Merge pull request #21 from Ensembl/jalvarez/sqlalchemy_updates

Make unit tests also compatible with SQLAlchemy 1.4.45+ and 2.0+

pyproject.toml

@@ -83,7 +83,9 @@ docs = [
     "mkdocstrings",
     "mkdocstrings-python",
 ]
-mysql = [ "mysqlclient" ]
+mysql = [
+    "mysqlclient",
+]
 
 [project.urls]
 Homepage = "https://www.ensembl.org"

src/ensembl/utils/__init__.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 """Ensembl Python general-purpose utils library."""
 
-__version__ = "0.4.1"
+__version__ = "0.4.2"
 
 __all__ = [
     "StrPath",

src/ensembl/utils/database/unittestdb.py

@@ -52,6 +52,7 @@
 from ensembl.utils import StrPath
 from ensembl.utils.database.dbconnection import DBConnection, StrURL
 
+
 TEST_USERNAME = os.environ.get("USER", "pytestuser")
 
 

tests/database/test_dbconnection.py

@@ -18,28 +18,38 @@
 
 import pytest
 from pytest import FixtureRequest, param
-from sqlalchemy import text, VARCHAR
-from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
+from sqlalchemy_utils import create_database, database_exists, drop_database
+from sqlalchemy import Integer, text, Sequence, String
+from sqlalchemy.orm import Mapped
 from sqlalchemy.engine.url import make_url
 from sqlalchemy.exc import IntegrityError
 from sqlalchemy.ext.automap import automap_base
-from sqlalchemy_utils import create_database, database_exists, drop_database
 
-from ensembl.utils.database import DBConnection, UnitTestDB
-from ensembl.utils.database.unittestdb import TEST_USERNAME
+# Support both SQLAlchemy 1.4+ and 2.0+
+try:
+    from sqlalchemy.orm import DeclarativeBase, mapped_column
 
+    class MockBase(DeclarativeBase):
+        """Mock Base for testing."""
 
-class MockBase(DeclarativeBase):
-    """Mock Base for testing."""
+except ImportError:
+    from sqlalchemy.orm import declarative_base
+    from sqlalchemy.schema import Column as mapped_column  # type: ignore
+
+    MockBase = declarative_base()  # type: ignore
+
+from ensembl.utils.database import DBConnection, UnitTestDB
+from ensembl.utils.database.unittestdb import TEST_USERNAME
 
 
 class MockTable(MockBase):
     """Mock Table for testing."""
 
     __tablename__ = "mock_table"
-    id: Mapped[int] = mapped_column(primary_key=True)
-    grp: Mapped[str] = mapped_column(VARCHAR(30))
-    value: Mapped[int]
+
+    id: Mapped[int] = mapped_column(Integer, Sequence("id_seq"), primary_key=True)
+    grp: Mapped[str] = mapped_column(String(30))
+    value: Mapped[int] = mapped_column(Integer)
 
 
 mock_metadata = MockBase.metadata
@@ -93,7 +103,7 @@ def test_db_name(self) -> None:
     def test_url(self) -> None:
         """Tests `DBConnection.url` property."""
         expected_url = make_url(self.server).set(database=self.dbc.db_name)
-        assert self.dbc.url == expected_url.render_as_string(hide_password=False)
+        assert self.dbc.url == expected_url.render_as_string(hide_password=False)  # pylint: disable=no-member
 
     @pytest.mark.dependency(depends=["test_init"], scope="class")
     def test_host(self) -> None:
@@ -230,7 +240,7 @@ def test_test_session_scope(self) -> None:
                 self.dbc.dialect == "mysql"
                 and self.dbc.tables["gibberish"].dialect_options["mysql"]["engine"] == "MyISAM"
             ):
-                assert len(results.all()) == 2, f"SQLite/MyISAM: 2 rows permanently added to ID {identifier}"
+                assert len(results.all()) == 2, f"MyISAM: 2 rows permanently added to ID {identifier}"
             else:
                 assert (
                     not results.fetchall()

tests/database/test_unittestdb.py

@@ -20,25 +20,35 @@
 
 import pytest
 from pytest import FixtureRequest, param, raises
-from sqlalchemy import text, VARCHAR
-from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
-from sqlalchemy.schema import MetaData
 from sqlalchemy_utils.functions import database_exists
+from sqlalchemy import Integer, text, Sequence, String
+from sqlalchemy.orm import Mapped
+from sqlalchemy.schema import MetaData
 
-from ensembl.utils.database import UnitTestDB
+# Support both SQLAlchemy 1.4+ and 2.0+
+try:
+    from sqlalchemy.orm import DeclarativeBase, mapped_column
 
+    class MockBase(DeclarativeBase):
+        """Mock Base for testing."""
 
-class MockBase(DeclarativeBase):
-    """Mock Base for testing."""
+except ImportError:
+    from sqlalchemy.orm import declarative_base
+    from sqlalchemy.schema import Column as mapped_column  # type: ignore
+
+    MockBase = declarative_base()  # type: ignore
+
+from ensembl.utils.database import UnitTestDB
 
 
 class MockTable(MockBase):
     """Mock Table for testing."""
 
     __tablename__ = "mock_table"
-    id: Mapped[int] = mapped_column(primary_key=True)
-    grp: Mapped[str] = mapped_column(VARCHAR(30))
-    value: Mapped[int]
+
+    id: Mapped[int] = mapped_column(Integer, Sequence("id_seq"), primary_key=True)
+    grp: Mapped[str] = mapped_column(String(30))
+    value: Mapped[int] = mapped_column(Integer)
 
 
 mock_metadata = MockBase.metadata

tests/database/test_unittestdb/mock_db/table.sql

@@ -1,7 +1,7 @@
-CREATE TABLE `gibberish` (
-    `id`    INTEGER NOT NULL,
-    `grp`   VARCHAR(20) DEFAULT "",
-    `value` INT DEFAULT NULL,
-    PRIMARY KEY (`id`, `grp`)
+CREATE TABLE gibberish (
+    id    INTEGER NOT NULL,
+    grp   VARCHAR(20) DEFAULT '',
+    value INT DEFAULT NULL,
+    PRIMARY KEY (id, grp)
 );
-CREATE INDEX `id_idx` ON `gibberish` (`id`);
+CREATE INDEX id_idx ON gibberish (id);