Testing

fence/sync/sync_users.py

@@ -659,9 +659,13 @@ def _parse_csv(self, file_dict, sess, dbgap_config={}, encrypted=True):
                         tags["pi"] = row["downloader for names"]
 
                     user_info[username] = {
-                        "email": row.get("email") or user_info[username].get('email') or "",
+                        "email": row.get("email")
+                        or user_info[username].get("email")
+                        or "",
                         "display_name": display_name,
-                        "phone_number": row.get("phone") or user_info[username].get('phone_number') or "",
+                        "phone_number": row.get("phone")
+                        or user_info[username].get("phone_number")
+                        or "",
                         "tags": tags,
                     }
 
@@ -967,10 +971,10 @@ def sync_to_storage_backend(self, user_project, user_info, sess, expires):
             google_group_user_mapping = {}
             get_or_create_proxy_group_id(
                 expires=expires,
-                user_id=user_info['user_id'],
-                username=user_info['username'],
+                user_id=user_info["user_id"],
+                username=user_info["username"],
                 session=sess,
-                storage_manager=self.storage_manager
+                storage_manager=self.storage_manager,
             )
 
         # TODO: eventually it'd be nice to remove this step but it's required
@@ -987,14 +991,11 @@ def sync_to_storage_backend(self, user_project, user_info, sess, expires):
             for project, _ in projects.items():
                 syncing_user_project_list.add((username.lower(), project))
 
-
         to_add = set(syncing_user_project_list)
 
         # when updating users we want to maintain case sensitivity in the username so
         # pass the original, non-lowered user_info dict
-        self._upsert_userinfo(sess, {
-            user_info['username'].lower(): user_info
-        })
+        self._upsert_userinfo(sess, {user_info["username"].lower(): user_info})
 
         self._grant_from_storage(
             to_add,
@@ -1473,6 +1474,7 @@ def _process_user_projects(
         dbgap_config,
         sess,
     ):
+        user_projects_to_modify = copy.deepcopy(user_projects)
         for username in user_projects.keys():
             for project in user_projects[username].keys():
                 phsid = project.split(".")
@@ -1509,7 +1511,7 @@ def _process_user_projects(
                             privileges,
                             username,
                             sess,
-                            user_projects,
+                            user_projects_to_modify,
                             dbgap_config,
                         )
 
@@ -1520,9 +1522,12 @@ def _process_user_projects(
                     privileges,
                     username,
                     sess,
-                    user_projects,
+                    user_projects_to_modify,
                     dbgap_config,
                 )
+        for k, v in user_projects.items():
+            if v != user_projects_to_modify[k]:
+                user_projects[k] = user_projects_to_modify[k]
 
     def sync(self):
         if self.session:
@@ -2485,8 +2490,8 @@ def sync_single_user_visas(self, user, ga4gh_visas, sess=None, expires=None):
             projects = {**projects, **project}
             parsed_visas.append(visa)
 
-        info['user_id'] = user.id
-        info['username'] = user.username
+        info["user_id"] = user.id
+        info["username"] = user.username
         user_projects[user.username] = projects
 
         user_projects = self.parse_projects(user_projects)
@@ -2511,9 +2516,7 @@ def sync_single_user_visas(self, user, ga4gh_visas, sess=None, expires=None):
 
         if user_projects:
             self.logger.info("Sync to storage backend [sync_single_user_visas]")
-            self.sync_to_storage_backend(
-                user_projects, info, sess, expires=expires
-            )
+            self.sync_to_storage_backend(user_projects, info, sess, expires=expires)
         else:
             self.logger.info("No users for syncing")