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Source code for galaxy.model.security
import logging
import socket
from datetime import (
datetime,
timedelta,
)
from typing import List
from sqlalchemy import (
and_,
false,
func,
not_,
or_,
select,
)
from sqlalchemy.orm import joinedload
import galaxy.model
from galaxy.model import (
Dataset,
DatasetPermissions,
Group,
GroupRoleAssociation,
HistoryDatasetAssociationDisplayAtAuthorization,
Library,
LibraryDataset,
LibraryDatasetDatasetAssociation,
LibraryDatasetPermissions,
LibraryPermissions,
Role,
User,
UserGroupAssociation,
UserRoleAssociation,
)
from galaxy.model.base import transaction
from galaxy.security import (
Action,
get_permitted_actions,
RBACAgent,
)
from galaxy.util import listify
from galaxy.util.bunch import Bunch
log = logging.getLogger(__name__)
[docs]class GalaxyRBACAgent(RBACAgent):
[docs] def __init__(self, model, permitted_actions=None):
self.model = model
if permitted_actions:
self.permitted_actions = permitted_actions
# List of "library_item" objects and their associated permissions and info template objects
self.library_item_assocs = (
(self.model.Library, self.model.LibraryPermissions),
(self.model.LibraryFolder, self.model.LibraryFolderPermissions),
(self.model.LibraryDataset, self.model.LibraryDatasetPermissions),
(self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions),
)
@property
def sa_session(self):
"""Returns a SQLAlchemy session"""
return self.model.context
[docs] def sort_by_attr(self, seq, attr):
"""
Sort the sequence of objects by object's attribute
Arguments:
seq - the list or any sequence (including immutable one) of objects to sort.
attr - the name of attribute to sort by
"""
# Use the "Schwartzian transform"
# Create the auxiliary list of tuples where every i-th tuple has form
# (seq[i].attr, i, seq[i]) and sort it. The second item of tuple is needed not
# only to provide stable sorting, but mainly to eliminate comparison of objects
# (which can be expensive or prohibited) in case of equal attribute values.
intermed = [(getattr(v, attr), i, v) for i, v in enumerate(seq)]
intermed.sort()
return [_[-1] for _ in intermed]
def _get_npns_roles(self, trans):
"""
non-private, non-sharing roles
"""
stmt = (
select(Role)
.where(and_(Role.deleted == false(), Role.type != Role.types.PRIVATE, Role.type != Role.types.SHARING))
.order_by(Role.name)
)
return trans.sa_session.scalars(stmt)
[docs] def get_all_roles(self, trans, cntrller):
admin_controller = cntrller in ["library_admin"]
roles = set()
if not trans.user:
return self._get_npns_roles(trans)
if admin_controller:
# The library is public and the user is an admin, so all roles are legitimate
stmt = select(Role).where(Role.deleted == false()).order_by(Role.name)
for role in trans.sa_session.scalars(stmt):
roles.add(role)
else:
# Add the current user's private role
roles.add(self.get_private_user_role(trans.user))
# Add the current user's sharing roles
for role in self.get_sharing_roles(trans.user):
roles.add(role)
# Add all remaining non-private, non-sharing roles
for role in self._get_npns_roles(trans):
roles.add(role)
return self.sort_by_attr([role for role in roles], "name")
[docs] def get_roles_for_action(self, item, action):
"""
Return a list containing the roles associated with given action on given item
where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation,
LibraryDataset, Dataset.
"""
roles = []
for item_permission in item.actions:
permission_action = self.get_action(item_permission.action)
if permission_action == action:
roles.append(item_permission.role)
return roles
[docs] def get_valid_roles(self, trans, item, query=None, page=None, page_limit=None, is_library_access=False):
"""
This method retrieves the list of possible roles that user can select
in the item permissions form. Admins can select any role so the
results are paginated in order to save the bandwidth and to speed
things up.
Standard users can select their own private role, any of their
sharing roles and any public role (not private and not sharing).
"""
roles = []
if query not in [None, ""]:
query = query.strip().replace("_", "/_").replace("%", "/%").replace("/", "//")
search_query = f"{query}%"
else:
search_query = None
# Limit the query only to get the page needed
if page is not None and page_limit is not None:
limit = page * page_limit
else:
limit = None
total_count = None
if isinstance(item, self.model.Library) and self.library_is_public(item):
is_public_item = True
elif isinstance(item, self.model.Dataset) and self.dataset_is_public(item):
is_public_item = True
elif isinstance(item, self.model.LibraryFolder):
is_public_item = True
else:
is_public_item = False
# Admins can always choose from all non-deleted roles
if trans.user_is_admin or trans.app.config.expose_user_email:
if trans.user_is_admin:
stmt = select(Role).where(Role.deleted == false())
else:
# User is not an admin but the configuration exposes all private roles to all users.
stmt = select(Role).where(and_(Role.deleted == false(), Role.type == Role.types.PRIVATE))
if search_query:
stmt = stmt.where(Role.name.like(search_query, escape="/"))
count_stmt = select(func.count()).select_from(stmt)
total_count = trans.sa_session.scalar(count_stmt)
if limit is not None:
# Takes the least number of results from beginning that includes the requested page
stmt = stmt.order_by(Role.name).limit(limit)
page_start = (page * page_limit) - page_limit
page_end = page_start + page_limit
if total_count < page_start + 1:
# Return empty list if there are less results than the requested position
roles = []
else:
roles = trans.sa_session.scalars(stmt).all()
roles = roles[page_start:page_end]
else:
stmt = stmt.order_by(Role.name)
roles = trans.sa_session.scalars(stmt).all()
# Non-admin and public item
elif is_public_item:
# Add the current user's private role
roles.append(self.get_private_user_role(trans.user))
# Add the current user's sharing roles
for role in self.get_sharing_roles(trans.user):
roles.append(role)
# Add all remaining non-private, non-sharing roles
for role in self._get_npns_roles(trans):
roles.append(role)
# User will see all the roles derived from the access roles on the item
else:
# If item has roles associated with the access permission, we need to start with them.
access_roles = item.get_access_roles(self)
for role in access_roles:
if self.ok_to_display(trans.user, role):
roles.append(role)
# Each role potentially has users. We need to find all roles that each of those users have.
for ura in role.users:
user = ura.user
for ura2 in user.roles:
if self.ok_to_display(trans.user, ura2.role):
roles.append(ura2.role)
# Each role also potentially has groups which, in turn, have members ( users ). We need to
# find all roles that each group's members have.
for gra in role.groups:
group = gra.group
for uga in group.users:
user = uga.user
for ura in user.roles:
if self.ok_to_display(trans.user, ura.role):
roles.append(ura.role)
# Omit duplicated roles by converting to set
return_roles = set(roles)
if total_count is None:
total_count = len(return_roles)
return self.sort_by_attr([role for role in return_roles], "name"), total_count
[docs] def get_legitimate_roles(self, trans, item, cntrller):
"""
Return a sorted list of legitimate roles that can be associated with a permission on
item where item is a Library or a Dataset. The cntrller param is the controller from
which the request is sent. We cannot use trans.user_is_admin because the controller is
what is important since admin users do not necessarily have permission to do things
on items outside of the admin view.
If cntrller is from the admin side ( e.g., library_admin ):
- if item is public, all roles, including private roles, are legitimate.
