_join**
-        are joined via the table_groups_nodes table.
-        from **joined_entity** as group to **enitity_to_join** as node.
-        (**enitity_to_join** is *with_group* **joined_entity**)
-        """
-        _check_dbentities((joined_entity, self._entities.Group), (entity_to_join, self._entities.Node), 'with_group')
-        aliased_group_nodes = aliased(self._entities.table_groups_nodes)
-        new_query = query.join(aliased_group_nodes, aliased_group_nodes.c.dbgroup_id == joined_entity.id).join(
-            entity_to_join, entity_to_join.id == aliased_group_nodes.c.dbnode_id, isouter=isouterjoin
-        )
-        return JoinReturn(new_query, aliased_group_nodes)
-
-    def _join_groups(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: The (aliased) node in the database
-        :param entity_to_join: The (aliased) Group
-
-        **joined_entity** and **entity_to_join** are
-        joined via the table_groups_nodes table.
-        from **joined_entity** as node to **enitity_to_join** as group.
-        (**enitity_to_join** is a group *with_node* **joined_entity**)
-        """
-        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Group), 'with_node')
-        aliased_group_nodes = aliased(self._entities.table_groups_nodes)
-        new_query = query.join(aliased_group_nodes, aliased_group_nodes.c.dbnode_id == joined_entity.id).join(
-            entity_to_join, entity_to_join.id == aliased_group_nodes.c.dbgroup_id, isouter=isouterjoin
-        )
-        return JoinReturn(new_query, aliased_group_nodes)
-
-    def _join_creator_of(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: the aliased node
-        :param entity_to_join: the aliased user to join to that node
-        """
-        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.User), 'with_node')
-        new_query = query.join(entity_to_join, entity_to_join.id == joined_entity.user_id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_created_by(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: the aliased user you want to join to
-        :param entity_to_join: the (aliased) node or group in the DB to join with
-        """
-        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Node), 'with_user')
-        new_query = query.join(entity_to_join, entity_to_join.user_id == joined_entity.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_to_computer_used(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: the (aliased) computer entity
-        :param entity_to_join: the (aliased) node entity
-
-        """
-        _check_dbentities((joined_entity, self._entities.Computer), (entity_to_join, self._entities.Node),
-                          'with_computer')
-        new_query = query.join(entity_to_join, entity_to_join.dbcomputer_id == joined_entity.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_computer(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An entity that can use a computer (eg a node)
-        :param entity_to_join: aliased dbcomputer entity
-        """
-        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Computer), 'with_node')
-        new_query = query.join(entity_to_join, joined_entity.dbcomputer_id == entity_to_join.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_group_user(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased dbgroup
-        :param entity_to_join: aliased dbuser
-        """
-        _check_dbentities((joined_entity, self._entities.Group), (entity_to_join, self._entities.User), 'with_group')
-        new_query = query.join(entity_to_join, joined_entity.user_id == entity_to_join.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_user_group(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased user
-        :param entity_to_join: aliased group
-        """
-        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Group), 'with_user')
-        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.user_id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_node_comment(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased node
-        :param entity_to_join: aliased comment
-        """
-        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Comment), 'with_node')
-        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.dbnode_id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_comment_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased comment
-        :param entity_to_join: aliased node
-        """
-        _check_dbentities((joined_entity, self._entities.Comment), (entity_to_join, self._entities.Node),
-                          'with_comment')
-        new_query = query.join(entity_to_join, joined_entity.dbnode_id == entity_to_join.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_node_log(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased node
-        :param entity_to_join: aliased log
-        """
-        _check_dbentities((joined_entity, self._entities.Node), (entity_to_join, self._entities.Log), 'with_node')
-        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.dbnode_id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_log_node(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased log
-        :param entity_to_join: aliased node
-        """
-        _check_dbentities((joined_entity, self._entities.Log), (entity_to_join, self._entities.Node), 'with_log')
-        new_query = query.join(entity_to_join, joined_entity.dbnode_id == entity_to_join.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_user_comment(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased user
-        :param entity_to_join: aliased comment
-        """
-        _check_dbentities((joined_entity, self._entities.User), (entity_to_join, self._entities.Comment), 'with_user')
-        new_query = query.join(entity_to_join, joined_entity.id == entity_to_join.user_id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
-    def _join_comment_user(self, query: Query, joined_entity, entity_to_join, isouterjoin: bool, **_kw):
-        """
-        :param joined_entity: An aliased comment
-        :param entity_to_join: aliased user
-        """
-        _check_dbentities((joined_entity, self._entities.Comment), (entity_to_join, self._entities.User),
-                          'with_comment')
-        new_query = query.join(entity_to_join, joined_entity.user_id == entity_to_join.id, isouter=isouterjoin)
-        return JoinReturn(new_query)
-
 
