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-rw-r--r--.gitignore1
-rw-r--r--MANIFEST.in4
-rw-r--r--changelog.d/2380.bugfix1
-rw-r--r--changelog.d/3436.bugfix1
-rw-r--r--changelog.d/4088.bugfix1
-rw-r--r--changelog.d/6084.misc1
-rw-r--r--changelog.d/6114.feature1
-rw-r--r--changelog.d/6127.misc1
-rw-r--r--changelog.d/6137.misc1
-rw-r--r--changelog.d/6155.bugfix1
-rw-r--r--changelog.d/6156.misc1
-rw-r--r--changelog.d/6168.bugfix1
-rw-r--r--changelog.d/6184.misc1
-rw-r--r--changelog.d/6186.bugfix1
-rw-r--r--changelog.d/6187.bugfix1
-rw-r--r--changelog.d/6191.misc1
-rw-r--r--changelog.d/6195.bugfix1
-rw-r--r--docs/sample_config.yaml1
-rw-r--r--mypy.ini16
-rw-r--r--snap/snapcraft.yaml22
-rw-r--r--synapse/__init__.py8
-rw-r--r--synapse/app/homeserver.py6
-rw-r--r--synapse/config/_base.py191
-rw-r--r--synapse/config/_base.pyi135
-rw-r--r--synapse/config/api.py2
-rw-r--r--synapse/config/appservice.py2
-rw-r--r--synapse/config/captcha.py2
-rw-r--r--synapse/config/cas.py5
-rw-r--r--synapse/config/consent_config.py3
-rw-r--r--synapse/config/database.py2
-rw-r--r--synapse/config/emailconfig.py2
-rw-r--r--synapse/config/groups.py2
-rw-r--r--synapse/config/homeserver.py68
-rw-r--r--synapse/config/jwt_config.py2
-rw-r--r--synapse/config/key.py2
-rw-r--r--synapse/config/logger.py2
-rw-r--r--synapse/config/metrics.py2
-rw-r--r--synapse/config/password.py2
-rw-r--r--synapse/config/password_auth_providers.py2
-rw-r--r--synapse/config/push.py2
-rw-r--r--synapse/config/ratelimiting.py2
-rw-r--r--synapse/config/registration.py4
-rw-r--r--synapse/config/repository.py2
-rw-r--r--synapse/config/room_directory.py2
-rw-r--r--synapse/config/saml2_config.py2
-rw-r--r--synapse/config/server.py2
-rw-r--r--synapse/config/server_notices_config.py2
-rw-r--r--synapse/config/spam_checker.py2
-rw-r--r--synapse/config/stats.py2
-rw-r--r--synapse/config/third_party_event_rules.py2
-rw-r--r--synapse/config/tls.py9
-rw-r--r--synapse/config/tracer.py2
-rw-r--r--synapse/config/user_directory.py2
-rw-r--r--synapse/config/voip.py2
-rw-r--r--synapse/config/workers.py2
-rw-r--r--synapse/groups/groups_server.py20
-rw-r--r--synapse/handlers/presence.py16
-rw-r--r--synapse/handlers/room.py4
-rw-r--r--synapse/handlers/room_member.py62
-rw-r--r--synapse/handlers/stats.py12
-rw-r--r--synapse/handlers/user_directory.py17
-rw-r--r--synapse/http/server.py2
-rw-r--r--synapse/logging/opentracing.py14
-rw-r--r--synapse/rest/client/v1/login.py4
-rw-r--r--synapse/rest/client/v2_alpha/filter.py12
-rw-r--r--synapse/rest/client/v2_alpha/sync.py41
-rw-r--r--synapse/rest/media/v1/preview_url_resource.py4
-rw-r--r--synapse/storage/_base.py56
-rw-r--r--synapse/storage/deviceinbox.py14
-rw-r--r--synapse/storage/devices.py14
-rw-r--r--synapse/storage/engines/postgres.py13
-rw-r--r--synapse/storage/engines/sqlite.py6
-rw-r--r--synapse/storage/event_federation.py9
-rw-r--r--synapse/storage/events.py44
-rw-r--r--synapse/storage/events_bg_updates.py55
-rw-r--r--synapse/storage/events_worker.py28
-rw-r--r--synapse/storage/filtering.py4
-rw-r--r--synapse/storage/monthly_active_users.py101
-rw-r--r--synapse/storage/presence.py14
-rw-r--r--synapse/storage/pusher.py2
-rw-r--r--synapse/storage/receipts.py53
-rw-r--r--synapse/storage/roommember.py18
-rw-r--r--synapse/storage/schema/delta/56/redaction_censor3_fix_update.sql.postgres17
-rw-r--r--synapse/storage/schema/delta/56/unique_user_filter_index.py58
-rw-r--r--synapse/storage/search.py13
-rw-r--r--synapse/storage/state_deltas.py38
-rw-r--r--synapse/storage/user_erasure_store.py18
-rw-r--r--synapse/util/patch_inline_callbacks.py219
-rw-r--r--tests/__init__.py4
-rw-r--r--tests/config/test_tls.py25
-rw-r--r--tests/handlers/test_typing.py2
-rw-r--r--tests/patch_inline_callbacks.py94
-rw-r--r--tests/rest/admin/test_admin.py2
-rw-r--r--tests/rest/client/v1/test_rooms.py9
-rw-r--r--tests/rest/client/v2_alpha/test_filter.py2
-rw-r--r--tests/storage/test_event_federation.py2
-rw-r--r--tests/storage/test_monthly_active_users.py58
-rw-r--r--tox.ini3
98 files changed, 1269 insertions, 474 deletions
diff --git a/.gitignore b/.gitignore
index 747b8714d7..af36c00cfa 100644
--- a/.gitignore
+++ b/.gitignore
@@ -7,6 +7,7 @@
 *.egg-info
 *.lock
 *.pyc
+*.snap
 *.tac
 _trial_temp/
 _trial_temp*/
diff --git a/MANIFEST.in b/MANIFEST.in
index 9c2902b8d2..b22be58f3d 100644
--- a/MANIFEST.in
+++ b/MANIFEST.in
@@ -47,7 +47,5 @@ prune debian
 prune demo/etc
 prune docker
 prune mypy.ini
+prune snap
 prune stubs
-
-exclude jenkins*
-recursive-exclude jenkins *.sh
diff --git a/changelog.d/2380.bugfix b/changelog.d/2380.bugfix
new file mode 100644
index 0000000000..eae3206031
--- /dev/null
+++ b/changelog.d/2380.bugfix
@@ -0,0 +1 @@
+Return an HTTP 404 instead of 400 when requesting a filter by ID that is unknown to the server. Thanks to @krombel for contributing this!
diff --git a/changelog.d/3436.bugfix b/changelog.d/3436.bugfix
new file mode 100644
index 0000000000..15714a11e0
--- /dev/null
+++ b/changelog.d/3436.bugfix
@@ -0,0 +1 @@
+Fix a problem where users could be invited twice to the same group.
diff --git a/changelog.d/4088.bugfix b/changelog.d/4088.bugfix
new file mode 100644
index 0000000000..61722b6224
--- /dev/null
+++ b/changelog.d/4088.bugfix
@@ -0,0 +1 @@
+Added domain validation when including a list of invitees upon room creation.
\ No newline at end of file
diff --git a/changelog.d/6084.misc b/changelog.d/6084.misc
new file mode 100644
index 0000000000..3c33701651
--- /dev/null
+++ b/changelog.d/6084.misc
@@ -0,0 +1 @@
+Add snapcraft packaging information. Contributed by @devec0.
diff --git a/changelog.d/6114.feature b/changelog.d/6114.feature
new file mode 100644
index 0000000000..a34ab12148
--- /dev/null
+++ b/changelog.d/6114.feature
@@ -0,0 +1 @@
+CAS login now provides a default display name for users if a `displayname_attribute` is set in the configuration file.
diff --git a/changelog.d/6127.misc b/changelog.d/6127.misc
new file mode 100644
index 0000000000..7bfbcfc252
--- /dev/null
+++ b/changelog.d/6127.misc
@@ -0,0 +1 @@
+Add env var to turn on tracking of log context changes.
diff --git a/changelog.d/6137.misc b/changelog.d/6137.misc
new file mode 100644
index 0000000000..92a02e71c3
--- /dev/null
+++ b/changelog.d/6137.misc
@@ -0,0 +1 @@
+Refactor configuration loading to allow better typechecking.
diff --git a/changelog.d/6155.bugfix b/changelog.d/6155.bugfix
new file mode 100644
index 0000000000..e32c0dce09
--- /dev/null
+++ b/changelog.d/6155.bugfix
@@ -0,0 +1 @@
+Fix transferring notifications and tags when joining an upgraded room that is new to your server.
\ No newline at end of file
diff --git a/changelog.d/6156.misc b/changelog.d/6156.misc
new file mode 100644
index 0000000000..49525e9416
--- /dev/null
+++ b/changelog.d/6156.misc
@@ -0,0 +1 @@
+Use Postgres ANY for selecting many values.
diff --git a/changelog.d/6168.bugfix b/changelog.d/6168.bugfix
new file mode 100644
index 0000000000..39e8e9d019
--- /dev/null
+++ b/changelog.d/6168.bugfix
@@ -0,0 +1 @@
+Fix monthly active user reaping where reserved users are specified.
diff --git a/changelog.d/6184.misc b/changelog.d/6184.misc
new file mode 100644
index 0000000000..30b3e56082
--- /dev/null
+++ b/changelog.d/6184.misc
@@ -0,0 +1 @@
+Update `user_filters` table to have a unique index, and non-null columns. Thanks to @pik for contributing this.
\ No newline at end of file
diff --git a/changelog.d/6186.bugfix b/changelog.d/6186.bugfix
new file mode 100644
index 0000000000..199ec69032
--- /dev/null
+++ b/changelog.d/6186.bugfix
@@ -0,0 +1 @@
+Fix bug where we were updating censored events as bytes rather than text, occaisonally causing invalid JSON being inserted breaking APIs that attempted to fetch such events.
diff --git a/changelog.d/6187.bugfix b/changelog.d/6187.bugfix
new file mode 100644
index 0000000000..6142c5b98d
--- /dev/null
+++ b/changelog.d/6187.bugfix
@@ -0,0 +1 @@
+Fix occasional missed updates in the room and user directories.
\ No newline at end of file
diff --git a/changelog.d/6191.misc b/changelog.d/6191.misc
new file mode 100644
index 0000000000..3c33701651
--- /dev/null
+++ b/changelog.d/6191.misc
@@ -0,0 +1 @@
+Add snapcraft packaging information. Contributed by @devec0.
diff --git a/changelog.d/6195.bugfix b/changelog.d/6195.bugfix
new file mode 100644
index 0000000000..d22935dbcd
--- /dev/null
+++ b/changelog.d/6195.bugfix
@@ -0,0 +1 @@
+Fix tracing of non-JSON APIs, /media, /key etc.
diff --git a/docs/sample_config.yaml b/docs/sample_config.yaml
index 43893399ad..8226978ba6 100644
--- a/docs/sample_config.yaml
+++ b/docs/sample_config.yaml
@@ -1220,6 +1220,7 @@ saml2_config:
 #   enabled: true
 #   server_url: "https://cas-server.com"
 #   service_url: "https://homeserver.domain.com:8448"
+#   #displayname_attribute: name
 #   #required_attributes:
 #   #    name: value
 
diff --git a/mypy.ini b/mypy.ini
index 8788574ee3..ffadaddc0b 100644
--- a/mypy.ini
+++ b/mypy.ini
@@ -4,10 +4,6 @@ plugins=mypy_zope:plugin
 follow_imports=skip
 mypy_path=stubs
 
-[mypy-synapse.config.homeserver]
-# this is a mess because of the metaclass shenanigans
-ignore_errors = True
-
 [mypy-zope]
 ignore_missing_imports = True
 
@@ -52,3 +48,15 @@ ignore_missing_imports = True
 
 [mypy-signedjson.*]
 ignore_missing_imports = True
+
+[mypy-prometheus_client.*]
+ignore_missing_imports = True
+
+[mypy-service_identity.*]
+ignore_missing_imports = True
+
+[mypy-daemonize]
+ignore_missing_imports = True
+
+[mypy-sentry_sdk]
+ignore_missing_imports = True
diff --git a/snap/snapcraft.yaml b/snap/snapcraft.yaml
new file mode 100644
index 0000000000..1f7df71db2
--- /dev/null
+++ b/snap/snapcraft.yaml
@@ -0,0 +1,22 @@
+name: matrix-synapse
+base: core18
+version: git 
+summary: Reference Matrix homeserver
+description: |
+  Synapse is the reference Matrix homeserver.
+  Matrix is a federated and decentralised instant messaging and VoIP system.
+
+grade: stable 
+confinement: strict 
+
+apps:
+  matrix-synapse: 
+    command: synctl --no-daemonize start $SNAP_COMMON/homeserver.yaml
+    stop-command: synctl -c $SNAP_COMMON stop
+    plugs: [network-bind, network]
+    daemon: simple 
+parts:
+  matrix-synapse:
+    source: .
+    plugin: python
+    python-version: python3
diff --git a/synapse/__init__.py b/synapse/__init__.py
index 2d52d26af5..56df3f5ac6 100644
--- a/synapse/__init__.py
+++ b/synapse/__init__.py
@@ -17,6 +17,7 @@
 """ This is a reference implementation of a Matrix home server.
 """
 
+import os
 import sys
 
 # Check that we're not running on an unsupported Python version.
@@ -36,3 +37,10 @@ except ImportError:
     pass
 
 __version__ = "1.4.0"
+
+if bool(os.environ.get("SYNAPSE_TEST_PATCH_LOG_CONTEXTS", False)):
+    # We import here so that we don't have to install a bunch of deps when
+    # running the packaging tox test.
+    from synapse.util.patch_inline_callbacks import do_patch
+
+    do_patch()
diff --git a/synapse/app/homeserver.py b/synapse/app/homeserver.py
index 774326dff9..eb54f56853 100644
--- a/synapse/app/homeserver.py
+++ b/synapse/app/homeserver.py
@@ -605,13 +605,13 @@ def run(hs):
     @defer.inlineCallbacks
     def generate_monthly_active_users():
         current_mau_count = 0
-        reserved_count = 0
+        reserved_users = ()
         store = hs.get_datastore()
         if hs.config.limit_usage_by_mau or hs.config.mau_stats_only:
             current_mau_count = yield store.get_monthly_active_count()
-            reserved_count = yield store.get_registered_reserved_users_count()
+            reserved_users = yield store.get_registered_reserved_users()
         current_mau_gauge.set(float(current_mau_count))
-        registered_reserved_users_mau_gauge.set(float(reserved_count))
+        registered_reserved_users_mau_gauge.set(float(len(reserved_users)))
         max_mau_gauge.set(float(hs.config.max_mau_value))
 
     def start_generate_monthly_active_users():
diff --git a/synapse/config/_base.py b/synapse/config/_base.py
index 31f6530978..08619404bb 100644
--- a/synapse/config/_base.py
+++ b/synapse/config/_base.py
@@ -18,7 +18,9 @@
 import argparse
 import errno
 import os
+from collections import OrderedDict
 from textwrap import dedent
+from typing import Any, MutableMapping, Optional
 
 from six import integer_types
 
@@ -51,7 +53,56 @@ Missing mandatory `server_name` config option.
 """
 
 
+def path_exists(file_path):
+    """Check if a file exists
+
+    Unlike os.path.exists, this throws an exception if there is an error
+    checking if the file exists (for example, if there is a perms error on
+    the parent dir).
+
+    Returns:
+        bool: True if the file exists; False if not.
+    """
+    try:
+        os.stat(file_path)
+        return True
+    except OSError as e:
+        if e.errno != errno.ENOENT:
+            raise e
+        return False
+
+
 class Config(object):
+    """
+    A configuration section, containing configuration keys and values.
+
+    Attributes:
+        section (str): The section title of this config object, such as
+            "tls" or "logger". This is used to refer to it on the root
+            logger (for example, `config.tls.some_option`). Must be
+            defined in subclasses.
+    """
+
+    section = None
+
+    def __init__(self, root_config=None):
+        self.root = root_config
+
+    def __getattr__(self, item: str) -> Any:
+        """
+        Try and fetch a configuration option that does not exist on this class.
+
+        This is so that existing configs that rely on `self.value`, where value
+        is actually from a different config section, continue to work.
+        """
+        if item in ["generate_config_section", "read_config"]:
+            raise AttributeError(item)
+
+        if self.root is None:
+            raise AttributeError(item)
+        else:
+            return self.root._get_unclassed_config(self.section, item)
+
     @staticmethod
     def parse_size(value):
         if isinstance(value, integer_types):
@@ -88,22 +139,7 @@ class Config(object):
 