- if item is restricted, legitimate roles are derived from the users and groups associated
with each role that is associated with the access permission ( i.e., DATASET_MANAGE_PERMISSIONS or
LIBRARY_MANAGE ) on item. Legitimate roles will include private roles.
If cntrller is not from the admin side ( e.g., root, library ):
- if item is public, all non-private roles, except for the current user's private role,
are legitimate.
- if item is restricted, legitimate roles are derived from the users and groups associated
with each role that is associated with the access permission on item. Private roles, except
for the current user's private role, will be excluded.
"""
admin_controller = cntrller in ["library_admin"]
roles = set()
if (isinstance(item, self.model.Library) and self.library_is_public(item)) or (
isinstance(item, self.model.Dataset) and self.dataset_is_public(item)
):
return self.get_all_roles(trans, cntrller)
# If item has roles associated with the access permission, we need to start with them.
access_roles = item.get_access_roles(self)
for role in access_roles:
if admin_controller or self.ok_to_display(trans.user, role):
roles.add(role)
# Each role potentially has users. We need to find all roles that each of those users have.
for ura in role.users:
user = ura.user
for ura2 in user.roles:
if admin_controller or self.ok_to_display(trans.user, ura2.role):
roles.add(ura2.role)
# Each role also potentially has groups which, in turn, have members ( users ). We need to
# find all roles that each group's members have.
for gra in role.groups:
group = gra.group
for uga in group.users:
user = uga.user
for ura in user.roles:
if admin_controller or self.ok_to_display(trans.user, ura.role):
roles.add(ura.role)
return self.sort_by_attr([role for role in roles], "name")
[docs] def ok_to_display(self, user, role):
"""
Method for checking if:
- a role is private and is the current user's private role
- a role is a sharing role and belongs to the current user
"""
role_type = role.type
if user:
if role_type == self.model.Role.types.PRIVATE:
return role == self.get_private_user_role(user)
if role_type == self.model.Role.types.SHARING:
return role in self.get_sharing_roles(user)
# If role_type is neither private nor sharing, it's ok to display
return True
return role_type != self.model.Role.types.PRIVATE and role_type != self.model.Role.types.SHARING
[docs] def allow_action(self, roles, action, item):
"""
Method for checking a permission for the current user ( based on roles ) to perform a
specific action on an item, which must be one of:
Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
"""
# SM: Note that calling get_item_actions will emit a query.
item_actions = self.get_item_actions(action, item)
if not item_actions:
return action.model == "restrict"
ret_val = False
# For DATASET_ACCESS only, user must have ALL associated roles
if action == self.permitted_actions.DATASET_ACCESS:
for item_action in item_actions:
if item_action.role not in roles:
break
else:
ret_val = True
# For remaining actions, user must have any associated role
else:
for item_action in item_actions:
if item_action.role in roles:
ret_val = True
break
return ret_val
[docs] def get_actions_for_items(self, trans, action, permission_items):
# TODO: Rename this; it's a replacement for get_item_actions, but it
# doesn't represent what it's really doing, which is confusing.
# TODO: Make this work for other classes besides lib_datasets.
# That should be as easy as checking the type and writing a query for each;
# we're avoiding using the SQLAlchemy backrefs because they can cause lots
# of queries to be generated.
#
# Originally, get_item_actions did:
# return [ permission for permission in item.actions if permission.action == action.action ]
# The "item" can be just about anything with permissions, and referencing
# item.actions causes the item's permissions to be retrieved.
# This method will retrieve all permissions for all "items" and only
# return the permissions associated with that given action.
# We initialize the permissions list to be empty; we will return an
# empty list by default.
#
# If the dataset id has no corresponding action in its permissions,
# then the returned permissions will not carry an entry for the dataset.
ret_permissions = {}
if len(permission_items) > 0:
# SM: NB: LibraryDatasets became Datasets for some odd reason.
if isinstance(permission_items[0], trans.model.LibraryDataset):
ids = [item.library_dataset_id for item in permission_items]
stmt = select(LibraryDatasetPermissions).where(
and_(
LibraryDatasetPermissions.library_dataset_id.in_(ids),
LibraryDatasetPermissions.action == action.action,
)
)
permissions = trans.sa_session.scalars(stmt)
# Massage the return data. We will return a list of permissions
# for each library dataset. So we initialize the return list to
# have an empty list for each dataset. Then each permission is
# appended to the right lib dataset.
# TODO: Consider eliminating the initialization and just return
# empty values for each library dataset id.
for item in permission_items:
ret_permissions[item.library_dataset_id] = []
for permission in permissions:
ret_permissions[permission.library_dataset_id].append(permission)
elif isinstance(permission_items[0], trans.model.Dataset):
ids = [item.id for item in permission_items]
stmt = select(DatasetPermissions).where(
and_(DatasetPermissions.dataset_id.in_(ids), DatasetPermissions.action == action.action)
)
permissions = trans.sa_session.scalars(stmt)
# Massage the return data. We will return a list of permissions
# for each library dataset. So we initialize the return list to
# have an empty list for each dataset. Then each permission is
# appended to the right lib dataset.
# TODO: Consider eliminating the initialization and just return
# empty values for each library dataset id.
for item in permission_items:
ret_permissions[item.id] = []
for permission in permissions:
ret_permissions[permission.dataset_id].append(permission)
# Test that we get the same response from get_item_actions each item:
test_code = False
if test_code:
try:
log.debug("get_actions_for_items: Test start")
for item in permission_items:
base_result = self.get_item_actions(action, item)
new_result = ret_permissions[item.library_dataset_id]
# For now, just test against LibraryDatasetIds; other classes
# are not tested yet.
if len(base_result) == len(new_result):
common_result = set(base_result).intersection(new_result)
if len(common_result) == len(base_result):
log.debug("Match on permissions for id %d" % item.library_dataset_id)
# TODO: Fix this failure message:
else:
log.debug(
"Error: dataset %d; originally: %s; now: %s"
% (item.library_dataset_id, base_result, new_result)
)
else:
log.debug(
"Error: dataset %d: had %d entries, now %d entries"
% (item.library_dataset_id, len(base_result), len(new_result))
)
log.debug("get_actions_for_items: Test end")
except Exception as e:
log.debug(f"Exception in test code: {e}")
return ret_permissions
[docs] def allow_action_on_libitems(self, trans, user_roles, action, items):
"""
This should be the equivalent of allow_action defined on multiple items.
It is meant to specifically replace allow_action for multiple
LibraryDatasets, but it could be reproduced or modified for
allow_action's permitted classes - Dataset, Library, LibraryFolder, and
LDDAs.