 def _check_dbentities(entities_cls_joined, entities_cls_to_join, relationship: str):
     """Type check for entities
diff --git a/tests/orm/test_querybuilder.py b/tests/orm/test_querybuilder.py
index e6e366dba0..75f626ecd1 100644
--- a/tests/orm/test_querybuilder.py
+++ b/tests/orm/test_querybuilder.py
@@ -1084,6 +1084,26 @@ def test_joins3_user_group(self):
 
         assert qb.count() == 1, 'The expected user that owns the selected group was not found.'
 
+    def test_joins_authinfo(self):
+        """Test querying for AuthInfo with specific computer/user."""
+        user = orm.User(email='email@new.com').store()
+        computer = orm.Computer(
+            label='new', hostname='localhost', transport_type='core.local', scheduler_type='core.direct'
+        ).store()
+        authinfo = computer.configure(user)
+
+        # Search for the user of the authinfo
+        qb = orm.QueryBuilder()
+        qb.append(orm.User, tag='user', filters={'id': {'==': user.id}})
+        qb.append(orm.AuthInfo, with_user='user', filters={'id': {'==': authinfo.id}})
+        assert qb.count() == 1, 'The expected user that owns the selected authinfo was not found.'
+
+        # Search for the computer of the authinfo
+        qb = orm.QueryBuilder()
+        qb.append(orm.Computer, tag='computer', filters={'id': {'==': computer.id}})
+        qb.append(orm.AuthInfo, with_computer='computer', filters={'id': {'==': authinfo.id}})
+        assert qb.count() == 1, 'The expected computer that owns the selected authinfo was not found.'
+
     def test_joins_group_node(self):
         """
         This test checks that the querying for the nodes that belong to a group works correctly (using QueryBuilder).

From dfbd49760922602014d4fe85c50517253d3d836b Mon Sep 17 00:00:00 2001
From: Chris Sewell <chrisj_sewell@hotmail.com>
Date: Tue, 26 Oct 2021 07:06:08 +0200
Subject: [PATCH 4/5] =?UTF-8?q?=F0=9F=91=8C=20IMPROVE:=20Get=20session=20f?=
 =?UTF-8?q?rom=20backend=20in=20`SqlaModelEntity`=20(#5199)?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

Replace `get_scoped_session()` with `self.backend.get_session()`.
Note currently `SqlaBackend.get_session` simply calls
`get_scoped_session()`, so this does not change any logic.
But eventually `SqlaBackend` instances will manage their own session,
and `get_scoped_session()` will be removed.
---
 .../orm/implementation/sqlalchemy/authinfos.py  |  6 ++----
 aiida/orm/implementation/sqlalchemy/comments.py |  5 ++---
 .../orm/implementation/sqlalchemy/computers.py  | 10 ++++------
 aiida/orm/implementation/sqlalchemy/groups.py   | 17 ++++++-----------
 aiida/orm/implementation/sqlalchemy/logs.py     |  5 ++---
 aiida/orm/implementation/sqlalchemy/nodes.py    | 11 +++++------
 6 files changed, 21 insertions(+), 33 deletions(-)

diff --git a/aiida/orm/implementation/sqlalchemy/authinfos.py b/aiida/orm/implementation/sqlalchemy/authinfos.py
index 5f8b266ca0..bad9053d29 100644
--- a/aiida/orm/implementation/sqlalchemy/authinfos.py
+++ b/aiida/orm/implementation/sqlalchemy/authinfos.py
@@ -8,8 +8,6 @@
 # For further information please visit http://www.aiida.net               #
 ###########################################################################
 """Module for the SqlAlchemy backend implementation of the `AuthInfo` ORM class."""
-
-from aiida.backends.sqlalchemy import get_scoped_session
 from aiida.backends.sqlalchemy.models.authinfo import DbAuthInfo
 from aiida.common import exceptions
 from aiida.common.lang import type_check
@@ -123,7 +121,7 @@ def delete(self, pk):
         # pylint: disable=import-error,no-name-in-module
         from sqlalchemy.orm.exc import NoResultFound
 