     @classmethod
     def path_exists(cls, file_path):
-        """Check if a file exists
-
-        Unlike os.path.exists, this throws an exception if there is an error
-        checking if the file exists (for example, if there is a perms error on
-        the parent dir).
-
-        Returns:
-            bool: True if the file exists; False if not.
-        """
-        try:
-            os.stat(file_path)
-            return True
-        except OSError as e:
-            if e.errno != errno.ENOENT:
-                raise e
-            return False
+        return path_exists(file_path)
 
     @classmethod
     def check_file(cls, file_path, config_name):
@@ -136,42 +172,106 @@ class Config(object):
         with open(file_path) as file_stream:
             return file_stream.read()
 
-    def invoke_all(self, name, *args, **kargs):
-        """Invoke all instance methods with the given name and arguments in the
-        class's MRO.
+
+class RootConfig(object):
+    """
+    Holder of an application's configuration.
+
+    What configuration this object holds is defined by `config_classes`, a list
+    of Config classes that will be instantiated and given the contents of a
+    configuration file to read. They can then be accessed on this class by their
+    section name, defined in the Config or dynamically set to be the name of the
+    class, lower-cased and with "Config" removed.
+    """
+
+    config_classes = []
+
+    def __init__(self):
+        self._configs = OrderedDict()
+
+        for config_class in self.config_classes:
+            if config_class.section is None:
+                raise ValueError("%r requires a section name" % (config_class,))
+
+            try:
+                conf = config_class(self)
+            except Exception as e:
+                raise Exception("Failed making %s: %r" % (config_class.section, e))
+            self._configs[config_class.section] = conf
+
+    def __getattr__(self, item: str) -> Any:
+        """
+        Redirect lookups on this object either to config objects, or values on
+        config objects, so that `config.tls.blah` works, as well as legacy uses
+        of things like `config.server_name`. It will first look up the config
+        section name, and then values on those config classes.
+        """
+        if item in self._configs.keys():
+            return self._configs[item]
+
+        return self._get_unclassed_config(None, item)
+
+    def _get_unclassed_config(self, asking_section: Optional[str], item: str):
+        """
+        Fetch a config value from one of the instantiated config classes that
+        has not been fetched directly.
+
+        Args:
+            asking_section: If this check is coming from a Config child, which
+                one? This section will not be asked if it has the value.
+            item: The configuration value key.
+
+        Raises:
+            AttributeError if no config classes have the config key. The body
+                will contain what sections were checked.
+        """
+        for key, val in self._configs.items():
+            if key == asking_section:
+                continue
+
+            if item in dir(val):
+                return getattr(val, item)
+
+        raise AttributeError(item, "not found in %s" % (list(self._configs.keys()),))
+
+    def invoke_all(self, func_name: str, *args, **kwargs) -> MutableMapping[str, Any]:
+        """
+        Invoke a function on all instantiated config objects this RootConfig is
+        configured to use.
 
         Args:
-            name (str): Name of function to invoke
+            func_name: Name of function to invoke
             *args
             **kwargs
-
         Returns:
-            list: The list of the return values from each method called
+            ordered dictionary of config section name and the result of the
+            function from it.
         """
-        results = []
-        for cls in type(self).mro():
-            if name in cls.__dict__:
-                results.append(getattr(cls, name)(self, *args, **kargs))
-        return results
+        res = OrderedDict()
+
+        for name, config in self._configs.items():
+            if hasattr(config, func_name):
+                res[name] = getattr(config, func_name)(*args, **kwargs)
+
+        return res
 
     @classmethod
-    def invoke_all_static(cls, name, *args, **kargs):
-        """Invoke all static methods with the given name and arguments in the
-        class's MRO.
+    def invoke_all_static(cls, func_name: str, *args, **kwargs):
+        """
+        Invoke a static function on config objects this RootConfig is
+        configured to use.
 
         Args:
-            name (str): Name of function to invoke
+            func_name: Name of function to invoke
             *args
             **kwargs
-
         Returns:
-            list: The list of the return values from each method called
+            ordered dictionary of config section name and the result of the
+            function from it.
         """
-        results = []
-        for c in cls.mro():
-            if name in c.__dict__:
-                results.append(getattr(c, name)(*args, **kargs))
-        return results
+        for config in cls.config_classes:
+            if hasattr(config, func_name):
+                getattr(config, func_name)(*args, **kwargs)
 
     def generate_config(
         self,
@@ -187,7 +287,8 @@ class Config(object):
         tls_private_key_path=None,
         acme_domain=None,
     ):
-        """Build a default configuration file
+        """
+        Build a default configuration file
 
         This is used when the user explicitly asks us to generate a config file
         (eg with --generate_config).
@@ -242,6 +343,7 @@ class Config(object):
         Returns:
             str: the yaml config file
         """
+
         return "\n\n".join(
             dedent(conf)
             for conf in self.invoke_all(
@@ -257,7 +359,7 @@ class Config(object):
                 tls_certificate_path=tls_certificate_path,
                 tls_private_key_path=tls_private_key_path,
                 acme_domain=acme_domain,
-            )
+            ).values()
         )
 
     @classmethod
@@ -444,7 +546,7 @@ class Config(object):
                 )
 
             (config_path,) = config_files
-            if not cls.path_exists(config_path):
+            if not path_exists(config_path):
                 print("Generating config file %s" % (config_path,))
 
                 if config_args.data_directory:
@@ -469,7 +571,7 @@ class Config(object):
                     open_private_ports=config_args.open_private_ports,
                 )
 
-                if not cls.path_exists(config_dir_path):
+                if not path_exists(config_dir_path):
                     os.makedirs(config_dir_path)
                 with open(config_path, "w") as config_file:
                     config_file.write("# vim:ft=yaml\n\n")
@@ -518,7 +620,7 @@ class Config(object):
 
         return obj
 
-    def parse_config_dict(self, config_dict, config_dir_path, data_dir_path):
+    def parse_config_dict(self, config_dict, config_dir_path=None, data_dir_path=None):
         """Read the information from the config dict into this Config object.
 
         Args:
@@ -607,3 +709,6 @@ def find_config_files(search_paths):
             else:
                 config_files.append(config_path)
     return config_files
+
+
+__all__ = ["Config", "RootConfig"]
diff --git a/synapse/config/_base.pyi b/synapse/config/_base.pyi
new file mode 100644
index 0000000000..86bc965ee4
--- /dev/null
+++ b/synapse/config/_base.pyi
@@ -0,0 +1,135 @@
+from typing import Any, List, Optional
+
+from synapse.config import (
+    api,
+    appservice,
+    captcha,
+    cas,
+    consent_config,
+    database,
+    emailconfig,
+    groups,
+    jwt_config,
+    key,
+    logger,
+    metrics,
+    password,
+    password_auth_providers,
+    push,
+    ratelimiting,
+    registration,
+    repository,
+    room_directory,
+    saml2_config,
+    server,
+    server_notices_config,
+    spam_checker,
+    stats,
+    third_party_event_rules,
+    tls,
+    tracer,
+    user_directory,
+    voip,
+    workers,
+)
+
+class ConfigError(Exception): ...
+
+MISSING_REPORT_STATS_CONFIG_INSTRUCTIONS: str
+MISSING_REPORT_STATS_SPIEL: str
+MISSING_SERVER_NAME: str
+
+def path_exists(file_path: str): ...
+
+class RootConfig:
+    server: server.ServerConfig
+    tls: tls.TlsConfig
+    database: database.DatabaseConfig
+    logging: logger.LoggingConfig
+    ratelimit: ratelimiting.RatelimitConfig
+    media: repository.ContentRepositoryConfig
+    captcha: captcha.CaptchaConfig
+    voip: voip.VoipConfig
+    registration: registration.RegistrationConfig
+    metrics: metrics.MetricsConfig
+    api: api.ApiConfig
+    appservice: appservice.AppServiceConfig
+    key: key.KeyConfig
+    saml2: saml2_config.SAML2Config
+    cas: cas.CasConfig
+    jwt: jwt_config.JWTConfig
+    password: password.PasswordConfig
+    email: emailconfig.EmailConfig
+    worker: workers.WorkerConfig
+    authproviders: password_auth_providers.PasswordAuthProviderConfig
+    push: push.PushConfig
+    spamchecker: spam_checker.SpamCheckerConfig
+    groups: groups.GroupsConfig
+    userdirectory: user_directory.UserDirectoryConfig
+    consent: consent_config.ConsentConfig
+    stats: stats.StatsConfig
+    servernotices: server_notices_config.ServerNoticesConfig
+    roomdirectory: room_directory.RoomDirectoryConfig
+    thirdpartyrules: third_party_event_rules.ThirdPartyRulesConfig
+    tracer: tracer.TracerConfig
+
+    config_classes: List = ...
+    def __init__(self) -> None: ...
+    def invoke_all(self, func_name: str, *args: Any, **kwargs: Any): ...
+    @classmethod
+    def invoke_all_static(cls, func_name: str, *args: Any, **kwargs: Any) -> None: ...
+    def __getattr__(self, item: str): ...
+    def parse_config_dict(
+        self,
+        config_dict: Any,
+        config_dir_path: Optional[Any] = ...,
+        data_dir_path: Optional[Any] = ...,
+    ) -> None: ...
+    read_config: Any = ...
+    def generate_config(
+        self,
+        config_dir_path: str,
+        data_dir_path: str,
+        server_name: str,
+        generate_secrets: bool = ...,
+        report_stats: Optional[str] = ...,
+        open_private_ports: bool = ...,
+        listeners: Optional[Any] = ...,
+        database_conf: Optional[Any] = ...,
+        tls_certificate_path: Optional[str] = ...,
+        tls_private_key_path: Optional[str] = ...,
+        acme_domain: Optional[str] = ...,
+    ): ...
+    @classmethod
+    def load_or_generate_config(cls, description: Any, argv: Any): ...
+    @classmethod
+    def load_config(cls, description: Any, argv: Any): ...
+    @classmethod
+    def add_arguments_to_parser(cls, config_parser: Any) -> None: ...
+    @classmethod
+    def load_config_with_parser(cls, parser: Any, argv: Any): ...
+    def generate_missing_files(
+        self, config_dict: dict, config_dir_path: str
+    ) -> None: ...
+
+class Config:
+    root: RootConfig
+    def __init__(self, root_config: Optional[RootConfig] = ...) -> None: ...
+    def __getattr__(self, item: str, from_root: bool = ...): ...
+    @staticmethod
+    def parse_size(value: Any): ...
+    @staticmethod
+    def parse_duration(value: Any): ...
+    @staticmethod
+    def abspath(file_path: Optional[str]): ...
+    @classmethod
+    def path_exists(cls, file_path: str): ...
+    @classmethod
+    def check_file(cls, file_path: str, config_name: str): ...
+    @classmethod
+    def ensure_directory(cls, dir_path: str): ...
+    @classmethod
+    def read_file(cls, file_path: str, config_name: str): ...
+
+def read_config_files(config_files: List[str]): ...
+def find_config_files(search_paths: List[str]): ...
diff --git a/synapse/config/api.py b/synapse/config/api.py
index dddea79a8a..74cd53a8ed 100644
--- a/synapse/config/api.py
+++ b/synapse/config/api.py
@@ -18,6 +18,8 @@ from ._base import Config
 
 
 class ApiConfig(Config):
+    section = "api"
+
     def read_config(self, config, **kwargs):
         self.room_invite_state_types = config.get(
             "room_invite_state_types",
diff --git a/synapse/config/appservice.py b/synapse/config/appservice.py
index 28d36b1bc3..9b4682222d 100644
--- a/synapse/config/appservice.py
+++ b/synapse/config/appservice.py
@@ -30,6 +30,8 @@ logger = logging.getLogger(__name__)
 
 
 class AppServiceConfig(Config):
+    section = "appservice"
+
     def read_config(self, config, **kwargs):
         self.app_service_config_files = config.get("app_service_config_files", [])
         self.notify_appservices = config.get("notify_appservices", True)
diff --git a/synapse/config/captcha.py b/synapse/config/captcha.py
index 8dac8152cf..44bd5c6799 100644
--- a/synapse/config/captcha.py
+++ b/synapse/config/captcha.py
@@ -16,6 +16,8 @@ from ._base import Config
 
 
 class CaptchaConfig(Config):
+    section = "captcha"
+
     def read_config(self, config, **kwargs):
         self.recaptcha_private_key = config.get("recaptcha_private_key")
         self.recaptcha_public_key = config.get("recaptcha_public_key")
diff --git a/synapse/config/cas.py b/synapse/config/cas.py
index ebe34d933b..4526c1a67b 100644
--- a/synapse/config/cas.py
+++ b/synapse/config/cas.py
@@ -22,17 +22,21 @@ class CasConfig(Config):
     cas_server_url: URL of CAS server
     """
 
+    section = "cas"
+
     def read_config(self, config, **kwargs):
         cas_config = config.get("cas_config", None)
         if cas_config:
             self.cas_enabled = cas_config.get("enabled", True)
             self.cas_server_url = cas_config["server_url"]
             self.cas_service_url = cas_config["service_url"]
+            self.cas_displayname_attribute = cas_config.get("displayname_attribute")
             self.cas_required_attributes = cas_config.get("required_attributes", {})
         else:
             self.cas_enabled = False
             self.cas_server_url = None
             self.cas_service_url = None
+            self.cas_displayname_attribute = None
             self.cas_required_attributes = {}
 
     def generate_config_section(self, config_dir_path, server_name, **kwargs):
@@ -43,6 +47,7 @@ class CasConfig(Config):
         #   enabled: true
         #   server_url: "https://cas-server.com"
         #   service_url: "https://homeserver.domain.com:8448"
+        #   #displayname_attribute: name
         #   #required_attributes:
         #   #    name: value
         """
diff --git a/synapse/config/consent_config.py b/synapse/config/consent_config.py
index 48976e17b1..62c4c44d60 100644
--- a/synapse/config/consent_config.py
+++ b/synapse/config/consent_config.py
@@ -73,6 +73,9 @@ DEFAULT_CONFIG = """\
 
 
 class ConsentConfig(Config):
+
+    section = "consent"
+
     def __init__(self, *args):
         super(ConsentConfig, self).__init__(*args)
 
diff --git a/synapse/config/database.py b/synapse/config/database.py
index 118aafbd4a..0e2509f0b1 100644
--- a/synapse/config/database.py
+++ b/synapse/config/database.py
@@ -21,6 +21,8 @@ from ._base import Config
 
 
 class DatabaseConfig(Config):
+    section = "database"
+
     def read_config(self, config, **kwargs):
         self.event_cache_size = self.parse_size(config.get("event_cache_size", "10K"))
 
diff --git a/synapse/config/emailconfig.py b/synapse/config/emailconfig.py
index d9b43de660..658897a77e 100644
--- a/synapse/config/emailconfig.py
+++ b/synapse/config/emailconfig.py
@@ -28,6 +28,8 @@ from ._base import Config, ConfigError
 
 
 class EmailConfig(Config):
+    section = "email"
+
     def read_config(self, config, **kwargs):
         # TODO: We should separate better the email configuration from the notification
         # and account validity config.
diff --git a/synapse/config/groups.py b/synapse/config/groups.py
index 2a522b5f44..d6862d9a64 100644
--- a/synapse/config/groups.py
+++ b/synapse/config/groups.py
@@ -17,6 +17,8 @@ from ._base import Config
 
 
 class GroupsConfig(Config):
+    section = "groups"
+
     def read_config(self, config, **kwargs):
         self.enable_group_creation = config.get("enable_group_creation", False)
         self.group_creation_prefix = config.get("group_creation_prefix", "")
diff --git a/synapse/config/homeserver.py b/synapse/config/homeserver.py
index 72acad4f18..6e348671c7 100644
--- a/synapse/config/homeserver.py
+++ b/synapse/config/homeserver.py
@@ -14,6 +14,7 @@
 # See the License for the specific language governing permissions and
 # limitations under the License.
 
