Perhaps the missing self in paginate_endpoint is causing:

2022-02-04 03:50:11,016,16ms [PID: 1542143] workers.pull_request_worker.50471 [DEBUG] Pull Requests model. ERROR: organize_needed_data() takes from 3 to 4 positional arguments but 5 were given
Traceback (most recent call last):
  File "/bigdisk/augur-vmware/workers/pull_request_worker/pull_request_worker.py", line 723, in pull_requests_model
    pk_source_prs = self._get_pk_source_prs()
  File "/bigdisk/augur-vmware/workers/pull_request_worker/pull_request_worker.py", line 676, in _get_pk_source_prs
    source_prs = self.paginate_endpoint(
  File "/bigdisk/augur-vmware/workers/worker_git_integration.py", line 1274, in paginate_endpoint
    need_insertion, need_update = self.organize_needed_data(
TypeError: organize_needed_data() takes from 3 to 4 positional arguments but 5 were given
2022-02-04 03:50:11,046,46ms [PID: 1542143] workers.pull_request_worker.50471 [INFO] Worker completed this task in -64.56478452682495 seconds.

I'm running out of logical guesses about what broke here.

workers/pull_request_worker/pull_request_worker.py

@@ -674,7 +674,7 @@ def bulk_insert(
         # )
 
         source_prs = self.paginate_endpoint(
-            pr_url, action_map=pr_action_map, table=self.pull_requests_table,
+            self, pr_url, action_map=pr_action_map, table=self.pull_requests_table,
             where_clause=self.pull_requests_table.c.repo_id == self.repo_id,
             stagger=True,
             insertion_method=pk_source_increment_insert