"""
all_items_actions = self.get_actions_for_items(trans, action, items)
ret_allow_action = {}
# Change item to lib_dataset or vice-versa.
for item in items:
if item.id in all_items_actions:
item_actions = all_items_actions[item.id]
if self.permitted_actions.DATASET_ACCESS == action:
ret_allow_action[item.id] = True
for item_action in item_actions:
if item_action.role not in user_roles:
ret_allow_action[item.id] = False
break
# Else look for just one dataset role to be in the list of
# acceptable user roles:
else:
ret_allow_action[item.id] = False
for item_action in item_actions:
if item_action.role in user_roles:
ret_allow_action[item.id] = True
break
else:
if "restrict" == action.model:
ret_allow_action[item.id] = True
else:
ret_allow_action[item.id] = False
# Test it: the result for each dataset should match the result for
# allow_action:
test_code = False
if test_code:
log.debug("allow_action_for_items: test start")
for item in items:
orig_value = self.allow_action(user_roles, action, item)
if orig_value == ret_allow_action[item.id]:
log.debug("Item %d: success" % item.id)
else:
log.debug("Item %d: fail: original: %s; new: %s" % (item.id, orig_value, ret_allow_action[item.id]))
log.debug("allow_action_for_items: test end")
return ret_allow_action
# DELETEME: SM: DO NOT TOUCH! This actually works.
[docs] def dataset_access_mapping(self, trans, user_roles, datasets):
"""
For the given list of datasets, return a mapping of the datasets' ids
to whether they can be accessed by the user or not. The datasets input
is expected to be a simple list of Dataset objects.
"""
datasets_public_map = self.datasets_are_public(trans, datasets)
datasets_allow_action_map = self.allow_action_on_libitems(
trans, user_roles, self.permitted_actions.DATASET_ACCESS, datasets
)
can_access = {}
for dataset in datasets:
can_access[dataset.id] = datasets_public_map[dataset.id] or datasets_allow_action_map[dataset.id]
return can_access
[docs] def dataset_permission_map_for_access(self, trans, user_roles, libitems):
"""
For a given list of library items (e.g., Datasets), return a map of the
datasets' ids to whether they can have permission to use that action
(e.g., "access" or "modify") on the dataset. The libitems input is
expected to be a simple list of library items, such as Datasets or
LibraryDatasets.
NB: This is currently only usable for Datasets; it was intended to
be used for any library item.
"""
# Map the library items to whether they are publicly accessible or not.
# Then determine what actions are allowed on the item (in case it's not
# public). Finally, the item is accessible if it's publicly available
# or the right permissions are enabled.
# TODO: This only works for Datasets; other code is using X_is_public,
# so this will have to be rewritten to support other items.
libitems_public_map = self.datasets_are_public(trans, libitems)
libitems_allow_action_map = self.allow_action_on_libitems(
trans, user_roles, self.permitted_actions.DATASET_ACCESS, libitems
)
can_access = {}
for libitem in libitems:
can_access[libitem.id] = libitems_public_map[libitem.id] or libitems_allow_action_map[libitem.id]
return can_access
[docs] def item_permission_map_for_modify(self, trans, user_roles, libitems):
return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_MODIFY, libitems)
[docs] def item_permission_map_for_manage(self, trans, user_roles, libitems):
return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_MANAGE, libitems)
[docs] def item_permission_map_for_add(self, trans, user_roles, libitems):
return self.allow_action_on_libitems(trans, user_roles, self.permitted_actions.LIBRARY_ADD, libitems)
[docs] def can_access_dataset(self, user_roles, dataset: galaxy.model.Dataset):
# SM: dataset_is_public will access dataset.actions, which is a
# backref that causes a query to be made to DatasetPermissions
retval = self.dataset_is_public(dataset) or self.allow_action(
user_roles, self.permitted_actions.DATASET_ACCESS, dataset
)
return retval
[docs] def can_access_datasets(self, user_roles, action_tuples):
user_role_ids = [galaxy.model.cached_id(r) for r in user_roles]
# For DATASET_ACCESS, user must have ALL associated roles
for action, user_role_id in action_tuples:
if action == self.permitted_actions.DATASET_ACCESS.action:
if user_role_id not in user_role_ids:
return False
return True
[docs] def can_access_collection(self, user_roles: List[galaxy.model.Role], collection: galaxy.model.DatasetCollection):
action_tuples = collection.dataset_action_tuples
if not self.can_access_datasets(user_roles, action_tuples):
return False
return True
[docs] def can_manage_dataset(self, roles, dataset):
return self.allow_action(roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset)
[docs] def can_access_library(self, roles, library):
return self.library_is_public(library) or self.allow_action(
roles, self.permitted_actions.LIBRARY_ACCESS, library
)
[docs] def get_accessible_libraries(self, trans, user):
"""Return all data libraries that the received user can access"""
accessible_libraries = []
current_user_role_ids = [role.id for role in user.all_roles()]
library_access_action = self.permitted_actions.LIBRARY_ACCESS.action
stmt = select(LibraryPermissions).where(LibraryPermissions.action == library_access_action).distinct()
restricted_library_ids = [lp.library_id for lp in trans.sa_session.scalars(stmt)]
stmt = select(LibraryPermissions).where(
and_(
LibraryPermissions.action == library_access_action,
LibraryPermissions.role_id.in_(current_user_role_ids),
)
)
accessible_restricted_library_ids = [lp.library_id for lp in trans.sa_session.scalars(stmt)]
# Filter to get libraries accessible by the current user. Get both
# public libraries and restricted libraries accessible by the current user.
stmt = (
select(Library)
.where(
and_(
Library.deleted == false(),
or_(
not_(Library.id.in_(restricted_library_ids)),
Library.id.in_(accessible_restricted_library_ids),
),
)
)
.order_by(Library.name)
)
for library in trans.sa_session.scalars(stmt):
accessible_libraries.append(library)
return accessible_libraries
[docs] def has_accessible_folders(self, trans, folder, user, roles, search_downward=True):
if (
self.has_accessible_library_datasets(trans, folder, user, roles, search_downward=search_downward)
or self.can_add_library_item(roles, folder)
or self.can_modify_library_item(roles, folder)
or self.can_manage_library_item(roles, folder)
):
return True
if search_downward:
for active_folder in folder.active_folders:
return self.has_accessible_folders(trans, active_folder, user, roles, search_downward=search_downward)
return False
[docs] def has_accessible_library_datasets(self, trans, folder, user, roles, search_downward=True):
stmt = select(LibraryDataset).where(
and_(LibraryDataset.deleted == false(), LibraryDataset.folder_id == folder.id)
)
for library_dataset in trans.sa_session.scalars(stmt):
if self.can_access_library_item(roles, library_dataset, user):
return True
if search_downward:
return self.__active_folders_have_accessible_library_datasets(trans, folder, user, roles)
return False
def __active_folders_have_accessible_library_datasets(self, trans, folder, user, roles):
for active_folder in folder.active_folders:
if self.has_accessible_library_datasets(trans, active_folder, user, roles):
return True
return False
[docs] def can_access_library_item(self, roles, item, user):
if isinstance(item, self.model.Library):
return self.can_access_library(roles, item)
elif isinstance(item, self.model.LibraryFolder):
return (
self.can_access_library(roles, item.parent_library) and self.check_folder_contents(user, roles, item)[0]
)
elif isinstance(item, self.model.LibraryDataset):
return self.can_access_library(roles, item.folder.parent_library) and self.can_access_dataset(
roles, item.library_dataset_dataset_association.dataset
)
elif isinstance(item, self.model.LibraryDatasetDatasetAssociation):
return self.can_access_library(
roles, item.library_dataset.folder.parent_library
) and self.can_access_dataset(roles, item.dataset)
elif isinstance(item, self.model.LibraryDatasetCollectionAssociation):
return self.can_access_library(roles, item.folder.parent_library)
else:
log.warning(f"Unknown library item type: {type(item)}")
return False
[docs] def can_add_library_item(self, roles, item):
return self.allow_action(roles, self.permitted_actions.LIBRARY_ADD, item)
[docs] def can_modify_library_item(self, roles, item):
return self.allow_action(roles, self.permitted_actions.LIBRARY_MODIFY, item)
[docs] def can_manage_library_item(self, roles, item):
return self.allow_action(roles, self.permitted_actions.LIBRARY_MANAGE, item)
[docs] def get_item_actions(self, action, item):
# item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation
# SM: Accessing item.actions emits a query to Library_Dataset_Permissions
# if the item is a LibraryDataset:
# TODO: Pass in the item's actions - the item isn't needed
return [permission for permission in item.actions if permission.action == action.action]
[docs] def guess_derived_permissions_for_datasets(self, datasets=None):
"""Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets"""
datasets = datasets or []
perms = {}
for dataset in datasets:
if not isinstance(dataset, self.model.Dataset):
dataset = dataset.dataset
these_perms = {}
# initialize blank perms
for action in self.get_actions():
these_perms[action] = []
# collect this dataset's perms
these_perms = self.get_permissions(dataset)
# join or intersect this dataset's permissions with others
for action, roles in these_perms.items():
if action not in perms.keys():
perms[action] = roles
else:
if action.model == "grant":
# intersect existing roles with new roles
perms[action] = [_ for _ in roles if _ in perms[action]]
elif action.model == "restrict":
# join existing roles with new roles
perms[action].extend([_ for _ in roles if _ not in perms[action]])
return perms
[docs] def guess_derived_permissions(self, all_input_permissions):
"""Returns a dict of { action : [ role_id, role_id, ... ] } for the output dataset based upon input dataset permissions.