+from ._base import RootConfig
 from .api import ApiConfig
 from .appservice import AppServiceConfig
 from .captcha import CaptchaConfig
@@ -46,36 +47,37 @@ from .voip import VoipConfig
 from .workers import WorkerConfig
 
 
-class HomeServerConfig(
-    ServerConfig,
-    TlsConfig,
-    DatabaseConfig,
-    LoggingConfig,
-    RatelimitConfig,
-    ContentRepositoryConfig,
-    CaptchaConfig,
-    VoipConfig,
-    RegistrationConfig,
-    MetricsConfig,
-    ApiConfig,
-    AppServiceConfig,
-    KeyConfig,
-    SAML2Config,
-    CasConfig,
-    JWTConfig,
-    PasswordConfig,
-    EmailConfig,
-    WorkerConfig,
-    PasswordAuthProviderConfig,
-    PushConfig,
-    SpamCheckerConfig,
-    GroupsConfig,
-    UserDirectoryConfig,
-    ConsentConfig,
-    StatsConfig,
-    ServerNoticesConfig,
-    RoomDirectoryConfig,
-    ThirdPartyRulesConfig,
-    TracerConfig,
-):
-    pass
+class HomeServerConfig(RootConfig):
+
+    config_classes = [
+        ServerConfig,
+        TlsConfig,
+        DatabaseConfig,
+        LoggingConfig,
+        RatelimitConfig,
+        ContentRepositoryConfig,
+        CaptchaConfig,
+        VoipConfig,
+        RegistrationConfig,
+        MetricsConfig,
+        ApiConfig,
+        AppServiceConfig,
+        KeyConfig,
+        SAML2Config,
+        CasConfig,
+        JWTConfig,
+        PasswordConfig,
+        EmailConfig,
+        WorkerConfig,
+        PasswordAuthProviderConfig,
+        PushConfig,
+        SpamCheckerConfig,
+        GroupsConfig,
+        UserDirectoryConfig,
+        ConsentConfig,
+        StatsConfig,
+        ServerNoticesConfig,
+        RoomDirectoryConfig,
+        ThirdPartyRulesConfig,
+        TracerConfig,
+    ]
diff --git a/synapse/config/jwt_config.py b/synapse/config/jwt_config.py
index 36d87cef03..a568726985 100644
--- a/synapse/config/jwt_config.py
+++ b/synapse/config/jwt_config.py
@@ -23,6 +23,8 @@ MISSING_JWT = """Missing jwt library. This is required for jwt login.
 
 
 class JWTConfig(Config):
+    section = "jwt"
+
     def read_config(self, config, **kwargs):
         jwt_config = config.get("jwt_config", None)
         if jwt_config:
diff --git a/synapse/config/key.py b/synapse/config/key.py
index f039f96e9c..ec5d430afb 100644
--- a/synapse/config/key.py
+++ b/synapse/config/key.py
@@ -92,6 +92,8 @@ class TrustedKeyServer(object):
 
 
 class KeyConfig(Config):
+    section = "key"
+
     def read_config(self, config, config_dir_path, **kwargs):
         # the signing key can be specified inline or in a separate file
         if "signing_key" in config:
diff --git a/synapse/config/logger.py b/synapse/config/logger.py
index 767ecfdf09..d609ec111b 100644
--- a/synapse/config/logger.py
+++ b/synapse/config/logger.py
@@ -84,6 +84,8 @@ root:
 
 
 class LoggingConfig(Config):
+    section = "logging"
+
     def read_config(self, config, **kwargs):
         self.log_config = self.abspath(config.get("log_config"))
         self.no_redirect_stdio = config.get("no_redirect_stdio", False)
diff --git a/synapse/config/metrics.py b/synapse/config/metrics.py
index ec35a6b868..282a43bddb 100644
--- a/synapse/config/metrics.py
+++ b/synapse/config/metrics.py
@@ -34,6 +34,8 @@ class MetricsFlags(object):
 
 
 class MetricsConfig(Config):
+    section = "metrics"
+
     def read_config(self, config, **kwargs):
         self.enable_metrics = config.get("enable_metrics", False)
         self.report_stats = config.get("report_stats", None)
diff --git a/synapse/config/password.py b/synapse/config/password.py
index d5b5953f2f..2a634ac751 100644
--- a/synapse/config/password.py
+++ b/synapse/config/password.py
@@ -20,6 +20,8 @@ class PasswordConfig(Config):
     """Password login configuration
     """
 
+    section = "password"
+
     def read_config(self, config, **kwargs):
         password_config = config.get("password_config", {})
         if password_config is None:
diff --git a/synapse/config/password_auth_providers.py b/synapse/config/password_auth_providers.py
index c50e244394..9746bbc681 100644
--- a/synapse/config/password_auth_providers.py
+++ b/synapse/config/password_auth_providers.py
@@ -23,6 +23,8 @@ LDAP_PROVIDER = "ldap_auth_provider.LdapAuthProvider"
 
 
 class PasswordAuthProviderConfig(Config):
+    section = "authproviders"
+
     def read_config(self, config, **kwargs):
         self.password_providers = []  # type: List[Any]
         providers = []
diff --git a/synapse/config/push.py b/synapse/config/push.py
index 1b932722a5..0910958649 100644
--- a/synapse/config/push.py
+++ b/synapse/config/push.py
@@ -18,6 +18,8 @@ from ._base import Config
 
 
 class PushConfig(Config):
+    section = "push"
+
     def read_config(self, config, **kwargs):
         push_config = config.get("push", {})
         self.push_include_content = push_config.get("include_content", True)
diff --git a/synapse/config/ratelimiting.py b/synapse/config/ratelimiting.py
index 587e2862b7..947f653e03 100644
--- a/synapse/config/ratelimiting.py
+++ b/synapse/config/ratelimiting.py
@@ -36,6 +36,8 @@ class FederationRateLimitConfig(object):
 
 
 class RatelimitConfig(Config):
+    section = "ratelimiting"
+
     def read_config(self, config, **kwargs):
 
         # Load the new-style messages config if it exists. Otherwise fall back
diff --git a/synapse/config/registration.py b/synapse/config/registration.py
index bef89e2bf4..b3e3e6dda2 100644
--- a/synapse/config/registration.py
+++ b/synapse/config/registration.py
@@ -24,6 +24,8 @@ from synapse.util.stringutils import random_string_with_symbols
 
 
 class AccountValidityConfig(Config):
+    section = "accountvalidity"
+
     def __init__(self, config, synapse_config):
         self.enabled = config.get("enabled", False)
         self.renew_by_email_enabled = "renew_at" in config
@@ -77,6 +79,8 @@ class AccountValidityConfig(Config):
 
 
 class RegistrationConfig(Config):
+    section = "registration"
+
     def read_config(self, config, **kwargs):
         self.enable_registration = bool(
             strtobool(str(config.get("enable_registration", False)))
diff --git a/synapse/config/repository.py b/synapse/config/repository.py
index 14740891f3..d0205e14b9 100644
--- a/synapse/config/repository.py
+++ b/synapse/config/repository.py
@@ -78,6 +78,8 @@ def parse_thumbnail_requirements(thumbnail_sizes):
 
 
 class ContentRepositoryConfig(Config):
+    section = "media"
+
     def read_config(self, config, **kwargs):
 
         # Only enable the media repo if either the media repo is enabled or the
diff --git a/synapse/config/room_directory.py b/synapse/config/room_directory.py
index a92693017b..7c9f05bde4 100644
--- a/synapse/config/room_directory.py
+++ b/synapse/config/room_directory.py
@@ -19,6 +19,8 @@ from ._base import Config, ConfigError
 
 
 class RoomDirectoryConfig(Config):
+    section = "roomdirectory"
+
     def read_config(self, config, **kwargs):
         self.enable_room_list_search = config.get("enable_room_list_search", True)
 
diff --git a/synapse/config/saml2_config.py b/synapse/config/saml2_config.py
index ab34b41ca8..c407e13680 100644
--- a/synapse/config/saml2_config.py
+++ b/synapse/config/saml2_config.py
@@ -55,6 +55,8 @@ def _dict_merge(merge_dict, into_dict):
 
 
 class SAML2Config(Config):
+    section = "saml2"
+
     def read_config(self, config, **kwargs):
         self.saml2_enabled = False
 
diff --git a/synapse/config/server.py b/synapse/config/server.py
index 709bd387e5..afc4d6a4ab 100644
--- a/synapse/config/server.py
+++ b/synapse/config/server.py
@@ -58,6 +58,8 @@ on how to configure the new listener.
 
 
 class ServerConfig(Config):
+    section = "server"
+
     def read_config(self, config, **kwargs):
         self.server_name = config["server_name"]
         self.server_context = config.get("server_context", None)
diff --git a/synapse/config/server_notices_config.py b/synapse/config/server_notices_config.py
index 6d4285ef93..6ea2ea8869 100644
--- a/synapse/config/server_notices_config.py
+++ b/synapse/config/server_notices_config.py
@@ -59,6 +59,8 @@ class ServerNoticesConfig(Config):
             None if server notices are not enabled.
     """
 
+    section = "servernotices"
+
     def __init__(self, *args):
         super(ServerNoticesConfig, self).__init__(*args)
         self.server_notices_mxid = None
diff --git a/synapse/config/spam_checker.py b/synapse/config/spam_checker.py
index e40797ab50..36e0ddab5c 100644
--- a/synapse/config/spam_checker.py
+++ b/synapse/config/spam_checker.py
@@ -19,6 +19,8 @@ from ._base import Config
 
 
 class SpamCheckerConfig(Config):
+    section = "spamchecker"
+
     def read_config(self, config, **kwargs):
         self.spam_checker = None
 
diff --git a/synapse/config/stats.py b/synapse/config/stats.py
index b18ddbd1fa..62485189ea 100644
--- a/synapse/config/stats.py
+++ b/synapse/config/stats.py
@@ -25,6 +25,8 @@ class StatsConfig(Config):
     Configuration for the behaviour of synapse's stats engine
     """
 
+    section = "stats"
+
     def read_config(self, config, **kwargs):
         self.stats_enabled = True
         self.stats_bucket_size = 86400 * 1000
diff --git a/synapse/config/third_party_event_rules.py b/synapse/config/third_party_event_rules.py
index b3431441b9..10a99c792e 100644
--- a/synapse/config/third_party_event_rules.py
+++ b/synapse/config/third_party_event_rules.py
@@ -19,6 +19,8 @@ from ._base import Config
 
 
 class ThirdPartyRulesConfig(Config):
+    section = "thirdpartyrules"
+
     def read_config(self, config, **kwargs):
         self.third_party_event_rules = None
 
diff --git a/synapse/config/tls.py b/synapse/config/tls.py
index fc47ba3e9a..f06341eb67 100644
--- a/synapse/config/tls.py
+++ b/synapse/config/tls.py
@@ -18,6 +18,7 @@ import os
 import warnings
 from datetime import datetime
 from hashlib import sha256
+from typing import List
 
 import six
 
@@ -33,7 +34,9 @@ logger = logging.getLogger(__name__)
 
 
 class TlsConfig(Config):
-    def read_config(self, config, config_dir_path, **kwargs):
+    section = "tls"
+
+    def read_config(self, config: dict, config_dir_path: str, **kwargs):
 
         acme_config = config.get("acme", None)
         if acme_config is None:
@@ -57,7 +60,7 @@ class TlsConfig(Config):
         self.tls_certificate_file = self.abspath(config.get("tls_certificate_path"))
         self.tls_private_key_file = self.abspath(config.get("tls_private_key_path"))
 
-        if self.has_tls_listener():
+        if self.root.server.has_tls_listener():
             if not self.tls_certificate_file:
                 raise ConfigError(
                     "tls_certificate_path must be specified if TLS-enabled listeners are "
@@ -108,7 +111,7 @@ class TlsConfig(Config):
         )
 
         # Support globs (*) in whitelist values
-        self.federation_certificate_verification_whitelist = []
+        self.federation_certificate_verification_whitelist = []  # type: List[str]
         for entry in fed_whitelist_entries:
             try:
                 entry_regex = glob_to_regex(entry.encode("ascii").decode("ascii"))
diff --git a/synapse/config/tracer.py b/synapse/config/tracer.py
index 85d99a3166..8be1346113 100644
--- a/synapse/config/tracer.py
+++ b/synapse/config/tracer.py
@@ -19,6 +19,8 @@ from ._base import Config, ConfigError
 
 
 class TracerConfig(Config):
+    section = "tracing"
+
     def read_config(self, config, **kwargs):
         opentracing_config = config.get("opentracing")
         if opentracing_config is None:
diff --git a/synapse/config/user_directory.py b/synapse/config/user_directory.py
index f6313e17d4..c8d19c5d6b 100644
--- a/synapse/config/user_directory.py
+++ b/synapse/config/user_directory.py
@@ -21,6 +21,8 @@ class UserDirectoryConfig(Config):
     Configuration for the behaviour of the /user_directory API
     """
 
+    section = "userdirectory"
+
     def read_config(self, config, **kwargs):
         self.user_directory_search_enabled = True
         self.user_directory_search_all_users = False
diff --git a/synapse/config/voip.py b/synapse/config/voip.py
index 2ca0e1cf70..a68a3068aa 100644
--- a/synapse/config/voip.py
+++ b/synapse/config/voip.py
@@ -16,6 +16,8 @@ from ._base import Config
 
 
 class VoipConfig(Config):
+    section = "voip"
+
     def read_config(self, config, **kwargs):
         self.turn_uris = config.get("turn_uris", [])
         self.turn_shared_secret = config.get("turn_shared_secret")
diff --git a/synapse/config/workers.py b/synapse/config/workers.py
index 1ec4998625..fef72ed974 100644
--- a/synapse/config/workers.py
+++ b/synapse/config/workers.py
@@ -21,6 +21,8 @@ class WorkerConfig(Config):
     They have their own pid_file and listener configuration. They use the
     replication_url to talk to the main synapse process."""
 
+    section = "worker"
+
     def read_config(self, config, **kwargs):
         self.worker_app = config.get("worker_app")
 
diff --git a/synapse/groups/groups_server.py b/synapse/groups/groups_server.py
index d50e691436..8f10b6adbb 100644
--- a/synapse/groups/groups_server.py
+++ b/synapse/groups/groups_server.py
@@ -1,6 +1,7 @@
 # -*- coding: utf-8 -*-
 # Copyright 2017 Vector Creations Ltd
 # Copyright 2018 New Vector Ltd
+# Copyright 2019 Michael Telatynski <7t3chguy@gmail.com>
 #
 # Licensed under the Apache License, Version 2.0 (the "License");
 # you may not use this file except in compliance with the License.
@@ -20,16 +21,16 @@ from six import string_types
 
 from twisted.internet import defer
 
-from synapse.api.errors import SynapseError
+from synapse.api.errors import Codes, SynapseError
 from synapse.types import GroupID, RoomID, UserID, get_domain_from_id
 from synapse.util.async_helpers import concurrently_execute
 
 logger = logging.getLogger(__name__)
 
 
-# TODO: Allow users to "knock" or simpkly join depending on rules
+# TODO: Allow users to "knock" or simply join depending on rules
 # TODO: Federation admin APIs
-# TODO: is_priveged flag to users and is_public to users and rooms
+# TODO: is_privileged flag to users and is_public to users and rooms
 # TODO: Audit log for admins (profile updates, membership changes, users who tried
 #       to join but were rejected, etc)
 # TODO: Flairs
@@ -590,7 +591,18 @@ class GroupsServerHandler(object):
         )
 
         # TODO: Check if user knocked
-        # TODO: Check if user is already invited
+
+        invited_users = yield self.store.get_invited_users_in_group(group_id)
+        if user_id in invited_users:
+            raise SynapseError(
+                400, "User already invited to group", errcode=Codes.BAD_STATE
+            )
+
+        user_results = yield self.store.get_users_in_group(
+            group_id, include_private=True
+        )
+        if user_id in [user_result["user_id"] for user_result in user_results]:
+            raise SynapseError(400, "User already in group")
 
         content = {
             "profile": {"name": group["name"], "avatar_url": group["avatar_url"]},
diff --git a/synapse/handlers/presence.py b/synapse/handlers/presence.py
index 053cf66b28..2a5f1a007d 100644
--- a/synapse/handlers/presence.py
+++ b/synapse/handlers/presence.py
@@ -803,17 +803,25 @@ class PresenceHandler(object):
         # Loop round handling deltas until we're up to date
         while True:
             with Measure(self.clock, "presence_delta"):
-                deltas = yield self.store.get_current_state_deltas(self._event_pos)
-                if not deltas:
+                room_max_stream_ordering = self.store.get_room_max_stream_ordering()
+                if self._event_pos == room_max_stream_ordering:
                     return
 
