diff --git a/synapse/storage/schema/delta/16/remote_media_cache_index.sql b/synapse/storage/schema/delta/16/remote_media_cache_index.sql
new file mode 100644
index 0000000000..7a15265cb1
--- /dev/null
+++ b/synapse/storage/schema/delta/16/remote_media_cache_index.sql
@@ -0,0 +1,2 @@
+CREATE INDEX IF NOT EXISTS remote_media_cache_thumbnails_media_id
+ ON remote_media_cache_thumbnails (media_id);
\ No newline at end of file
diff --git a/synapse/storage/schema/delta/16/unique_constraints.sql b/synapse/storage/schema/delta/16/unique_constraints.sql
new file mode 100644
index 0000000000..b2b677e510
--- /dev/null
+++ b/synapse/storage/schema/delta/16/unique_constraints.sql
@@ -0,0 +1,64 @@
+
+-- We can use SQLite features here, since mysql support was only added in v16
+
+--
+DELETE FROM current_state_events WHERE rowid not in (
+ SELECT MIN(rowid) FROM current_state_events GROUP BY event_id
+);
+
+CREATE UNIQUE INDEX current_state_events_event_id ON current_state_events(event_id);
+
+--
+DELETE FROM room_memberships WHERE rowid not in (
+ SELECT MIN(rowid) FROM room_memberships GROUP BY event_id
+);
+
+CREATE UNIQUE INDEX room_memberships_event_id ON room_memberships(event_id);
+
+--
+DELETE FROM feedback WHERE rowid not in (
+ SELECT MIN(rowid) FROM feedback GROUP BY event_id
+);
+
+CREATE UNIQUE INDEX feedback_event_id ON feedback(event_id);
+
+--
+DELETE FROM topics WHERE rowid not in (
+ SELECT MIN(rowid) FROM topics GROUP BY event_id
+);
+
+CREATE UNIQUE INDEX topics_event_id ON topics(event_id);
+
+--
+DELETE FROM room_names WHERE rowid not in (
+ SELECT MIN(rowid) FROM room_names GROUP BY event_id
+);
+
+CREATE UNIQUE INDEX room_names_id ON room_names(event_id);
+
+--
+DELETE FROM presence WHERE rowid not in (
+ SELECT MIN(rowid) FROM presence GROUP BY user_id
+);
+
+CREATE UNIQUE INDEX presence_id ON presence(user_id);
+
+--
+DELETE FROM presence_allow_inbound WHERE rowid not in (
+ SELECT MIN(rowid) FROM presence_allow_inbound
+ GROUP BY observed_user_id, observer_user_id
+);
+
+CREATE UNIQUE INDEX presence_allow_inbound_observers ON presence_allow_inbound(
+ observed_user_id, observer_user_id
+);
+
+--
+DELETE FROM presence_list WHERE rowid not in (
+ SELECT MIN(rowid) FROM presence_list
+ GROUP BY user_id, observed_user_id
+);
+
+CREATE UNIQUE INDEX presence_list_observers ON presence_list(
+ user_id, observed_user_id
+);
diff --git a/synapse/storage/schema/delta/16/users.sql b/synapse/storage/schema/delta/16/users.sql
new file mode 100644
index 0000000000..1bbd1c0a17
--- /dev/null
+++ b/synapse/storage/schema/delta/16/users.sql
@@ -0,0 +1,56 @@
+-- Convert `access_tokens`.user from rowids to user strings.
+-- MUST BE DONE BEFORE REMOVING ID COLUMN FROM USERS TABLE BELOW
+CREATE TABLE IF NOT EXISTS new_access_tokens(
+ id BIGINT PRIMARY KEY,
+ user_id VARCHAR(150) NOT NULL,
+ device_id VARCHAR(150),
+ token VARCHAR(150) NOT NULL,
+ last_used BIGINT,
+ UNIQUE(token)
+);
+
+INSERT INTO new_access_tokens
+ SELECT a.id, u.name, a.device_id, a.token, a.last_used
+ FROM access_tokens as a
+ INNER JOIN users as u ON u.id = a.user_id;
+
+DROP TABLE access_tokens;
+
+ALTER TABLE new_access_tokens RENAME TO access_tokens;
+
+-- Remove ID column from `users` table
+CREATE TABLE IF NOT EXISTS new_users(
+ name VARCHAR(150),
+ password_hash VARCHAR(150),
+ creation_ts BIGINT,
+ admin BOOL DEFAULT 0 NOT NULL,
+ UNIQUE(name)
+);
+
+INSERT INTO new_users SELECT name, password_hash, creation_ts, admin FROM users;
+
+DROP TABLE users;
+
+ALTER TABLE new_users RENAME TO users;
+
+
+-- Remove UNIQUE constraint from `user_ips` table
+CREATE TABLE IF NOT EXISTS new_user_ips (
+ user VARCHAR(150) NOT NULL,
+ access_token VARCHAR(150) NOT NULL,
+ device_id VARCHAR(150),
+ ip VARCHAR(150) NOT NULL,
+ user_agent VARCHAR(150) NOT NULL,
+ last_seen BIGINT NOT NULL
+);
+
+INSERT INTO new_user_ips
+ SELECT user, access_token, device_id, ip, user_agent, last_seen FROM user_ips;
+
+DROP TABLE user_ips;
+
+ALTER TABLE new_user_ips RENAME TO user_ips;
+
+CREATE INDEX IF NOT EXISTS user_ips_user ON user_ips(user);
+CREATE INDEX IF NOT EXISTS user_ips_user_ip ON user_ips(user, access_token, ip);
+
diff --git a/synapse/storage/schema/full_schemas/16/application_services.sql b/synapse/storage/schema/full_schemas/16/application_services.sql
new file mode 100644
index 0000000000..7a5c2510d2
--- /dev/null
+++ b/synapse/storage/schema/full_schemas/16/application_services.sql
@@ -0,0 +1,48 @@
+/* Copyright 2015 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.