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(DbAuthInfo).filter_by(id=pk).one().delete()
@@ -143,7 +141,7 @@ def get(self, computer, user):
         # pylint: disable=import-error,no-name-in-module
         from sqlalchemy.orm.exc import MultipleResultsFound, NoResultFound
 
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             authinfo = session.query(DbAuthInfo).filter_by(dbcomputer_id=computer.id, aiidauser_id=user.id).one()
diff --git a/aiida/orm/implementation/sqlalchemy/comments.py b/aiida/orm/implementation/sqlalchemy/comments.py
index 618aa021bf..f67a008478 100644
--- a/aiida/orm/implementation/sqlalchemy/comments.py
+++ b/aiida/orm/implementation/sqlalchemy/comments.py
@@ -14,7 +14,6 @@
 
 from sqlalchemy.orm.exc import NoResultFound
 
-from aiida.backends.sqlalchemy import get_scoped_session
 from aiida.backends.sqlalchemy.models import comment as models
 from aiida.common import exceptions, lang
 
@@ -125,7 +124,7 @@ def delete(self, comment_id):
         if not isinstance(comment_id, int):
             raise TypeError('comment_id must be an int')
 
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(models.DbComment).filter_by(id=comment_id).one().delete()
@@ -140,7 +139,7 @@ def delete_all(self):
 
         :raises `~aiida.common.exceptions.IntegrityError`: if all Comments could not be deleted
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(models.DbComment).delete()
diff --git a/aiida/orm/implementation/sqlalchemy/computers.py b/aiida/orm/implementation/sqlalchemy/computers.py
index 525fae15b4..6cebd9b351 100644
--- a/aiida/orm/implementation/sqlalchemy/computers.py
+++ b/aiida/orm/implementation/sqlalchemy/computers.py
@@ -15,7 +15,6 @@
 from sqlalchemy.exc import SQLAlchemyError
 from sqlalchemy.orm.session import make_transient
 
-from aiida.backends.sqlalchemy import get_scoped_session
 from aiida.backends.sqlalchemy.models.computer import DbComputer
 from aiida.common import exceptions
 from aiida.orm.implementation.computers import BackendComputer, BackendComputerCollection
@@ -52,7 +51,7 @@ def is_stored(self):
 
     def copy(self):
         """Create an unstored clone of an already stored `Computer`."""
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         if not self.is_stored:
             raise exceptions.InvalidOperation('You can copy a computer only after having stored it')
@@ -128,14 +127,13 @@ class SqlaComputerCollection(BackendComputerCollection):
 
     ENTITY_CLASS = SqlaComputer
 
-    @staticmethod
-    def list_names():
-        session = get_scoped_session()
+    def list_names(self):
+        session = self.backend.get_session()
         return session.query(DbComputer.label).all()
 
     def delete(self, pk):
         try:
-            session = get_scoped_session()
+            session = self.backend.get_session()
             session.get(DbComputer, pk).delete()
             session.commit()
         except SQLAlchemyError as exc:
diff --git a/aiida/orm/implementation/sqlalchemy/groups.py b/aiida/orm/implementation/sqlalchemy/groups.py
index 8b8e991c3b..6c5744bcb4 100644
--- a/aiida/orm/implementation/sqlalchemy/groups.py
+++ b/aiida/orm/implementation/sqlalchemy/groups.py
@@ -12,7 +12,6 @@
 from collections.abc import Iterable
 import logging
 
-from aiida.backends import sqlalchemy as sa
 from aiida.backends.sqlalchemy.models.group import DbGroup, table_groups_nodes
 from aiida.backends.sqlalchemy.models.node import DbNode
 from aiida.common.exceptions import UniquenessError
@@ -124,14 +123,12 @@ def count(self):
 