+                logger.debug(
+                    "Processing presence stats %s->%s",
+                    self._event_pos,
+                    room_max_stream_ordering,
+                )
+                max_pos, deltas = yield self.store.get_current_state_deltas(
+                    self._event_pos, room_max_stream_ordering
+                )
                 yield self._handle_state_delta(deltas)
 
-                self._event_pos = deltas[-1]["stream_id"]
+                self._event_pos = max_pos
 
                 # Expose current event processing position to prometheus
                 synapse.metrics.event_processing_positions.labels("presence").set(
-                    self._event_pos
+                    max_pos
                 )
 
     @defer.inlineCallbacks
diff --git a/synapse/handlers/room.py b/synapse/handlers/room.py
index 970be3c846..2816bd8f87 100644
--- a/synapse/handlers/room.py
+++ b/synapse/handlers/room.py
@@ -28,6 +28,7 @@ from twisted.internet import defer
 from synapse.api.constants import EventTypes, JoinRules, RoomCreationPreset
 from synapse.api.errors import AuthError, Codes, NotFoundError, StoreError, SynapseError
 from synapse.api.room_versions import KNOWN_ROOM_VERSIONS
+from synapse.http.endpoint import parse_and_validate_server_name
 from synapse.storage.state import StateFilter
 from synapse.types import RoomAlias, RoomID, RoomStreamToken, StreamToken, UserID
 from synapse.util import stringutils
@@ -554,7 +555,8 @@ class RoomCreationHandler(BaseHandler):
         invite_list = config.get("invite", [])
         for i in invite_list:
             try:
-                UserID.from_string(i)
+                uid = UserID.from_string(i)
+                parse_and_validate_server_name(uid.domain)
             except Exception:
                 raise SynapseError(400, "Invalid user_id: %s" % (i,))
 
diff --git a/synapse/handlers/room_member.py b/synapse/handlers/room_member.py
index 95a244d86c..380e2fad5e 100644
--- a/synapse/handlers/room_member.py
+++ b/synapse/handlers/room_member.py
@@ -203,23 +203,11 @@ class RoomMemberHandler(object):
                 prev_member_event = yield self.store.get_event(prev_member_event_id)
                 newly_joined = prev_member_event.membership != Membership.JOIN
             if newly_joined:
-                yield self._user_joined_room(target, room_id)
-
-            # Copy over direct message status and room tags if this is a join
-            # on an upgraded room
-
-            # Check if this is an upgraded room
-            predecessor = yield self.store.get_room_predecessor(room_id)
-
-            if predecessor:
-                # It is an upgraded room. Copy over old tags
-                self.copy_room_tags_and_direct_to_room(
-                    predecessor["room_id"], room_id, user_id
-                )
-                # Copy over push rules
-                yield self.store.copy_push_rules_from_room_to_room_for_user(
-                    predecessor["room_id"], room_id, user_id
+                # Copy over user state if we're joining an upgraded room
+                yield self.copy_user_state_if_room_upgrade(
+                    room_id, requester.user.to_string()
                 )
+                yield self._user_joined_room(target, room_id)
         elif event.membership == Membership.LEAVE:
             if prev_member_event_id:
                 prev_member_event = yield self.store.get_event(prev_member_event_id)
@@ -463,10 +451,16 @@ class RoomMemberHandler(object):
                 if requester.is_guest:
                     content["kind"] = "guest"
 
-                ret = yield self._remote_join(
+                remote_join_response = yield self._remote_join(
                     requester, remote_room_hosts, room_id, target, content
                 )
-                return ret
+
+                # Copy over user state if this is a join on an remote upgraded room
+                yield self.copy_user_state_if_room_upgrade(
+                    room_id, requester.user.to_string()
+                )
+
+                return remote_join_response
 
         elif effective_membership_state == Membership.LEAVE:
             if not is_host_in_room:
@@ -504,6 +498,38 @@ class RoomMemberHandler(object):
         return res
 
     @defer.inlineCallbacks
+    def copy_user_state_if_room_upgrade(self, new_room_id, user_id):
+        """Copy user-specific information when they join a new room if that new room is the
+        result of a room upgrade
+
+        Args:
+            new_room_id (str): The ID of the room the user is joining
+            user_id (str): The ID of the user
+
+        Returns:
+            Deferred
+        """
+        # Check if the new room is an upgraded room
+        predecessor = yield self.store.get_room_predecessor(new_room_id)
+        if not predecessor:
+            return
+
+        logger.debug(
+            "Found predecessor for %s: %s. Copying over room tags and push " "rules",
+            new_room_id,
+            predecessor,
+        )
+
+        # It is an upgraded room. Copy over old tags
+        yield self.copy_room_tags_and_direct_to_room(
+            predecessor["room_id"], new_room_id, user_id
+        )
+        # Copy over push rules
+        yield self.store.copy_push_rules_from_room_to_room_for_user(
+            predecessor["room_id"], new_room_id, user_id
+        )
+
+    @defer.inlineCallbacks
     def send_membership_event(self, requester, event, context, ratelimit=True):
         """
         Change the membership status of a user in a room.
diff --git a/synapse/handlers/stats.py b/synapse/handlers/stats.py
index c62b113115..466daf9202 100644
--- a/synapse/handlers/stats.py
+++ b/synapse/handlers/stats.py
@@ -87,21 +87,23 @@ class StatsHandler(StateDeltasHandler):
             # Be sure to read the max stream_ordering *before* checking if there are any outstanding
             # deltas, since there is otherwise a chance that we could miss updates which arrive
             # after we check the deltas.
-            room_max_stream_ordering = yield self.store.get_room_max_stream_ordering()
+            room_max_stream_ordering = self.store.get_room_max_stream_ordering()
             if self.pos == room_max_stream_ordering:
                 break
 
-            deltas = yield self.store.get_current_state_deltas(self.pos)
+            logger.debug(
+                "Processing room stats %s->%s", self.pos, room_max_stream_ordering
+            )
+            max_pos, deltas = yield self.store.get_current_state_deltas(
+                self.pos, room_max_stream_ordering
+            )
 
             if deltas:
                 logger.debug("Handling %d state deltas", len(deltas))
                 room_deltas, user_deltas = yield self._handle_deltas(deltas)
-
-                max_pos = deltas[-1]["stream_id"]
             else:
                 room_deltas = {}
                 user_deltas = {}
-                max_pos = room_max_stream_ordering
 
             # Then count deltas for total_events and total_event_bytes.
             room_count, user_count = yield self.store.get_changes_room_total_events_and_bytes(
diff --git a/synapse/handlers/user_directory.py b/synapse/handlers/user_directory.py
index e53669e40d..624f05ab5b 100644
--- a/synapse/handlers/user_directory.py
+++ b/synapse/handlers/user_directory.py
@@ -138,21 +138,28 @@ class UserDirectoryHandler(StateDeltasHandler):
         # Loop round handling deltas until we're up to date
         while True:
             with Measure(self.clock, "user_dir_delta"):
-                deltas = yield self.store.get_current_state_deltas(self.pos)
-                if not deltas:
+                room_max_stream_ordering = self.store.get_room_max_stream_ordering()
+                if self.pos == room_max_stream_ordering:
                     return
 
+                logger.debug(
+                    "Processing user stats %s->%s", self.pos, room_max_stream_ordering
+                )
+                max_pos, deltas = yield self.store.get_current_state_deltas(
+                    self.pos, room_max_stream_ordering
+                )
+
                 logger.info("Handling %d state deltas", len(deltas))
                 yield self._handle_deltas(deltas)
 
-                self.pos = deltas[-1]["stream_id"]
+                self.pos = max_pos
 
                 # Expose current event processing position to prometheus
                 synapse.metrics.event_processing_positions.labels("user_dir").set(
-                    self.pos
+                    max_pos
                 )
 
-                yield self.store.update_user_directory_stream_pos(self.pos)
+                yield self.store.update_user_directory_stream_pos(max_pos)
 
     @defer.inlineCallbacks
     def _handle_deltas(self, deltas):
diff --git a/synapse/http/server.py b/synapse/http/server.py
index cb9158fe1b..2ccb210fd6 100644
--- a/synapse/http/server.py
+++ b/synapse/http/server.py
@@ -388,7 +388,7 @@ class DirectServeResource(resource.Resource):
         if not callback:
             return super().render(request)
 
-        resp = callback(request)
+        resp = trace_servlet(self.__class__.__name__)(callback)(request)
 
         # If it's a coroutine, turn it into a Deferred
         if isinstance(resp, types.CoroutineType):
diff --git a/synapse/logging/opentracing.py b/synapse/logging/opentracing.py
index cd1ff6a518..0638cec429 100644
--- a/synapse/logging/opentracing.py
+++ b/synapse/logging/opentracing.py
@@ -169,6 +169,7 @@ import contextlib
 import inspect
 import logging
 import re
+import types
 from functools import wraps
 from typing import Dict
 
@@ -778,8 +779,7 @@ def trace_servlet(servlet_name, extract_context=False):
             return func
 
         @wraps(func)
-        @defer.inlineCallbacks
-        def _trace_servlet_inner(request, *args, **kwargs):
+        async def _trace_servlet_inner(request, *args, **kwargs):
             request_tags = {
                 "request_id": request.get_request_id(),
                 tags.SPAN_KIND: tags.SPAN_KIND_RPC_SERVER,
@@ -796,8 +796,14 @@ def trace_servlet(servlet_name, extract_context=False):
                 scope = start_active_span(servlet_name, tags=request_tags)
 
             with scope:
-                result = yield defer.maybeDeferred(func, request, *args, **kwargs)
-                return result
+                result = func(request, *args, **kwargs)
+
+                if not isinstance(result, (types.CoroutineType, defer.Deferred)):
+                    # Some servlets aren't async and just return results
+                    # directly, so we handle that here.
+                    return result
+
+                return await result
 
         return _trace_servlet_inner
 
diff --git a/synapse/rest/client/v1/login.py b/synapse/rest/client/v1/login.py
index 9cddbc752a..8414af08cb 100644
--- a/synapse/rest/client/v1/login.py
+++ b/synapse/rest/client/v1/login.py
@@ -377,6 +377,7 @@ class CasTicketServlet(RestServlet):
         super(CasTicketServlet, self).__init__()
         self.cas_server_url = hs.config.cas_server_url
         self.cas_service_url = hs.config.cas_service_url
+        self.cas_displayname_attribute = hs.config.cas_displayname_attribute
         self.cas_required_attributes = hs.config.cas_required_attributes
         self._sso_auth_handler = SSOAuthHandler(hs)
         self._http_client = hs.get_simple_http_client()
@@ -400,6 +401,7 @@ class CasTicketServlet(RestServlet):
 
     def handle_cas_response(self, request, cas_response_body, client_redirect_url):
         user, attributes = self.parse_cas_response(cas_response_body)
+        displayname = attributes.pop(self.cas_displayname_attribute, None)
 
         for required_attribute, required_value in self.cas_required_attributes.items():
             # If required attribute was not in CAS Response - Forbidden
@@ -414,7 +416,7 @@ class CasTicketServlet(RestServlet):
                     raise LoginError(401, "Unauthorized", errcode=Codes.UNAUTHORIZED)
 
         return self._sso_auth_handler.on_successful_auth(
-            user, request, client_redirect_url
+            user, request, client_redirect_url, displayname
         )
 
     def parse_cas_response(self, cas_response_body):
diff --git a/synapse/rest/client/v2_alpha/filter.py b/synapse/rest/client/v2_alpha/filter.py
index c6ddf24c8d..17a8bc7366 100644
--- a/synapse/rest/client/v2_alpha/filter.py
+++ b/synapse/rest/client/v2_alpha/filter.py
@@ -17,7 +17,7 @@ import logging
 
 from twisted.internet import defer
 
-from synapse.api.errors import AuthError, Codes, StoreError, SynapseError
+from synapse.api.errors import AuthError, NotFoundError, StoreError, SynapseError
 from synapse.http.servlet import RestServlet, parse_json_object_from_request
 from synapse.types import UserID
 
@@ -52,13 +52,15 @@ class GetFilterRestServlet(RestServlet):
             raise SynapseError(400, "Invalid filter_id")
 
         try:
-            filter = yield self.filtering.get_user_filter(
+            filter_collection = yield self.filtering.get_user_filter(
                 user_localpart=target_user.localpart, filter_id=filter_id
             )
+        except StoreError as e:
+            if e.code != 404:
+                raise
+            raise NotFoundError("No such filter")
 
-            return 200, filter.get_filter_json()
-        except (KeyError, StoreError):
-            raise SynapseError(400, "No such filter", errcode=Codes.NOT_FOUND)
+        return 200, filter_collection.get_filter_json()
 
 
 class CreateFilterRestServlet(RestServlet):
diff --git a/synapse/rest/client/v2_alpha/sync.py b/synapse/rest/client/v2_alpha/sync.py
index c98c5a3802..a883c8adda 100644
--- a/synapse/rest/client/v2_alpha/sync.py
+++ b/synapse/rest/client/v2_alpha/sync.py
@@ -21,7 +21,7 @@ from canonicaljson import json
 from twisted.internet import defer
 
 from synapse.api.constants import PresenceState
-from synapse.api.errors import SynapseError
+from synapse.api.errors import Codes, StoreError, SynapseError
 from synapse.api.filtering import DEFAULT_FILTER_COLLECTION, FilterCollection
 from synapse.events.utils import (
     format_event_for_client_v2_without_room_id,
@@ -119,25 +119,32 @@ class SyncRestServlet(RestServlet):
 
         request_key = (user, timeout, since, filter_id, full_state, device_id)
 
-        if filter_id:
-            if filter_id.startswith("{"):
-                try:
-                    filter_object = json.loads(filter_id)
-                    set_timeline_upper_limit(
-                        filter_object, self.hs.config.filter_timeline_limit
-                    )
-                except Exception:
-                    raise SynapseError(400, "Invalid filter JSON")
-                self.filtering.check_valid_filter(filter_object)
-                filter = FilterCollection(filter_object)
-            else:
-                filter = yield self.filtering.get_user_filter(user.localpart, filter_id)
+        if filter_id is None:
+            filter_collection = DEFAULT_FILTER_COLLECTION
+        elif filter_id.startswith("{"):
+            try:
+                filter_object = json.loads(filter_id)
+                set_timeline_upper_limit(
+                    filter_object, self.hs.config.filter_timeline_limit
+                )
+            except Exception:
+                raise SynapseError(400, "Invalid filter JSON")
+            self.filtering.check_valid_filter(filter_object)
+            filter_collection = FilterCollection(filter_object)
         else:
-            filter = DEFAULT_FILTER_COLLECTION
+            try:
+                filter_collection = yield self.filtering.get_user_filter(
+                    user.localpart, filter_id
+                )
+            except StoreError as err:
+                if err.code != 404:
+                    raise
+                # fix up the description and errcode to be more useful
+                raise SynapseError(400, "No such filter", errcode=Codes.INVALID_PARAM)
 
         sync_config = SyncConfig(
             user=user,
-            filter_collection=filter,
+            filter_collection=filter_collection,
             is_guest=requester.is_guest,
             request_key=request_key,
             device_id=device_id,
@@ -171,7 +178,7 @@ class SyncRestServlet(RestServlet):
 
         time_now = self.clock.time_msec()
         response_content = yield self.encode_response(
-            time_now, sync_result, requester.access_token_id, filter
+            time_now, sync_result, requester.access_token_id, filter_collection
         )
 
         return 200, response_content
diff --git a/synapse/rest/media/v1/preview_url_resource.py b/synapse/rest/media/v1/preview_url_resource.py
index 7a56cd4b6c..0c68c3aad5 100644
--- a/synapse/rest/media/v1/preview_url_resource.py
+++ b/synapse/rest/media/v1/preview_url_resource.py
@@ -270,7 +270,7 @@ class PreviewUrlResource(DirectServeResource):
 
         logger.debug("Calculated OG for %s as %s" % (url, og))
 
-        jsonog = json.dumps(og).encode("utf8")
+        jsonog = json.dumps(og)
 
