Merge pull request #743 from dbmi-bgm/drr_purge_fix

Purge permissions fix

CHANGELOG.rst

@@ -6,6 +6,14 @@ cgap-portal
 Change Log
 ----------
 
+14.1.1
+======
+`PR 743: Purge permissions fix <https://github.com/dbmi-bgm/cgap-portal/pull/743>`_
+
+* Update set_user_info_property to true to allow admins to purge items
+* Bring in updated snovault to fix impersonation bug
+
+
 14.1.0
 ======
 `PR 739: Bm babel updates <https://github.com/dbmi-bgm/cgap-portal/pull/739>`_

pyproject.toml

@@ -1,7 +1,7 @@
 [tool.poetry]
 # Note: Various modules refer to this system as "encoded", not "cgap-portal".
 name = "encoded"
-version = "14.1.0"
+version = "14.1.1"
 description = "Computational Genome Analysis Platform"
 authors = ["4DN-DCIC Team <[email protected]>"]
 license = "MIT"
@@ -49,7 +49,7 @@ codeguru-profiler-agent = "^1.2.4"
 cryptography = "39.0.2"
 colorama = "0.3.3"
 dcicpyvcf = "1.0.0.1b0"  # "^1.0.0"
-dcicsnovault = "9.0.0"
+dcicsnovault = "9.1.1"
 #dcicutils = "^7.4.0"
 #dcicutils = "7.4.4.5b21"
 dcicutils = "^7.5.0"

src/encoded/commands/owltools.py

@@ -76,7 +76,7 @@ def get_last_bit(uri_string):
 
 def isBlankNode(aClass):
     ''' Checks for an RDF blank node '''
-    if type(aClass) == BNode:
+    if type(aClass) is BNode:
         return True
     else:
         return False

src/encoded/project/authentication.py

@@ -8,7 +8,7 @@ def login(self, context, request, *, samesite):
         return super().login(context, request, samesite=samesite)
 
     def namespaced_authentication_policy_authenticated_userid(self, namespaced_authentication_policy, request, set_user_info_property):
-        set_user_info_property = False
+        set_user_info_property = True
         return super().namespaced_authentication_policy_authenticated_userid(namespaced_authentication_policy, request, set_user_info_property)
 
     def note_auth0_authentication_policy_unauthenticated_userid(self, auth0_authentication_policy, request, email, id_token):

src/encoded/search/search.py

@@ -1017,7 +1017,7 @@ def build_table_columns(self):
             type_infos = [self.request.registry[TYPES][t] for t in self.doc_types if t != 'Item']
             for ti in type_infos:
                 # We use `type` instead of `isinstance` since we don't want to catch subclasses.
-                if type(ti) == AbstractTypeInfo:
+                if type(ti) is AbstractTypeInfo:
                     any_abstract_types = True
                     break
 

src/encoded/tests/test_permissions.py

@@ -1,10 +1,10 @@
+from typing import Any, Dict
+
 import pytest
-# import webtest
+from webtest.app import TestApp
 
-# from datetime import date
-# from urllib.parse import urlencode
-# from ..types.institution import Institution
 from .datafixtures import remote_user_testapp
+from .utils import get_identifier_path
 
 
 pytestmark = [pytest.mark.setone, pytest.mark.working, pytest.mark.schema]
@@ -461,3 +461,9 @@ def test_public_item_wo_project_can_be_posted_by_project_member(bgm_user_testapp
     # need to have a uniquename
     to_post['name'] = 'another section name'
     bgm_user_testapp.post_json('/static_section', to_post, status=201)
+
+
+def test_admin_can_purge(testapp: TestApp, file: Dict[str, Any]) -> None:
+    file_path = get_identifier_path(file.get("uuid"))
+    testapp.patch_json(file_path, {"status": "deleted"}, status=200)
+    testapp.delete_json(f"{file_path}/?purge=True", {}, status=200)