         :return: integer number of entities contained within the group
         """
-        from aiida.backends.sqlalchemy import get_scoped_session
-        session = get_scoped_session()
+        session = self.backend.get_session()
         return session.query(self.MODEL_CLASS).join(self.MODEL_CLASS.dbnodes).filter(DbGroup.id == self.pk).count()
 
     def clear(self):
         """Remove all the nodes from this group."""
-        from aiida.backends.sqlalchemy import get_scoped_session
-        session = get_scoped_session()
+        session = self.backend.get_session()
         # Note we have to call `dbmodel` and `_dbmodel` to circumvent the `ModelWrapper`
         self.dbmodel.dbnodes = []
         session.commit()
@@ -184,7 +181,6 @@ def add_nodes(self, nodes, **kwargs):
         from sqlalchemy.dialects.postgresql import insert  # pylint: disable=import-error, no-name-in-module
         from sqlalchemy.exc import IntegrityError  # pylint: disable=import-error, no-name-in-module
 
-        from aiida.backends.sqlalchemy import get_scoped_session
         from aiida.backends.sqlalchemy.models.base import Base
         from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode
 
@@ -199,7 +195,7 @@ def check_node(given_node):
             if not given_node.is_stored:
                 raise ValueError('At least one of the provided nodes is unstored, stopping...')
 
-        with utils.disable_expire_on_commit(get_scoped_session()) as session:
+        with utils.disable_expire_on_commit(self.backend.get_session()) as session:
             if not skip_orm:
                 # Get dbnodes here ONCE, otherwise each call to dbnodes will re-read the current value in the database
                 dbnodes = self._dbmodel.dbnodes
@@ -241,7 +237,6 @@ def remove_nodes(self, nodes, **kwargs):
         """
         from sqlalchemy import and_
 
-        from aiida.backends.sqlalchemy import get_scoped_session
         from aiida.backends.sqlalchemy.models.base import Base
         from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode
 
@@ -260,7 +255,7 @@ def check_node(node):
 
         list_nodes = []
 
-        with utils.disable_expire_on_commit(get_scoped_session()) as session:
+        with utils.disable_expire_on_commit(self.backend.get_session()) as session:
             if not skip_orm:
                 for node in nodes:
                     check_node(node)
@@ -303,7 +298,7 @@ def query(
         # pylint: disable=too-many-branches
         from aiida.orm.implementation.sqlalchemy.nodes import SqlaNode
 
-        session = sa.get_scoped_session()
+        session = self.backend.get_session()
 
         filters = []
 
@@ -366,7 +361,7 @@ def query(
         return [SqlaGroup.from_dbmodel(group, self._backend) for group in groups]  # pylint: disable=no-member
 
     def delete(self, id):  # pylint: disable=redefined-builtin
-        session = sa.get_scoped_session()
+        session = self.backend.get_session()
 
         session.get(DbGroup, id).delete()
         session.commit()
diff --git a/aiida/orm/implementation/sqlalchemy/logs.py b/aiida/orm/implementation/sqlalchemy/logs.py
index 62a973171d..8abc1c8e53 100644
--- a/aiida/orm/implementation/sqlalchemy/logs.py
+++ b/aiida/orm/implementation/sqlalchemy/logs.py
@@ -12,7 +12,6 @@
 
 from sqlalchemy.orm.exc import NoResultFound
 
-from aiida.backends.sqlalchemy import get_scoped_session
 from aiida.backends.sqlalchemy.models import log as models
 from aiida.common import exceptions
 
@@ -107,7 +106,7 @@ def delete(self, log_id):
         if not isinstance(log_id, int):
             raise TypeError('log_id must be an int')
 
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(models.DbLog).filter_by(id=log_id).one().delete()
@@ -122,7 +121,7 @@ def delete_all(self):
 