         # store OG in history-aware DB cache
         yield self.store.store_url_cache(
@@ -283,7 +283,7 @@ class PreviewUrlResource(DirectServeResource):
             media_info["created_ts"],
         )
 
-        return jsonog
+        return jsonog.encode("utf8")
 
     @defer.inlineCallbacks
     def _download_url(self, url, user):
diff --git a/synapse/storage/_base.py b/synapse/storage/_base.py
index abe16334ec..f5906fcd54 100644
--- a/synapse/storage/_base.py
+++ b/synapse/storage/_base.py
@@ -20,6 +20,7 @@ import random
 import sys
 import threading
 import time
+from typing import Iterable, Tuple
 
 from six import PY2, iteritems, iterkeys, itervalues
 from six.moves import builtins, intern, range
@@ -30,7 +31,7 @@ from prometheus_client import Histogram
 from twisted.internet import defer
 
 from synapse.api.errors import StoreError
-from synapse.logging.context import LoggingContext, PreserveLoggingContext
+from synapse.logging.context import LoggingContext, make_deferred_yieldable
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.storage.engines import PostgresEngine, Sqlite3Engine
 from synapse.types import get_domain_from_id
@@ -550,8 +551,9 @@ class SQLBaseStore(object):
 
                 return func(conn, *args, **kwargs)
 
-        with PreserveLoggingContext():
-            result = yield self._db_pool.runWithConnection(inner_func, *args, **kwargs)
+        result = yield make_deferred_yieldable(
+            self._db_pool.runWithConnection(inner_func, *args, **kwargs)
+        )
 
         return result
 
@@ -1162,19 +1164,18 @@ class SQLBaseStore(object):
         if not iterable:
             return []
 
-        sql = "SELECT %s FROM %s" % (", ".join(retcols), table)
-
-        clauses = []
-        values = []
-        clauses.append("%s IN (%s)" % (column, ",".join("?" for _ in iterable)))
-        values.extend(iterable)
+        clause, values = make_in_list_sql_clause(txn.database_engine, column, iterable)
+        clauses = [clause]
 
         for key, value in iteritems(keyvalues):
             clauses.append("%s = ?" % (key,))
             values.append(value)
 
-        if clauses:
-            sql = "%s WHERE %s" % (sql, " AND ".join(clauses))
+        sql = "SELECT %s FROM %s WHERE %s" % (
+            ", ".join(retcols),
+            table,
+            " AND ".join(clauses),
+        )
 
         txn.execute(sql, values)
         return cls.cursor_to_dict(txn)
@@ -1323,10 +1324,8 @@ class SQLBaseStore(object):
 
         sql = "DELETE FROM %s" % table
 
-        clauses = []
-        values = []
-        clauses.append("%s IN (%s)" % (column, ",".join("?" for _ in iterable)))
-        values.extend(iterable)
+        clause, values = make_in_list_sql_clause(txn.database_engine, column, iterable)
+        clauses = [clause]
 
         for key, value in iteritems(keyvalues):
             clauses.append("%s = ?" % (key,))
@@ -1693,3 +1692,30 @@ def db_to_json(db_content):
     except Exception:
         logging.warning("Tried to decode '%r' as JSON and failed", db_content)
         raise
+
+
+def make_in_list_sql_clause(
+    database_engine, column: str, iterable: Iterable
+) -> Tuple[str, Iterable]:
+    """Returns an SQL clause that checks the given column is in the iterable.
+
+    On SQLite this expands to `column IN (?, ?, ...)`, whereas on Postgres
+    it expands to `column = ANY(?)`. While both DBs support the `IN` form,
+    using the `ANY` form on postgres means that it views queries with
+    different length iterables as the same, helping the query stats.
+
+    Args:
+        database_engine
+        column: Name of the column
+        iterable: The values to check the column against.
+
+    Returns:
+        A tuple of SQL query and the args
+    """
+
+    if database_engine.supports_using_any_list:
+        # This should hopefully be faster, but also makes postgres query
+        # stats easier to understand.
+        return "%s = ANY(?)" % (column,), [list(iterable)]
+    else:
+        return "%s IN (%s)" % (column, ",".join("?" for _ in iterable)), list(iterable)
diff --git a/synapse/storage/deviceinbox.py b/synapse/storage/deviceinbox.py
index 70bc2bb2cc..f04aad0743 100644
--- a/synapse/storage/deviceinbox.py
+++ b/synapse/storage/deviceinbox.py
@@ -20,7 +20,7 @@ from canonicaljson import json
 from twisted.internet import defer
 
 from synapse.logging.opentracing import log_kv, set_tag, trace
-from synapse.storage._base import SQLBaseStore
+from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
 from synapse.storage.background_updates import BackgroundUpdateStore
 from synapse.util.caches.expiringcache import ExpiringCache
 
@@ -378,15 +378,15 @@ class DeviceInboxStore(DeviceInboxWorkerStore, DeviceInboxBackgroundUpdateStore)
             else:
                 if not devices:
                     continue
-                sql = (
-                    "SELECT device_id FROM devices"
-                    " WHERE user_id = ? AND device_id IN ("
-                    + ",".join("?" * len(devices))
-                    + ")"
+
+                clause, args = make_in_list_sql_clause(
+                    txn.database_engine, "device_id", devices
                 )
+                sql = "SELECT device_id FROM devices WHERE user_id = ? AND " + clause
+
                 # TODO: Maybe this needs to be done in batches if there are
                 # too many local devices for a given user.
-                txn.execute(sql, [user_id] + devices)
+                txn.execute(sql, [user_id] + list(args))
                 for row in txn:
                     # Only insert into the local inbox if the device exists on
                     # this server
diff --git a/synapse/storage/devices.py b/synapse/storage/devices.py
index 111bfb3d64..ac5239e50a 100644
--- a/synapse/storage/devices.py
+++ b/synapse/storage/devices.py
@@ -28,7 +28,12 @@ from synapse.logging.opentracing import (
     whitelisted_homeserver,
 )
 from synapse.metrics.background_process_metrics import run_as_background_process
-from synapse.storage._base import Cache, SQLBaseStore, db_to_json
+from synapse.storage._base import (
+    Cache,
+    SQLBaseStore,
+    db_to_json,
+    make_in_list_sql_clause,
+)
 from synapse.storage.background_updates import BackgroundUpdateStore
 from synapse.util import batch_iter
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks, cachedList
@@ -448,11 +453,14 @@ class DeviceWorkerStore(SQLBaseStore):
             sql = """
                 SELECT DISTINCT user_id FROM device_lists_stream
                 WHERE stream_id > ?
-                AND user_id IN (%s)
+                AND
             """
 
             for chunk in batch_iter(to_check, 100):
-                txn.execute(sql % (",".join("?" for _ in chunk),), (from_key,) + chunk)
+                clause, args = make_in_list_sql_clause(
+                    txn.database_engine, "user_id", chunk
+                )
+                txn.execute(sql + clause, (from_key,) + tuple(args))
                 changes.update(user_id for user_id, in txn)
 
             return changes
diff --git a/synapse/storage/engines/postgres.py b/synapse/storage/engines/postgres.py
index 601617b21e..b7c4eda338 100644
--- a/synapse/storage/engines/postgres.py
+++ b/synapse/storage/engines/postgres.py
@@ -22,6 +22,13 @@ class PostgresEngine(object):
     def __init__(self, database_module, database_config):
         self.module = database_module
         self.module.extensions.register_type(self.module.extensions.UNICODE)
+
+        # Disables passing `bytes` to txn.execute, c.f. #6186. If you do
+        # actually want to use bytes than wrap it in `bytearray`.
+        def _disable_bytes_adapter(_):
+            raise Exception("Passing bytes to DB is disabled.")
+
+        self.module.extensions.register_adapter(bytes, _disable_bytes_adapter)
         self.synchronous_commit = database_config.get("synchronous_commit", True)
         self._version = None  # unknown as yet
 
@@ -79,6 +86,12 @@ class PostgresEngine(object):
         """
         return True
 
+    @property
+    def supports_using_any_list(self):
+        """Do we support using `a = ANY(?)` and passing a list
+        """
+        return True
+
     def is_deadlock(self, error):
         if isinstance(error, self.module.DatabaseError):
             # https://www.postgresql.org/docs/current/static/errcodes-appendix.html
diff --git a/synapse/storage/engines/sqlite.py b/synapse/storage/engines/sqlite.py
index ac92109366..ddad17dc5a 100644
--- a/synapse/storage/engines/sqlite.py
+++ b/synapse/storage/engines/sqlite.py
@@ -46,6 +46,12 @@ class Sqlite3Engine(object):
         """
         return self.module.sqlite_version_info >= (3, 15, 0)
 
+    @property
+    def supports_using_any_list(self):
+        """Do we support using `a = ANY(?)` and passing a list
+        """
+        return False
+
     def check_database(self, txn):
         pass
 
diff --git a/synapse/storage/event_federation.py b/synapse/storage/event_federation.py
index f5e8c39262..47cc10d32a 100644
--- a/synapse/storage/event_federation.py
+++ b/synapse/storage/event_federation.py
@@ -25,7 +25,7 @@ from twisted.internet import defer
 
 from synapse.api.errors import StoreError
 from synapse.metrics.background_process_metrics import run_as_background_process
-from synapse.storage._base import SQLBaseStore
+from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
 from synapse.storage.events_worker import EventsWorkerStore
 from synapse.storage.signatures import SignatureWorkerStore
 from synapse.util.caches.descriptors import cached
@@ -68,7 +68,7 @@ class EventFederationWorkerStore(EventsWorkerStore, SignatureWorkerStore, SQLBas
         else:
             results = set()
 
-        base_sql = "SELECT auth_id FROM event_auth WHERE event_id IN (%s)"
+        base_sql = "SELECT auth_id FROM event_auth WHERE "
 
         front = set(event_ids)
         while front:
@@ -76,7 +76,10 @@ class EventFederationWorkerStore(EventsWorkerStore, SignatureWorkerStore, SQLBas
             front_list = list(front)
             chunks = [front_list[x : x + 100] for x in range(0, len(front), 100)]
             for chunk in chunks:
-                txn.execute(base_sql % (",".join(["?"] * len(chunk)),), chunk)
+                clause, args = make_in_list_sql_clause(
+                    txn.database_engine, "event_id", chunk
+                )
+                txn.execute(base_sql + clause, list(args))
                 new_front.update([r[0] for r in txn])
 
             new_front -= results
diff --git a/synapse/storage/events.py b/synapse/storage/events.py
index bb6ff0595a..ee49ef235d 100644
--- a/synapse/storage/events.py
+++ b/synapse/storage/events.py
@@ -39,6 +39,7 @@ from synapse.logging.utils import log_function
 from synapse.metrics import BucketCollector
 from synapse.metrics.background_process_metrics import run_as_background_process
 from synapse.state import StateResolutionStore
+from synapse.storage._base import make_in_list_sql_clause
 from synapse.storage.background_updates import BackgroundUpdateStore
 from synapse.storage.event_federation import EventFederationStore
 from synapse.storage.events_worker import EventsWorkerStore
@@ -641,14 +642,16 @@ class EventsStore(
                 LEFT JOIN rejections USING (event_id)
                 LEFT JOIN event_json USING (event_id)
             WHERE
-                prev_event_id IN (%s)
-                AND NOT events.outlier
+                NOT events.outlier
                 AND rejections.event_id IS NULL
-            """ % (
-                ",".join("?" for _ in batch),
+                AND
+            """
+
+            clause, args = make_in_list_sql_clause(
+                self.database_engine, "prev_event_id", batch
             )
 
-            txn.execute(sql, batch)
+            txn.execute(sql + clause, args)
             results.extend(r[0] for r in txn if not json.loads(r[1]).get("soft_failed"))
 
         for chunk in batch_iter(event_ids, 100):
@@ -695,13 +698,15 @@ class EventsStore(
                     LEFT JOIN rejections USING (event_id)
                     LEFT JOIN event_json USING (event_id)
                 WHERE
-                    event_id IN (%s)
-                    AND NOT events.outlier
-                """ % (
-                    ",".join("?" for _ in to_recursively_check),
+                    NOT events.outlier
+                    AND
+                """
+
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "event_id", to_recursively_check
                 )
 
-                txn.execute(sql, to_recursively_check)
+                txn.execute(sql + clause, args)
                 to_recursively_check = []
 
                 for event_id, prev_event_id, metadata, rejected in txn:
@@ -1543,10 +1548,14 @@ class EventsStore(
                 " FROM events as e"
                 " LEFT JOIN rejections as rej USING (event_id)"
                 " LEFT JOIN redactions as r ON e.event_id = r.redacts"
-                " WHERE e.event_id IN (%s)"
-            ) % (",".join(["?"] * len(ev_map)),)
+                " WHERE "
+            )
+
+            clause, args = make_in_list_sql_clause(
+                self.database_engine, "e.event_id", list(ev_map)
+            )
 
-            txn.execute(sql, list(ev_map))
+            txn.execute(sql + clause, args)
             rows = self.cursor_to_dict(txn)
             for row in rows:
                 event = ev_map[row["event_id"]]
@@ -2249,11 +2258,12 @@ class EventsStore(
             sql = """
                 SELECT DISTINCT state_group FROM event_to_state_groups
                 LEFT JOIN events_to_purge AS ep USING (event_id)
-                WHERE state_group IN (%s) AND ep.event_id IS NULL
-            """ % (
-                ",".join("?" for _ in current_search),
+                WHERE ep.event_id IS NULL AND
+            """
+            clause, args = make_in_list_sql_clause(
+                txn.database_engine, "state_group", current_search
             )
-            txn.execute(sql, list(current_search))
+            txn.execute(sql + clause, list(args))
 
             referenced = set(sg for sg, in txn)
             referenced_groups |= referenced
diff --git a/synapse/storage/events_bg_updates.py b/synapse/storage/events_bg_updates.py
index 5717baf48c..31ea6f917f 100644
--- a/synapse/storage/events_bg_updates.py
+++ b/synapse/storage/events_bg_updates.py
@@ -21,6 +21,7 @@ from canonicaljson import json
 
 from twisted.internet import defer
 
+from synapse.storage._base import make_in_list_sql_clause
 from synapse.storage.background_updates import BackgroundUpdateStore
 
 logger = logging.getLogger(__name__)
@@ -71,6 +72,19 @@ class EventsBackgroundUpdatesStore(BackgroundUpdateStore):
             "redactions_received_ts", self._redactions_received_ts
         )
 
+        # This index gets deleted in `event_fix_redactions_bytes` update
+        self.register_background_index_update(
+            "event_fix_redactions_bytes_create_index",
+            index_name="redactions_censored_redacts",
+            table="redactions",
+            columns=["redacts"],
+            where_clause="have_censored",
+        )
+
+        self.register_background_update_handler(
+            "event_fix_redactions_bytes", self._event_fix_redactions_bytes
+        )
+
     @defer.inlineCallbacks
     def _background_reindex_fields_sender(self, progress, batch_size):
         target_min_stream_id = progress["target_min_stream_id_inclusive"]
@@ -312,12 +326,13 @@ class EventsBackgroundUpdatesStore(BackgroundUpdateStore):
                     INNER JOIN event_json USING (event_id)
                     LEFT JOIN rejections USING (event_id)
                     WHERE
-                        prev_event_id IN (%s)
-                        AND NOT events.outlier
-                """ % (
-                    ",".join("?" for _ in to_check),
+                        NOT events.outlier
+                        AND
+                """
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "prev_event_id", to_check
                 )
-                txn.execute(sql, to_check)
+                txn.execute(sql + clause, list(args))
 
                 for prev_event_id, event_id, metadata, rejected in txn:
                     if event_id in graph:
@@ -458,3 +473,33 @@ class EventsBackgroundUpdatesStore(BackgroundUpdateStore):
             yield self._end_background_update("redactions_received_ts")
 
         return count
+
+    @defer.inlineCallbacks
+    def _event_fix_redactions_bytes(self, progress, batch_size):
+        """Undoes hex encoded censored redacted event JSON.
+        """
+
+        def _event_fix_redactions_bytes_txn(txn):
+            # This update is quite fast due to new index.
+            txn.execute(
+                """
+                UPDATE event_json
+                SET
+                    json = convert_from(json::bytea, 'utf8')
+                FROM redactions
+                WHERE
+                    redactions.have_censored
+                    AND event_json.event_id = redactions.redacts
+                    AND json NOT LIKE '{%';
+                """
+            )
+
+            txn.execute("DROP INDEX redactions_censored_redacts")
+
+        yield self.runInteraction(
+            "_event_fix_redactions_bytes", _event_fix_redactions_bytes_txn
+        )
+
+        yield self._end_background_update("event_fix_redactions_bytes")
+
+        return 1
diff --git a/synapse/storage/events_worker.py b/synapse/storage/events_worker.py
index 57ce0304e9..4c4b76bd93 100644
--- a/synapse/storage/events_worker.py
+++ b/synapse/storage/events_worker.py
@@ -31,12 +31,11 @@ from synapse.events.snapshot import EventContext  # noqa: F401
 from synapse.events.utils import prune_event
 from synapse.logging.context import LoggingContext, PreserveLoggingContext
 from synapse.metrics.background_process_metrics import run_as_background_process
+from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
 from synapse.types import get_domain_from_id
 from synapse.util import batch_iter
 from synapse.util.metrics import Measure
 