all_input_permissions should be of the form {action_name: set(role_ids)}
"""
perms = {}
for action_name, role_ids in all_input_permissions.items():
if not role_ids:
continue
action = self.get_action(action_name)
if action not in perms.keys():
perms[action] = list(role_ids)
else:
if action.model == "grant":
# intersect existing roles with new roles
perms[action] = [_ for _ in role_ids if _ in perms[action]]
elif action.model == "restrict":
# join existing roles with new roles
perms[action].extend([_ for _ in role_ids if _ not in perms[action]])
return perms
[docs] def associate_components(self, **kwd):
if "user" in kwd:
if "group" in kwd:
return self.associate_user_group(kwd["user"], kwd["group"])
elif "role" in kwd:
return self.associate_user_role(kwd["user"], kwd["role"])
elif "role" in kwd:
if "group" in kwd:
return self.associate_group_role(kwd["group"], kwd["role"])
if "action" in kwd:
if "dataset" in kwd and "role" in kwd:
return self.associate_action_dataset_role(kwd["action"], kwd["dataset"], kwd["role"])
raise Exception(f"No valid method of associating provided components: {kwd}")
[docs] def associate_user_group(self, user, group):
assoc = self.model.UserGroupAssociation(user, group)
self.sa_session.add(assoc)
with transaction(self.sa_session):
self.sa_session.commit()
return assoc
[docs] def associate_user_role(self, user, role):
assoc = self.model.UserRoleAssociation(user, role)
self.sa_session.add(assoc)
with transaction(self.sa_session):
self.sa_session.commit()
return assoc
[docs] def associate_group_role(self, group, role):
assoc = self.model.GroupRoleAssociation(group, role)
self.sa_session.add(assoc)
with transaction(self.sa_session):
self.sa_session.commit()
return assoc
[docs] def associate_action_dataset_role(self, action, dataset, role):
assoc = self.model.DatasetPermissions(action, dataset, role)
self.sa_session.add(assoc)
with transaction(self.sa_session):
self.sa_session.commit()
return assoc
[docs] def create_user_role(self, user, app):
# Create private user role if necessary
self.get_private_user_role(user, auto_create=True)
# Create default user permissions if necessary
if not user.default_permissions:
if hasattr(app.config, "new_user_dataset_access_role_default_private"):
permissions = app.config.new_user_dataset_access_role_default_private
self.user_set_default_permissions(user, default_access_private=permissions)
else:
self.user_set_default_permissions(user, history=True, dataset=True)
[docs] def create_private_user_role(self, user):
user.attempt_create_private_role()
return self.get_private_user_role(user)
[docs] def get_private_user_role(self, user, auto_create=False):
stmt = (
select(Role)
.where(
and_(
UserRoleAssociation.user_id == user.id,
Role.id == UserRoleAssociation.role_id,
Role.type == Role.types.PRIVATE,
)
)
.distinct()
)
role = self.sa_session.execute(stmt).scalar_one_or_none()
if not role:
if auto_create:
return self.create_private_user_role(user)
else:
return None
return role
[docs] def get_role(self, name, type=None):
type = type or self.model.Role.types.SYSTEM
# will raise exception if not found
stmt = select(Role).where(and_(Role.name == name, Role.type == type))
return self.sa_session.execute(stmt).scalar_one()
[docs] def create_role(self, name, description, in_users, in_groups, create_group_for_role=False, type=None):
type = type or self.model.Role.types.SYSTEM
role = self.model.Role(name=name, description=description, type=type)
self.sa_session.add(role)
# Create the UserRoleAssociations
for user in [self.sa_session.get(User, x) for x in in_users]:
self.associate_user_role(user, role)
# Create the GroupRoleAssociations
for group in [self.sa_session.get(Group, x) for x in in_groups]:
self.associate_group_role(group, role)
if create_group_for_role:
# Create the group
group = self.model.Group(name=name)
self.sa_session.add(group)
# Associate the group with the role
self.associate_group_role(group, role)
num_in_groups = len(in_groups) + 1
else:
num_in_groups = len(in_groups)
with transaction(self.sa_session):
self.sa_session.commit()
return role, num_in_groups
[docs] def get_sharing_roles(self, user):
stmt = select(Role).where(
and_((Role.name).like(f"Sharing role for: %{user.email}%"), Role.type == Role.types.SHARING)
)
return self.sa_session.scalars(stmt)
[docs] def user_set_default_permissions(
self,
user,
permissions=None,
history=False,
dataset=False,
bypass_manage_permission=False,
default_access_private=False,
):
# bypass_manage_permission is used to change permissions of datasets in a userless history when logging in
flush_needed = False
permissions = permissions or {}
if user is None:
return None
if not permissions:
# default permissions
permissions = {
self.permitted_actions.DATASET_MANAGE_PERMISSIONS: [self.get_private_user_role(user, auto_create=True)]
}
# new_user_dataset_access_role_default_private is set as True in config file
if default_access_private:
permissions[self.permitted_actions.DATASET_ACCESS] = next(iter(permissions.values()))
# Delete all of the current default permissions for the user
for dup in user.default_permissions:
self.sa_session.delete(dup)
flush_needed = True
# Add the new default permissions for the user
for action, roles in permissions.items():
if isinstance(action, Action):
action = action.action
for dup in [self.model.DefaultUserPermissions(user, action, role) for role in roles]:
self.sa_session.add(dup)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
if history:
for history in user.active_histories:
self.history_set_default_permissions(
history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission
)
[docs] def user_get_default_permissions(self, user):
permissions = {}
for dup in user.default_permissions:
action = self.get_action(dup.action)
if action in permissions:
permissions[action].append(dup.role)
else:
permissions[action] = [dup.role]
return permissions
[docs] def history_set_default_permissions(self, history, permissions=None, dataset=False, bypass_manage_permission=False):
# bypass_manage_permission is used to change permissions of datasets in a user-less history when logging in
flush_needed = False
permissions = permissions or {}
user = history.user
if not user:
# default permissions on a user-less history are None
return None
if not permissions:
permissions = self.user_get_default_permissions(user)
# Delete all of the current default permission for the history
for dhp in history.default_permissions:
self.sa_session.delete(dhp)
flush_needed = True
# Add the new default permissions for the history
for action, roles in permissions.items():
if isinstance(action, Action):
action = action.action
for dhp in [self.model.DefaultHistoryPermissions(history, action, role) for role in roles]:
self.sa_session.add(dhp)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
if dataset:
# Only deal with datasets that are not purged
for hda in history.activatable_datasets:
dataset = hda.dataset
if dataset.library_associations:
# Don't change permissions on a dataset associated with a library
continue
if [assoc for assoc in dataset.history_associations if assoc.history not in user.histories]:
# Don't change permissions on a dataset associated with a history not owned by the user
continue
if bypass_manage_permission or self.can_manage_dataset(user.all_roles(), dataset):
self.set_all_dataset_permissions(dataset, permissions)
[docs] def history_get_default_permissions(self, history):
permissions = {}
for dhp in history.default_permissions:
action = self.get_action(dhp.action)
if action in permissions:
permissions[action].append(dhp.role)
else:
permissions[action] = [dhp.role]
return permissions
[docs] def set_all_dataset_permissions(self, dataset, permissions=None, new=False, flush=True):
"""
Set new full permissions on a dataset, eliminating all current permissions.
