Merge remote-tracking branch 'origin/develop' into matrix-org-hotfixes

CHANGES.md

@@ -1,3 +1,10 @@
+# Synapse 1.104.0 (2024-04-02)
+
+### Bugfixes
+
+- Fix regression when using OIDC provider. Introduced in v1.104.0rc1. ([\#17031](https://github.com/element-hq/synapse/issues/17031))
+
+
 # Synapse 1.104.0rc1 (2024-03-26)
 
 ### Features

changelog.d/16930.bugfix

@@ -0,0 +1 @@
+Fix various long-standing bugs which could cause incorrect state to be returned from `/sync` in certain situations.

changelog.d/16932.bugfix

@@ -0,0 +1 @@
+Fix various long-standing bugs which could cause incorrect state to be returned from `/sync` in certain situations.

changelog.d/16942.bugfix

@@ -0,0 +1 @@
+Fix various long-standing bugs which could cause incorrect state to be returned from `/sync` in certain situations.

changelog.d/17031.feature

@@ -1 +0,0 @@
-OIDC: try to JWT decode userinfo response if JSON parsing failed.

changelog.d/17044.misc

@@ -0,0 +1 @@
+Refactor auth chain fetching to reduce duplication.

changelog.d/17045.misc

@@ -0,0 +1 @@
+Improve database performance by adding a missing index to `access_tokens.refresh_token_id`.

changelog.d/17049.misc

@@ -0,0 +1 @@
+Improve database performance by reducing number of receipts fetched when sending push notifications.

debian/changelog

@@ -1,3 +1,9 @@
+matrix-synapse-py3 (1.104.0) stable; urgency=medium
+
+  * New Synapse release 1.104.0.
+
+ -- Synapse Packaging team <packages@matrix.org>  Tue, 02 Apr 2024 17:15:45 +0100
+
 matrix-synapse-py3 (1.104.0~rc1) stable; urgency=medium
 
   * New Synapse release 1.104.0rc1.

pyproject.toml

@@ -96,7 +96,7 @@ module-name = "synapse.synapse_rust"
 
 [tool.poetry]
 name = "matrix-synapse"
-version = "1.104.0rc1"
+version = "1.104.0"
 description = "Homeserver for the Matrix decentralised comms protocol"
 authors = ["Matrix.org Team and Contributors <packages@matrix.org>"]
 license = "AGPL-3.0-or-later"

synapse/handlers/sync.py

@@ -953,7 +953,7 @@ class SyncHandler:
         batch: TimelineBatch,
         sync_config: SyncConfig,
         since_token: Optional[StreamToken],
-        now_token: StreamToken,
+        end_token: StreamToken,
         full_state: bool,
     ) -> MutableStateMap[EventBase]:
         """Works out the difference in state between the end of the previous sync and
@@ -964,7 +964,9 @@ class SyncHandler:
             batch: The timeline batch for the room that will be sent to the user.
             sync_config:
             since_token: Token of the end of the previous batch. May be `None`.
-            now_token: Token of the end of the current batch.
+            end_token: Token of the end of the current batch. Normally this will be
+                the same as the global "now_token", but if the user has left the room,
+                the point just after their leave event.
             full_state: Whether to force returning the full state.
                 `lazy_load_members` still applies when `full_state` is `True`.
 
@@ -1044,7 +1046,7 @@ class SyncHandler:
                     room_id,
                     sync_config.user,
                     batch,
-                    now_token,
+                    end_token,
                     members_to_fetch,
                     timeline_state,
                 )
@@ -1058,7 +1060,7 @@ class SyncHandler:
                     room_id,
                     batch,
                     since_token,
-                    now_token,
+                    end_token,
                     members_to_fetch,
                     timeline_state,
                 )
@@ -1130,7 +1132,7 @@ class SyncHandler:
         room_id: str,
         syncing_user: UserID,
         batch: TimelineBatch,
-        now_token: StreamToken,
+        end_token: StreamToken,
         members_to_fetch: Optional[Set[str]],
         timeline_state: StateMap[str],
     ) -> StateMap[str]:
@@ -1143,7 +1145,9 @@ class SyncHandler:
             room_id: The room we are calculating for.
             syncing_user: The user that is calling `/sync`.
             batch: The timeline batch for the room that will be sent to the user.
-            now_token: Token of the end of the current batch.
+            end_token: Token of the end of the current batch. Normally this will be
+                the same as the global "now_token", but if the user has left the room,
+                the point just after their leave event.
             members_to_fetch: If lazy-loading is enabled, the memberships needed for
                 events in the timeline.
             timeline_state: The contribution to the room state from state events in
@@ -1183,15 +1187,16 @@ class SyncHandler:
             await_full_state = True
             lazy_load_members = False
 
-        if batch:
+        state_at_timeline_end = await self.get_state_at(
-            state_at_timeline_end = (
+            room_id,
-                await self._state_storage_controller.get_state_ids_for_event(
+            stream_position=end_token,
-                    batch.events[-1].event_id,
+            state_filter=state_filter,
-                    state_filter=state_filter,
+            await_full_state=await_full_state,
-                    await_full_state=await_full_state,
+        )
-                )
-            )
 