-from ._base import SQLBaseStore
-
 logger = logging.getLogger(__name__)
 
 
@@ -623,10 +622,14 @@ class EventsWorkerStore(SQLBaseStore):
                 " rej.reason "
                 " FROM event_json as e"
                 " LEFT JOIN rejections as rej USING (event_id)"
-                " WHERE e.event_id IN (%s)"
-            ) % (",".join(["?"] * len(evs)),)
+                " WHERE "
+            )
 
-            txn.execute(sql, evs)
+            clause, args = make_in_list_sql_clause(
+                txn.database_engine, "e.event_id", evs
+            )
+
+            txn.execute(sql + clause, args)
 
             for row in txn:
                 event_id = row[0]
@@ -640,11 +643,11 @@ class EventsWorkerStore(SQLBaseStore):
                 }
 
             # check for redactions
-            redactions_sql = (
-                "SELECT event_id, redacts FROM redactions WHERE redacts IN (%s)"
-            ) % (",".join(["?"] * len(evs)),)
+            redactions_sql = "SELECT event_id, redacts FROM redactions WHERE "
+
+            clause, args = make_in_list_sql_clause(txn.database_engine, "redacts", evs)
 
-            txn.execute(redactions_sql, evs)
+            txn.execute(redactions_sql + clause, args)
 
             for (redacter, redacted) in txn:
                 d = event_dict.get(redacted)
@@ -753,10 +756,11 @@ class EventsWorkerStore(SQLBaseStore):
         results = set()
 
         def have_seen_events_txn(txn, chunk):
-            sql = "SELECT event_id FROM events as e WHERE e.event_id IN (%s)" % (
-                ",".join("?" * len(chunk)),
+            sql = "SELECT event_id FROM events as e WHERE "
+            clause, args = make_in_list_sql_clause(
+                txn.database_engine, "e.event_id", chunk
             )
-            txn.execute(sql, chunk)
+            txn.execute(sql + clause, args)
             for (event_id,) in txn:
                 results.add(event_id)
 
diff --git a/synapse/storage/filtering.py b/synapse/storage/filtering.py
index 23b48f6cea..7c2a7da836 100644
--- a/synapse/storage/filtering.py
+++ b/synapse/storage/filtering.py
@@ -51,7 +51,7 @@ class FilteringStore(SQLBaseStore):
                 "SELECT filter_id FROM user_filters "
                 "WHERE user_id = ? AND filter_json = ?"
             )
-            txn.execute(sql, (user_localpart, def_json))
+            txn.execute(sql, (user_localpart, bytearray(def_json)))
             filter_id_response = txn.fetchone()
             if filter_id_response is not None:
                 return filter_id_response[0]
@@ -68,7 +68,7 @@ class FilteringStore(SQLBaseStore):
                 "INSERT INTO user_filters (user_id, filter_id, filter_json)"
                 "VALUES(?, ?, ?)"
             )
-            txn.execute(sql, (user_localpart, filter_id, def_json))
+            txn.execute(sql, (user_localpart, filter_id, bytearray(def_json)))
 
             return filter_id
 
diff --git a/synapse/storage/monthly_active_users.py b/synapse/storage/monthly_active_users.py
index 752e9788a2..3803604be7 100644
--- a/synapse/storage/monthly_active_users.py
+++ b/synapse/storage/monthly_active_users.py
@@ -32,7 +32,6 @@ class MonthlyActiveUsersStore(SQLBaseStore):
         super(MonthlyActiveUsersStore, self).__init__(None, hs)
         self._clock = hs.get_clock()
         self.hs = hs
-        self.reserved_users = ()
         # Do not add more reserved users than the total allowable number
         self._new_transaction(
             dbconn,
@@ -51,7 +50,6 @@ class MonthlyActiveUsersStore(SQLBaseStore):
             txn (cursor):
             threepids (list[dict]): List of threepid dicts to reserve
         """
-        reserved_user_list = []
 
         for tp in threepids:
             user_id = self.get_user_id_by_threepid_txn(txn, tp["medium"], tp["address"])
@@ -60,10 +58,8 @@ class MonthlyActiveUsersStore(SQLBaseStore):
                 is_support = self.is_support_user_txn(txn, user_id)
                 if not is_support:
                     self.upsert_monthly_active_user_txn(txn, user_id)
-                    reserved_user_list.append(user_id)
             else:
                 logger.warning("mau limit reserved threepid %s not found in db" % tp)
-        self.reserved_users = tuple(reserved_user_list)
 
     @defer.inlineCallbacks
     def reap_monthly_active_users(self):
@@ -74,8 +70,11 @@ class MonthlyActiveUsersStore(SQLBaseStore):
             Deferred[]
         """
 
-        def _reap_users(txn):
-            # Purge stale users
+        def _reap_users(txn, reserved_users):
+            """
+            Args:
+                reserved_users (tuple): reserved users to preserve
+            """
 
             thirty_days_ago = int(self._clock.time_msec()) - (1000 * 60 * 60 * 24 * 30)
             query_args = [thirty_days_ago]
@@ -83,20 +82,19 @@ class MonthlyActiveUsersStore(SQLBaseStore):
 
             # Need if/else since 'AND user_id NOT IN ({})' fails on Postgres
             # when len(reserved_users) == 0. Works fine on sqlite.
-            if len(self.reserved_users) > 0:
+            if len(reserved_users) > 0:
                 # questionmarks is a hack to overcome sqlite not supporting
                 # tuples in 'WHERE IN %s'
-                questionmarks = "?" * len(self.reserved_users)
+                question_marks = ",".join("?" * len(reserved_users))
 
-                query_args.extend(self.reserved_users)
-                sql = base_sql + """ AND user_id NOT IN ({})""".format(
-                    ",".join(questionmarks)
-                )
+                query_args.extend(reserved_users)
+                sql = base_sql + " AND user_id NOT IN ({})".format(question_marks)
             else:
                 sql = base_sql
 
             txn.execute(sql, query_args)
 
+            max_mau_value = self.hs.config.max_mau_value
             if self.hs.config.limit_usage_by_mau:
                 # If MAU user count still exceeds the MAU threshold, then delete on
                 # a least recently active basis.
@@ -106,31 +104,52 @@ class MonthlyActiveUsersStore(SQLBaseStore):
                 # While Postgres does not require 'LIMIT', but also does not support
                 # negative LIMIT values. So there is no way to write it that both can
                 # support
-                safe_guard = self.hs.config.max_mau_value - len(self.reserved_users)
-                # Must be greater than zero for postgres
-                safe_guard = safe_guard if safe_guard > 0 else 0
-                query_args = [safe_guard]
-
-                base_sql = """
-                    DELETE FROM monthly_active_users
-                    WHERE user_id NOT IN (
-                        SELECT user_id FROM monthly_active_users
-                        ORDER BY timestamp DESC
-                        LIMIT ?
+                if len(reserved_users) == 0:
+                    sql = """
+                        DELETE FROM monthly_active_users
+                        WHERE user_id NOT IN (
+                            SELECT user_id FROM monthly_active_users
+                            ORDER BY timestamp DESC
+                            LIMIT ?
                         )
-                    """
+                        """
+                    txn.execute(sql, (max_mau_value,))
                 # Need if/else since 'AND user_id NOT IN ({})' fails on Postgres
                 # when len(reserved_users) == 0. Works fine on sqlite.
-                if len(self.reserved_users) > 0:
-                    query_args.extend(self.reserved_users)
-                    sql = base_sql + """ AND user_id NOT IN ({})""".format(
-                        ",".join(questionmarks)
-                    )
                 else:
-                    sql = base_sql
-                txn.execute(sql, query_args)
+                    # Must be >= 0 for postgres
+                    num_of_non_reserved_users_to_remove = max(
+                        max_mau_value - len(reserved_users), 0
+                    )
+
+                    # It is important to filter reserved users twice to guard
+                    # against the case where the reserved user is present in the
+                    # SELECT, meaning that a legitmate mau is deleted.
+                    sql = """
+                        DELETE FROM monthly_active_users
+                        WHERE user_id NOT IN (
+                            SELECT user_id FROM monthly_active_users
+                            WHERE user_id NOT IN ({})
+                            ORDER BY timestamp DESC
+                            LIMIT ?
+                        )
+                        AND user_id NOT IN ({})
+                    """.format(
+                        question_marks, question_marks
+                    )
+
+                    query_args = [
+                        *reserved_users,
+                        num_of_non_reserved_users_to_remove,
+                        *reserved_users,
+                    ]
 
-        yield self.runInteraction("reap_monthly_active_users", _reap_users)
+                    txn.execute(sql, query_args)
+
+        reserved_users = yield self.get_registered_reserved_users()
+        yield self.runInteraction(
+            "reap_monthly_active_users", _reap_users, reserved_users
+        )
         # It seems poor to invalidate the whole cache, Postgres supports
         # 'Returning' which would allow me to invalidate only the
         # specific users, but sqlite has no way to do this and instead
@@ -159,21 +178,25 @@ class MonthlyActiveUsersStore(SQLBaseStore):
         return self.runInteraction("count_users", _count_users)
 
     @defer.inlineCallbacks
-    def get_registered_reserved_users_count(self):
-        """Of the reserved threepids defined in config, how many are associated
+    def get_registered_reserved_users(self):
+        """Of the reserved threepids defined in config, which are associated
         with registered users?
 
         Returns:
-            Defered[int]: Number of real reserved users
+            Defered[list]: Real reserved users
         """
-        count = 0
-        for tp in self.hs.config.mau_limits_reserved_threepids:
+        users = []
+
+        for tp in self.hs.config.mau_limits_reserved_threepids[
+            : self.hs.config.max_mau_value
+        ]:
             user_id = yield self.hs.get_datastore().get_user_id_by_threepid(
                 tp["medium"], tp["address"]
             )
             if user_id:
-                count = count + 1
-        return count
+                users.append(user_id)
+
+        return users
 
     @defer.inlineCallbacks
     def upsert_monthly_active_user(self, user_id):
diff --git a/synapse/storage/presence.py b/synapse/storage/presence.py
index 5db6f2d84a..3a641f538b 100644
--- a/synapse/storage/presence.py
+++ b/synapse/storage/presence.py
@@ -18,11 +18,10 @@ from collections import namedtuple
 from twisted.internet import defer
 
 from synapse.api.constants import PresenceState
+from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
 from synapse.util import batch_iter
 from synapse.util.caches.descriptors import cached, cachedList
 
-from ._base import SQLBaseStore
-
 
 class UserPresenceState(
     namedtuple(
@@ -119,14 +118,13 @@ class PresenceStore(SQLBaseStore):
         )
 
         # Delete old rows to stop database from getting really big
-        sql = (
-            "DELETE FROM presence_stream WHERE" " stream_id < ?" " AND user_id IN (%s)"
-        )
+        sql = "DELETE FROM presence_stream WHERE stream_id < ? AND "
 
         for states in batch_iter(presence_states, 50):
-            args = [stream_id]
-            args.extend(s.user_id for s in states)
-            txn.execute(sql % (",".join("?" for _ in states),), args)
+            clause, args = make_in_list_sql_clause(
+                self.database_engine, "user_id", [s.user_id for s in states]
+            )
+            txn.execute(sql + clause, [stream_id] + list(args))
 
     def get_all_presence_updates(self, last_id, current_id):
         if last_id == current_id:
diff --git a/synapse/storage/pusher.py b/synapse/storage/pusher.py
index 3e0e834a62..b12e80440a 100644
--- a/synapse/storage/pusher.py
+++ b/synapse/storage/pusher.py
@@ -241,7 +241,7 @@ class PusherStore(PusherWorkerStore):
                     "device_display_name": device_display_name,
                     "ts": pushkey_ts,
                     "lang": lang,
-                    "data": encode_canonical_json(data),
+                    "data": bytearray(encode_canonical_json(data)),
                     "last_stream_ordering": last_stream_ordering,
                     "profile_tag": profile_tag,
                     "id": stream_id,
diff --git a/synapse/storage/receipts.py b/synapse/storage/receipts.py
index 290ddb30e8..0c24430f28 100644
--- a/synapse/storage/receipts.py
+++ b/synapse/storage/receipts.py
@@ -21,12 +21,11 @@ from canonicaljson import json
 
 from twisted.internet import defer
 
+from synapse.storage._base import SQLBaseStore, make_in_list_sql_clause
+from synapse.storage.util.id_generators import StreamIdGenerator
 from synapse.util.caches.descriptors import cached, cachedInlineCallbacks, cachedList
 from synapse.util.caches.stream_change_cache import StreamChangeCache
 
-from ._base import SQLBaseStore
-from .util.id_generators import StreamIdGenerator
-
 logger = logging.getLogger(__name__)
 
 
@@ -217,24 +216,26 @@ class ReceiptsWorkerStore(SQLBaseStore):
 
         def f(txn):
             if from_key:
-                sql = (
-                    "SELECT * FROM receipts_linearized WHERE"
-                    " room_id IN (%s) AND stream_id > ? AND stream_id <= ?"
-                ) % (",".join(["?"] * len(room_ids)))
-                args = list(room_ids)
-                args.extend([from_key, to_key])
+                sql = """
+                    SELECT * FROM receipts_linearized WHERE
+                    stream_id > ? AND stream_id <= ? AND
+                """
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "room_id", room_ids
+                )
 
-                txn.execute(sql, args)
+                txn.execute(sql + clause, [from_key, to_key] + list(args))
             else:
-                sql = (
-                    "SELECT * FROM receipts_linearized WHERE"
-                    " room_id IN (%s) AND stream_id <= ?"
-                ) % (",".join(["?"] * len(room_ids)))
+                sql = """
+                    SELECT * FROM receipts_linearized WHERE
+                    stream_id <= ? AND
+                """
 
-                args = list(room_ids)
-                args.append(to_key)
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "room_id", room_ids
+                )
 
-                txn.execute(sql, args)
+                txn.execute(sql + clause, [to_key] + list(args))
 
             return self.cursor_to_dict(txn)
 
@@ -433,13 +434,19 @@ class ReceiptsStore(ReceiptsWorkerStore):
             # we need to points in graph -> linearized form.
             # TODO: Make this better.
             def graph_to_linear(txn):
-                query = (
-                    "SELECT event_id WHERE room_id = ? AND stream_ordering IN ("
-                    " SELECT max(stream_ordering) WHERE event_id IN (%s)"
-                    ")"
-                ) % (",".join(["?"] * len(event_ids)))
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "event_id", event_ids
+                )
+
+                sql = """
+                    SELECT event_id WHERE room_id = ? AND stream_ordering IN (
+                        SELECT max(stream_ordering) WHERE %s
+                    )
+                """ % (
+                    clause,
+                )
 