Permission looks like: { Action : [ Role, Role ] }
"""
# Make sure that DATASET_MANAGE_PERMISSIONS is associated with at least 1 role
has_dataset_manage_permissions = False
permissions = permissions or {}
for _ in _walk_action_roles(permissions, self.permitted_actions.DATASET_MANAGE_PERMISSIONS):
has_dataset_manage_permissions = True
break
if not has_dataset_manage_permissions:
return "At least 1 role must be associated with manage permissions on this dataset."
# If this is new, the objectstore likely hasn't been set yet - defer check until
# the job handler assigns it.
if not new and not dataset.shareable:
# ensure dataset not shared.
dataset_access_roles = []
for _, roles in _walk_action_roles(permissions, self.permitted_actions.DATASET_ACCESS):
dataset_access_roles.extend(roles)
if len(dataset_access_roles) != 1 or dataset_access_roles[0].type != self.model.Role.types.PRIVATE:
return galaxy.model.CANNOT_SHARE_PRIVATE_DATASET_MESSAGE
flush_needed = False
# Delete all of the current permissions on the dataset
if not new:
for dp in dataset.actions:
self.sa_session.delete(dp)
flush_needed = True
# Add the new permissions on the dataset
for action, roles in permissions.items():
if isinstance(action, Action):
action = action.action
for role in roles:
if hasattr(role, "id"):
role_id = role.id
else:
role_id = role
dp = self.model.DatasetPermissions(action, dataset, role_id=role_id)
self.sa_session.add(dp)
flush_needed = True
if flush_needed and flush:
with transaction(self.sa_session):
self.sa_session.commit()
return ""
[docs] def set_dataset_permission(self, dataset, permission=None):
"""
Set a specific permission on a dataset, leaving all other current permissions on the dataset alone.
Permission looks like: { Action.action : [ Role, Role ] }
"""
permission = permission or {}
# if modifying access - ensure it is shareable.
for _ in _walk_action_roles(permission, self.permitted_actions.DATASET_ACCESS):
dataset.ensure_shareable()
break
flush_needed = False
for action, roles in permission.items():
if isinstance(action, Action):
action = action.action
# Delete the current specific permission on the dataset if one exists
for dp in dataset.actions:
if dp.action == action:
self.sa_session.delete(dp)
flush_needed = True
# Add the new specific permission on the dataset
for dp in [self.model.DatasetPermissions(action, dataset, role) for role in roles]:
self.sa_session.add(dp)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def get_permissions(self, item):
"""
Return a dictionary containing the actions and associated roles on item
where item is one of Library, LibraryFolder, LibraryDatasetDatasetAssociation,
LibraryDataset, Dataset. The dictionary looks like: { Action : [ Role, Role ] }.
"""
permissions = {}
for item_permission in item.actions:
action = self.get_action(item_permission.action)
if action in permissions:
permissions[action].append(item_permission.role)
else:
permissions[action] = [item_permission.role]
return permissions
[docs] def copy_dataset_permissions(self, src, dst, flush=True):
if not isinstance(src, self.model.Dataset):
src = src.dataset
if not isinstance(dst, self.model.Dataset):
dst = dst.dataset
self.set_all_dataset_permissions(dst, self.get_permissions(src), flush=flush)
[docs] def set_all_library_permissions(self, trans, library_item, permissions=None):
# Set new permissions on library_item, eliminating all current permissions
flush_needed = False
permissions = permissions or {}
for role_assoc in library_item.actions:
self.sa_session.delete(role_assoc)
flush_needed = True
# Add the new permissions on library_item
for item_class, permission_class in self.library_item_assocs:
if isinstance(library_item, item_class):
for action, roles in list(permissions.items()):
if isinstance(action, Action):
action = action.action
for role_assoc in [permission_class(action, library_item, role) for role in roles]:
self.sa_session.add(role_assoc)
flush_needed = True
if isinstance(library_item, self.model.LibraryDatasetDatasetAssociation):
# Permission setting related to DATASET_MANAGE_PERMISSIONS was broken for a period of time,
# so it is possible that some Datasets have no roles associated with the DATASET_MANAGE_PERMISSIONS
# permission. In this case, we'll reset this permission to the library_item user's private role.
if not library_item.dataset.has_manage_permissions_roles(self):
# Well this looks like a bug, this should be looked at.
# Default permissions above is single hash that keeps getting reeditted here
# because permission is being defined instead of permissions. -John
permissions[self.permitted_actions.DATASET_MANAGE_PERMISSIONS] = [
trans.app.security_agent.get_private_user_role(library_item.user)
]
self.set_dataset_permission(library_item.dataset, permissions)
if action == self.permitted_actions.LIBRARY_MANAGE.action and roles:
# Handle the special case when we are setting the LIBRARY_MANAGE_PERMISSION on a
# library_dataset_dataset_association since the roles need to be applied to the
# DATASET_MANAGE_PERMISSIONS permission on the associated dataset.
permissions = {}
permissions[self.permitted_actions.DATASET_MANAGE_PERMISSIONS] = roles
self.set_dataset_permission(library_item.dataset, permissions)
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def set_library_item_permission(self, library_item, permission=None):
"""
Set a specific permission on a library item, leaving all other current permissions on the item alone.