+        if batch:
+            # Strictly speaking, this returns the state *after* the first event in the
+            # timeline, but that is good enough here.
             state_at_timeline_start = (
                 await self._state_storage_controller.get_state_ids_for_event(
                     batch.events[0].event_id,
@@ -1200,13 +1205,6 @@ class SyncHandler:
                 )
             )
         else:
-            state_at_timeline_end = await self.get_state_at(
-                room_id,
-                stream_position=now_token,
-                state_filter=state_filter,
-                await_full_state=await_full_state,
-            )
-
             state_at_timeline_start = state_at_timeline_end
 
         state_ids = _calculate_state(
@@ -1223,7 +1221,7 @@ class SyncHandler:
         room_id: str,
         batch: TimelineBatch,
         since_token: StreamToken,
-        now_token: StreamToken,
+        end_token: StreamToken,
         members_to_fetch: Optional[Set[str]],
         timeline_state: StateMap[str],
     ) -> StateMap[str]:
@@ -1239,7 +1237,9 @@ class SyncHandler:
             room_id: The room we are calculating for.
             batch: The timeline batch for the room that will be sent to the user.
             since_token: Token of the end of the previous batch.
-            now_token: Token of the end of the current batch.
+            end_token: Token of the end of the current batch. Normally this will be
+                the same as the global "now_token", but if the user has left the room,
+                the point just after their leave event.
             members_to_fetch: If lazy-loading is enabled, the memberships needed for
                 events in the timeline. Otherwise, `None`.
             timeline_state: The contribution to the room state from state events in
@@ -1259,25 +1259,25 @@ class SyncHandler:
             await_full_state = True
             lazy_load_members = False
 
-        if batch.limited:
+        if batch:
-            if batch:
+            state_at_timeline_start = (
-                state_at_timeline_start = (
+                await self._state_storage_controller.get_state_ids_for_event(
-                    await self._state_storage_controller.get_state_ids_for_event(
+                    batch.events[0].event_id,
-                        batch.events[0].event_id,
-                        state_filter=state_filter,
-                        await_full_state=await_full_state,
-                    )
-                )
-            else:
-                # We can get here if the user has ignored the senders of all
-                # the recent events.
-                state_at_timeline_start = await self.get_state_at(
-                    room_id,
-                    stream_position=now_token,
                     state_filter=state_filter,
                     await_full_state=await_full_state,
                 )
+            )
+        else:
+            # We can get here if the user has ignored the senders of all
+            # the recent events.
+            state_at_timeline_start = await self.get_state_at(
+                room_id,
+                stream_position=end_token,
+                state_filter=state_filter,
+                await_full_state=await_full_state,
+            )
 
+        if batch.limited:
             # for now, we disable LL for gappy syncs - see
             # https://github.com/vector-im/riot-web/issues/7211#issuecomment-419976346
             # N.B. this slows down incr syncs as we are now processing way
@@ -1292,58 +1292,28 @@ class SyncHandler:
             # about them).
             state_filter = StateFilter.all()
 
-            state_at_previous_sync = await self.get_state_at(
+        state_at_previous_sync = await self.get_state_at(
-                room_id,
+            room_id,
-                stream_position=since_token,
+            stream_position=since_token,
-                state_filter=state_filter,
+            state_filter=state_filter,
-                await_full_state=await_full_state,
+            await_full_state=await_full_state,
-            )
+        )
 
-            if batch:
+        state_at_timeline_end = await self.get_state_at(
-                state_at_timeline_end = (
+            room_id,
-                    await self._state_storage_controller.get_state_ids_for_event(
+            stream_position=end_token,
-                        batch.events[-1].event_id,
+            state_filter=state_filter,
-                        state_filter=state_filter,
+            await_full_state=await_full_state,
-                        await_full_state=await_full_state,
+        )
-                    )
-                )
-            else:
-                # We can get here if the user has ignored the senders of all
-                # the recent events.
-                state_at_timeline_end = await self.get_state_at(
-                    room_id,
-                    stream_position=now_token,
-                    state_filter=state_filter,
-                    await_full_state=await_full_state,
-                )
 
-            state_ids = _calculate_state(
+        state_ids = _calculate_state(
-                timeline_contains=timeline_state,
+            timeline_contains=timeline_state,
-                timeline_start=state_at_timeline_start,
+            timeline_start=state_at_timeline_start,
-                timeline_end=state_at_timeline_end,
+            timeline_end=state_at_timeline_end,
-                previous_timeline_end=state_at_previous_sync,
+            previous_timeline_end=state_at_previous_sync,
-                lazy_load_members=lazy_load_members,
+            lazy_load_members=lazy_load_members,
-            )
+        )
-        else:
-            state_ids = {}
-            if lazy_load_members:
-                if members_to_fetch and batch.events:
-                    # We're returning an incremental sync, with no
-                    # "gap" since the previous sync, so normally there would be
-                    # no state to return.
-                    # But we're lazy-loading, so the client might need some more
-                    # member events to understand the events in this timeline.
-                    # So we fish out all the member events corresponding to the
-                    # timeline here. The caller will then dedupe any redundant ones.
 
-                    state_ids = await self._state_storage_controller.get_state_ids_for_event(
-                        batch.events[0].event_id,
-                        # we only want members!
-                        state_filter=StateFilter.from_types(
-                            (EventTypes.Member, member) for member in members_to_fetch
-                        ),
-                        await_full_state=False,
-                    )
         return state_ids
 
     async def _find_missing_partial_state_memberships(
@@ -2344,6 +2314,7 @@ class SyncHandler:
                         full_state=False,
                         since_token=since_token,
                         upto_token=leave_token,
+                        end_token=leave_token,
                         out_of_band=leave_event.internal_metadata.is_out_of_band_membership(),
                     )
                 )
@@ -2381,6 +2352,7 @@ class SyncHandler:
                     full_state=False,
                     since_token=None if newly_joined else since_token,
                     upto_token=prev_batch_token,
+                    end_token=now_token,
                 )
             else:
                 entry = RoomSyncResultBuilder(
@@ -2391,6 +2363,7 @@ class SyncHandler:
                     full_state=False,
                     since_token=since_token,
                     upto_token=since_token,
+                    end_token=now_token,
                 )
 
             room_entries.append(entry)
@@ -2449,6 +2422,7 @@ class SyncHandler:
                         full_state=True,
                         since_token=since_token,
                         upto_token=now_token,
+                        end_token=now_token,
                     )
                 )
             elif event.membership == Membership.INVITE:
@@ -2478,6 +2452,7 @@ class SyncHandler:
                         full_state=True,
                         since_token=since_token,
                         upto_token=leave_token,
+                        end_token=leave_token,
                     )
                 )
 
