Add a unique index to state_group_edges to prevent duplicates being…

… accidentally introduced and the consequential impact to performance. (#12687)

changelog.d/12687.bugfix

@@ -0,0 +1 @@
+Add a unique index to `state_group_edges` to prevent duplicates being accidentally introduced and the consequential impact to performance.

docs/upgrade.md

@@ -89,6 +89,96 @@ process, for example:
     dpkg -i matrix-synapse-py3_1.3.0+stretch1_amd64.deb
     ```
 
+# Upgrading to v1.60.0
+
+## Adding a new unique index to `state_group_edges` could fail if your database is corrupted
+
+This release of Synapse will add a unique index to the `state_group_edges` table, in order
+to prevent accidentally introducing duplicate information (for example, because a database
+backup was restored multiple times).
+
+Duplicate rows being present in this table could cause drastic performance problems; see
+[issue 11779](https://github.com/matrix-org/synapse/issues/11779) for more details.
+
+If your Synapse database already has had duplicate rows introduced into this table,
+this could fail, with either of these errors:
+
+
+**On Postgres:**
+```
+synapse.storage.background_updates - 623 - INFO - background_updates-0 - Adding index state_group_edges_unique_idx to state_group_edges
+synapse.storage.background_updates - 282 - ERROR - background_updates-0 - Error doing update
+...
+psycopg2.errors.UniqueViolation: could not create unique index "state_group_edges_unique_idx"
+DETAIL:  Key (state_group, prev_state_group)=(2, 1) is duplicated.
+```
+(The numbers may be different.)
+
+**On SQLite:**
+```
+synapse.storage.background_updates - 623 - INFO - background_updates-0 - Adding index state_group_edges_unique_idx to state_group_edges
+synapse.storage.background_updates - 282 - ERROR - background_updates-0 - Error doing update
+...
+sqlite3.IntegrityError: UNIQUE constraint failed: state_group_edges.state_group, state_group_edges.prev_state_group
+```
+
+
+<details>
+<summary><b>Expand this section for steps to resolve this problem</b></summary>
+
+### On Postgres
+
+Connect to your database with `psql`.
+
+```sql
+BEGIN;
+DELETE FROM state_group_edges WHERE (ctid, state_group, prev_state_group) IN (
+  SELECT row_id, state_group, prev_state_group
+  FROM (
+    SELECT
+      ctid AS row_id,
+      MIN(ctid) OVER (PARTITION BY state_group, prev_state_group) AS min_row_id,
+      state_group,
+      prev_state_group
+    FROM state_group_edges
+  ) AS t1
+  WHERE row_id <> min_row_id
+);
+COMMIT;
+```
+
+
+### On SQLite
+
+At the command-line, use `sqlite3 path/to/your-homeserver-database.db`:
+
+```sql
+BEGIN;
+DELETE FROM state_group_edges WHERE (rowid, state_group, prev_state_group) IN (
+  SELECT row_id, state_group, prev_state_group
+  FROM (
+    SELECT
+      rowid AS row_id,
+      MIN(rowid) OVER (PARTITION BY state_group, prev_state_group) AS min_row_id,
+      state_group,
+      prev_state_group
+    FROM state_group_edges
+  )
+  WHERE row_id <> min_row_id
+);
+COMMIT;
+```
+
+
+### For more details
+
+[This comment on issue 11779](https://github.com/matrix-org/synapse/issues/11779#issuecomment-1131545970)
+has queries that can be used to check a database for this problem in advance.
+
+</details>
+
+
+
 # Upgrading to v1.59.0
 
 ## Device name lookup over federation has been disabled by default

synapse/storage/background_updates.py

@@ -535,6 +535,7 @@ def register_background_index_update(
         where_clause: Optional[str] = None,
         unique: bool = False,
         psql_only: bool = False,
+        replaces_index: Optional[str] = None,
     ) -> None:
         """Helper for store classes to do a background index addition
 
@@ -554,6 +555,8 @@ def register_background_index_update(
             unique: true to make a UNIQUE index
             psql_only: true to only create this index on psql databases (useful
                 for virtual sqlite tables)
+            replaces_index: The name of an index that this index replaces.
+                The named index will be dropped upon completion of the new index.
         """
 
         def create_index_psql(conn: Connection) -> None:
@@ -585,6 +588,12 @@ def create_index_psql(conn: Connection) -> None:
                 }
                 logger.debug("[SQL] %s", sql)
                 c.execute(sql)
+
+                if replaces_index is not None:
+                    # We drop the old index as the new index has now been created.
+                    sql = f"DROP INDEX IF EXISTS {replaces_index}"
+                    logger.debug("[SQL] %s", sql)
+                    c.execute(sql)
             finally:
                 conn.set_session(autocommit=False)  # type: ignore
 
@@ -613,6 +622,12 @@ def create_index_sqlite(conn: Connection) -> None:
             logger.debug("[SQL] %s", sql)
             c.execute(sql)
 
+            if replaces_index is not None:
+                # We drop the old index as the new index has now been created.
+                sql = f"DROP INDEX IF EXISTS {replaces_index}"
+                logger.debug("[SQL] %s", sql)
+                c.execute(sql)
+
         if isinstance(self.db_pool.engine, engines.PostgresEngine):
             runner: Optional[Callable[[Connection], None]] = create_index_psql
         elif psql_only:

synapse/storage/databases/state/bg_updates.py

@@ -195,6 +195,7 @@ class StateBackgroundUpdateStore(StateGroupBackgroundUpdateStore):
     STATE_GROUP_DEDUPLICATION_UPDATE_NAME = "state_group_state_deduplication"
     STATE_GROUP_INDEX_UPDATE_NAME = "state_group_state_type_index"
     STATE_GROUPS_ROOM_INDEX_UPDATE_NAME = "state_groups_room_id_idx"
+    STATE_GROUP_EDGES_UNIQUE_INDEX_UPDATE_NAME = "state_group_edges_unique_idx"
 
     def __init__(
         self,
@@ -217,6 +218,21 @@ def __init__(
             columns=["room_id"],
         )
 
+        # `state_group_edges` can cause severe performance issues if duplicate
+        # rows are introduced, which can accidentally be done by well-meaning
+        # server admins when trying to restore a database dump, etc.
+        # See https://github.com/matrix-org/synapse/issues/11779.
+        # Introduce a unique index to guard against that.
+        self.db_pool.updates.register_background_index_update(
+            self.STATE_GROUP_EDGES_UNIQUE_INDEX_UPDATE_NAME,
+            index_name="state_group_edges_unique_idx",
+            table="state_group_edges",
+            columns=["state_group", "prev_state_group"],
+            unique=True,
+            # The old index was on (state_group) and was not unique.
+            replaces_index="state_group_edges_idx",
+        )
+
     async def _background_deduplicate_state(
         self, progress: dict, batch_size: int
     ) -> int:

synapse/storage/schema/state/delta/70/08_state_group_edges_unique.sql

@@ -0,0 +1,17 @@
+/* Copyright 2022 The Matrix.org Foundation C.I.C
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *    http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+
+INSERT INTO background_updates (ordering, update_name, progress_json) VALUES
+    (7008, 'state_group_edges_unique_idx', '{}');