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sqlalchemy 2 compatibility

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- avoid backref warnings by adding objects to session explicitly before creating any relationships
- remove unnecessary `[]` around scalar query
- use `text()` wrapper on connection.execute
- engine.execute is removed
- update import of declarative_base
- ensure RemovedIn20Warning is available for warnings filters on sqlalchemy < 1.4 (needs editable install to avoid pytest path mismatch)
- explicitly relay password in engine.url to alembic
This commit is contained in:
Min RK
2023-01-18 09:44:35 +01:00
parent 0a84738fe9
commit 2db7c47fbf
12 changed files with 114 additions and 50 deletions
Download Patch File Download Diff File Expand all files Collapse all files

4
.github/workflows/test.yml vendored
View File

@@ -29,6 +29,7 @@ env:
# UTF-8 content may be interpreted as ascii and causes errors without this.
LANG: C.UTF-8
PYTEST_ADDOPTS: "--verbose --color=yes"
SQLALCHEMY_WARN_20: "1"
permissions:
contents: read
@@ -140,7 +141,7 @@ jobs:
- name: Install Python dependencies
run: |
pip install --upgrade pip
pip install ".[test]"
pip install -e ".[test]"
if [ "${{ matrix.oldest_dependencies }}" != "" ]; then
# take any dependencies in requirements.txt such as tornado>=5.0
@@ -152,6 +153,7 @@ jobs:
if [ "${{ matrix.main_dependencies }}" != "" ]; then
pip install git+https://github.com/ipython/traitlets#egg=traitlets --force
pip install --upgrade --pre sqlalchemy
fi
if [ "${{ matrix.legacy_notebook }}" != "" ]; then
pip uninstall jupyter_server --yes

6
jupyterhub/apihandlers/groups.py
View File

@@ -94,8 +94,9 @@ class GroupListAPIHandler(_GroupAPIHandler):
# create the group
self.log.info("Creating new group %s with %i users", name, len(users))
self.log.debug("Users: %s", usernames)
group = orm.Group(name=name, users=users)
group = orm.Group(name=name)
self.db.add(group)
group.users = users
self.db.commit()
created.append(group)
self.write(json.dumps([self.group_model(group) for group in created]))
@@ -131,8 +132,9 @@ class GroupAPIHandler(_GroupAPIHandler):
# create the group
self.log.info("Creating new group %s with %i users", group_name, len(users))
self.log.debug("Users: %s", usernames)
group = orm.Group(name=group_name, users=users)
group = orm.Group(name=group_name)
self.db.add(group)
group.users = users
self.db.commit()
self.write(json.dumps(self.group_model(group)))
self.set_status(201)

4
jupyterhub/app.py
View File

@@ -1962,9 +1962,9 @@ class JupyterHub(Application):
user = orm.User.find(db, name)
if user is None:
user = orm.User(name=name, admin=True)
db.add(user)
roles.assign_default_roles(self.db, entity=user)
new_users.append(user)
db.add(user)
else:
user.admin = True
# the admin_users config variable will never be used after this point.
@@ -2376,6 +2376,7 @@ class JupyterHub(Application):
if orm_service is None:
# not found, create a new one
orm_service = orm.Service(name=name)
self.db.add(orm_service)
if spec.get('admin', False):
self.log.warning(
f"Service {name} sets `admin: True`, which is deprecated in JupyterHub 2.0."
@@ -2384,7 +2385,6 @@ class JupyterHub(Application):
"the Service admin flag will be ignored."
)
roles.update_roles(self.db, entity=orm_service, roles=['admin'])
self.db.add(orm_service)
orm_service.admin = spec.get('admin', False)
self.db.commit()
service = Service(

4
jupyterhub/oauth/provider.py
View File

@@ -257,16 +257,16 @@ class JupyterHubRequestValidator(RequestValidator):
raise ValueError("No such client: %s" % client_id)
orm_code = orm.OAuthCode(
client=orm_client,
code=code['code'],
# oauth has 5 minutes to complete
expires_at=int(orm.OAuthCode.now() + 300),
scopes=list(request.scopes),
user=request.user.orm_user,
redirect_uri=orm_client.redirect_uri,
session_id=request.session_id,
)
self.db.add(orm_code)
orm_code.client = orm_client
orm_code.user = request.user.orm_user
self.db.commit()
def get_authorization_code_scopes(self, client_id, code, redirect_uri, request):