Permission looks like: { Action.action : [ Role, Role ] }
"""
permission = permission or {}
flush_needed = False
for action, roles in permission.items():
if isinstance(action, Action):
action = action.action
# Delete the current specific permission on the library item if one exists
for item_permission in library_item.actions:
if item_permission.action == action:
self.sa_session.delete(item_permission)
flush_needed = True
# Add the new specific permission on the library item
if isinstance(library_item, self.model.LibraryDataset):
for item_permission in [
self.model.LibraryDatasetPermissions(action, library_item, role) for role in roles
]:
self.sa_session.add(item_permission)
flush_needed = True
elif isinstance(library_item, self.model.LibraryPermissions):
for item_permission in [self.model.LibraryPermissions(action, library_item, role) for role in roles]:
self.sa_session.add(item_permission)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def library_is_public(self, library, contents=False):
if contents:
# Check all contained folders and datasets to find any that are not public
if not self.folder_is_public(library.root_folder):
return False
# A library is considered public if there are no "access" actions associated with it.
return self.permitted_actions.LIBRARY_ACCESS.action not in [a.action for a in library.actions]
[docs] def library_is_unrestricted(self, library):
# A library is considered unrestricted if there are no "access" actions associated with it.
return self.permitted_actions.LIBRARY_ACCESS.action not in [a.action for a in library.actions]
[docs] def make_library_public(self, library, contents=False):
flush_needed = False
if contents:
# Make all contained folders (include deleted folders, but not purged folders), public
self.make_folder_public(library.root_folder)
# A library is considered public if there are no LIBRARY_ACCESS actions associated with it.
for lp in library.actions:
if lp.action == self.permitted_actions.LIBRARY_ACCESS.action:
self.sa_session.delete(lp)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def folder_is_public(self, folder):
for sub_folder in folder.folders:
if not self.folder_is_public(sub_folder):
return False
for library_dataset in folder.datasets:
ldda = library_dataset.library_dataset_dataset_association
if ldda and ldda.dataset and not self.dataset_is_public(ldda.dataset):
return False
return True
[docs] def folder_is_unrestricted(self, folder):
# TODO implement folder restrictions
# for now all folders are _visible_ but the restricted datasets within are not visible
return True
[docs] def make_folder_public(self, folder):
# Make all of the contents (include deleted contents, but not purged contents) of folder public
for sub_folder in folder.folders:
if not sub_folder.purged:
self.make_folder_public(sub_folder)
for library_dataset in folder.datasets:
dataset = library_dataset.library_dataset_dataset_association.dataset
if not dataset.purged and not self.dataset_is_public(dataset):
self.make_dataset_public(dataset)
[docs] def dataset_is_public(self, dataset: galaxy.model.Dataset):
"""
A dataset is considered public if there are no "access" actions
associated with it. Any other actions ( 'manage permissions',
'edit metadata' ) are irrelevant. Accessing dataset.actions
will cause a query to be emitted.
"""
return self.permitted_actions.DATASET_ACCESS.action not in [a.action for a in dataset.actions]
[docs] def dataset_is_unrestricted(self, trans, dataset):
"""
Different implementation of the method above with signature:
def dataset_is_public( self, dataset )
"""
return len(dataset.library_dataset_dataset_association.get_access_roles(self)) == 0
[docs] def dataset_is_private_to_user(self, trans, dataset):
"""
If the Dataset object has exactly one access role and that is
the current user's private role then we consider the dataset private.
"""
private_role = self.get_private_user_role(trans.user)
access_roles = dataset.get_access_roles(self)
if len(access_roles) != 1 or private_role is None:
return False
else:
if access_roles[0].id == private_role.id:
return True
else:
return False
[docs] def dataset_is_private_to_a_user(self, dataset):
"""
If the Dataset object has exactly one access role and that is
the current user's private role then we consider the dataset private.
"""
access_roles = dataset.get_access_roles(self)
if len(access_roles) != 1:
return False
else:
access_role = access_roles[0]
return access_role.type == self.model.Role.types.PRIVATE
[docs] def datasets_are_public(self, trans, datasets):
"""
Given a transaction object and a list of Datasets, return
a mapping from Dataset ids to whether the Dataset is public
or not. All Dataset ids should be returned in the mapping's keys.
"""
# We go the other way around from dataset_is_public: we start with
# all datasets being marked as public. If there is an access action
# associated with the dataset, then we mark it as nonpublic:
datasets_public = {}
dataset_ids = [dataset.id for dataset in datasets]
for dataset_id in dataset_ids:
datasets_public[dataset_id] = True
# Now get all datasets which have DATASET_ACCESS actions:
stmt = select(DatasetPermissions).where(
and_(
DatasetPermissions.dataset_id.in_(dataset_ids),
DatasetPermissions.action == self.permitted_actions.DATASET_ACCESS.action,
)
)
access_data_perms = trans.sa_session.scalars(stmt)
# Every dataset returned has "access" privileges associated with it,
# so it's not public.
for permission in access_data_perms:
datasets_public[permission.dataset_id] = False
return datasets_public
[docs] def make_dataset_public(self, dataset):
# A dataset is considered public if there are no "access" actions associated with it. Any
# other actions ( 'manage permissions', 'edit metadata' ) are irrelevant.
dataset.ensure_shareable()
flush_needed = False
for dp in dataset.actions:
if dp.action == self.permitted_actions.DATASET_ACCESS.action:
self.sa_session.delete(dp)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def derive_roles_from_access(self, trans, item_id, cntrller, library=False, **kwd):
# Check the access permission on a dataset. If library is true, item_id refers to a library. If library
# is False, item_id refers to a dataset ( item_id must currently be decoded before being sent ). The
# cntrller param is the calling controller, which needs to be passed to get_legitimate_roles().
msg = ""
permissions = {}
# accessible will be True only if at least 1 user has every role in DATASET_ACCESS_in
accessible = False
# legitimate will be True only if all roles in DATASET_ACCESS_in are in the set of roles returned from
# get_legitimate_roles()
# legitimate = False # TODO: not used
# private_role_found will be true only if more than 1 role is being associated with the DATASET_ACCESS
# permission on item, and at least 1 of the roles is private.
private_role_found = False
error = False
for k, v in get_permitted_actions(filter="DATASET").items():
# Change for removing the prefix '_in' from the roles select box
in_roles = [self.sa_session.get(Role, x) for x in listify(kwd[k])]
if not in_roles:
in_roles = [self.sa_session.get(Role, x) for x in listify(kwd.get(f"{k}_in", []))]
if v == self.permitted_actions.DATASET_ACCESS and in_roles:
if library:
item = self.sa_session.get(Library, item_id)
else:
item = self.sa_session.get(Dataset, item_id)
if (library and not self.library_is_public(item)) or (not library and not self.dataset_is_public(item)):
# Ensure that roles being associated with DATASET_ACCESS are a subset of the legitimate roles
# derived from the roles associated with the access permission on item if it's not public. This
# will keep illegitimate roles from being associated with the DATASET_ACCESS permission on the
# dataset (i.e., in the case where item is .a library, if Role1 is associated with LIBRARY_ACCESS,
# then only those users that have Role1 should be associated with DATASET_ACCESS.
legitimate_roles = self.get_legitimate_roles(trans, item, cntrller)
illegitimate_roles = []
for role in in_roles:
if role not in legitimate_roles:
illegitimate_roles.append(role)
if illegitimate_roles:
# This condition should never occur since illegitimate roles are filtered out of the set of
# roles displayed on the forms, but just in case there is a bug somewhere that incorrectly
# filters, we'll display this message.
error = True
msg += "The following roles are not associated with users that have the 'access' permission on this "
msg += "item, so they were incorrectly displayed: "
for role in illegitimate_roles:
msg += f"{role.name}, "
msg = msg.rstrip(", ")
new_in_roles = []
for role in in_roles:
if role in legitimate_roles:
new_in_roles.append(role)
in_roles = new_in_roles
if len(in_roles) > 1:
