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diff --git a/tests/storage/test_cleanup_extrems.py b/tests/storage/test_cleanup_extrems.py
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+# -*- coding: utf-8 -*-
+# Copyright 2019 The Matrix.org Foundation C.I.C.
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#     http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an "AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import os.path
+
+from synapse.storage import prepare_database
+from synapse.types import Requester, UserID
+
+from tests.unittest import HomeserverTestCase
+
+
+class CleanupExtremBackgroundUpdateStoreTestCase(HomeserverTestCase):
+    """
+    Test the background update to clean forward extremities table.
+    """
+
+    def prepare(self, reactor, clock, homeserver):
+        self.store = homeserver.get_datastore()
+        self.room_creator = homeserver.get_room_creation_handler()
+
+        # Create a test user and room
+        self.user = UserID("alice", "test")
+        self.requester = Requester(self.user, None, False, None, None)
+        info = self.get_success(self.room_creator.create_room(self.requester, {}))
+        self.room_id = info["room_id"]
+
+    def run_background_update(self):
+        """Re run the background update to clean up the extremities.
+        """
+        # Make sure we don't clash with in progress updates.
+        self.assertTrue(self.store._all_done, "Background updates are still ongoing")
+
+        schema_path = os.path.join(
+            prepare_database.dir_path,
+            "schema",
+            "delta",
+            "54",
+            "delete_forward_extremities.sql",
+        )
+
+        def run_delta_file(txn):
+            prepare_database.executescript(txn, schema_path)
+
+        self.get_success(
+            self.store.runInteraction("test_delete_forward_extremities", run_delta_file)
+        )
+
+        # Ugh, have to reset this flag
+        self.store._all_done = False
+
+        while not self.get_success(self.store.has_completed_background_updates()):
+            self.get_success(self.store.do_next_background_update(100), by=0.1)
+
+    def test_soft_failed_extremities_handled_correctly(self):
+        """Test that extremities are correctly calculated in the presence of
+        soft failed events.
+
+        Tests a graph like:
+
+            A <- SF1 <- SF2 <- B
+
+        Where SF* are soft failed.
+        """
+
+        # Create the room graph
+        event_id_1 = self.create_and_send_event(self.room_id, self.user)
+        event_id_2 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_1]
+        )
+        event_id_3 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_2]
+        )
+        event_id_4 = self.create_and_send_event(
+            self.room_id, self.user, False, [event_id_3]
+        )
+
+        # Check the latest events are as expected
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+
+        self.assertEqual(latest_event_ids, [event_id_4])
+
+    def test_basic_cleanup(self):
+        """Test that extremities are correctly calculated in the presence of
+        soft failed events.
+
+        Tests a graph like:
+
+            A <- SF1 <- B
+
+        Where SF* are soft failed, and with extremities of A and B
+        """
+        # Create the room graph
+        event_id_a = self.create_and_send_event(self.room_id, self.user)
+        event_id_sf1 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_a]
+        )
+        event_id_b = self.create_and_send_event(
+            self.room_id, self.user, False, [event_id_sf1]
+        )
+
+        # Add the new extremity and check the latest events are as expected
+        self.add_extremity(self.room_id, event_id_a)
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(set(latest_event_ids), set((event_id_a, event_id_b)))
+
+        # Run the background update and check it did the right thing
+        self.run_background_update()
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(latest_event_ids, [event_id_b])
+
+    def test_chain_of_fail_cleanup(self):
+        """Test that extremities are correctly calculated in the presence of
+        soft failed events.
+
+        Tests a graph like:
+
+            A <- SF1 <- SF2 <- B
+
+        Where SF* are soft failed, and with extremities of A and B
+        """
+        # Create the room graph
+        event_id_a = self.create_and_send_event(self.room_id, self.user)
+        event_id_sf1 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_a]
+        )
+        event_id_sf2 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_sf1]
+        )
+        event_id_b = self.create_and_send_event(
+            self.room_id, self.user, False, [event_id_sf2]
+        )
+
+        # Add the new extremity and check the latest events are as expected
+        self.add_extremity(self.room_id, event_id_a)
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(set(latest_event_ids), set((event_id_a, event_id_b)))
+
+        # Run the background update and check it did the right thing
+        self.run_background_update()
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(latest_event_ids, [event_id_b])
+
+    def test_forked_graph_cleanup(self):
+        r"""Test that extremities are correctly calculated in the presence of
+        soft failed events.
+
+        Tests a graph like, where time flows down the page:
+
+                A     B
+               / \   /
+              /   \ /
+            SF1   SF2
+             |     |
+            SF3    |
+           /   \   |
+           |    \  |
+           C     SF4
+
+        Where SF* are soft failed, and with them A, B and C marked as
+        extremities. This should resolve to B and C being marked as extremity.
+        """
+
+        # Create the room graph
+        event_id_a = self.create_and_send_event(self.room_id, self.user)
+        event_id_b = self.create_and_send_event(self.room_id, self.user)
+        event_id_sf1 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_a]
+        )
+        event_id_sf2 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_a, event_id_b]
+        )
+        event_id_sf3 = self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_sf1]
+        )
+        self.create_and_send_event(
+            self.room_id, self.user, True, [event_id_sf2, event_id_sf3]
+        )  # SF4
+        event_id_c = self.create_and_send_event(
+            self.room_id, self.user, False, [event_id_sf3]
+        )
+
+        # Add the new extremity and check the latest events are as expected
+        self.add_extremity(self.room_id, event_id_a)
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(
+            set(latest_event_ids), set((event_id_a, event_id_b, event_id_c))
+        )
+
+        # Run the background update and check it did the right thing
+        self.run_background_update()
+
+        latest_event_ids = self.get_success(
+            self.store.get_latest_event_ids_in_room(self.room_id)
+        )
+        self.assertEqual(set(latest_event_ids), set([event_id_b, event_id_c]))