@@ -2548,6 +2523,7 @@ class SyncHandler:
                 {
                     "since_token": since_token,
                     "upto_token": upto_token,
+                    "end_token": room_builder.end_token,
                 }
             )
 
@@ -2621,7 +2597,7 @@ class SyncHandler:
                     batch,
                     sync_config,
                     since_token,
-                    now_token,
+                    room_builder.end_token,
                     full_state=full_state,
                 )
             else:
@@ -2781,6 +2757,61 @@ def _calculate_state(
             e for t, e in timeline_start.items() if t[0] == EventTypes.Member
         )
 
+    # Naively, we would just return the difference between the state at the start
+    # of the timeline (`timeline_start_ids`) and that at the end of the previous sync
+    # (`previous_timeline_end_ids`). However, that fails in the presence of forks in
+    # the DAG.
+    #
+    # For example, consider a DAG such as the following:
+    #
+    #       E1
+    #     ↗    ↖
+    #    |      S2
+    #    |      ↑
+    #  --|------|----
+    #    |      |
+    #    E3     |
+    #     ↖    /
+    #       E4
+    #
+    # ... and a filter that means we only return 2 events, represented by the dashed
+    # horizontal line. Assuming S2 was *not* included in the previous sync, we need to
+    # include it in the `state` section.
+    #
+    # Note that the state at the start of the timeline (E3) does not include S2. So,
+    # to make sure it gets included in the calculation here, we actually look at
+    # the state at the *end* of the timeline, and subtract any events that are present
+    # in the timeline.
+    #
+    # ----------
+    #
+    # Aside 1: You may then wonder if we need to include `timeline_start` in the
+    # calculation. Consider a linear DAG:
+    #
+    #      E1
+    #      ↑
+    #      S2
+    #      ↑
+    #  ----|------
+    #      |
+    #      E3
+    #      ↑
+    #      S4
+    #      ↑
+    #      E5
+    #
+    # ... where S2 and S4 change the same piece of state; and where we have a filter
+    # that returns 3 events (E3, S4, E5). We still need to tell the client about S2,
+    # because it might affect the display of E3. However, the state at the end of the
+    # timeline only tells us about S4; if we don't inspect `timeline_start` we won't
+    # find out about S2.
+    #
+    # (There are yet more complicated cases in which a state event is excluded from the
+    # timeline, but whose effect actually lands in the DAG in the *middle* of the
+    # timeline. We have no way to represent that in the /sync response, and we don't
+    # even try; it is ether omitted or plonked into `state` as if it were at the start
+    # of the timeline, depending on what else is in the timeline.)
+
     state_ids = (
         (timeline_end_ids | timeline_start_ids)
         - previous_timeline_end_ids
@@ -2883,13 +2914,30 @@ class RoomSyncResultBuilder:
 
     Attributes:
         room_id
+
         rtype: One of `"joined"` or `"archived"`
+
         events: List of events to include in the room (more events may be added
             when generating result).
+
         newly_joined: If the user has newly joined the room
+
         full_state: Whether the full state should be sent in result
+
         since_token: Earliest point to return events from, or None
-        upto_token: Latest point to return events from.
+
+        upto_token: Latest point to return events from. If `events` is populated,
+           this is set to the token at the start of `events`
+
+        end_token: The last point in the timeline that the client should see events
+           from. Normally this will be the same as the global `now_token`, but in
+           the case of rooms where the user has left the room, this will be the point
+           just after their leave event.
+
+           This is used in the calculation of the state which is returned in `state`:
+           any state changes *up to* `end_token` (and not beyond!) which are not
+           reflected in the timeline need to be returned in `state`.
+
         out_of_band: whether the events in the room are "out of band" events
             and the server isn't in the room.
     """
@@ -2901,5 +2949,5 @@ class RoomSyncResultBuilder:
     full_state: bool
     since_token: Optional[StreamToken]
     upto_token: StreamToken
-
+    end_token: StreamToken
     out_of_band: bool = False

synapse/storage/databases/main/event_federation.py

@@ -27,6 +27,7 @@ from typing import (
     Collection,
     Dict,
     FrozenSet,
+    Generator,
     Iterable,
     List,
     Optional,
@@ -279,64 +280,16 @@ class EventFederationWorkerStore(SignatureWorkerStore, EventsWorkerStore, SQLBas
 
         # Now we look up all links for the chains we have, adding chains that
         # are reachable from any event.
-        #
-        # This query is structured to first get all chain IDs reachable, and
-        # then pull out all links from those chains. This does pull out more
-        # rows than is strictly necessary, however there isn't a way of
-        # structuring the recursive part of query to pull out the links without
-        # also returning large quantities of redundant data (which can make it a
-        # lot slower).
-        sql = """
-            WITH RECURSIVE links(chain_id) AS (
-                SELECT
-                    DISTINCT origin_chain_id
-                FROM event_auth_chain_links WHERE %s
-                UNION
-                SELECT
-                    target_chain_id
-                FROM event_auth_chain_links
-                INNER JOIN links ON (chain_id = origin_chain_id)
-            )
-            SELECT
-                origin_chain_id, origin_sequence_number,
-                target_chain_id, target_sequence_number
-            FROM links
-            INNER JOIN event_auth_chain_links ON (chain_id = origin_chain_id)
-        """
 
