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optimize nonadmin and nonanon library list permission queries

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Before, the code would emit extra queries per each library to
find out whether the current user has permissions on it.
By pre-fetching all of them in one query and passing around as
 a dict object we should see a considerable speedup on Galaxies
with many libraries.
This commit is contained in:
Martin Cech
2018-02-14 19:38:13 -05:00
parent c20b68a5dd
commit 7457ce426f
2 changed files with 53 additions and 26 deletions
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lib/galaxy/managers/libraries.py
+51 -24
View File
@@ -3,7 +3,7 @@ Manager and Serializer for libraries.
"""
import logging
from sqlalchemy import and_, false, not_, or_, true
from sqlalchemy import false, not_, or_, true
from sqlalchemy.orm.exc import MultipleResultsFound
from sqlalchemy.orm.exc import NoResultFound
@@ -109,8 +109,11 @@ class LibraryManager(object):
:returns: query that will emit all accessible libraries
:rtype: sqlalchemy query
:returns: set of library ids that have restricted access (not public)
:rtype: set
:returns: dict of 3 sets with available actions for user's accessible
libraries and a set of ids of all public libraries. These are
used for limiting the number of queries when dictifying the
libraries later on.
:rtype: dict
"""
is_admin = trans.user_is_admin()
query = trans.sa_session.query(trans.app.model.Library)
@@ -119,6 +122,7 @@ class LibraryManager(object):
trans.sa_session.query(trans.model.LibraryPermissions).filter(
trans.model.LibraryPermissions.table.c.action == library_access_action
).distinct())}
prefetched_ids = {'restricted_library_ids': restricted_library_ids}
if is_admin:
if deleted is None:
# Flag is not specified, do not filter on it.
@@ -129,18 +133,33 @@ class LibraryManager(object):
query = query.filter(trans.app.model.Library.table.c.deleted == false())
else:
# Nonadmins can't see deleted libraries
query = query.filter(trans.app.model.Library.table.c.deleted == false())
current_user_role_ids = [role.id for role in trans.get_current_user_roles()]
accessible_restricted_library_ids = [lp.library_id for lp in (
trans.sa_session.query(trans.model.LibraryPermissions).filter(
and_(
trans.model.LibraryPermissions.table.c.action == library_access_action,
trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids)
)))]
all_actions = trans.sa_session.query(trans.model.LibraryPermissions).filter(trans.model.LibraryPermissions.table.c.role_id.in_(current_user_role_ids))
library_add_action = trans.app.security_agent.permitted_actions.LIBRARY_ADD.action
library_modify_action = trans.app.security_agent.permitted_actions.LIBRARY_MODIFY.action
library_manage_action = trans.app.security_agent.permitted_actions.LIBRARY_MANAGE.action
accessible_restricted_library_ids = []
allowed_library_add_ids = set([])
allowed_library_modify_ids = set([])
allowed_library_manage_ids = set([])
for action in all_actions:
if action.action == library_access_action:
accessible_restricted_library_ids.add(action.library_id)
if action.action == library_add_action:
allowed_library_add_ids.add(action.library_id)
if action.action == library_modify_action:
allowed_library_modify_ids.add(action.library_id)
if action.action == library_manage_action:
allowed_library_manage_ids.add(action.library_id)
query = query.filter(or_(
not_(trans.model.Library.table.c.id.in_(restricted_library_ids)),
trans.model.Library.table.c.id.in_(accessible_restricted_library_ids)
))
return query, restricted_library_ids
prefetched_ids['allowed_library_add_ids'] = allowed_library_add_ids
prefetched_ids['allowed_library_modify_ids'] = allowed_library_modify_ids
prefetched_ids['allowed_library_manage_ids'] = allowed_library_manage_ids
return query, prefetched_ids
def secure(self, trans, library, check_accessible=True):
"""
@@ -172,30 +191,38 @@ class LibraryManager(object):
else:
return library
def get_library_dict(self, trans, library, restricted_library_ids=None):
def get_library_dict(self, trans, library, prefetched_ids=None):
"""
Return library data in the form of a dictionary.
:param library: library
:type library: galaxy.model.Library
:param restricted_library_ids: ids of restricted libraries to speed up the
detection of public libraries
:type restricted_library_ids: list of ints
:param library: library
:type library: galaxy.model.Library
:param prefetched_ids: dict of 3 sets with available actions for user's accessible
libraries and a set of ids of all public libraries. These are
used for limiting the number of queries when dictifying a
set of libraries.
:type prefetched_ids: dict
:returns: dict with data about the library
:rtype: dictionary
"""
restricted_library_ids = prefetched_ids.get('restricted_library_ids', None) if prefetched_ids else None
allowed_library_add_ids = prefetched_ids.get('allowed_library_add_ids', None) if prefetched_ids else None
allowed_library_modify_ids = prefetched_ids.get('allowed_library_modify_ids', None) if prefetched_ids else None
allowed_library_manage_ids = prefetched_ids.get('allowed_library_manage_ids', None) if prefetched_ids else None
library_dict = library.to_dict(view='element', value_mapper={'id': trans.security.encode_id, 'root_folder_id': trans.security.encode_id})
if restricted_library_ids and library.id in restricted_library_ids:
library_dict['public'] = False
else:
library_dict['public'] = True
library_dict['public'] = False if (restricted_library_ids and library.id in restricted_library_ids) else True
library_dict['create_time_pretty'] = pretty_print_time_interval(library.create_time, precise=True)
if not trans.user_is_admin():
current_user_roles = trans.get_current_user_roles()
library_dict['can_user_add'] = trans.app.security_agent.can_add_library_item(current_user_roles, library)
library_dict['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, library)
library_dict['can_user_manage'] = trans.app.security_agent.can_manage_library_item(current_user_roles, library)
if prefetched_ids:
library_dict['can_user_add'] = True if (allowed_library_add_ids and library.id in allowed_library_add_ids) else False
library_dict['can_user_modify'] = True if (allowed_library_modify_ids and library.id in allowed_library_modify_ids) else False
library_dict['can_user_manage'] = True if (allowed_library_manage_ids and library.id in allowed_library_manage_ids) else False
else:
current_user_roles = trans.get_current_user_roles()
library_dict['can_user_add'] = trans.app.security_agent.can_add_library_item(current_user_roles, library)
library_dict['can_user_modify'] = trans.app.security_agent.can_modify_library_item(current_user_roles, library)
library_dict['can_user_manage'] = trans.app.security_agent.can_manage_library_item(current_user_roles, library)
else:
library_dict['can_user_add'] = True
library_dict['can_user_modify'] = True
lib/galaxy/webapps/galaxy/api/libraries.py
+2 -2
View File
@@ -46,10 +46,10 @@ class LibrariesController(BaseAPIController):
"""
deleted = util.string_as_bool_or_none(kwd.get('deleted', None))
query, restricted_library_ids = self.library_manager.list(trans, deleted)
query, prefetched_ids = self.library_manager.list(trans, deleted)
libraries = []
for library in query:
libraries.append(self.library_manager.get_library_dict(trans, library, restricted_library_ids))
libraries.append(self.library_manager.get_library_dict(trans, library, prefetched_ids))
return libraries
def __decode_id(self, trans, encoded_id, object_name=None):