+ */
+
+CREATE TABLE IF NOT EXISTS application_services(
+ id BIGINT PRIMARY KEY,
+ url VARCHAR(150),
+ token VARCHAR(150),
+ hs_token VARCHAR(150),
+ sender VARCHAR(150),
+ UNIQUE(token)
+);
+
+CREATE TABLE IF NOT EXISTS application_services_regex(
+ id BIGINT PRIMARY KEY,
+ as_id BIGINT NOT NULL,
+ namespace INTEGER, /* enum[room_id|room_alias|user_id] */
+ regex VARCHAR(150),
+ FOREIGN KEY(as_id) REFERENCES application_services(id)
+);
+
+CREATE TABLE IF NOT EXISTS application_services_state(
+ as_id VARCHAR(150) PRIMARY KEY,
+ state VARCHAR(5),
+ last_txn INTEGER
+);
+
+CREATE TABLE IF NOT EXISTS application_services_txns(
+ as_id VARCHAR(150) NOT NULL,
+ txn_id INTEGER NOT NULL,
+ event_ids BLOB NOT NULL,
+ UNIQUE(as_id, txn_id)
+);
+
+CREATE INDEX IF NOT EXISTS application_services_txns_id ON application_services_txns (
+ as_id
+);
diff --git a/synapse/storage/schema/full_schemas/16/presence.sql b/synapse/storage/schema/full_schemas/16/presence.sql
index f3f86e5634..15a6ad3c79 100644
--- a/synapse/storage/schema/full_schemas/16/presence.sql
+++ b/synapse/storage/schema/full_schemas/16/presence.sql
@@ -36,3 +36,5 @@ CREATE TABLE IF NOT EXISTS presence_list(
accepted BOOLEAN NOT NULL,
UNIQUE (user_id, observed_user_id)
);
+
+CREATE INDEX IF NOT EXISTS presence_list_user_id ON presence_list (user_id);
diff --git a/synapse/storage/schema/full_schemas/16/push.sql b/synapse/storage/schema/full_schemas/16/push.sql
new file mode 100644
index 0000000000..4c8faa9213
--- /dev/null
+++ b/synapse/storage/schema/full_schemas/16/push.sql
@@ -0,0 +1,73 @@
+/* Copyright 2015 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.
+ */
+
+CREATE TABLE IF NOT EXISTS rejections(
+ event_id VARCHAR(150) NOT NULL,
+ reason VARCHAR(150) NOT NULL,
+ last_check VARCHAR(150) NOT NULL,
+ UNIQUE (event_id)
+);
+
+-- Push notification endpoints that users have configured
+CREATE TABLE IF NOT EXISTS pushers (
+ id BIGINT PRIMARY KEY,
+ user_name VARCHAR(150) NOT NULL,
+ profile_tag VARCHAR(32) NOT NULL,
+ kind VARCHAR(8) NOT NULL,
+ app_id VARCHAR(64) NOT NULL,
+ app_display_name VARCHAR(64) NOT NULL,
+ device_display_name VARCHAR(128) NOT NULL,
+ pushkey VARBINARY(512) NOT NULL,
+ ts BIGINT NOT NULL,
+ lang VARCHAR(8),
+ data BLOB,
+ last_token TEXT,
+ last_success BIGINT,
+ failing_since BIGINT,
+ UNIQUE (app_id, pushkey)
+);
+
+CREATE TABLE IF NOT EXISTS push_rules (
+ id BIGINT PRIMARY KEY,
+ user_name VARCHAR(150) NOT NULL,
+ rule_id VARCHAR(150) NOT NULL,
+ priority_class TINYINT NOT NULL,
+ priority INTEGER NOT NULL DEFAULT 0,
+ conditions VARCHAR(150) NOT NULL,
+ actions VARCHAR(150) NOT NULL,
+ UNIQUE(user_name, rule_id)
+);
+
+CREATE INDEX IF NOT EXISTS push_rules_user_name on push_rules (user_name);
+
+CREATE TABLE IF NOT EXISTS user_filters(
+ user_id VARCHAR(150),
+ filter_id BIGINT,
+ filter_json BLOB
+);
+
+CREATE INDEX IF NOT EXISTS user_filters_by_user_id_filter_id ON user_filters(
+ user_id, filter_id
+);
+
+CREATE TABLE IF NOT EXISTS push_rules_enable (
+ id BIGINT PRIMARY KEY,
+ user_name VARCHAR(150) NOT NULL,
+ rule_id VARCHAR(150) NOT NULL,
+ enabled TINYINT,
+ UNIQUE(user_name, rule_id)
+);
+
+CREATE INDEX IF NOT EXISTS push_rules_enable_user_name on push_rules_enable (user_name);
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