         # A map from chain ID to max sequence number *reachable* from any event ID.
         chains: Dict[int, int] = {}
-
+        for links in self._get_chain_links(txn, set(event_chains.keys())):
-        # Add all linked chains reachable from initial set of chains.
-        chains_to_fetch = set(event_chains.keys())
-        while chains_to_fetch:
-            batch2 = tuple(itertools.islice(chains_to_fetch, 1000))
-            chains_to_fetch.difference_update(batch2)
-            clause, args = make_in_list_sql_clause(
-                txn.database_engine, "origin_chain_id", batch2
-            )
-            txn.execute(sql % (clause,), args)
-
-            links: Dict[int, List[Tuple[int, int, int]]] = {}
-
-            for (
-                origin_chain_id,
-                origin_sequence_number,
-                target_chain_id,
-                target_sequence_number,
-            ) in txn:
-                links.setdefault(origin_chain_id, []).append(
-                    (origin_sequence_number, target_chain_id, target_sequence_number)
-                )
-
             for chain_id in links:
                 if chain_id not in event_chains:
                     continue
 
                 _materialize(chain_id, event_chains[chain_id], links, chains)
 
-            chains_to_fetch.difference_update(chains)
-
         # Add the initial set of chains, excluding the sequence corresponding to
         # initial event.
         for chain_id, seq_no in event_chains.items():
@@ -380,6 +333,68 @@ class EventFederationWorkerStore(SignatureWorkerStore, EventsWorkerStore, SQLBas
 
         return results
 
+    @classmethod
+    def _get_chain_links(
+        cls, txn: LoggingTransaction, chains_to_fetch: Set[int]
+    ) -> Generator[Dict[int, List[Tuple[int, int, int]]], None, None]:
+        """Fetch all auth chain links from the given set of chains, and all
+        links from those chains, recursively.
+
+        Note: This may return links that are not reachable from the given
+        chains.
+
+        Returns a generator that produces dicts from origin chain ID to 3-tuple
+        of origin sequence number, target chain ID and target sequence number.
+        """
+
+        # This query is structured to first get all chain IDs reachable, and
+        # then pull out all links from those chains. This does pull out more
+        # rows than is strictly necessary, however there isn't a way of
+        # structuring the recursive part of query to pull out the links without
+        # also returning large quantities of redundant data (which can make it a
+        # lot slower).
+        sql = """
+            WITH RECURSIVE links(chain_id) AS (
+                SELECT
+                    DISTINCT origin_chain_id
+                FROM event_auth_chain_links WHERE %s
+                UNION
+                SELECT
+                    target_chain_id
+                FROM event_auth_chain_links
+                INNER JOIN links ON (chain_id = origin_chain_id)
+            )
+            SELECT
+                origin_chain_id, origin_sequence_number,
+                target_chain_id, target_sequence_number
+            FROM links
+            INNER JOIN event_auth_chain_links ON (chain_id = origin_chain_id)
+        """
+
+        while chains_to_fetch:
+            batch2 = tuple(itertools.islice(chains_to_fetch, 1000))
+            chains_to_fetch.difference_update(batch2)
+            clause, args = make_in_list_sql_clause(
+                txn.database_engine, "origin_chain_id", batch2
+            )
+            txn.execute(sql % (clause,), args)
+
+            links: Dict[int, List[Tuple[int, int, int]]] = {}
+
+            for (
+                origin_chain_id,
+                origin_sequence_number,
+                target_chain_id,
+                target_sequence_number,
+            ) in txn:
+                links.setdefault(origin_chain_id, []).append(
+                    (origin_sequence_number, target_chain_id, target_sequence_number)
+                )
+
+            chains_to_fetch.difference_update(links)
+
+            yield links
+
     def _get_auth_chain_ids_txn(
         self, txn: LoggingTransaction, event_ids: Collection[str], include_given: bool
     ) -> Set[str]:
@@ -564,53 +579,9 @@ class EventFederationWorkerStore(SignatureWorkerStore, EventsWorkerStore, SQLBas
 
         # Now we look up all links for the chains we have, adding chains that
         # are reachable from any event.
-        #
-        # This query is structured to first get all chain IDs reachable, and
-        # then pull out all links from those chains. This does pull out more
-        # rows than is strictly necessary, however there isn't a way of
-        # structuring the recursive part of query to pull out the links without
-        # also returning large quantities of redundant data (which can make it a
-        # lot slower).
-        sql = """
-            WITH RECURSIVE links(chain_id) AS (
-                SELECT
-                    DISTINCT origin_chain_id
-                FROM event_auth_chain_links WHERE %s
-                UNION
-                SELECT
-                    target_chain_id
-                FROM event_auth_chain_links
-                INNER JOIN links ON (chain_id = origin_chain_id)
-            )
-            SELECT
-                origin_chain_id, origin_sequence_number,
-                target_chain_id, target_sequence_number
-            FROM links
-            INNER JOIN event_auth_chain_links ON (chain_id = origin_chain_id)
-        """
-
-        # (We need to take a copy of `seen_chains` as we want to mutate it in
-        # the loop)
-        chains_to_fetch = set(seen_chains)
-        while chains_to_fetch:
-            batch2 = tuple(itertools.islice(chains_to_fetch, 1000))
-            clause, args = make_in_list_sql_clause(
-                txn.database_engine, "origin_chain_id", batch2
-            )
-            txn.execute(sql % (clause,), args)
-
-            links: Dict[int, List[Tuple[int, int, int]]] = {}
-
-            for (
-                origin_chain_id,
-                origin_sequence_number,
-                target_chain_id,
-                target_sequence_number,
-            ) in txn:
-                links.setdefault(origin_chain_id, []).append(
-                    (origin_sequence_number, target_chain_id, target_sequence_number)
-                )
 
+        # (We need to take a copy of `seen_chains` as the function mutates it)
+        for links in self._get_chain_links(txn, set(seen_chains)):
             for chains in set_to_chain:
                 for chain_id in links:
                     if chain_id not in chains:
@@ -618,7 +589,6 @@ class EventFederationWorkerStore(SignatureWorkerStore, EventsWorkerStore, SQLBas
 
                     _materialize(chain_id, chains[chain_id], links, chains)
 
-                chains_to_fetch.difference_update(chains)
                 seen_chains.update(chains)
 