-                txn.execute(query, [room_id] + event_ids)
+                txn.execute(sql, [room_id] + list(args))
                 rows = txn.fetchall()
                 if rows:
                     return rows[0][0]
diff --git a/synapse/storage/roommember.py b/synapse/storage/roommember.py
index 4e606a8380..ff63487823 100644
--- a/synapse/storage/roommember.py
+++ b/synapse/storage/roommember.py
@@ -26,7 +26,7 @@ from twisted.internet import defer
 from synapse.api.constants import EventTypes, Membership
 from synapse.metrics import LaterGauge
 from synapse.metrics.background_process_metrics import run_as_background_process
-from synapse.storage._base import LoggingTransaction
+from synapse.storage._base import LoggingTransaction, make_in_list_sql_clause
 from synapse.storage.background_updates import BackgroundUpdateStore
 from synapse.storage.engines import Sqlite3Engine
 from synapse.storage.events_worker import EventsWorkerStore
@@ -372,6 +372,9 @@ class RoomMemberWorkerStore(EventsWorkerStore):
         results = []
         if membership_list:
             if self._current_state_events_membership_up_to_date:
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "c.membership", membership_list
+                )
                 sql = """
                     SELECT room_id, e.sender, c.membership, event_id, e.stream_ordering
                     FROM current_state_events AS c
@@ -379,11 +382,14 @@ class RoomMemberWorkerStore(EventsWorkerStore):
                     WHERE
                         c.type = 'm.room.member'
                         AND state_key = ?
-                        AND c.membership IN (%s)
+                        AND %s
                 """ % (
-                    ",".join("?" * len(membership_list))
+                    clause,
                 )
             else:
+                clause, args = make_in_list_sql_clause(
+                    self.database_engine, "m.membership", membership_list
+                )
                 sql = """
                     SELECT room_id, e.sender, m.membership, event_id, e.stream_ordering
                     FROM current_state_events AS c
@@ -392,12 +398,12 @@ class RoomMemberWorkerStore(EventsWorkerStore):
                     WHERE
                         c.type = 'm.room.member'
                         AND state_key = ?
-                        AND m.membership IN (%s)
+                        AND %s
                 """ % (
-                    ",".join("?" * len(membership_list))
+                    clause,
                 )
 
-            txn.execute(sql, (user_id, *membership_list))
+            txn.execute(sql, (user_id, *args))
             results = [RoomsForUser(**r) for r in self.cursor_to_dict(txn)]
 
         if do_invite:
diff --git a/synapse/storage/schema/delta/56/redaction_censor3_fix_update.sql.postgres b/synapse/storage/schema/delta/56/redaction_censor3_fix_update.sql.postgres
index f7bcc5e2f2..67471f3ef5 100644
--- a/synapse/storage/schema/delta/56/redaction_censor3_fix_update.sql.postgres
+++ b/synapse/storage/schema/delta/56/redaction_censor3_fix_update.sql.postgres
@@ -15,12 +15,11 @@
 
 
 -- There was a bug where we may have updated censored redactions as bytes,
--- which can (somehow) cause json to be inserted hex encoded. This goes and
--- undoes any such hex encoded JSON.
-UPDATE event_json SET json = convert_from(json::bytea, 'utf8')
-WHERE event_id IN (
-  SELECT event_json.event_id
-  FROM event_json
-  INNER JOIN redactions ON (event_json.event_id = redacts)
-  WHERE have_censored AND json NOT LIKE '{%'
-);
+-- which can (somehow) cause json to be inserted hex encoded. These updates go
+-- and undoes any such hex encoded JSON.
+
+INSERT into background_updates (update_name, progress_json)
+  VALUES ('event_fix_redactions_bytes_create_index', '{}');
+
+INSERT into background_updates (update_name, progress_json, depends_on)
+  VALUES ('event_fix_redactions_bytes', '{}', 'event_fix_redactions_bytes_create_index');
diff --git a/synapse/storage/schema/delta/56/unique_user_filter_index.py b/synapse/storage/schema/delta/56/unique_user_filter_index.py
index 60031f23ca..1de8b54961 100644
--- a/synapse/storage/schema/delta/56/unique_user_filter_index.py
+++ b/synapse/storage/schema/delta/56/unique_user_filter_index.py
@@ -5,42 +5,48 @@ from synapse.storage.engines import PostgresEngine
 logger = logging.getLogger(__name__)
 
 
+"""
+This migration updates the user_filters table as follows:
+
+ - drops any (user_id, filter_id) duplicates
+ - makes the columns NON-NULLable
+ - turns the index into a UNIQUE index
+"""
+
+
 def run_upgrade(cur, database_engine, *args, **kwargs):
+    pass
+
+
+def run_create(cur, database_engine, *args, **kwargs):
     if isinstance(database_engine, PostgresEngine):
         select_clause = """
-        CREATE TEMPORARY TABLE user_filters_migration AS
             SELECT DISTINCT ON (user_id, filter_id) user_id, filter_id, filter_json
-            FROM user_filters;
+            FROM user_filters
         """
     else:
         select_clause = """
-        CREATE TEMPORARY TABLE user_filters_migration AS
-            SELECT * FROM user_filters GROUP BY user_id, filter_id;
+            SELECT * FROM user_filters GROUP BY user_id, filter_id
         """
-    sql = (
-        """
-        BEGIN;
-            %s
-            DROP INDEX user_filters_by_user_id_filter_id;
-            DELETE FROM user_filters;
-            ALTER TABLE user_filters
-               ALTER COLUMN user_id SET NOT NULL,
-               ALTER COLUMN filter_id SET NOT NULL,
-               ALTER COLUMN filter_json SET NOT NULL;
-            INSERT INTO user_filters(user_id, filter_id, filter_json)
-                SELECT * FROM user_filters_migration;
-            DROP TABLE user_filters_migration;
-            CREATE UNIQUE INDEX user_filters_by_user_id_filter_id_unique
-                ON user_filters(user_id, filter_id);
-        END;
-    """
-        % select_clause
+    sql = """
+            DROP TABLE IF EXISTS user_filters_migration;
+            DROP INDEX IF EXISTS user_filters_unique;
+            CREATE TABLE user_filters_migration (
+                user_id TEXT NOT NULL,
+                filter_id BIGINT NOT NULL,
+                filter_json BYTEA NOT NULL
+            );
+            INSERT INTO user_filters_migration (user_id, filter_id, filter_json)
+                %s;
+            CREATE UNIQUE INDEX user_filters_unique ON user_filters_migration
+                (user_id, filter_id);
+            DROP TABLE user_filters;
+            ALTER TABLE user_filters_migration RENAME TO user_filters;
+        """ % (
+        select_clause,
     )
+
     if isinstance(database_engine, PostgresEngine):
         cur.execute(sql)
     else:
         cur.executescript(sql)
-
-
-def run_create(cur, database_engine, *args, **kwargs):
-    pass
diff --git a/synapse/storage/search.py b/synapse/storage/search.py
index 6ba4190f1a..7695bf09fc 100644
--- a/synapse/storage/search.py
+++ b/synapse/storage/search.py
@@ -24,6 +24,7 @@ from canonicaljson import json
 from twisted.internet import defer
 
 from synapse.api.errors import SynapseError
+from synapse.storage._base import make_in_list_sql_clause
 from synapse.storage.engines import PostgresEngine, Sqlite3Engine
 
 from .background_updates import BackgroundUpdateStore
@@ -385,8 +386,10 @@ class SearchStore(SearchBackgroundUpdateStore):
         # Make sure we don't explode because the person is in too many rooms.
         # We filter the results below regardless.
         if len(room_ids) < 500:
-            clauses.append("room_id IN (%s)" % (",".join(["?"] * len(room_ids)),))
-            args.extend(room_ids)
+            clause, args = make_in_list_sql_clause(
+                self.database_engine, "room_id", room_ids
+            )
+            clauses = [clause]
 
         local_clauses = []
         for key in keys:
@@ -492,8 +495,10 @@ class SearchStore(SearchBackgroundUpdateStore):
         # Make sure we don't explode because the person is in too many rooms.
         # We filter the results below regardless.
         if len(room_ids) < 500:
-            clauses.append("room_id IN (%s)" % (",".join(["?"] * len(room_ids)),))
-            args.extend(room_ids)
+            clause, args = make_in_list_sql_clause(
+                self.database_engine, "room_id", room_ids
+            )
+            clauses = [clause]
 
         local_clauses = []
         for key in keys:
diff --git a/synapse/storage/state_deltas.py b/synapse/storage/state_deltas.py
index 5fdb442104..28f33ec18f 100644
--- a/synapse/storage/state_deltas.py
+++ b/synapse/storage/state_deltas.py
@@ -21,7 +21,7 @@ logger = logging.getLogger(__name__)
 
 
 class StateDeltasStore(SQLBaseStore):
-    def get_current_state_deltas(self, prev_stream_id):
+    def get_current_state_deltas(self, prev_stream_id: int, max_stream_id: int):
         """Fetch a list of room state changes since the given stream id
 
         Each entry in the result contains the following fields:
@@ -36,15 +36,27 @@ class StateDeltasStore(SQLBaseStore):
 
         Args:
             prev_stream_id (int): point to get changes since (exclusive)
+            max_stream_id (int): the point that we know has been correctly persisted
+               - ie, an upper limit to return changes from.
 
         Returns:
-            Deferred[list[dict]]: results
+            Deferred[tuple[int, list[dict]]: A tuple consisting of:
+               - the stream id which these results go up to
+               - list of current_state_delta_stream rows. If it is empty, we are
+                 up to date.
         """
         prev_stream_id = int(prev_stream_id)
+
+        # check we're not going backwards
+        assert prev_stream_id <= max_stream_id
+
         if not self._curr_state_delta_stream_cache.has_any_entity_changed(
             prev_stream_id
         ):
-            return []
+            # if the CSDs haven't changed between prev_stream_id and now, we
+            # know for certain that they haven't changed between prev_stream_id and
+            # max_stream_id.
+            return max_stream_id, []
 
         def get_current_state_deltas_txn(txn):
             # First we calculate the max stream id that will give us less than
@@ -54,21 +66,29 @@ class StateDeltasStore(SQLBaseStore):
             sql = """
                 SELECT stream_id, count(*)
                 FROM current_state_delta_stream
-                WHERE stream_id > ?
+                WHERE stream_id > ? AND stream_id <= ?
                 GROUP BY stream_id
                 ORDER BY stream_id ASC
                 LIMIT 100
             """
-            txn.execute(sql, (prev_stream_id,))
+            txn.execute(sql, (prev_stream_id, max_stream_id))
 
             total = 0
-            max_stream_id = prev_stream_id
-            for max_stream_id, count in txn:
+
+            for stream_id, count in txn:
                 total += count
                 if total > 100:
                     # We arbitarily limit to 100 entries to ensure we don't
                     # select toooo many.
+                    logger.debug(
+                        "Clipping current_state_delta_stream rows to stream_id %i",
+                        stream_id,
+                    )
+                    clipped_stream_id = stream_id
                     break
+            else:
+                # if there's no problem, we may as well go right up to the max_stream_id
+                clipped_stream_id = max_stream_id
 
             # Now actually get the deltas
             sql = """
@@ -77,8 +97,8 @@ class StateDeltasStore(SQLBaseStore):
                 WHERE ? < stream_id AND stream_id <= ?
                 ORDER BY stream_id ASC
             """
-            txn.execute(sql, (prev_stream_id, max_stream_id))
-            return self.cursor_to_dict(txn)
+            txn.execute(sql, (prev_stream_id, clipped_stream_id))
+            return clipped_stream_id, self.cursor_to_dict(txn)
 
         return self.runInteraction(
             "get_current_state_deltas", get_current_state_deltas_txn
diff --git a/synapse/storage/user_erasure_store.py b/synapse/storage/user_erasure_store.py
index 05cabc2282..aa4f0da5f0 100644
--- a/synapse/storage/user_erasure_store.py
+++ b/synapse/storage/user_erasure_store.py
@@ -56,15 +56,15 @@ class UserErasureWorkerStore(SQLBaseStore):
         # iterate it multiple times, and (b) avoiding duplicates.
         user_ids = tuple(set(user_ids))
 
-        def _get_erased_users(txn):
-            txn.execute(
-                "SELECT user_id FROM erased_users WHERE user_id IN (%s)"
-                % (",".join("?" * len(user_ids))),
-                user_ids,
-            )
-            return set(r[0] for r in txn)
-
-        erased_users = yield self.runInteraction("are_users_erased", _get_erased_users)
+        rows = yield self._simple_select_many_batch(
+            table="erased_users",
+            column="user_id",
+            iterable=user_ids,
+            retcols=("user_id",),
+            desc="are_users_erased",
+        )
+        erased_users = set(row["user_id"] for row in rows)
+
         res = dict((u, u in erased_users) for u in user_ids)
         return res
 
diff --git a/synapse/util/patch_inline_callbacks.py b/synapse/util/patch_inline_callbacks.py
new file mode 100644
index 0000000000..3925927f9f
--- /dev/null
+++ b/synapse/util/patch_inline_callbacks.py
@@ -0,0 +1,219 @@
+# -*- coding: utf-8 -*-
+# Copyright 2018 New Vector 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.
+
+from __future__ import print_function
+
+import functools
+import sys
+from typing import Any, Callable, List
+
+from twisted.internet import defer
+from twisted.internet.defer import Deferred
+from twisted.python.failure import Failure
+
+# Tracks if we've already patched inlineCallbacks
+_already_patched = False
+
+
+def do_patch():
+    """
+    Patch defer.inlineCallbacks so that it checks the state of the logcontext on exit
+    """
+
+    from synapse.logging.context import LoggingContext
+
+    global _already_patched
+
+    orig_inline_callbacks = defer.inlineCallbacks
+    if _already_patched:
+        return
+
+    def new_inline_callbacks(f):
+        @functools.wraps(f)
+        def wrapped(*args, **kwargs):
+            start_context = LoggingContext.current_context()
+            changes = []  # type: List[str]
+            orig = orig_inline_callbacks(_check_yield_points(f, changes))
+
+            try:
+                res = orig(*args, **kwargs)
+            except Exception:
+                if LoggingContext.current_context() != start_context:
+                    for err in changes:
+                        print(err, file=sys.stderr)
+
+                    err = "%s changed context from %s to %s on exception" % (
+                        f,
+                        start_context,
+                        LoggingContext.current_context(),
+                    )
+                    print(err, file=sys.stderr)
+                    raise Exception(err)
+                raise
+
+            if not isinstance(res, Deferred) or res.called:
+                if LoggingContext.current_context() != start_context:
+                    for err in changes:
+                        print(err, file=sys.stderr)
+
+                    err = "Completed %s changed context from %s to %s" % (
+                        f,
+                        start_context,
+                        LoggingContext.current_context(),
+                    )
+                    # print the error to stderr because otherwise all we
+                    # see in travis-ci is the 500 error
+                    print(err, file=sys.stderr)
+                    raise Exception(err)
+                return res
+
+            if LoggingContext.current_context() != LoggingContext.sentinel:
+                err = (
+                    "%s returned incomplete deferred in non-sentinel context "
+                    "%s (start was %s)"
+                ) % (f, LoggingContext.current_context(), start_context)
+                print(err, file=sys.stderr)
+                raise Exception(err)
+
+            def check_ctx(r):
+                if LoggingContext.current_context() != start_context:
+                    for err in changes:
+                        print(err, file=sys.stderr)
+                    err = "%s completion of %s changed context from %s to %s" % (
+                        "Failure" if isinstance(r, Failure) else "Success",
+                        f,
+                        start_context,
+                        LoggingContext.current_context(),
+                    )
+                    print(err, file=sys.stderr)
+                    raise Exception(err)
+                return r
+
+            res.addBoth(check_ctx)
+            return res
+
+        return wrapped
+
+    defer.inlineCallbacks = new_inline_callbacks
+    _already_patched = True
+
+
+def _check_yield_points(f: Callable, changes: List[str]):
+    """Wraps a generator that is about to be passed to defer.inlineCallbacks
+    checking that after every yield the log contexts are correct.
+
+    It's perfectly valid for log contexts to change within a function, e.g. due
+    to new Measure blocks, so such changes are added to the given `changes`
+    list instead of triggering an exception.
+
+    Args:
+        f: generator function to wrap
+        changes: A list of strings detailing how the contexts
+            changed within a function.
+
+    Returns:
+        function
+    """
+
+    from synapse.logging.context import LoggingContext
+
+    @functools.wraps(f)
+    def check_yield_points_inner(*args, **kwargs):
+        gen = f(*args, **kwargs)
+
+        last_yield_line_no = gen.gi_frame.f_lineno
+        result = None  # type: Any
+        while True:
+            expected_context = LoggingContext.current_context()
+
+            try:
+                isFailure = isinstance(result, Failure)
+                if isFailure:
+                    d = result.throwExceptionIntoGenerator(gen)
+                else:
+                    d = gen.send(result)
+            except (StopIteration, defer._DefGen_Return) as e:
+                if LoggingContext.current_context() != expected_context:
+                    # This happens when the context is lost sometime *after* the
+                    # final yield and returning. E.g. we forgot to yield on a
+                    # function that returns a deferred.
+                    #
+                    # We don't raise here as it's perfectly valid for contexts to
+                    # change in a function, as long as it sets the correct context
+                    # on resolving (which is checked separately).
+                    err = (
+                        "Function %r returned and changed context from %s to %s,"
+                        " in %s between %d and end of func"
+                        % (
+                            f.__qualname__,
+                            expected_context,
+                            LoggingContext.current_context(),
+                            f.__code__.co_filename,
+                            last_yield_line_no,
+                        )
+                    )
+                    changes.append(err)
+                return getattr(e, "value", None)
+
+            frame = gen.gi_frame
+
+            if isinstance(d, defer.Deferred) and not d.called:
+                # This happens if we yield on a deferred that doesn't follow
+                # the log context rules without wrapping in a `make_deferred_yieldable`.
+                # We raise here as this should never happen.
+                if LoggingContext.current_context() is not LoggingContext.sentinel:
+                    err = (
+                        "%s yielded with context %s rather than sentinel,"
+                        " yielded on line %d in %s"
+                        % (
+                            frame.f_code.co_name,
+                            LoggingContext.current_context(),
+                            frame.f_lineno,
+                            frame.f_code.co_filename,
+                        )
+                    )
+                    raise Exception(err)
+
+            try:
+                result = yield d
+            except Exception as e:
+                result = Failure(e)
+
+            if LoggingContext.current_context() != expected_context:
+
+                # This happens because the context is lost sometime *after* the
+                # previous yield and *after* the current yield. E.g. the
+                # deferred we waited on didn't follow the rules, or we forgot to
+                # yield on a function between the two yield points.
+                #
+                # We don't raise here as its perfectly valid for contexts to
+                # change in a function, as long as it sets the correct context
+                # on resolving (which is checked separately).
+                err = (
+                    "%s changed context from %s to %s, happened between lines %d and %d in %s"
+                    % (
+                        frame.f_code.co_name,
+                        expected_context,
+                        LoggingContext.current_context(),
+                        last_yield_line_no,
+                        frame.f_lineno,
+                        frame.f_code.co_filename,
+                    )
+                )
+                changes.append(err)
+
+            last_yield_line_no = frame.f_lineno
+
+    return check_yield_points_inner
diff --git a/tests/__init__.py b/tests/__init__.py
index f7fc502f01..ed805db1c2 100644
--- a/tests/__init__.py
+++ b/tests/__init__.py
@@ -16,9 +16,9 @@
 