# At least 1 user must have every role associated with the access
# permission on this dataset, or the dataset is not accessible.
# Since we have more than 1 role, none of them can be private.
for role in in_roles:
if role.type == self.model.Role.types.PRIVATE:
private_role_found = True
break
if len(in_roles) == 1:
accessible = True
else:
# At least 1 user must have every role associated with the access
# permission on this dataset, or the dataset is not accessible.
in_roles_set = set()
for role in in_roles:
in_roles_set.add(role)
users_set = set()
for role in in_roles:
for ura in role.users:
users_set.add(ura.user)
for gra in role.groups:
group = gra.group
for uga in group.users:
users_set.add(uga.user)
# Make sure that at least 1 user has every role being associated with the dataset.
for user in users_set:
user_roles_set = set()
for ura in user.roles:
user_roles_set.add(ura.role)
if in_roles_set.issubset(user_roles_set):
accessible = True
break
if private_role_found or not accessible:
error = True
# Don't set the permissions for DATASET_ACCESS if inaccessible or multiple roles with
# at least 1 private, but set all other permissions.
permissions[self.get_action(v.action)] = []
msg = "At least 1 user must have every role associated with accessing datasets. "
if private_role_found:
msg += "Since you are associating more than 1 role, no private roles are allowed."
if not accessible:
msg += "The roles you attempted to associate for access would make the datasets in-accessible by everyone."
else:
permissions[self.get_action(v.action)] = in_roles
else:
permissions[self.get_action(v.action)] = in_roles
return permissions, in_roles, error, msg
[docs] def copy_library_permissions(self, trans, source_library_item, target_library_item, user=None):
# Copy all relevant permissions from source.
permissions = {}
for role_assoc in source_library_item.actions:
if role_assoc.action != self.permitted_actions.LIBRARY_ACCESS.action:
# LIBRARY_ACCESS is a special permission that is set only at the library level.
if role_assoc.action in permissions:
permissions[role_assoc.action].append(role_assoc.role)
else:
permissions[role_assoc.action] = [role_assoc.role]
self.set_all_library_permissions(trans, target_library_item, permissions)
if user:
for item_class, permission_class in self.library_item_assocs:
if isinstance(target_library_item, item_class):
found_permission_class = permission_class
break
else:
raise Exception(
f"Invalid class ({target_library_item.__class__}) specified for target_library_item ({target_library_item.__class__.__name__})"
)
# Make sure user's private role is included
private_role = self.model.security_agent.get_private_user_role(user)
for action in self.permitted_actions.values():
if not found_permission_class.filter_by(role_id=private_role.id, action=action.action).first():
lp = found_permission_class(action.action, target_library_item, private_role)
self.sa_session.add(lp)
with transaction(self.sa_session):
self.sa_session.commit()
[docs] def get_permitted_libraries(self, trans, user, actions):
"""
This method is historical (it is not currently used), but may be useful again at some
point. It returns a dictionary whose keys are library objects and whose values are a
comma-separated string of folder ids. This method works with the show_library_item()
method below, and it returns libraries for which the received user has permission to
perform the received actions. Here is an example call to this method to return all
libraries for which the received user has LIBRARY_ADD permission::
libraries = trans.app.security_agent.get_permitted_libraries( trans, user,
[ trans.app.security_agent.permitted_actions.LIBRARY_ADD ] )
"""
stmt = select(Library).where(Library.deleted == false()).order_by(Library.name)
all_libraries = trans.sa_session.scalars(stmt)
roles = user.all_roles()
actions_to_check = actions
# The libraries dictionary looks like: { library : '1,2' }, library : '3' }
# Its keys are the libraries that should be displayed for the current user and whose values are a
# string of comma-separated folder ids, of the associated folders the should NOT be displayed.
# The folders that should not be displayed may not be a complete list, but it is ultimately passed
# to the calling method to keep from re-checking the same folders when the library / folder
# select lists are rendered.
libraries = {}
for library in all_libraries:
can_show, hidden_folder_ids = self.show_library_item(self, roles, library, actions_to_check)
if can_show:
libraries[library] = hidden_folder_ids
return libraries
[docs] def show_library_item(self, user, roles, library_item, actions_to_check, hidden_folder_ids=""):
"""
This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a
comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with
the string, True is returned if the current user has permission to perform any 1 of actions_to_check
on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets
this criteria, if it exists. This method does not necessarily scan the entire library as it returns
when it finds the first library_item that allows user to perform any one action in actions_to_check.
"""
for action in actions_to_check:
if self.allow_action(roles, action, library_item):
return True, hidden_folder_ids
if isinstance(library_item, self.model.Library):
return self.show_library_item(user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids="")
if isinstance(library_item, self.model.LibraryFolder):
for folder in library_item.active_folders:
can_show, hidden_folder_ids = self.show_library_item(
user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids
)
if can_show:
return True, hidden_folder_ids
if hidden_folder_ids:
hidden_folder_ids = "%s,%d" % (hidden_folder_ids, folder.id)
else:
hidden_folder_ids = "%d" % folder.id
return False, hidden_folder_ids
[docs] def get_showable_folders(
self, user, roles, library_item, actions_to_check, hidden_folder_ids=None, showable_folders=None
):
"""
This method must be sent an instance of Library(), all the folders of which are scanned to determine if
user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should
contain a list of folder IDs which was generated when the library was previously scanned
using the same actions_to_check. A list of showable folders is generated. This method scans the entire library.
"""
hidden_folder_ids = hidden_folder_ids or []
showable_folders = showable_folders or []
if isinstance(library_item, self.model.Library):
return self.get_showable_folders(
user, roles, library_item.root_folder, actions_to_check, showable_folders=[]
)
if isinstance(library_item, self.model.LibraryFolder):
if library_item.id not in hidden_folder_ids:
for action in actions_to_check:
if self.allow_action(roles, action, library_item):
showable_folders.append(library_item)
break
for folder in library_item.active_folders:
self.get_showable_folders(user, roles, folder, actions_to_check, showable_folders=showable_folders)
return showable_folders
[docs] def set_entity_user_associations(self, users=None, roles=None, groups=None, delete_existing_assocs=True):
users = users or []
roles = roles or []
groups = groups or []
for user in users:
if delete_existing_assocs:
flush_needed = False
for a in user.non_private_roles + user.groups:
self.sa_session.delete(a)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
self.sa_session.refresh(user)
for role in roles:
# Make sure we are not creating an additional association with a PRIVATE role
if role not in [x.role for x in user.roles]:
self.associate_components(user=user, role=role)
for group in groups:
self.associate_components(user=user, group=group)
[docs] def set_entity_group_associations(self, groups=None, users=None, roles=None, delete_existing_assocs=True):
users = users or []
roles = roles or []
groups = groups or []
for group in groups:
if delete_existing_assocs:
flush_needed = False
for a in group.roles + group.users:
self.sa_session.delete(a)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
for role in roles:
self.associate_components(group=group, role=role)
for user in users:
self.associate_components(group=group, user=user)
[docs] def set_entity_role_associations(self, roles=None, users=None, groups=None, delete_existing_assocs=True):
users = users or []
roles = roles or []
groups = groups or []
for role in roles:
if delete_existing_assocs:
flush_needed = False
for a in role.users + role.groups:
self.sa_session.delete(a)
flush_needed = True
if flush_needed:
with transaction(self.sa_session):
self.sa_session.commit()
for user in users:
self.associate_components(user=user, role=role)
for group in groups:
self.associate_components(group=group, role=role)
[docs] def get_component_associations(self, **kwd):
assert len(kwd) == 2, "You must specify exactly 2 Galaxy security components to check for associations."