         # Now for each chain we figure out the maximum sequence number reachable

synapse/storage/databases/main/event_push_actions.py

@@ -106,7 +106,7 @@ from synapse.storage.database import (
 )
 from synapse.storage.databases.main.receipts import ReceiptsWorkerStore
 from synapse.storage.databases.main.stream import StreamWorkerStore
-from synapse.types import JsonDict
+from synapse.types import JsonDict, StrCollection
 from synapse.util import json_encoder
 from synapse.util.caches.descriptors import cached
 
@@ -859,37 +859,86 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
 
         return await self.db_pool.runInteraction("get_push_action_users_in_range", f)
 
-    def _get_receipts_by_room_txn(
+    def _get_receipts_for_room_and_threads_txn(
-        self, txn: LoggingTransaction, user_id: str
+        self,
+        txn: LoggingTransaction,
+        user_id: str,
+        room_ids: StrCollection,
+        thread_ids: StrCollection,
     ) -> Dict[str, _RoomReceipt]:
         """
-        Generate a map of room ID to the latest stream ordering that has been
+        Get (private) read receipts for a user in each of the given room IDs
-        read by the given user.
+        and thread IDs.
 
-        Args:
+        Note: The corresponding room ID for each thread must appear in
-            txn:
+        `room_ids` arg.
-            user_id: The user to fetch receipts for.
 
         Returns:
             A map including all rooms the user is in with a receipt. It maps
             room IDs to _RoomReceipt instances
         """
-        receipt_types_clause, args = make_in_list_sql_clause(
+
+        receipt_types_clause, receipts_args = make_in_list_sql_clause(
             self.database_engine,
             "receipt_type",
             (ReceiptTypes.READ, ReceiptTypes.READ_PRIVATE),
         )
 
+        thread_ids_clause, thread_ids_args = make_in_list_sql_clause(
+            self.database_engine,
+            "thread_id",
+            thread_ids,
+        )
+
+        room_ids_clause, room_ids_args = make_in_list_sql_clause(
+            self.database_engine,
+            "room_id",
+            room_ids,
+        )
+
+        # We use the union of two (almost identical) queries here, the first to
+        # fetch the specific thread receipts and the second to fetch the
+        # unthreaded receipts.
+        #
+        # This SQL is optimized to use the indices we have on
+        # `receipts_linearized`.
+        #
+        # We compare room ID and thread IDs independently due to the above,
+        # which means that this query might return more rows than we need if the
+        # same thread ID appears across different rooms (e.g. 'main' thread ID).
+        # This doesn't cause any logic issues, and isn't a performance concern
+        # given this function generally gets called with only one room and
+        # thread ID.
         sql = f"""
             SELECT room_id, thread_id, MAX(stream_ordering)
             FROM receipts_linearized
             INNER JOIN events USING (room_id, event_id)
             WHERE {receipt_types_clause}
+                AND {thread_ids_clause}
+                AND {room_ids_clause}
+            AND user_id = ?
+            GROUP BY room_id, thread_id
+
+        UNION ALL
+
+            SELECT room_id, thread_id, MAX(stream_ordering)
+            FROM receipts_linearized
+            INNER JOIN events USING (room_id, event_id)
+            WHERE {receipt_types_clause}
+                AND {room_ids_clause}
+                AND thread_id IS NULL
             AND user_id = ?
             GROUP BY room_id, thread_id
         """
 
-        args.extend((user_id,))
+        args = list(receipts_args)
+        args.extend(thread_ids_args)
+        args.extend(room_ids_args)
+        args.append(user_id)
+        args.extend(receipts_args)
+        args.extend(room_ids_args)
+        args.append(user_id)
+
         txn.execute(sql, args)
 
         result: Dict[str, _RoomReceipt] = {}
@@ -925,12 +974,6 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             The list will have between 0~limit entries.
         """
 
-        receipts_by_room = await self.db_pool.runInteraction(
-            "get_unread_push_actions_for_user_in_range_http_receipts",
-            self._get_receipts_by_room_txn,
-            user_id=user_id,
-        )
-
         def get_push_actions_txn(
             txn: LoggingTransaction,
         ) -> List[Tuple[str, str, str, int, str, bool]]:
@@ -952,6 +995,27 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             "get_unread_push_actions_for_user_in_range_http", get_push_actions_txn
         )
 
+        room_ids = set()
+        thread_ids = []
+        for (
+            _,
+            room_id,
+            thread_id,
+            _,
+            _,
+            _,
+        ) in push_actions:
+            room_ids.add(room_id)
+            thread_ids.append(thread_id)
+
+        receipts_by_room = await self.db_pool.runInteraction(
+            "get_unread_push_actions_for_user_in_range_http_receipts",
+            self._get_receipts_for_room_and_threads_txn,
+            user_id=user_id,
+            room_ids=room_ids,
+            thread_ids=thread_ids,
+        )
+
         notifs = [
             HttpPushAction(
                 event_id=event_id,
@@ -998,12 +1062,6 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             The list will have between 0~limit entries.
         """
 
-        receipts_by_room = await self.db_pool.runInteraction(
-            "get_unread_push_actions_for_user_in_range_email_receipts",
-            self._get_receipts_by_room_txn,
-            user_id=user_id,
-        )
-
         def get_push_actions_txn(
             txn: LoggingTransaction,
         ) -> List[Tuple[str, str, str, int, str, bool, int]]:
@@ -1026,6 +1084,28 @@ class EventPushActionsWorkerStore(ReceiptsWorkerStore, StreamWorkerStore, SQLBas
             "get_unread_push_actions_for_user_in_range_email", get_push_actions_txn
         )
 
+        room_ids = set()
+        thread_ids = []
+        for (
+            _,
+            room_id,
+            thread_id,
+            _,
+            _,
+            _,
+            _,
+        ) in push_actions:
+            room_ids.add(room_id)
+            thread_ids.append(thread_id)
+
+        receipts_by_room = await self.db_pool.runInteraction(
+            "get_unread_push_actions_for_user_in_range_email_receipts",
+            self._get_receipts_for_room_and_threads_txn,
+            user_id=user_id,
+            room_ids=room_ids,
+            thread_ids=thread_ids,
+        )
+
         # Make a list of dicts from the two sets of results.
         notifs = [
             EmailPushAction(

synapse/storage/databases/main/registration.py

@@ -2266,6 +2266,13 @@ class RegistrationStore(StatsStore, RegistrationBackgroundUpdateStore):
     ):
         super().__init__(database, db_conn, hs)
 
+        self.db_pool.updates.register_background_index_update(
+            update_name="access_tokens_refresh_token_id_idx",
+            index_name="access_tokens_refresh_token_id_idx",
+            table="access_tokens",
+            columns=("refresh_token_id",),
+        )
+
         self._ignore_unknown_session_error = (
             hs.config.server.request_token_inhibit_3pid_errors
         )

tests/handlers/test_sync.py

@@ -17,14 +17,16 @@
 # [This file includes modifications made by New Vector Limited]
 #
 #
-from typing import Collection, List, Optional
+from typing import Collection, ContextManager, List, Optional
 from unittest.mock import AsyncMock, Mock, patch
 
+from parameterized import parameterized
+
 from twisted.test.proto_helpers import MemoryReactor
 
 from synapse.api.constants import EventTypes, JoinRules
 from synapse.api.errors import Codes, ResourceLimitError
-from synapse.api.filtering import Filtering
+from synapse.api.filtering import FilterCollection, Filtering
 from synapse.api.room_versions import RoomVersion, RoomVersions
 from synapse.events import EventBase
 from synapse.events.snapshot import EventContext
@@ -33,7 +35,7 @@ from synapse.handlers.sync import SyncConfig, SyncResult
 from synapse.rest import admin
 from synapse.rest.client import knock, login, room
 from synapse.server import HomeServer
-from synapse.types import UserID, create_requester
+from synapse.types import JsonDict, UserID, create_requester
 from synapse.util import Clock
 
 import tests.unittest
@@ -258,13 +260,7 @@ class SyncTestCase(tests.unittest.HomeserverTestCase):
         # Eve tries to join the room. We monkey patch the internal logic which selects
         # the prev_events used when creating the join event, such that the ban does not
         # precede the join.
-        mocked_get_prev_events = patch.object(
+        with self._patch_get_latest_events([last_room_creation_event_id]):
-            self.hs.get_datastores().main,
-            "get_prev_events_for_room",
-            new_callable=AsyncMock,
-            return_value=[last_room_creation_event_id],
-        )
-        with mocked_get_prev_events:
             self.helper.join(room_id, eve, tok=eve_token)
 
         # Eve makes a second, incremental sync.
@@ -288,6 +284,365 @@ class SyncTestCase(tests.unittest.HomeserverTestCase):
         )
         self.assertEqual(eve_initial_sync_after_join.joined, [])
 
+    def test_state_includes_changes_on_forks(self) -> None:
+        """State changes that happen on a fork of the DAG must be included in `state`
+
+        Given the following DAG:
+
+             E1
+           ↗    ↖
+          |      S2
+          |      ↑
+        --|------|----
+          |      |
+          E3     |
+           ↖    /
+             E4
+
+        ... and a filter that means we only return 2 events, represented by the dashed
+        horizontal line: `S2` must be included in the `state` section.
+        """
+        alice = self.register_user("alice", "password")
+        alice_tok = self.login(alice, "password")
+        alice_requester = create_requester(alice)
+        room_id = self.helper.create_room_as(alice, is_public=True, tok=alice_tok)
+
+        # Do an initial sync as Alice to get a known starting point.
+        initial_sync_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester, generate_sync_config(alice)
+            )
+        )
+        last_room_creation_event_id = (
+            initial_sync_result.joined[0].timeline.events[-1].event_id
+        )
+
+        # Send a state event, and a regular event, both using the same prev ID
+        with self._patch_get_latest_events([last_room_creation_event_id]):
+            s2_event = self.helper.send_state(room_id, "s2", {}, tok=alice_tok)[
+                "event_id"
+            ]
+            e3_event = self.helper.send(room_id, "e3", tok=alice_tok)["event_id"]
+
+        # Send a final event, joining the two branches of the dag
+        e4_event = self.helper.send(room_id, "e4", tok=alice_tok)["event_id"]
+
+        # do an incremental sync, with a filter that will ensure we only get two of
+        # the three new events.
+        incremental_sync = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester,
+                generate_sync_config(
+                    alice,
+                    filter_collection=FilterCollection(
+                        self.hs, {"room": {"timeline": {"limit": 2}}}
+                    ),
+                ),
+                since_token=initial_sync_result.next_batch,
+            )
+        )
+
+        # The state event should appear in the 'state' section of the response.
+        room_sync = incremental_sync.joined[0]
+        self.assertEqual(room_sync.room_id, room_id)
+        self.assertTrue(room_sync.timeline.limited)
+        self.assertEqual(
+            [e.event_id for e in room_sync.timeline.events],
+            [e3_event, e4_event],
+        )
+        self.assertEqual(
+            [e.event_id for e in room_sync.state.values()],
+            [s2_event],
+        )
+
+    def test_state_includes_changes_on_forks_when_events_excluded(self) -> None:
+        """A variation on the previous test, but where one event is filtered
+
+        The DAG is the same as the previous test, but E4 is excluded by the filter.
+
+             E1
+           ↗    ↖
+          |      S2
+          |      ↑
+        --|------|----
+          |      |
+          E3     |
+           ↖    /
+            (E4)
+
+        """
+
+        alice = self.register_user("alice", "password")
+        alice_tok = self.login(alice, "password")
+        alice_requester = create_requester(alice)
+        room_id = self.helper.create_room_as(alice, is_public=True, tok=alice_tok)
+
+        # Do an initial sync as Alice to get a known starting point.
+        initial_sync_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester, generate_sync_config(alice)
+            )
+        )
+        last_room_creation_event_id = (
+            initial_sync_result.joined[0].timeline.events[-1].event_id
+        )
+
+        # Send a state event, and a regular event, both using the same prev ID
+        with self._patch_get_latest_events([last_room_creation_event_id]):
+            s2_event = self.helper.send_state(room_id, "s2", {}, tok=alice_tok)[
+                "event_id"
+            ]
+            e3_event = self.helper.send(room_id, "e3", tok=alice_tok)["event_id"]
+
+        # Send a final event, joining the two branches of the dag
+        self.helper.send(room_id, "e4", type="not_a_normal_message", tok=alice_tok)[
+            "event_id"
+        ]
+
+        # do an incremental sync, with a filter that will only return E3, excluding S2
+        # and E4.
+        incremental_sync = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester,
+                generate_sync_config(
+                    alice,
+                    filter_collection=FilterCollection(
+                        self.hs,
+                        {
+                            "room": {
+                                "timeline": {
+                                    "limit": 1,
+                                    "not_types": ["not_a_normal_message"],
+                                }
+                            }
+                        },
+                    ),
+                ),
+                since_token=initial_sync_result.next_batch,
+            )
+        )
+
+        # The state event should appear in the 'state' section of the response.
+        room_sync = incremental_sync.joined[0]
+        self.assertEqual(room_sync.room_id, room_id)
+        self.assertTrue(room_sync.timeline.limited)
+        self.assertEqual(
+            [e.event_id for e in room_sync.timeline.events],
+            [e3_event],
+        )
+        self.assertEqual(
+            [e.event_id for e in room_sync.state.values()],
+            [s2_event],
+        )
+
+    def test_state_includes_changes_on_ungappy_syncs(self) -> None:
+        """Test `state` where the sync is not gappy.
+
+        We start with a DAG like this:
+
+             E1
+           ↗    ↖
+          |      S2
+          |
+        --|---
+          |
+          E3
+
+        ... and initialsync with `limit=1`, represented by the horizontal dashed line.
+        At this point, we do not expect S2 to appear in the response at all (since
+        it is excluded from the timeline by the `limit`, and the state is based on the
+        state after the most recent event before the sync token (E3), which doesn't
+        include S2.
+
+        Now more events arrive, and we do an incremental sync:
+
+             E1
+           ↗    ↖
+          |      S2
+          |      ↑
+          E3     |
+          ↑      |
+        --|------|----
+          |      |
+          E4     |
+           ↖    /
+             E5
+
+        This is the last chance for us to tell the client about S2, so it *must* be
+        included in the response.
+        """
+        alice = self.register_user("alice", "password")
+        alice_tok = self.login(alice, "password")
+        alice_requester = create_requester(alice)
+        room_id = self.helper.create_room_as(alice, is_public=True, tok=alice_tok)
+
+        # Do an initial sync to get a known starting point.
+        initial_sync_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester, generate_sync_config(alice)
+            )
+        )
+        last_room_creation_event_id = (
+            initial_sync_result.joined[0].timeline.events[-1].event_id
+        )
+
+        # Send a state event, and a regular event, both using the same prev ID
+        with self._patch_get_latest_events([last_room_creation_event_id]):
+            s2_event = self.helper.send_state(room_id, "s2", {}, tok=alice_tok)[
+                "event_id"
+            ]
+            e3_event = self.helper.send(room_id, "e3", tok=alice_tok)["event_id"]
+
+        # Another initial sync, with limit=1
+        initial_sync_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester,
+                generate_sync_config(
+                    alice,
+                    filter_collection=FilterCollection(
+                        self.hs, {"room": {"timeline": {"limit": 1}}}
+                    ),
+                ),
+            )
+        )
+        room_sync = initial_sync_result.joined[0]
+        self.assertEqual(room_sync.room_id, room_id)
+        self.assertEqual(
+            [e.event_id for e in room_sync.timeline.events],
+            [e3_event],
+        )
+        self.assertNotIn(s2_event, [e.event_id for e in room_sync.state.values()])
+
+        # More events, E4 and E5
+        with self._patch_get_latest_events([e3_event]):
+            e4_event = self.helper.send(room_id, "e4", tok=alice_tok)["event_id"]
+        e5_event = self.helper.send(room_id, "e5", tok=alice_tok)["event_id"]
+
+        # Now incremental sync
+        incremental_sync = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                alice_requester,
+                generate_sync_config(alice),
+                since_token=initial_sync_result.next_batch,
+            )
+        )
+
+        # The state event should appear in the 'state' section of the response.
+        room_sync = incremental_sync.joined[0]
+        self.assertEqual(room_sync.room_id, room_id)
+        self.assertFalse(room_sync.timeline.limited)
+        self.assertEqual(
+            [e.event_id for e in room_sync.timeline.events],
+            [e4_event, e5_event],
+        )
+        self.assertEqual(
+            [e.event_id for e in room_sync.state.values()],
+            [s2_event],
+        )
+
+    @parameterized.expand(
+        [
+            (False, False),
+            (True, False),
+            (False, True),
+            (True, True),
+        ]
+    )
+    def test_archived_rooms_do_not_include_state_after_leave(
+        self, initial_sync: bool, empty_timeline: bool
+    ) -> None:
+        """If the user leaves the room, state changes that happen after they leave are not returned.
+
+        We try with both a zero and a normal timeline limit,
+        and we try both an initial sync and an incremental sync for both.
+        """
+        if empty_timeline and not initial_sync:
+            # FIXME synapse doesn't return the room at all in this situation!
+            self.skipTest("Synapse does not correctly handle this case")
+
+        # Alice creates the room, and bob joins.
+        alice = self.register_user("alice", "password")
+        alice_tok = self.login(alice, "password")
+
+        bob = self.register_user("bob", "password")
+        bob_tok = self.login(bob, "password")
+        bob_requester = create_requester(bob)
+
+        room_id = self.helper.create_room_as(alice, is_public=True, tok=alice_tok)
+        self.helper.join(room_id, bob, tok=bob_tok)
+
+        initial_sync_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                bob_requester, generate_sync_config(bob)
+            )
+        )
+
+        # Alice sends a message and a state
+        before_message_event = self.helper.send(room_id, "before", tok=alice_tok)[
+            "event_id"
+        ]
+        before_state_event = self.helper.send_state(
+            room_id, "test_state", {"body": "before"}, tok=alice_tok
+        )["event_id"]
+
+        # Bob leaves
+        leave_event = self.helper.leave(room_id, bob, tok=bob_tok)["event_id"]
+
+        # Alice sends some more stuff
+        self.helper.send(room_id, "after", tok=alice_tok)["event_id"]
+        self.helper.send_state(room_id, "test_state", {"body": "after"}, tok=alice_tok)[
+            "event_id"
+        ]
+
+        # And now, Bob resyncs.
+        filter_dict: JsonDict = {"room": {"include_leave": True}}
+        if empty_timeline:
+            filter_dict["room"]["timeline"] = {"limit": 0}
+        sync_room_result = self.get_success(
+            self.sync_handler.wait_for_sync_for_user(
+                bob_requester,
+                generate_sync_config(
+                    bob, filter_collection=FilterCollection(self.hs, filter_dict)
+                ),
+                since_token=None if initial_sync else initial_sync_result.next_batch,
+            )
+        ).archived[0]
+
+        if empty_timeline:
+            # The timeline should be empty
+            self.assertEqual(sync_room_result.timeline.events, [])
+
+            # And the state should include the leave event...
+            self.assertEqual(
+                sync_room_result.state[("m.room.member", bob)].event_id, leave_event
+            )
+            # ... and the state change before he left.
+            self.assertEqual(
+                sync_room_result.state[("test_state", "")].event_id, before_state_event
+            )
+        else:
+            # The last three events in the timeline should be those leading up to the
+            # leave
+            self.assertEqual(
+                [e.event_id for e in sync_room_result.timeline.events[-3:]],
+                [before_message_event, before_state_event, leave_event],
+            )
+            # ... And the state should be empty
+            self.assertEqual(sync_room_result.state, {})
+
+    def _patch_get_latest_events(self, latest_events: List[str]) -> ContextManager:
+        """Monkey-patch `get_prev_events_for_room`
+
+        Returns a context manager which will replace the implementation of
+        `get_prev_events_for_room` with one which returns `latest_events`.
+        """
+        return patch.object(
+            self.hs.get_datastores().main,
+            "get_prev_events_for_room",
+            new_callable=AsyncMock,
+            return_value=latest_events,
+        )
+
     def test_call_invite_in_public_room_not_returned(self) -> None:
         user = self.register_user("alice", "password")
         tok = self.login(user, "password")
@@ -401,14 +756,26 @@ _request_key = 0
 
