Source code for

"""Tool Shed Security"""
import logging

from sqlalchemy import (

from galaxy.util import listify
from galaxy.util.bunch import Bunch

log = logging.getLogger(__name__)

[docs]class Action:
[docs] def __init__(self, action, description, model): self.action = action self.description = description self.model = model
[docs]class RBACAgent: """Handle Galaxy Tool Shed security""" permitted_actions = Bunch()
[docs] def associate_components(self, **kwd): raise Exception(f"No valid method of associating provided components: {kwd}")
[docs] def associate_user_role(self, user, role): raise Exception("No valid method of associating a user with a role")
[docs] def convert_permitted_action_strings(self, permitted_action_strings): """ When getting permitted actions from an untrusted source like a form, ensure that they match our actual permitted actions. """ return [ x for x in [self.permitted_actions.get(action_string) for action_string in permitted_action_strings] if x is not None ]
[docs] def create_user_role(self, user, app): raise Exception("Unimplemented Method")
[docs] def create_private_user_role(self, user): raise Exception("Unimplemented Method")
[docs] def get_action(self, name, default=None): """Get a permitted action by its dict key or action name""" for k, v in self.permitted_actions.items(): if k == name or v.action == name: return v return default
[docs] def get_actions(self): """Get all permitted actions as a list of Action objects""" return list(self.permitted_actions.__dict__.values())
[docs] def get_item_actions(self, action, item): raise Exception(f"No valid method of retrieving action ({action}) for item {item}.")
[docs] def get_private_user_role(self, user): raise Exception("Unimplemented Method")
[docs]class CommunityRBACAgent(RBACAgent):
[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, roles, action, item): """ Method for checking a permission for the current user ( based on roles ) to perform a specific action on an item """ item_actions = self.get_item_actions(action, item) if not item_actions: return action.model == "restrict" ret_val = False for item_action in item_actions: if item_action.role in roles: ret_val = True break return ret_val
[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"]) elif "repository" in kwd: return self.associate_repository_category(kwd["repository"], kwd["category"]) raise Exception(f"No valid method of associating provided components: {kwd}")
[docs] def associate_group_role(self, group, role): assoc = self.model.GroupRoleAssociation(group, role) self.sa_session.add(assoc) self.sa_session.flush() return assoc
[docs] def associate_user_group(self, user, group): assoc = self.model.UserGroupAssociation(user, group) self.sa_session.add(assoc) self.sa_session.flush() return assoc
[docs] def associate_user_role(self, user, role): assoc = self.model.UserRoleAssociation(user, role) self.sa_session.add(assoc) self.sa_session.flush() return assoc
[docs] def associate_repository_category(self, repository, category): assoc = self.model.RepositoryCategoryAssociation(repository, category) self.sa_session.add(assoc) self.sa_session.flush() return assoc
[docs] def create_private_user_role(self, user): # Create private role role = self.model.Role(, description=f"Private Role for {}", type=self.model.Role.types.PRIVATE ) self.sa_session.add(role) self.sa_session.flush() # Add user to role self.associate_components(role=role, user=user) return role
[docs] def create_user_role(self, user, app): self.get_private_user_role(user, auto_create=True)
[docs] def get_item_actions(self, action, item): # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation return [permission for permission in item.actions if permission.action == action.action]
[docs] def get_private_user_role(self, user, auto_create=False): role = ( self.sa_session.query(self.model.Role) .filter( and_( ==, self.model.Role.table.c.type == self.model.Role.types.PRIVATE, ) ) .first() ) if not role: if auto_create: return self.create_private_user_role(user) else: return None return role
[docs] def set_entity_group_associations(self, groups=None, users=None, roles=None, delete_existing_assocs=True): if groups is None: groups = [] if users is None: users = [] if roles is None: roles = [] for group in groups: if delete_existing_assocs: for a in group.roles + group.users: self.sa_session.delete(a) self.sa_session.flush() 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, repositories=None, delete_existing_assocs=True ): if roles is None: roles = [] if users is None: users = [] if groups is None: groups = [] if repositories is None: repositories = [] for role in roles: if delete_existing_assocs: for a in role.users + role.groups: self.sa_session.delete(a) self.sa_session.flush() for user in users: self.associate_components(user=user, role=role) for group in groups: self.associate_components(group=group, role=role)
[docs] def set_entity_user_associations(self, users=None, roles=None, groups=None, delete_existing_assocs=True): if users is None: users = [] if roles is None: roles = [] if groups is None: groups = [] for user in users: if delete_existing_assocs: for a in user.non_private_roles + user.groups: self.sa_session.delete(a) self.sa_session.flush() 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 user.roles: self.associate_components(user=user, role=role) for group in groups: self.associate_components(user=user, group=group)
[docs] def can_push(self, app, user, repository): if user: return user.username in listify(repository.allow_push()) return False
[docs] def user_can_administer_repository(self, user, repository): """Return True if the received user can administer the received repository.""" if user: if repository: repository_admin_role = repository.admin_role for rra in repository.roles: role = rra.role if == # We have the repository's admin role, so see if the user is associated with it. for ura in role.users: role_member = ura.user if == return True # The user is not directly associated with the role, so see if they are a member # of a group that is associated with the role. for gra in role.groups: group = for uga in group.users: member = uga.user if == return True return False
[docs] def user_can_import_repository_archive(self, user, archive_owner): # This method should be called only if the current user is not an admin. if user.username == archive_owner: return True # A member of the IUC is authorized to create new repositories that are owned by another user. iuc_group = ( self.sa_session.query(self.model.Group) .filter( and_( == "Intergalactic Utilities Commission", self.model.Group.table.c.deleted == false(), ) ) .first() ) if iuc_group is not None: for uga in iuc_group.users: if == return True return False
[docs]def get_permitted_actions(filter=None): """Utility method to return a subset of RBACAgent's permitted actions""" if filter is None: return RBACAgent.permitted_actions tmp_bunch = Bunch() [tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith(filter)] return tmp_bunch