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Fixes for LDDA manager - clearly that didn't work at all.

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This commit is contained in:
John Chilton
2021-10-25 20:24:01 -04:00
parent 00c30ca493
commit d8fc9b3ab4
2 changed files with 5 additions and 56 deletions
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lib/galaxy/managers/lddas.py
+5 -54
View File
@@ -1,6 +1,6 @@
import logging
from galaxy import model, util
from galaxy import model
from galaxy.managers import base as manager_base
from galaxy.managers.datasets import DatasetAssociationManager
from galaxy.structured_app import MinimalManagerApp
@@ -18,6 +18,7 @@ class LDDAManager(DatasetAssociationManager):
"""
Set up and initialize other managers needed by lddas.
"""
super().__init__(app)
def get(self, trans, id, check_accessible=True):
return manager_base.get_object(trans, id,
@@ -26,56 +27,6 @@ class LDDAManager(DatasetAssociationManager):
check_accessible=check_accessible)
def _set_permissions(self, trans, library_dataset, role_ids_dict):
dataset = library_dataset.library_dataset_dataset_association.dataset
new_access_roles_ids = role_ids_dict["DATASET_ACCESS"]
new_manage_roles_ids = role_ids_dict["DATASET_MANAGE_PERMISSIONS"]
new_modify_roles_ids = role_ids_dict["LIBRARY_MODIFY"]
# ACCESS DATASET ROLES
valid_access_roles = []
invalid_access_roles_ids = []
valid_roles_for_dataset, total_roles = trans.app.security_agent.get_valid_roles(trans, dataset)
if new_access_roles_ids is None:
trans.app.security_agent.make_dataset_public(dataset)
else:
for role_id in new_access_roles_ids:
role = self.role_manager.get(trans, self.app, role_id)
if role in valid_roles_for_dataset:
valid_access_roles.append(role)
else:
invalid_access_roles_ids.append(role_id)
if len(invalid_access_roles_ids) > 0:
log.warning(f"The following roles could not be added to the dataset access permission: {str(invalid_access_roles_ids)}")
access_permission = dict(access=valid_access_roles)
trans.app.security_agent.set_dataset_permission(dataset, access_permission)
# MANAGE DATASET ROLES
valid_manage_roles = []
invalid_manage_roles_ids = []
new_manage_roles_ids = util.listify(new_manage_roles_ids)
for role_id in new_manage_roles_ids:
role = self.role_manager.get(trans, self.app, role_id)
if role in valid_roles_for_dataset:
valid_manage_roles.append(role)
else:
invalid_manage_roles_ids.append(role_id)
if len(invalid_manage_roles_ids) > 0:
log.warning(f"The following roles could not be added to the dataset manage permission: {str(invalid_manage_roles_ids)}")
manage_permission = {trans.app.security_agent.permitted_actions.DATASET_MANAGE_PERMISSIONS: valid_manage_roles}
trans.app.security_agent.set_dataset_permission(dataset, manage_permission)
# MODIFY LIBRARY ITEM ROLES
valid_modify_roles = []
invalid_modify_roles_ids = []
new_modify_roles_ids = util.listify(new_modify_roles_ids)
for role_id in new_modify_roles_ids:
role = self.role_manager.get(trans, self.app, role_id)
if role in valid_roles_for_dataset:
valid_modify_roles.append(role)
else:
invalid_modify_roles_ids.append(role_id)
if len(invalid_modify_roles_ids) > 0:
log.warning(f"The following roles could not be added to the dataset modify permission: {str(invalid_modify_roles_ids)}")
modify_permission = {trans.app.security_agent.permitted_actions.LIBRARY_MODIFY: valid_modify_roles}
trans.app.security_agent.set_library_item_permission(library_dataset, modify_permission)
# Check Git history for an older broken implementation, but it was broken
# and security related and had not test coverage so it was deleted.
raise NotImplementedError()
setup.cfg
-2
View File
@@ -589,8 +589,6 @@ check_untyped_defs = False
check_untyped_defs = False
[mypy-galaxy.metadata.set_metadata]
check_untyped_defs = False
[mypy-galaxy.managers.lddas]
check_untyped_defs = False
[mypy-galaxy.tools.error_reports]
check_untyped_defs = False
[mypy-galaxy.jobs.dynamic_tool_destination]