refactor: Clean up DB sessions consistently

.github/workflows/ci.yml

@@ -15,7 +15,7 @@ env:
 jobs:
   test_quetz:
     # timeout for the whole job
-    timeout-minutes: 10
+    timeout-minutes: 15
     runs-on: ${{ matrix.os }}
     strategy:
       fail-fast: false
@@ -79,7 +79,7 @@ jobs:
       - name: Testing server
         shell: bash -l -eo pipefail {0}
         # timeout for the step
-        timeout-minutes: 5
+        timeout-minutes: 15
         env:
           TEST_DB_BACKEND: ${{ matrix.test_database }}
           QUETZ_TEST_DBINIT: ${{ matrix.db_init }}

.pre-commit-config.yaml

@@ -15,7 +15,6 @@ repos:
       - id: mypy
         files: ^quetz/
         additional_dependencies:
-          - sqlalchemy-stubs
           - types-click
           - types-Jinja2
           - types-mock

environment.yml

@@ -9,7 +9,7 @@ dependencies:
   - authlib=0.15.5
   - psycopg2
   - httpx>=0.22.0
-  - sqlalchemy
+  - sqlalchemy >= 2, <3
   - sqlalchemy-utils
   - sqlite
   - python-multipart

init_db.py

@@ -21,11 +21,10 @@
 def init_test_db():
     config = Config()
     init_db(config.sqlalchemy_database_url)
-    db = get_session(config.sqlalchemy_database_url)
 
-    testUsers = []
+    with get_session(config) as db:
+        testUsers = []
 
-    try:
         for index, username in enumerate(["alice", "bob", "carol", "dave"]):
             user = User(id=uuid.uuid4().bytes, username=username)
 
@@ -102,8 +101,6 @@ def init_test_db():
 
             db.add(channel_member)
         db.commit()
-    finally:
-        db.close()
 
 
 if __name__ == "__main__":

plugins/quetz_conda_suggest/quetz_conda_suggest/main.py

@@ -4,7 +4,7 @@
 
 import quetz
 from quetz.config import Config
-from quetz.database import get_db_manager
+from quetz.database import get_session
 from quetz.db_models import PackageVersion
 from quetz.utils import add_entry_for_index
 
@@ -45,7 +45,7 @@ def post_add_package_version(version, condainfo):
             if command not in suggest_map:
                 suggest_map[command] = package
 
-    with get_db_manager() as db:
+    with get_session() as db:
         if not version.binfiles:
             metadata = db_models.CondaSuggestMetadata(
                 version_id=version.id, data=json.dumps(suggest_map)

plugins/quetz_conda_suggest/tests/conftest.py

@@ -77,7 +77,7 @@ def package_version(user, channel, db, dao, package):
         package_format,
         "linux-64",
         "0.1",
-        "0",
+        0,
         "0",
         "test-package-0.1-0.tar.bz2",
         package_info,

plugins/quetz_conda_suggest/tests/test_quetz_conda_suggest.py

@@ -2,7 +2,6 @@
 import shutil
 import tarfile
 import tempfile
-from contextlib import contextmanager
 from unittest import mock
 
 import pytest
@@ -18,7 +17,7 @@
     assert response.json() == None  # noqa: E711
 
 
-def test_post_add_package_version(package_version, db, config):
+def test_post_add_package_version(package_version, db, config, session_maker):
     filename = "test-package-0.1-0.tar.bz2"
 
     with tempfile.SpooledTemporaryFile(mode="wb") as target:
@@ -27,13 +26,9 @@
         target.seek(0)
         condainfo = CondaInfo(target, filename)
 
-    @contextmanager
-    def get_db():
-        yield db
-
     from quetz_conda_suggest import main
 
-    with mock.patch("quetz_conda_suggest.main.get_db_manager", get_db):
+    with mock.patch("quetz_conda_suggest.main.get_session", session_maker):
         main.post_add_package_version(package_version, condainfo)
 
     meta = db.query(db_models.CondaSuggestMetadata).first()
@@ -50,8 +45,8 @@
         b"lib/libtpkg.so\n",
         b"lib/pkgconfig/libtpkg.pc\n",
     ]
-    with mock.patch("quetz_conda_suggest.main.get_db_manager", get_db):
+    with mock.patch("quetz_conda_suggest.main.get_session", session_maker):
         main.post_add_package_version(package_version, condainfo)
 
     meta = db.query(db_models.CondaSuggestMetadata).all()
 
@@ -76,7 +71,6 @@
     response = client.get("/api/dummylogin/madhurt")
     filename = "test-package-0.1-0.tar.bz2"
 
-    @contextmanager
     def get_db():
         yield db
 
@@ -114,10 +108,10 @@
     tar.addfile(t, io.BytesIO(b))
     tar.close()
 
-    with mock.patch("quetz_conda_suggest.main.get_db_manager", get_db):
+    with mock.patch("quetz_conda_suggest.main.get_session", get_db):
         url = f"/api/channels/{channel.name}/files/"
         files = {"files": (filename, open(filename, "rb"))}
         response = client.post(url, files=files)
 
         assert response.status_code == 201
 

plugins/quetz_content_trust/quetz_content_trust/api.py

@@ -8,7 +8,7 @@
 
 from quetz import authorization
 from quetz.config import Config
-from quetz.database import get_db_manager
+from quetz.database import get_session
 from quetz.deps import get_rules
 
 from . import db_models
@@ -102,7 +102,7 @@ def post_role(
 ):
     auth.assert_channel_roles(channel, ["owner"])
 
-    with get_db_manager() as db:
+    with get_session() as db:
         existing_role_count = (
             db.query(db_models.ContentTrustRole)
             .filter(
@@ -190,7 +190,7 @@ def get_role(
 ):
     auth.assert_channel_roles(channel, ["owner", "maintainer", "member"])
 
-    with get_db_manager() as db:
+    with get_session() as db:
         query = (
             db.query(db_models.ContentTrustRole)
             .filter(db_models.ContentTrustRole.channel == channel)
@@ -211,7 +211,7 @@ def get_new_key(secret: bool = False):
     mamba_key = libmamba_api.Key.from_ed25519(key.public_key)
     private_key = key.private_key
 
-    with get_db_manager() as db:
+    with get_session() as db:
         db.add(key)
         db.commit()
 

plugins/quetz_content_trust/quetz_content_trust/main.py

@@ -4,7 +4,7 @@
 from sqlalchemy import desc
 
 import quetz
-from quetz.database import get_db_manager
+from quetz.database import get_session
 
 from . import db_models
 from .api import router
@@ -21,7 +21,7 @@ def register_router():
 def post_index_creation(raw_repodata: dict, channel_name, subdir):
     """Use available online keys to sign packages"""
 
-    with get_db_manager() as db:
+    with get_session() as db:
         query = (
             db.query(db_models.SigningKey)
             .join(db_models.RoleDelegation.keys)

plugins/quetz_repodata_patching/quetz_repodata_patching/main.py

@@ -9,7 +9,7 @@
 
 import quetz
 from quetz.config import Config
-from quetz.database import get_db_manager
+from quetz.database import get_session
 from quetz.db_models import PackageFormatEnum, PackageVersion
 from quetz.utils import add_temp_static_file
 
@@ -107,7 +107,7 @@ def _load_instructions(tar, path):
 
 @quetz.hookimpl(tryfirst=True)
 def post_package_indexing(tempdir: Path, channel_name, subdirs, files, packages):
-    with get_db_manager() as db:
+    with get_session() as db:
         query = (
             db.query(PackageVersion)
             .filter(