44
jupyterhub/orm.py
View File

@@ -8,7 +8,9 @@ from datetime import datetime, timedelta
import alembic.command
import alembic.config
import sqlalchemy
from alembic.script import ScriptDirectory
from packaging.version import parse as parse_version
from sqlalchemy import (
Boolean,
Column,
@@ -24,8 +26,8 @@ from sqlalchemy import (
inspect,
or_,
select,
text,
)
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.orm import (
Session,
backref,
@@ -34,6 +36,13 @@ from sqlalchemy.orm import (
relationship,
sessionmaker,
)
try:
from sqlalchemy.orm import declarative_base
except ImportError:
# sqlalchemy < 1.4
from sqlalchemy.ext.declarative import declarative_base
from sqlalchemy.pool import StaticPool
from sqlalchemy.types import LargeBinary, Text, TypeDecorator
from tornado.log import app_log
@@ -750,6 +759,7 @@ class APIToken(Hashed, Base):
session_id=session_id,
scopes=list(scopes),
)
db.add(orm_token)
orm_token.token = token
if user:
assert user.id is not None
@@ -760,7 +770,6 @@ class APIToken(Hashed, Base):
if expires_in is not None:
orm_token.expires_at = cls.now() + timedelta(seconds=expires_in)
db.add(orm_token)
db.commit()
return token
@@ -902,7 +911,7 @@ def register_ping_connection(engine):
"""
@event.listens_for(engine, "engine_connect")
def ping_connection(connection, branch):
def ping_connection(connection, branch=None):
if branch:
# "branch" refers to a sub-connection of a connection,
# we don't want to bother pinging on these.
@@ -913,11 +922,17 @@ def register_ping_connection(engine):
save_should_close_with_result = connection.should_close_with_result
connection.should_close_with_result = False
if parse_version(sqlalchemy.__version__) < parse_version("1.4"):
one = [1]
else:
one = 1
try:
# run a SELECT 1. use a core select() so that
# the SELECT of a scalar value without a table is
# appropriately formatted for the backend
connection.scalar(select([1]))
with connection.begin() as transaction:
connection.scalar(select(one))
except exc.DBAPIError as err:
# catch SQLAlchemy's DBAPIError, which is a wrapper
# for the DBAPI's exception. It includes a .connection_invalidated
@@ -932,7 +947,8 @@ def register_ping_connection(engine):
# itself and establish a new connection. The disconnect detection
# here also causes the whole connection pool to be invalidated
# so that all stale connections are discarded.
connection.scalar(select([1]))
with connection.begin() as transaction:
connection.scalar(select(one))
else:
raise
finally:
@@ -956,7 +972,13 @@ def check_db_revision(engine):
from .dbutil import _temp_alembic_ini
with _temp_alembic_ini(engine.url) as ini:
if hasattr(engine.url, "render_as_string"):
# sqlalchemy >= 1.4
engine_url = engine.url.render_as_string(hide_password=False)
else:
engine_url = str(engine.url)
with _temp_alembic_ini(engine_url) as ini:
cfg = alembic.config.Config(ini)
scripts = ScriptDirectory.from_config(cfg)
head = scripts.get_heads()[0]
@@ -991,8 +1013,9 @@ def check_db_revision(engine):
# check database schema version
# it should always be defined at this point
alembic_revision = engine.execute(
'SELECT version_num FROM alembic_version'
with engine.begin() as connection:
alembic_revision = connection.execute(
text('SELECT version_num FROM alembic_version')
).first()[0]
if alembic_revision == head:
app_log.debug("database schema version found: %s", alembic_revision)
@@ -1010,11 +1033,14 @@ def mysql_large_prefix_check(engine):
"""Check mysql has innodb_large_prefix set"""
if not str(engine.url).startswith('mysql'):
return False
with engine.begin() as connection:
variables = dict(
engine.execute(
connection.execute(
text(
'show variables where variable_name like '
'"innodb_large_prefix" or '
'variable_name like "innodb_file_format";'
)
).fetchall()
)
if (

9
jupyterhub/tests/test_api.py
View File

@@ -444,11 +444,12 @@ async def test_get_self(app):
db.add(oauth_client)
db.commit()
oauth_token = orm.APIToken(
user=u.orm_user,
oauth_client=oauth_client,
token=token,
)
db.add(oauth_token)
oauth_token.user = u.orm_user
oauth_token.oauth_client = oauth_client
db.commit()
r = await api_request(
app,
@@ -2131,13 +2132,13 @@ def test_shutdown(app):
def stop():
stop.called = True
loop.call_later(1, real_stop)
loop.call_later(2, real_stop)
real_cleanup = app.cleanup
def cleanup():
cleanup.called = True
return real_cleanup()
loop.call_later(1, real_cleanup)
app.cleanup = cleanup

34
jupyterhub/tests/test_orm.py
View File

@@ -323,7 +323,9 @@ def test_spawner_delete_cascade(db):
db.add(user)
db.commit()
spawner = orm.Spawner(user=user)
spawner = orm.Spawner()
db.add(spawner)
spawner.user = user
db.commit()
spawner.server = server = orm.Server()
db.commit()
@@ -350,16 +352,19 @@ def test_user_delete_cascade(db):
# these should all be deleted automatically when the user goes away
user.new_api_token()
api_token = user.api_tokens[0]
spawner = orm.Spawner(user=user)
spawner = orm.Spawner()
db.add(spawner)
spawner.user = user
db.commit()
spawner.server = server = orm.Server()
oauth_code = orm.OAuthCode(client=oauth_client, user=user)
oauth_code = orm.OAuthCode()
db.add(oauth_code)
oauth_token = orm.APIToken(
oauth_client=oauth_client,
user=user,
)
oauth_code.client = oauth_client
oauth_code.user = user
oauth_token = orm.APIToken()
db.add(oauth_token)
oauth_token.oauth_client = oauth_client
oauth_token.user = user
db.commit()
# record all of the ids
@@ -390,13 +395,14 @@ def test_oauth_client_delete_cascade(db):
# create a bunch of objects that reference the User
# these should all be deleted automatically when the user goes away
oauth_code = orm.OAuthCode(client=oauth_client, user=user)
oauth_code = orm.OAuthCode()
db.add(oauth_code)
oauth_token = orm.APIToken(
oauth_client=oauth_client,
user=user,
)
oauth_code.client = oauth_client
oauth_code.user = user
oauth_token = orm.APIToken()
db.add(oauth_token)
oauth_token.oauth_client = oauth_client
oauth_token.user = user
db.commit()
assert user.api_tokens == [oauth_token]
@@ -517,11 +523,11 @@ def test_expiring_oauth_token(app, user):
db.add(client)
orm_token = orm.APIToken(
token=token,
oauth_client=client,
user=user,
expires_at=now() + timedelta(seconds=30),
)
db.add(orm_token)
orm_token.oauth_client = client
orm_token.user = user
db.commit()
found = orm.APIToken.find(db, token)

7
jupyterhub/tests/test_pages.py
View File

@@ -1033,11 +1033,10 @@ async def test_oauth_token_page(app):
user = app.users[orm.User.find(app.db, name)]
client = orm.OAuthClient(identifier='token')
app.db.add(client)
oauth_token = orm.APIToken(
oauth_client=client,
user=user,
)
oauth_token = orm.APIToken()
app.db.add(oauth_token)
oauth_token.oauth_client = client
oauth_token.user = user
app.db.commit()
r = await get_page('token', app, cookies=cookies)
r.raise_for_status()

8
jupyterhub/tests/test_roles.py
View File

@@ -3,9 +3,11 @@
# Distributed under the terms of the Modified BSD License.
import json
import os
import warnings
import pytest
from pytest import mark
from sqlalchemy.exc import SADeprecationWarning
from tornado.log import app_log
from .. import orm, roles
@@ -343,7 +345,13 @@ async def test_creating_roles(app, role, role_def, response_type, response):
# make sure no warnings/info logged when the role exists and its definition hasn't been changed
elif response_type == 'no-log':
with pytest.warns(response) as record:
# don't catch already-suppressed sqlalchemy warnings
warnings.simplefilter("ignore", SADeprecationWarning)
roles.create_role(db, role_def)
for warning in record.list:
# show warnings for debugging
print("Unexpected warning", warning)
assert not record.list
role = orm.Role.find(db, role_def['name'])
assert role is not None

19
jupyterhub/tests/utils.py
View File

@@ -6,6 +6,7 @@ from concurrent.futures import ThreadPoolExecutor
import pytest
import requests
from certipy import Certipy
from sqlalchemy import text
from tornado.httputil import url_concat
from jupyterhub import metrics, orm
@@ -13,6 +14,20 @@ from jupyterhub.objects import Server
from jupyterhub.roles import assign_default_roles, update_roles
from jupyterhub.utils import url_path_join as ujoin
try:
from sqlalchemy.exc import RemovedIn20Warning
except ImportError:
class RemovedIn20Warning(DeprecationWarning):
"""
I only exist so I can be used in warnings filters in pytest.ini
I will never be displayed.
sqlalchemy 1.4 introduces RemovedIn20Warning,
but we still test against older sqlalchemy.
"""
class _AsyncRequests:
"""Wrapper around requests to return a Future from request methods
@@ -85,8 +100,8 @@ def check_db_locks(func):
def _check(_=None):
temp_session = app.session_factory()
try:
temp_session.execute('CREATE TABLE dummy (foo INT)')
temp_session.execute('DROP TABLE dummy')
temp_session.execute(text('CREATE TABLE dummy (foo INT)'))
temp_session.execute(text('DROP TABLE dummy'))
finally:
temp_session.close()

5
jupyterhub/user.py
View File

@@ -416,9 +416,10 @@ class User:
yield orm_spawner
def _new_orm_spawner(self, server_name):
"""Creat the low-level orm Spawner object"""
orm_spawner = orm.Spawner(user=self.orm_user, name=server_name)
"""Create the low-level orm Spawner object"""
orm_spawner = orm.Spawner(name=server_name)
self.db.add(orm_spawner)
orm_spawner.user = self.orm_user
self.db.commit()
assert server_name in self.orm_spawners
return orm_spawner

4
pytest.ini
View File

@@ -18,3 +18,7 @@ markers =
slow: mark a test as slow
role: mark as a test for roles
selenium: web tests that run with selenium
filterwarnings =
error:.*:jupyterhub.tests.utils.RemovedIn20Warning
ignore:.*event listener has changed as of version 2.0.*:sqlalchemy.exc.SADeprecationWarning