         :raises `~aiida.common.exceptions.IntegrityError`: if all Logs could not be deleted
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(models.DbLog).delete()
diff --git a/aiida/orm/implementation/sqlalchemy/nodes.py b/aiida/orm/implementation/sqlalchemy/nodes.py
index db324ba280..1bcc841548 100644
--- a/aiida/orm/implementation/sqlalchemy/nodes.py
+++ b/aiida/orm/implementation/sqlalchemy/nodes.py
@@ -15,7 +15,6 @@
 from sqlalchemy.exc import SQLAlchemyError
 from sqlalchemy.orm.exc import NoResultFound
 
-from aiida.backends.sqlalchemy import get_scoped_session
 from aiida.backends.sqlalchemy.models import node as models
 from aiida.common import exceptions
 from aiida.common.lang import type_check
@@ -158,7 +157,7 @@ def add_incoming(self, source, link_type, link_label):
         :return: True if the proposed link is allowed, False otherwise
         :raise aiida.common.ModificationNotAllowed: if either source or target node is not stored
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         type_check(source, SqlaNode)
 
@@ -180,7 +179,7 @@ def _add_link(self, source, link_type, link_label):
         """
         from aiida.backends.sqlalchemy.models.node import DbLink
 
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             with session.begin_nested():
@@ -200,7 +199,7 @@ def store(self, links=None, with_transaction=True, clean=True):  # pylint: disab
         :param with_transaction: if False, do not use a transaction because the caller will already have opened one.
         :param clean: boolean, if True, will clean the attributes and extras before attempting to store
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         if clean:
             self.clean_values()
@@ -231,7 +230,7 @@ def get(self, pk):
 
         :param pk: id of the node
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             return self.ENTITY_CLASS.from_dbmodel(session.query(models.DbNode).filter_by(id=pk).one(), self.backend)
@@ -243,7 +242,7 @@ def delete(self, pk):
 
         :param pk: id of the node to delete
         """
-        session = get_scoped_session()
+        session = self.backend.get_session()
 
         try:
             session.query(models.DbNode).filter_by(id=pk).one().delete()

From 78c7b7281669b1000ab328a1f731fb0cd3a1aef3 Mon Sep 17 00:00:00 2001
From: "Jason.Yu" <jusong.yeu@gmail.com>
Date: Tue, 26 Oct 2021 07:18:56 +0200
Subject: [PATCH 5/5] =?UTF-8?q?=F0=9F=93=9A=20DOCS:=20howto=20set=20PYTHON?=
 =?UTF-8?q?PATH=20for=20local=20work=20chains=20(#5191)?=
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Co-authored-by: Chris Sewell <chrisj_sewell@hotmail.com>
---
 docs/source/howto/faq.rst | 10 +++++++++-
 1 file changed, 9 insertions(+), 1 deletion(-)

diff --git a/docs/source/howto/faq.rst b/docs/source/howto/faq.rst
index 41b8803ec3..b62778c98e 100644
--- a/docs/source/howto/faq.rst
+++ b/docs/source/howto/faq.rst
@@ -74,9 +74,17 @@ To determine exactly what might be going wrong, first :ref:`set the loglevel <in
 
 Then restart the daemon with ``verdi daemon restart`` for the changes to take effect.
 Run the command ``verdi daemon logshow`` in a separate terminal to see the logging output of the daemon and then submit the problematic calculation or workflow again.
+
 If the root cause is indeed due to an import problem, it will probably appear as an ``ImportError`` exception in the daemon log.
 To solve these issues, make sure that all the Python code that is being run is properly importable, which means that it is part of the `PYTHONPATH <https://docs.python.org/3/using/cmdline.html#envvar-PYTHONPATH>`_.
-Make sure that the PYTHONPATH is correctly defined automatically when starting your shell, so for example if you are using bash, add it to your ``.bashrc``.
+Make sure that the PYTHONPATH is correctly defined automatically when starting your shell, so for example if you are using bash, add it to your ``.bashrc`` and completely reset daemon.
+For example, go to the directory that contains the file where you defined the process and run:
+
+.. code-block:: console
+
+    $ echo "export PYTHONPATH=\$PYTHONPATH:$PWD" >> $HOME/.bashrc
+    $ source $HOME/.bashrc
+    $ verdi daemon restart --reset
 
 .. _how-to:faq:caching-not-enabled: