Merge branch 'develop' of github.com:matrix-org/synapse into erikj/fed_reader

12 files changed, 552 insertions, 120 deletions

diff --git a/synapse/storage/background_updates.py b/synapse/storage/background_updates.py
index 66a995157d..30d0e4c5dc 100644
--- a/synapse/storage/background_updates.py
+++ b/synapse/storage/background_updates.py
@@ -14,6 +14,7 @@
 # limitations under the License.
 
 from ._base import SQLBaseStore
+from . import engines
 
 from twisted.internet import defer
 
@@ -87,10 +88,12 @@ class BackgroundUpdateStore(SQLBaseStore):
 
     @defer.inlineCallbacks
     def start_doing_background_updates(self):
-        while True:
-            if self._background_update_timer is not None:
-                return
+        assert self._background_update_timer is None, \
+            "background updates already running"
+
+        logger.info("Starting background schema updates")
 
+        while True:
             sleep = defer.Deferred()
             self._background_update_timer = self._clock.call_later(
                 self.BACKGROUND_UPDATE_INTERVAL_MS / 1000., sleep.callback, None
@@ -101,22 +104,23 @@ class BackgroundUpdateStore(SQLBaseStore):
                 self._background_update_timer = None
 
             try:
-                result = yield self.do_background_update(
+                result = yield self.do_next_background_update(
                     self.BACKGROUND_UPDATE_DURATION_MS
                 )
             except:
                 logger.exception("Error doing update")
-
-            if result is None:
-                logger.info(
-                    "No more background updates to do."
-                    " Unscheduling background update task."
-                )
-                return
+            else:
+                if result is None:
+                    logger.info(
+                        "No more background updates to do."
+                        " Unscheduling background update task."
+                    )
+                    defer.returnValue(None)
 
     @defer.inlineCallbacks
-    def do_background_update(self, desired_duration_ms):
-        """Does some amount of work on a background update
+    def do_next_background_update(self, desired_duration_ms):
+        """Does some amount of work on the next queued background update
+
         Args:
             desired_duration_ms(float): How long we want to spend
                 updating.
@@ -135,11 +139,21 @@ class BackgroundUpdateStore(SQLBaseStore):
                 self._background_update_queue.append(update['update_name'])
 
         if not self._background_update_queue:
+            # no work left to do
             defer.returnValue(None)
 
+        # pop from the front, and add back to the back
         update_name = self._background_update_queue.pop(0)
         self._background_update_queue.append(update_name)
 
+        res = yield self._do_background_update(update_name, desired_duration_ms)
+        defer.returnValue(res)
+
+    @defer.inlineCallbacks
+    def _do_background_update(self, update_name, desired_duration_ms):
+        logger.info("Starting update batch on background update '%s'",
+                    update_name)
+
         update_handler = self._background_update_handlers[update_name]
 
         performance = self._background_update_performance.get(update_name)
@@ -202,6 +216,64 @@ class BackgroundUpdateStore(SQLBaseStore):
         """
         self._background_update_handlers[update_name] = update_handler
 
+    def register_background_index_update(self, update_name, index_name,
+                                         table, columns):
+        """Helper for store classes to do a background index addition
+
+        To use:
+
+        1. use a schema delta file to add a background update. Example:
+            INSERT INTO background_updates (update_name, progress_json) VALUES
+                ('my_new_index', '{}');
+
+        2. In the Store constructor, call this method
+
+        Args:
+            update_name (str): update_name to register for
+            index_name (str): name of index to add
+            table (str): table to add index to
+            columns (list[str]): columns/expressions to include in index
+        """
+
+        # if this is postgres, we add the indexes concurrently. Otherwise
+        # we fall back to doing it inline
+        if isinstance(self.database_engine, engines.PostgresEngine):
+            conc = True
+        else:
+            conc = False
+
+        sql = "CREATE INDEX %(conc)s %(name)s ON %(table)s (%(columns)s)" \
+              % {
+                  "conc": "CONCURRENTLY" if conc else "",
+                  "name": index_name,
+                  "table": table,
+                  "columns": ", ".join(columns),
+              }
+
+        def create_index_concurrently(conn):
+            conn.rollback()
+            # postgres insists on autocommit for the index
+            conn.set_session(autocommit=True)
+            c = conn.cursor()
+            c.execute(sql)
+            conn.set_session(autocommit=False)
+
+        def create_index(conn):
+            c = conn.cursor()
+            c.execute(sql)
+
+        @defer.inlineCallbacks
+        def updater(progress, batch_size):
+            logger.info("Adding index %s to %s", index_name, table)
+            if conc:
+                yield self.runWithConnection(create_index_concurrently)
+            else:
+                yield self.runWithConnection(create_index)
+            yield self._end_background_update(update_name)
+            defer.returnValue(1)
+
+        self.register_background_update_handler(update_name, updater)
+
     def start_background_update(self, update_name, progress):
         """Starts a background update running.
 
diff --git a/synapse/storage/client_ips.py b/synapse/storage/client_ips.py
index e31fa53c3f..71e5ea112f 100644
--- a/synapse/storage/client_ips.py
+++ b/synapse/storage/client_ips.py
@@ -15,10 +15,11 @@
 
 import logging
 
-from ._base import SQLBaseStore, Cache
-
 from twisted.internet import defer
 
+from ._base import Cache
+from . import background_updates
+
 logger = logging.getLogger(__name__)
 
 # Number of msec of granularity to store the user IP 'last seen' time. Smaller
@@ -27,8 +28,7 @@ logger = logging.getLogger(__name__)
 LAST_SEEN_GRANULARITY = 120 * 1000
 
 
-class ClientIpStore(SQLBaseStore):
-
+class ClientIpStore(background_updates.BackgroundUpdateStore):
     def __init__(self, hs):
         self.client_ip_last_seen = Cache(
             name="client_ip_last_seen",
@@ -37,6 +37,13 @@ class ClientIpStore(SQLBaseStore):
 
         super(ClientIpStore, self).__init__(hs)
 
+        self.register_background_index_update(
+            "user_ips_device_index",
+            index_name="user_ips_device_id",
+            table="user_ips",
+            columns=["user_id", "device_id", "last_seen"],
+        )
+
     @defer.inlineCallbacks
     def insert_client_ip(self, user, access_token, ip, user_agent, device_id):
         now = int(self._clock.time_msec())
diff --git a/synapse/storage/devices.py b/synapse/storage/devices.py
index 1cc6e07f2b..afd6530cab 100644
--- a/synapse/storage/devices.py
+++ b/synapse/storage/devices.py
@@ -76,6 +76,46 @@ class DeviceStore(SQLBaseStore):
             desc="get_device",
         )
 
+    def delete_device(self, user_id, device_id):
+        """Delete a device.
+
+        Args:
+            user_id (str): The ID of the user which owns the device
+            device_id (str): The ID of the device to delete
+        Returns:
+            defer.Deferred
+        """
+        return self._simple_delete_one(
+            table="devices",
+            keyvalues={"user_id": user_id, "device_id": device_id},
+            desc="delete_device",
+        )
+
+    def update_device(self, user_id, device_id, new_display_name=None):
+        """Update a device.
+
+        Args:
+            user_id (str): The ID of the user which owns the device
+            device_id (str): The ID of the device to update
+            new_display_name (str|None): new displayname for device; None
+               to leave unchanged
+        Raises:
+            StoreError: if the device is not found
+        Returns:
+            defer.Deferred
+        """
+        updates = {}
+        if new_display_name is not None:
+            updates["display_name"] = new_display_name
+        if not updates:
+            return defer.succeed(None)
+        return self._simple_update_one(
+            table="devices",
+            keyvalues={"user_id": user_id, "device_id": device_id},
+            updatevalues=updates,
+            desc="update_device",
+        )
+
     @defer.inlineCallbacks
     def get_devices_by_user(self, user_id):
         """Retrieve all of a user's registered devices.
diff --git a/synapse/storage/end_to_end_keys.py b/synapse/storage/end_to_end_keys.py
index 2e89066515..62b7790e91 100644
--- a/synapse/storage/end_to_end_keys.py
+++ b/synapse/storage/end_to_end_keys.py
@@ -13,6 +13,8 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+import twisted.internet.defer
+
 from ._base import SQLBaseStore
 
 
@@ -123,3 +125,16 @@ class EndToEndKeyStore(SQLBaseStore):
         return self.runInteraction(
             "claim_e2e_one_time_keys", _claim_e2e_one_time_keys
         )
+
+    @twisted.internet.defer.inlineCallbacks
+    def delete_e2e_keys_by_device(self, user_id, device_id):
+        yield self._simple_delete(
+            table="e2e_device_keys_json",
+            keyvalues={"user_id": user_id, "device_id": device_id},
+            desc="delete_e2e_device_keys_by_device"
+        )
+        yield self._simple_delete(
+            table="e2e_one_time_keys_json",
+            keyvalues={"user_id": user_id, "device_id": device_id},
+            desc="delete_e2e_one_time_keys_by_device"
+        )
diff --git a/synapse/storage/event_push_actions.py b/synapse/storage/event_push_actions.py
index 3d93285f84..df4000d0da 100644
--- a/synapse/storage/event_push_actions.py
+++ b/synapse/storage/event_push_actions.py
@@ -117,24 +117,42 @@ class EventPushActionsStore(SQLBaseStore):
         defer.returnValue(ret)
 
     @defer.inlineCallbacks
-    def get_unread_push_actions_for_user_in_range(self, user_id,
-                                                  min_stream_ordering,
-                                                  max_stream_ordering=None,
-                                                  limit=20):
+    def get_unread_push_actions_for_user_in_range_for_http(
+        self, user_id, min_stream_ordering, max_stream_ordering, limit=20
+    ):
+        """Get a list of the most recent unread push actions for a given user,
+        within the given stream ordering range. Called by the httppusher.
+
+        Args:
+            user_id (str): The user to fetch push actions for.
+            min_stream_ordering(int): The exclusive lower bound on the
+                stream ordering of event push actions to fetch.
+            max_stream_ordering(int): The inclusive upper bound on the
+                stream ordering of event push actions to fetch.
+            limit (int): The maximum number of rows to return.
+        Returns:
+            A promise which resolves to a list of dicts with the keys "event_id",
+            "room_id", "stream_ordering", "actions".
+            The list will be ordered by ascending stream_ordering.
+            The list will have between 0~limit entries.
+        """
+        # find rooms that have a read receipt in them and return the next
+        # push actions
         def get_after_receipt(txn):
+            # find rooms that have a read receipt in them and return the next
+            # push actions
             sql = (
-                "SELECT ep.event_id, ep.room_id, ep.stream_ordering, ep.actions, "
-                "e.received_ts "
-                "FROM ("
-                "   SELECT room_id, user_id, "
-                "       max(topological_ordering) as topological_ordering, "
-                "       max(stream_ordering) as stream_ordering "
-                "       FROM events"
-                "   NATURAL JOIN receipts_linearized WHERE receipt_type = 'm.read'"
-                "   GROUP BY room_id, user_id"
+                "SELECT ep.event_id, ep.room_id, ep.stream_ordering, ep.actions"
+                " FROM ("
+                "   SELECT room_id,"
+                "       MAX(topological_ordering) as topological_ordering,"
+                "       MAX(stream_ordering) as stream_ordering"
+                "   FROM events"
+                "   INNER JOIN receipts_linearized USING (room_id, event_id)"
+                "   WHERE receipt_type = 'm.read' AND user_id = ?"
+                "   GROUP BY room_id"
                 ") AS rl,"
                 " event_push_actions AS ep"
-                " INNER JOIN events AS e USING (room_id, event_id)"
                 " WHERE"
                 "   ep.room_id = rl.room_id"
                 "   AND ("
@@ -144,44 +162,159 @@ class EventPushActionsStore(SQLBaseStore):
                 "           AND ep.stream_ordering > rl.stream_ordering"
                 "       )"
                 "   )"
-                "   AND ep.stream_ordering > ?"
                 "   AND ep.user_id = ?"
-                "   AND ep.user_id = rl.user_id"
+                "   AND ep.stream_ordering > ?"
+                "   AND ep.stream_ordering <= ?"
+                " ORDER BY ep.stream_ordering ASC LIMIT ?"
             )
-            args = [min_stream_ordering, user_id]
-            if max_stream_ordering is not None:
-                sql += " AND ep.stream_ordering <= ?"
-                args.append(max_stream_ordering)
-            sql += " ORDER BY ep.stream_ordering DESC LIMIT ?"
-            args.append(limit)
+            args = [
+                user_id, user_id,
+                min_stream_ordering, max_stream_ordering, limit,
+            ]
             txn.execute(sql, args)
             return txn.fetchall()
         after_read_receipt = yield self.runInteraction(
-            "get_unread_push_actions_for_user_in_range", get_after_receipt
+            "get_unread_push_actions_for_user_in_range_http_arr", get_after_receipt
         )
 
+        # There are rooms with push actions in them but you don't have a read receipt in
+        # them e.g. rooms you've been invited to, so get push actions for rooms which do
+        # not have read receipts in them too.
         def get_no_receipt(txn):
             sql = (
                 "SELECT ep.event_id, ep.room_id, ep.stream_ordering, ep.actions,"
                 " e.received_ts"
                 " FROM event_push_actions AS ep"
-                " JOIN events e ON ep.room_id = e.room_id AND ep.event_id = e.event_id"
-                " WHERE ep.room_id not in ("
-                "   SELECT room_id FROM events NATURAL JOIN receipts_linearized"
+                " INNER JOIN events AS e USING (room_id, event_id)"
+                " WHERE"
+                "   ep.room_id NOT IN ("
+                "     SELECT room_id FROM receipts_linearized"
+                "       WHERE receipt_type = 'm.read' AND user_id = ?"
+                "       GROUP BY room_id"
+                "   )"
+                "   AND ep.user_id = ?"
+                "   AND ep.stream_ordering > ?"
+                "   AND ep.stream_ordering <= ?"
+                " ORDER BY ep.stream_ordering ASC LIMIT ?"
+            )
+            args = [
+                user_id, user_id,
+                min_stream_ordering, max_stream_ordering, limit,
+            ]
+            txn.execute(sql, args)
+            return txn.fetchall()
+        no_read_receipt = yield self.runInteraction(
+            "get_unread_push_actions_for_user_in_range_http_nrr", get_no_receipt
+        )
+
+        notifs = [
+            {
+                "event_id": row[0],
+                "room_id": row[1],
+                "stream_ordering": row[2],
+                "actions": json.loads(row[3]),
+            } for row in after_read_receipt + no_read_receipt
+        ]
+
+        # Now sort it so it's ordered correctly, since currently it will
+        # contain results from the first query, correctly ordered, followed
+        # by results from the second query, but we want them all ordered
+        # by stream_ordering, oldest first.
+        notifs.sort(key=lambda r: r['stream_ordering'])
+
+        # Take only up to the limit. We have to stop at the limit because
+        # one of the subqueries may have hit the limit.
+        defer.returnValue(notifs[:limit])
+
+    @defer.inlineCallbacks
+    def get_unread_push_actions_for_user_in_range_for_email(
+        self, user_id, min_stream_ordering, max_stream_ordering, limit=20
+    ):
+        """Get a list of the most recent unread push actions for a given user,
+        within the given stream ordering range. Called by the emailpusher
+
+        Args:
+            user_id (str): The user to fetch push actions for.
+            min_stream_ordering(int): The exclusive lower bound on the
+                stream ordering of event push actions to fetch.
+            max_stream_ordering(int): The inclusive upper bound on the
+                stream ordering of event push actions to fetch.
+            limit (int): The maximum number of rows to return.
+        Returns:
+            A promise which resolves to a list of dicts with the keys "event_id",
+            "room_id", "stream_ordering", "actions", "received_ts".
+            The list will be ordered by descending received_ts.
+            The list will have between 0~limit entries.
+        """
+        # find rooms that have a read receipt in them and return the most recent
+        # push actions
+        def get_after_receipt(txn):
+            sql = (
+                "SELECT ep.event_id, ep.room_id, ep.stream_ordering, ep.actions,"
+                "  e.received_ts"
+                " FROM ("
+                "   SELECT room_id,"
+                "       MAX(topological_ordering) as topological_ordering,"
+                "       MAX(stream_ordering) as stream_ordering"
+                "   FROM events"
+                "   INNER JOIN receipts_linearized USING (room_id, event_id)"
                 "   WHERE receipt_type = 'm.read' AND user_id = ?"
                 "   GROUP BY room_id"
-                ") AND ep.user_id = ? AND ep.stream_ordering > ?"
+                ") AS rl,"
+                " event_push_actions AS ep"
+                " INNER JOIN events AS e USING (room_id, event_id)"
+                " WHERE"
+                "   ep.room_id = rl.room_id"
+                "   AND ("
+                "       ep.topological_ordering > rl.topological_ordering"
+                "       OR ("
+                "           ep.topological_ordering = rl.topological_ordering"
+                "           AND ep.stream_ordering > rl.stream_ordering"
+                "       )"
+                "   )"
+                "   AND ep.user_id = ?"
+                "   AND ep.stream_ordering > ?"
+                "   AND ep.stream_ordering <= ?"
+                " ORDER BY ep.stream_ordering DESC LIMIT ?"
+            )
+            args = [
+                user_id, user_id,
+                min_stream_ordering, max_stream_ordering, limit,
+            ]
+            txn.execute(sql, args)
+            return txn.fetchall()
+        after_read_receipt = yield self.runInteraction(
+            "get_unread_push_actions_for_user_in_range_email_arr", get_after_receipt
+        )
+
+        # There are rooms with push actions in them but you don't have a read receipt in
+        # them e.g. rooms you've been invited to, so get push actions for rooms which do
+        # not have read receipts in them too.
+        def get_no_receipt(txn):
+            sql = (
+                "SELECT ep.event_id, ep.room_id, ep.stream_ordering, ep.actions,"
+                " e.received_ts"
+                " FROM event_push_actions AS ep"
+                " INNER JOIN events AS e USING (room_id, event_id)"
+                " WHERE"
+                "   ep.room_id NOT IN ("
+                "     SELECT room_id FROM receipts_linearized"
+                "       WHERE receipt_type = 'm.read' AND user_id = ?"
+                "       GROUP BY room_id"
+                "   )"
+                "   AND ep.user_id = ?"
+                "   AND ep.stream_ordering > ?"
+                "   AND ep.stream_ordering <= ?"
+                " ORDER BY ep.stream_ordering DESC LIMIT ?"
             )
-            args = [user_id, user_id, min_stream_ordering]
-            if max_stream_ordering is not None:
-                sql += " AND ep.stream_ordering <= ?"
-                args.append(max_stream_ordering)
-            sql += " ORDER BY ep.stream_ordering DESC LIMIT ?"
-            args.append(limit)
+            args = [
+                user_id, user_id,
+                min_stream_ordering, max_stream_ordering, limit,
+            ]
             txn.execute(sql, args)
             return txn.fetchall()
         no_read_receipt = yield self.runInteraction(
-            "get_unread_push_actions_for_user_in_range", get_no_receipt
+            "get_unread_push_actions_for_user_in_range_email_nrr", get_no_receipt
         )
 
         # Make a list of dicts from the two sets of results.
@@ -198,7 +331,7 @@ class EventPushActionsStore(SQLBaseStore):
         # Now sort it so it's ordered correctly, since currently it will
         # contain results from the first query, correctly ordered, followed
         # by results from the second query, but we want them all ordered
-        # by received_ts
+        # by received_ts (most recent first)
         notifs.sort(key=lambda r: -(r['received_ts'] or 0))
 
         # Now return the first `limit`
diff --git a/synapse/storage/events.py b/synapse/storage/events.py
index 6610549281..c63ca36df6 100644
--- a/synapse/storage/events.py
+++ b/synapse/storage/events.py
@@ -397,6 +397,12 @@ class EventsStore(SQLBaseStore):
 
     @log_function
     def _persist_events_txn(self, txn, events_and_contexts, backfilled):
+        """Insert some number of room events into the necessary database tables.
+
+        Rejected events are only inserted into the events table, the events_json table,
+        and the rejections table. Things reading from those table will need to check
+        whether the event was rejected.
+        """
         depth_updates = {}
         for event, context in events_and_contexts:
             # Remove the any existing cache entries for the event_ids
@@ -407,21 +413,11 @@ class EventsStore(SQLBaseStore):
                     event.room_id, event.internal_metadata.stream_ordering,
                 )
 
-            if not event.internal_metadata.is_outlier():
+            if not event.internal_metadata.is_outlier() and not context.rejected:
                 depth_updates[event.room_id] = max(
                     event.depth, depth_updates.get(event.room_id, event.depth)
                 )
 
-            if context.push_actions:
-                self._set_push_actions_for_event_and_users_txn(
-                    txn, event, context.push_actions
-                )
-
-        if event.type == EventTypes.Redaction and event.redacts is not None:
-            self._remove_push_actions_for_event_id_txn(
-                txn, event.room_id, event.redacts
-            )
-
         for room_id, depth in depth_updates.items():
             self._update_min_depth_for_room_txn(txn, room_id, depth)
 
@@ -431,14 +427,24 @@ class EventsStore(SQLBaseStore):
             ),
             [event.event_id for event, _ in events_and_contexts]
         )
+
         have_persisted = {
             event_id: outlier
             for event_id, outlier in txn.fetchall()
         }
 
+        # Remove the events that we've seen before.
         event_map = {}
         to_remove = set()
         for event, context in events_and_contexts:
+            if context.rejected:
+                # If the event is rejected then we don't care if the event
+                # was an outlier or not.
+                if event.event_id in have_persisted:
+                    # If we have already seen the event then ignore it.
+                    to_remove.add(event)
+                continue
+
             # Handle the case of the list including the same event multiple
             # times. The tricky thing here is when they differ by whether
             # they are an outlier.
@@ -463,6 +469,12 @@ class EventsStore(SQLBaseStore):
 
             outlier_persisted = have_persisted[event.event_id]
             if not event.internal_metadata.is_outlier() and outlier_persisted:
+                # We received a copy of an event that we had already stored as
+                # an outlier in the database. We now have some state at that
+                # so we need to update the state_groups table with that state.
+
+                # insert into the state_group, state_groups_state and
+                # event_to_state_groups tables.
                 self._store_mult_state_groups_txn(txn, ((event, context),))
 
                 metadata_json = encode_json(
@@ -478,6 +490,8 @@ class EventsStore(SQLBaseStore):
                     (metadata_json, event.event_id,)
                 )
 
+                # Add an entry to the ex_outlier_stream table to replicate the
+                # change in outlier status to our workers.
                 stream_order = event.internal_metadata.stream_ordering
                 state_group_id = context.state_group or context.new_state_group_id
                 self._simple_insert_txn(
@@ -499,6 +513,8 @@ class EventsStore(SQLBaseStore):
                     (False, event.event_id,)
                 )
 
+                # Update the event_backward_extremities table now that this
+                # event isn't an outlier any more.
                 self._update_extremeties(txn, [event])
 
         events_and_contexts = [
@@ -506,38 +522,12 @@ class EventsStore(SQLBaseStore):
         ]
 
         if not events_and_contexts:
+            # Make sure we don't pass an empty list to functions that expect to
+            # be storing at least one element.
             return
 
-        self._store_mult_state_groups_txn(txn, events_and_contexts)
-
-        self._handle_mult_prev_events(
-            txn,
-            events=[event for event, _ in events_and_contexts],
-        )
-
-        for event, _ in events_and_contexts:
-            if event.type == EventTypes.Name:
-                self._store_room_name_txn(txn, event)
-            elif event.type == EventTypes.Topic:
-                self._store_room_topic_txn(txn, event)
-            elif event.type == EventTypes.Message:
-                self._store_room_message_txn(txn, event)
-            elif event.type == EventTypes.Redaction:
-                self._store_redaction(txn, event)
-            elif event.type == EventTypes.RoomHistoryVisibility:
-                self._store_history_visibility_txn(txn, event)
-            elif event.type == EventTypes.GuestAccess:
-                self._store_guest_access_txn(txn, event)
-
-        self._store_room_members_txn(
-            txn,
-            [
-                event
-                for event, _ in events_and_contexts
-                if event.type == EventTypes.Member
-            ],
-            backfilled=backfilled,
-        )
+        # From this point onwards the events are only events that we haven't
+        # seen before.
 
         def event_dict(event):
             return {
@@ -591,10 +581,41 @@ class EventsStore(SQLBaseStore):
             ],
         )
 
-        if context.rejected:
-            self._store_rejections_txn(
-                txn, event.event_id, context.rejected
-            )
+        # Remove the rejected events from the list now that we've added them
+        # to the events table and the events_json table.
+        to_remove = set()
+        for event, context in events_and_contexts:
+            if context.rejected:
+                # Insert the event_id into the rejections table
+                self._store_rejections_txn(
+                    txn, event.event_id, context.rejected
+                )
+                to_remove.add(event)
+
+        events_and_contexts = [
+            ec for ec in events_and_contexts if ec[0] not in to_remove
+        ]
+
+        if not events_and_contexts:
+            # Make sure we don't pass an empty list to functions that expect to
+            # be storing at least one element.
+            return
+
+        # From this point onwards the events are only ones that weren't rejected.
+
+        for event, context in events_and_contexts:
+            # Insert all the push actions into the event_push_actions table.
+            if context.push_actions:
+                self._set_push_actions_for_event_and_users_txn(
+                    txn, event, context.push_actions
+                )
+
+            if event.type == EventTypes.Redaction and event.redacts is not None:
+                # Remove the entries in the event_push_actions table for the
+                # redacted event.
+                self._remove_push_actions_for_event_id_txn(
+                    txn, event.room_id, event.redacts
+                )
 
         self._simple_insert_many_txn(
             txn,
@@ -610,6 +631,49 @@ class EventsStore(SQLBaseStore):
             ],
         )
 
+        # Insert into the state_groups, state_groups_state, and
+        # event_to_state_groups tables.
+        self._store_mult_state_groups_txn(txn, events_and_contexts)
+
+        # Update the event_forward_extremities, event_backward_extremities and
+        # event_edges tables.
+        self._handle_mult_prev_events(
+            txn,
+            events=[event for event, _ in events_and_contexts],
+        )
+
+        for event, _ in events_and_contexts:
+            if event.type == EventTypes.Name:
+                # Insert into the room_names and event_search tables.
+                self._store_room_name_txn(txn, event)
+            elif event.type == EventTypes.Topic:
+                # Insert into the topics table and event_search table.
+                self._store_room_topic_txn(txn, event)
+            elif event.type == EventTypes.Message:
+                # Insert into the event_search table.
+                self._store_room_message_txn(txn, event)
+            elif event.type == EventTypes.Redaction:
+                # Insert into the redactions table.
+                self._store_redaction(txn, event)
+            elif event.type == EventTypes.RoomHistoryVisibility:
+                # Insert into the event_search table.
+                self._store_history_visibility_txn(txn, event)
+            elif event.type == EventTypes.GuestAccess:
+                # Insert into the event_search table.
+                self._store_guest_access_txn(txn, event)
+
+        # Insert into the room_memberships table.
+        self._store_room_members_txn(
+            txn,
+            [
+                event
+                for event, _ in events_and_contexts
+                if event.type == EventTypes.Member
+            ],
+            backfilled=backfilled,
+        )
+
+        # Insert event_reference_hashes table.
         self._store_event_reference_hashes_txn(
             txn, [event for event, _ in events_and_contexts]
         )
@@ -654,6 +718,7 @@ class EventsStore(SQLBaseStore):
             ],
         )
 
+        # Prefill the event cache
         self._add_to_cache(txn, events_and_contexts)
 
         if backfilled:
@@ -666,11 +731,6 @@ class EventsStore(SQLBaseStore):
                 # Outlier events shouldn't clobber the current state.
                 continue
 
-            if context.rejected:
-                # If the event failed it's auth checks then it shouldn't
-                # clobbler the current state.
-                continue
-
             txn.call_after(
                 self._get_current_state_for_key.invalidate,
                 (event.room_id, event.type, event.state_key,)
diff --git a/synapse/storage/registration.py b/synapse/storage/registration.py
index 9a92b35361..7e7d32eb66 100644
--- a/synapse/storage/registration.py
+++ b/synapse/storage/registration.py
@@ -18,18 +18,31 @@ import re
 from twisted.internet import defer
 
 from synapse.api.errors import StoreError, Codes
-
-from ._base import SQLBaseStore
+from synapse.storage import background_updates
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks
 
 
-class RegistrationStore(SQLBaseStore):
+class RegistrationStore(background_updates.BackgroundUpdateStore):
 
     def __init__(self, hs):
         super(RegistrationStore, self).__init__(hs)
 
         self.clock = hs.get_clock()
 
+        self.register_background_index_update(
+            "access_tokens_device_index",
+            index_name="access_tokens_device_id",
+            table="access_tokens",
+            columns=["user_id", "device_id"],
+        )
+
+        self.register_background_index_update(
+            "refresh_tokens_device_index",
+            index_name="refresh_tokens_device_id",
+            table="refresh_tokens",
+            columns=["user_id", "device_id"],
+        )
+
     @defer.inlineCallbacks
     def add_access_token_to_user(self, user_id, token, device_id=None):
         """Adds an access token for the given user.
@@ -238,16 +251,37 @@ class RegistrationStore(SQLBaseStore):
         self.get_user_by_id.invalidate((user_id,))
 
     @defer.inlineCallbacks
-    def user_delete_access_tokens(self, user_id, except_token_ids=[]):
-        def f(txn):
-            sql = "SELECT token FROM access_tokens WHERE user_id = ?"
+    def user_delete_access_tokens(self, user_id, except_token_ids=[],
+                                  device_id=None,
+                                  delete_refresh_tokens=False):
+        """
+        Invalidate access/refresh tokens belonging to a user
+
+        Args:
+            user_id (str):  ID of user the tokens belong to
+            except_token_ids (list[str]): list of access_tokens which should
+                *not* be deleted
+            device_id (str|None):  ID of device the tokens are associated with.
+                If None, tokens associated with any device (or no device) will
+                be deleted
+            delete_refresh_tokens (bool):  True to delete refresh tokens as
+                well as access tokens.
+        Returns:
+            defer.Deferred:
+        """
+        def f(txn, table, except_tokens, call_after_delete):
+            sql = "SELECT token FROM %s WHERE user_id = ?" % table
             clauses = [user_id]
 
-            if except_token_ids:
+            if device_id is not None:
+                sql += " AND device_id = ?"
+                clauses.append(device_id)
+
+            if except_tokens:
                 sql += " AND id NOT IN (%s)" % (
-                    ",".join(["?" for _ in except_token_ids]),
+                    ",".join(["?" for _ in except_tokens]),
                 )
-                clauses += except_token_ids
+                clauses += except_tokens
 
             txn.execute(sql, clauses)
 
@@ -256,16 +290,33 @@ class RegistrationStore(SQLBaseStore):
             n = 100
             chunks = [rows[i:i + n] for i in xrange(0, len(rows), n)]
             for chunk in chunks:
-                for row in chunk:
-                    txn.call_after(self.get_user_by_access_token.invalidate, (row[0],))
+                if call_after_delete:
+                    for row in chunk:
+                        txn.call_after(call_after_delete, (row[0],))
 
                 txn.execute(
-                    "DELETE FROM access_tokens WHERE token in (%s)" % (
+                    "DELETE FROM %s WHERE token in (%s)" % (
+                        table,
                         ",".join(["?" for _ in chunk]),
                     ), [r[0] for r in chunk]
                 )
 
-        yield self.runInteraction("user_delete_access_tokens", f)
+        # delete refresh tokens first, to stop new access tokens being
+        # allocated while our backs are turned
+        if delete_refresh_tokens:
+            yield self.runInteraction(
+                "user_delete_access_tokens", f,
+                table="refresh_tokens",
+                except_tokens=[],
+                call_after_delete=None,
+            )
+
+        yield self.runInteraction(
+            "user_delete_access_tokens", f,
+            table="access_tokens",
+            except_tokens=except_token_ids,
+            call_after_delete=self.get_user_by_access_token.invalidate,
+        )
 
     def delete_access_token(self, access_token):
         def f(txn):
@@ -288,9 +339,8 @@ class RegistrationStore(SQLBaseStore):
         Args:
             token (str): The access token of a user.
         Returns:
-            dict: Including the name (user_id) and the ID of their access token.
-        Raises:
-            StoreError if no user was found.
+            defer.Deferred: None, if the token did not match, otherwise dict
+                including the keys `name`, `is_guest`, `device_id`, `token_id`.
         """
         return self.runInteraction(
             "get_user_by_access_token",
diff --git a/synapse/storage/schema/delta/33/access_tokens_device_index.sql b/synapse/storage/schema/delta/33/access_tokens_device_index.sql
new file mode 100644
index 0000000000..61ad3fe3e8
--- /dev/null
+++ b/synapse/storage/schema/delta/33/access_tokens_device_index.sql
@@ -0,0 +1,17 @@
+/* Copyright 2016 OpenMarket Ltd
+ *
+ * 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.
+ */
+
+INSERT INTO background_updates (update_name, progress_json) VALUES
+  ('access_tokens_device_index', '{}');
diff --git a/synapse/storage/schema/delta/33/devices_for_e2e_keys.sql b/synapse/storage/schema/delta/33/devices_for_e2e_keys.sql
new file mode 100644
index 0000000000..140f2b63e0
--- /dev/null
+++ b/synapse/storage/schema/delta/33/devices_for_e2e_keys.sql
@@ -0,0 +1,19 @@
+/* Copyright 2016 OpenMarket Ltd
+ *
+ * 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.
+ */
+
+-- make sure that we have a device record for each set of E2E keys, so that the
+-- user can delete them if they like.
+INSERT INTO devices
+    SELECT user_id, device_id, 'unknown device' FROM e2e_device_keys_json;
diff --git a/synapse/storage/schema/delta/33/refreshtoken_device_index.sql b/synapse/storage/schema/delta/33/refreshtoken_device_index.sql
new file mode 100644
index 0000000000..bb225dafbf
--- /dev/null
+++ b/synapse/storage/schema/delta/33/refreshtoken_device_index.sql
@@ -0,0 +1,17 @@
+/* Copyright 2016 OpenMarket Ltd
+ *
+ * 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.
+ */
+
+INSERT INTO background_updates (update_name, progress_json) VALUES
+  ('refresh_tokens_device_index', '{}');
diff --git a/synapse/storage/schema/delta/33/user_ips_index.sql b/synapse/storage/schema/delta/33/user_ips_index.sql
index 8a05677d42..473f75a78e 100644
--- a/synapse/storage/schema/delta/33/user_ips_index.sql
+++ b/synapse/storage/schema/delta/33/user_ips_index.sql
@@ -13,4 +13,5 @@
  * limitations under the License.
  */
 
-CREATE INDEX user_ips_device_id ON user_ips(user_id, device_id, last_seen);
+INSERT INTO background_updates (update_name, progress_json) VALUES
+  ('user_ips_device_index', '{}');
diff --git a/synapse/storage/transactions.py b/synapse/storage/transactions.py
index 6c7481a728..6258ff1725 100644
--- a/synapse/storage/transactions.py
+++ b/synapse/storage/transactions.py
@@ -24,6 +24,7 @@ from collections import namedtuple
 
 import itertools
 import logging
+import ujson as json
 
 logger = logging.getLogger(__name__)
 
@@ -101,7 +102,7 @@ class TransactionStore(SQLBaseStore):
         )
 
         if result and result["response_code"]:
-            return result["response_code"], result["response_json"]
+            return result["response_code"], json.loads(str(result["response_json"]))
         else:
             return None