 from twisted.trial import util
 
-import tests.patch_inline_callbacks
+from synapse.util.patch_inline_callbacks import do_patch
 
 # attempt to do the patch before we load any synapse code
-tests.patch_inline_callbacks.do_patch()
+do_patch()
 
 util.DEFAULT_TIMEOUT_DURATION = 20
diff --git a/tests/config/test_tls.py b/tests/config/test_tls.py
index b02780772a..1be6ff563b 100644
--- a/tests/config/test_tls.py
+++ b/tests/config/test_tls.py
@@ -21,17 +21,24 @@ import yaml
 
 from OpenSSL import SSL
 
+from synapse.config._base import Config, RootConfig
 from synapse.config.tls import ConfigError, TlsConfig
 from synapse.crypto.context_factory import ClientTLSOptionsFactory
 
 from tests.unittest import TestCase
 
 
-class TestConfig(TlsConfig):
+class FakeServer(Config):
+    section = "server"
+
     def has_tls_listener(self):
         return False
 
 
+class TestConfig(RootConfig):
+    config_classes = [FakeServer, TlsConfig]
+
+
 class TLSConfigTests(TestCase):
     def test_warn_self_signed(self):
         """
@@ -202,13 +209,13 @@ s4niecZKPBizL6aucT59CsunNmmb5Glq8rlAcU+1ZTZZzGYqVYhF6axB9Qg=
         conf = TestConfig()
         conf.read_config(
             yaml.safe_load(
-                TestConfig().generate_config_section(
+                TestConfig().generate_config(
                     "/config_dir_path",
                     "my_super_secure_server",
                     "/data_dir_path",
-                    "/tls_cert_path",
-                    "tls_private_key",
-                    None,  # This is the acme_domain
+                    tls_certificate_path="/tls_cert_path",
+                    tls_private_key_path="tls_private_key",
+                    acme_domain=None,  # This is the acme_domain
                 )
             ),
             "/config_dir_path",
@@ -223,13 +230,13 @@ s4niecZKPBizL6aucT59CsunNmmb5Glq8rlAcU+1ZTZZzGYqVYhF6axB9Qg=
         conf = TestConfig()
         conf.read_config(
             yaml.safe_load(
-                TestConfig().generate_config_section(
+                TestConfig().generate_config(
                     "/config_dir_path",
                     "my_super_secure_server",
                     "/data_dir_path",
-                    "/tls_cert_path",
-                    "tls_private_key",
-                    "my_supe_secure_server",  # This is the acme_domain
+                    tls_certificate_path="/tls_cert_path",
+                    tls_private_key_path="tls_private_key",
+                    acme_domain="my_supe_secure_server",  # This is the acme_domain
                 )
             ),
             "/config_dir_path",
diff --git a/tests/handlers/test_typing.py b/tests/handlers/test_typing.py
index 1f2ef5d01f..67f1013051 100644
--- a/tests/handlers/test_typing.py
+++ b/tests/handlers/test_typing.py
@@ -139,7 +139,7 @@ class TypingNotificationsTestCase(unittest.HomeserverTestCase):
             defer.succeed(1)
         )
 
-        self.datastore.get_current_state_deltas.return_value = None
+        self.datastore.get_current_state_deltas.return_value = (0, None)
 
         self.datastore.get_to_device_stream_token = lambda: 0
         self.datastore.get_new_device_msgs_for_remote = lambda *args, **kargs: ([], 0)
diff --git a/tests/patch_inline_callbacks.py b/tests/patch_inline_callbacks.py
deleted file mode 100644
index 220884311c..0000000000
--- a/tests/patch_inline_callbacks.py
+++ /dev/null
@@ -1,94 +0,0 @@
-# -*- coding: utf-8 -*-
-# Copyright 2018 New Vector 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.
-
-from __future__ import print_function
-
-import functools
-import sys
-
-from twisted.internet import defer
-from twisted.internet.defer import Deferred
-from twisted.python.failure import Failure
-
-
-def do_patch():
-    """
-    Patch defer.inlineCallbacks so that it checks the state of the logcontext on exit
-    """
-
-    from synapse.logging.context import LoggingContext
-
-    orig_inline_callbacks = defer.inlineCallbacks
-
-    def new_inline_callbacks(f):
-
-        orig = orig_inline_callbacks(f)
-
-        @functools.wraps(f)
-        def wrapped(*args, **kwargs):
-            start_context = LoggingContext.current_context()
-
-            try:
-                res = orig(*args, **kwargs)
-            except Exception:
-                if LoggingContext.current_context() != start_context:
-                    err = "%s changed context from %s to %s on exception" % (
-                        f,
-                        start_context,
-                        LoggingContext.current_context(),
-                    )
-                    print(err, file=sys.stderr)
-                    raise Exception(err)
-                raise
-
-            if not isinstance(res, Deferred) or res.called:
-                if LoggingContext.current_context() != start_context:
-                    err = "%s changed context from %s to %s" % (
-                        f,
-                        start_context,
-                        LoggingContext.current_context(),
-                    )
-                    # print the error to stderr because otherwise all we
-                    # see in travis-ci is the 500 error
-                    print(err, file=sys.stderr)
-                    raise Exception(err)
-                return res
-
-            if LoggingContext.current_context() != LoggingContext.sentinel:
-                err = (
-                    "%s returned incomplete deferred in non-sentinel context "
-                    "%s (start was %s)"
-                ) % (f, LoggingContext.current_context(), start_context)
-                print(err, file=sys.stderr)
-                raise Exception(err)
-
-            def check_ctx(r):
-                if LoggingContext.current_context() != start_context:
-                    err = "%s completion of %s changed context from %s to %s" % (
-                        "Failure" if isinstance(r, Failure) else "Success",
-                        f,
-                        start_context,
-                        LoggingContext.current_context(),
-                    )
-                    print(err, file=sys.stderr)
-                    raise Exception(err)
-                return r
-
-            res.addBoth(check_ctx)
-            return res
-
-        return wrapped
-
-    defer.inlineCallbacks = new_inline_callbacks
diff --git a/tests/rest/admin/test_admin.py b/tests/rest/admin/test_admin.py
index 5877bb2133..d3a4f717f7 100644
--- a/tests/rest/admin/test_admin.py
+++ b/tests/rest/admin/test_admin.py
@@ -62,7 +62,7 @@ class UserRegisterTestCase(unittest.HomeserverTestCase):
         self.device_handler.check_device_registered = Mock(return_value="FAKE")
 
         self.datastore = Mock(return_value=Mock())
-        self.datastore.get_current_state_deltas = Mock(return_value=[])
+        self.datastore.get_current_state_deltas = Mock(return_value=(0, []))
 
         self.secrets = Mock()
 
diff --git a/tests/rest/client/v1/test_rooms.py b/tests/rest/client/v1/test_rooms.py
index fe741637f5..2f2ca74611 100644
--- a/tests/rest/client/v1/test_rooms.py
+++ b/tests/rest/client/v1/test_rooms.py
@@ -484,6 +484,15 @@ class RoomsCreateTestCase(RoomBase):
         self.render(request)
         self.assertEquals(400, channel.code)
 
+    def test_post_room_invitees_invalid_mxid(self):
+        # POST with invalid invitee, see https://github.com/matrix-org/synapse/issues/4088
+        # Note the trailing space in the MXID here!
+        request, channel = self.make_request(
+            "POST", "/createRoom", b'{"invite":["@alice:example.com "]}'
+        )
+        self.render(request)
+        self.assertEquals(400, channel.code)
+
 
 class RoomTopicTestCase(RoomBase):
     """ Tests /rooms/$room_id/topic REST events. """
diff --git a/tests/rest/client/v2_alpha/test_filter.py b/tests/rest/client/v2_alpha/test_filter.py
index f42a8efbf4..e0e9e94fbf 100644
--- a/tests/rest/client/v2_alpha/test_filter.py
+++ b/tests/rest/client/v2_alpha/test_filter.py
@@ -92,7 +92,7 @@ class FilterTestCase(unittest.HomeserverTestCase):
         )
         self.render(request)
 
-        self.assertEqual(channel.result["code"], b"400")
+        self.assertEqual(channel.result["code"], b"404")
         self.assertEquals(channel.json_body["errcode"], Codes.NOT_FOUND)
 
     # Currently invalid params do not have an appropriate errcode
diff --git a/tests/storage/test_event_federation.py b/tests/storage/test_event_federation.py
index b58386994e..2fe50377f8 100644
--- a/tests/storage/test_event_federation.py
+++ b/tests/storage/test_event_federation.py
@@ -57,7 +57,7 @@ class EventFederationWorkerStoreTestCase(tests.unittest.TestCase):
                     "(event_id, algorithm, hash) "
                     "VALUES (?, 'sha256', ?)"
                 ),
-                (event_id, b"ffff"),
+                (event_id, bytearray(b"ffff")),
             )
 
         for i in range(0, 11):
diff --git a/tests/storage/test_monthly_active_users.py b/tests/storage/test_monthly_active_users.py
index 1494650d10..90a63dc477 100644
--- a/tests/storage/test_monthly_active_users.py
+++ b/tests/storage/test_monthly_active_users.py
@@ -50,6 +50,7 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
             {"medium": "email", "address": user2_email},
             {"medium": "email", "address": user3_email},
         ]
+        self.hs.config.mau_limits_reserved_threepids = threepids
         # -1 because user3 is a support user and does not count
         user_num = len(threepids) - 1
 
@@ -84,6 +85,7 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
         self.hs.config.max_mau_value = 0
 
         self.reactor.advance(FORTY_DAYS)
+        self.hs.config.max_mau_value = 5
 
         self.store.reap_monthly_active_users()
         self.pump()
@@ -147,9 +149,7 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
         self.store.reap_monthly_active_users()
         self.pump()
         count = self.store.get_monthly_active_count()
-        self.assertEquals(
-            self.get_success(count), initial_users - self.hs.config.max_mau_value
-        )
+        self.assertEquals(self.get_success(count), self.hs.config.max_mau_value)
 
         self.reactor.advance(FORTY_DAYS)
         self.store.reap_monthly_active_users()
@@ -158,6 +158,44 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
         count = self.store.get_monthly_active_count()
         self.assertEquals(self.get_success(count), 0)
 
+    def test_reap_monthly_active_users_reserved_users(self):
+        """ Tests that reaping correctly handles reaping where reserved users are
+        present"""
+
+        self.hs.config.max_mau_value = 5
+        initial_users = 5
+        reserved_user_number = initial_users - 1
+        threepids = []
+        for i in range(initial_users):
+            user = "@user%d:server" % i
+            email = "user%d@example.com" % i
+            self.get_success(self.store.upsert_monthly_active_user(user))
+            threepids.append({"medium": "email", "address": email})
+            # Need to ensure that the most recent entries in the
+            # monthly_active_users table are reserved
+            now = int(self.hs.get_clock().time_msec())
+            if i != 0:
+                self.get_success(
+                    self.store.register_user(user_id=user, password_hash=None)
+                )
+                self.get_success(
+                    self.store.user_add_threepid(user, "email", email, now, now)
+                )
+
+        self.hs.config.mau_limits_reserved_threepids = threepids
+        self.store.runInteraction(
+            "initialise", self.store._initialise_reserved_users, threepids
+        )
+        count = self.store.get_monthly_active_count()
+        self.assertTrue(self.get_success(count), initial_users)
+
+        users = self.store.get_registered_reserved_users()
+        self.assertEquals(len(self.get_success(users)), reserved_user_number)
+
+        self.get_success(self.store.reap_monthly_active_users())
+        count = self.store.get_monthly_active_count()
+        self.assertEquals(self.get_success(count), self.hs.config.max_mau_value)
+
     def test_populate_monthly_users_is_guest(self):
         # Test that guest users are not added to mau list
         user_id = "@user_id:host"
@@ -192,12 +230,13 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
 
     def test_get_reserved_real_user_account(self):
         # Test no reserved users, or reserved threepids
-        count = self.store.get_registered_reserved_users_count()
-        self.assertEquals(self.get_success(count), 0)
+        users = self.get_success(self.store.get_registered_reserved_users())
+        self.assertEquals(len(users), 0)
         # Test reserved users but no registered users
 
         user1 = "@user1:example.com"
         user2 = "@user2:example.com"
+
         user1_email = "user1@example.com"
         user2_email = "user2@example.com"
         threepids = [
@@ -210,8 +249,8 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
         )
 
         self.pump()
-        count = self.store.get_registered_reserved_users_count()
-        self.assertEquals(self.get_success(count), 0)
+        users = self.get_success(self.store.get_registered_reserved_users())
+        self.assertEquals(len(users), 0)
 
         # Test reserved registed users
         self.store.register_user(user_id=user1, password_hash=None)
@@ -221,8 +260,9 @@ class MonthlyActiveUsersTestCase(unittest.HomeserverTestCase):
         now = int(self.hs.get_clock().time_msec())
         self.store.user_add_threepid(user1, "email", user1_email, now, now)
         self.store.user_add_threepid(user2, "email", user2_email, now, now)
-        count = self.store.get_registered_reserved_users_count()
-        self.assertEquals(self.get_success(count), len(threepids))
+
+        users = self.get_success(self.store.get_registered_reserved_users())
+        self.assertEquals(len(users), len(threepids))
 
     def test_support_user_not_add_to_mau_limits(self):
         support_user_id = "@support:test"
diff --git a/tox.ini b/tox.ini
index 1bce10a4ce..367cc2ccf2 100644
--- a/tox.ini
+++ b/tox.ini
@@ -163,10 +163,9 @@ deps =
     {[base]deps}
     mypy
     mypy-zope
-    typeshed
 env =
     MYPYPATH = stubs/
 extras = all
-commands = mypy --show-traceback \
+commands = mypy --show-traceback --check-untyped-defs --show-error-codes --follow-imports=normal \
             synapse/logging/ \
             synapse/config/