 
 def generate_sync_config(
-    user_id: str, device_id: Optional[str] = "device_id"
+    user_id: str,
+    device_id: Optional[str] = "device_id",
+    filter_collection: Optional[FilterCollection] = None,
 ) -> SyncConfig:
-    """Generate a sync config (with a unique request key)."""
+    """Generate a sync config (with a unique request key).
+
+    Args:
+        user_id: user who is syncing.
+        device_id: device that is syncing. Defaults to "device_id".
+        filter_collection: filter to apply. Defaults to the default filter (ie,
+           return everything, with a default limit)
+    """
+    if filter_collection is None:
+        filter_collection = Filtering(Mock()).DEFAULT_FILTER_COLLECTION
+
     global _request_key
     _request_key += 1
     return SyncConfig(
         user=UserID.from_string(user_id),
-        filter_collection=Filtering(Mock()).DEFAULT_FILTER_COLLECTION,
+        filter_collection=filter_collection,
         is_guest=False,
         request_key=("request_key", _request_key),
         device_id=device_id,

tests/rest/client/utils.py

@@ -170,8 +170,8 @@ class RestHelper:
         targ: Optional[str] = None,
         expect_code: int = HTTPStatus.OK,
         tok: Optional[str] = None,
-    ) -> None:
+    ) -> JsonDict:
-        self.change_membership(
+        return self.change_membership(
             room=room,
             src=src,
             targ=targ,
@@ -189,8 +189,8 @@ class RestHelper:
         appservice_user_id: Optional[str] = None,
         expect_errcode: Optional[Codes] = None,
         expect_additional_fields: Optional[dict] = None,
-    ) -> None:
+    ) -> JsonDict:
-        self.change_membership(
+        return self.change_membership(
             room=room,
             src=user,
             targ=user,
@@ -242,8 +242,8 @@ class RestHelper:
         user: Optional[str] = None,
         expect_code: int = HTTPStatus.OK,
         tok: Optional[str] = None,
-    ) -> None:
+    ) -> JsonDict:
-        self.change_membership(
+        return self.change_membership(
             room=room,
             src=user,
             targ=user,
@@ -282,7 +282,7 @@ class RestHelper:
         expect_code: int = HTTPStatus.OK,
         expect_errcode: Optional[str] = None,
         expect_additional_fields: Optional[dict] = None,
-    ) -> None:
+    ) -> JsonDict:
         """
         Send a membership state event into a room.
 
@@ -298,6 +298,9 @@ class RestHelper:
                 using an application service access token in `tok`.
             expect_code: The expected HTTP response code
             expect_errcode: The expected Matrix error code
+
+        Returns:
+            The JSON response
         """
         temp_id = self.auth_user_id
         self.auth_user_id = src
@@ -356,6 +359,7 @@ class RestHelper:
                 )
 
         self.auth_user_id = temp_id
+        return channel.json_body
 
     def send(
         self,