if "dataset" in kwd:
if "action" in kwd:
stmt = (
select(DatasetPermissions)
.filter_by(action=kwd["action"].action, dataset_id=kwd["dataset"].id)
.limit(1)
)
return self.sa_session.scalars(stmt).first()
elif "user" in kwd:
if "group" in kwd:
stmt = select(UserGroupAssociation).filter_by(group_id=kwd["group"].id, user_id=kwd["user"].id).limit(1)
return self.sa_session.scalars(stmt).first()
elif "role" in kwd:
stmt = select(UserRoleAssociation).filter_by(role_id=kwd["role"].id, user_id=kwd["user"].id).limit(1)
return self.sa_session.scalars(stmt).first()
elif "group" in kwd:
if "role" in kwd:
stmt = select(GroupRoleAssociation).filter_by(role_id=kwd["role"].id, group_id=kwd["group"].id).limit(1)
return self.sa_session.scalars(stmt).first()
raise Exception(f"No valid method of associating provided components: {kwd}")
[docs] def check_folder_contents(self, user, roles, folder, hidden_folder_ids=""):
"""
This method must always be sent an instance of LibraryFolder(). Recursive execution produces a
comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along
with the string, True is returned if the current user has permission to access folder. Otherwise,
cycle through all sub-folders in folder until one is found that meets this criteria, if it exists.
This method does not necessarily scan the entire library as it returns when it finds the first
folder that is accessible to user.
"""
# If a folder is writeable, it's accessable and we need not go further
if self.can_add_library_item(roles, folder):
return True, ""
action = self.permitted_actions.DATASET_ACCESS
stmt = (
select(LibraryDatasetDatasetAssociation)
.join(LibraryDatasetDatasetAssociation.library_dataset)
.where(LibraryDataset.folder == folder)
.join(Dataset)
.options(joinedload(LibraryDatasetDatasetAssociation.dataset).joinedload(Dataset.actions))
)
lddas = self.sa_session.scalars(stmt).unique()
for ldda in lddas:
ldda_access_permissions = self.get_item_actions(action, ldda.dataset)
if not ldda_access_permissions:
# Dataset is public
return True, hidden_folder_ids
for ldda_access_permission in ldda_access_permissions:
if ldda_access_permission.role in roles:
# The current user has access permission on the dataset
return True, hidden_folder_ids
for sub_folder in folder.active_folders:
can_access, hidden_folder_ids = self.check_folder_contents(
user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids
)
if can_access:
return True, hidden_folder_ids
if hidden_folder_ids:
hidden_folder_ids = "%s,%d" % (hidden_folder_ids, sub_folder.id)
else:
hidden_folder_ids = "%d" % sub_folder.id
return False, hidden_folder_ids
[docs]class HostAgent(RBACAgent):
"""
A simple security agent which allows access to datasets based on host.
This exists so that externals sites such as UCSC can gain access to
datasets which have permissions which would normally prevent such access.
"""
# TODO: Make sites user configurable
sites = Bunch(
ucsc_main=(
"hgw1.cse.ucsc.edu",
"hgw2.cse.ucsc.edu",
"hgw3.cse.ucsc.edu",
"hgw4.cse.ucsc.edu",
"hgw5.cse.ucsc.edu",
"hgw6.cse.ucsc.edu",
"hgw7.cse.ucsc.edu",
"hgw8.cse.ucsc.edu",
),
ucsc_test=("hgwdev.cse.ucsc.edu",),
ucsc_archaea=("lowepub.cse.ucsc.edu",),
)
[docs] def __init__(self, model, permitted_actions=None):
self.model = model
if permitted_actions:
self.permitted_actions = permitted_actions
@property
def sa_session(self):
"""Returns a SQLAlchemy session"""
return self.model.context
[docs] def allow_action(self, addr, action, **kwd):
if "dataset" in kwd and action == self.permitted_actions.DATASET_ACCESS:
hda = kwd["dataset"]
if action == self.permitted_actions.DATASET_ACCESS and action.action not in [
dp.action for dp in hda.dataset.actions
]:
log.debug("Allowing access to public dataset with hda: %i." % hda.id)
return True # dataset has no roles associated with the access permission, thus is already public
stmt = (
select(HistoryDatasetAssociationDisplayAtAuthorization)
.filter_by(history_dataset_association_id=hda.id)
.limit(1)
)
hdadaa = self.sa_session.scalars(stmt).first()
if not hdadaa:
log.debug(
"Denying access to private dataset with hda: %i. No hdadaa record for this dataset." % hda.id
)
return False # no auth
# We could just look up the reverse of addr, but then we'd also
# have to verify it with the forward address and special case any
# IPs (instead of hosts) in the server list.
#
# This would be improved by caching, but that's what the OS's name
# service cache daemon is for (you ARE running nscd, right?).
for server in HostAgent.sites.get(hdadaa.site, []):
# We're going to search in order, but if the remote site is load
# balancing their connections (as UCSC does), this is okay.
try:
if socket.gethostbyname(server) == addr:
break # remote host is in the server list
except (OSError, socket.gaierror):
pass # can't resolve, try next
else:
log.debug(
"Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s."
% (hda.id, hdadaa.site)
)
return False # remote addr is not in the server list
if (datetime.utcnow() - hdadaa.update_time) > timedelta(seconds=60):
log.debug(
"Denying access to private dataset with hda: %i. Authorization was granted, but has expired."
% hda.id
)
return False # not authz'd in the last 60 seconds
log.debug("Allowing access to private dataset with hda: %i. Remote server is: %s." % (hda.id, server))
return True
else:
raise Exception("The dataset access permission is the only valid permission in the host security agent.")
[docs] def set_dataset_permissions(self, hda, user, site):
stmt = (
select(HistoryDatasetAssociationDisplayAtAuthorization)
.filter_by(history_dataset_association_id=hda.id)
.limit(1)
)
hdadaa = self.sa_session.scalars(stmt).first()
if hdadaa:
hdadaa.update_time = datetime.utcnow()
else:
hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization(hda=hda, user=user, site=site)
self.sa_session.add(hdadaa)
with transaction(self.sa_session):
self.sa_session.commit()
def _walk_action_roles(permissions, query_action):
for action, roles in permissions.items():
if isinstance(action, Action):
if action == query_action and roles:
yield action, roles
elif action == query_action.action and roles:
yield action, roles