Merge pull request #14 from Ensembl/jalvarez/update_dbc

Update database connection and plan next release

src/ensembl/utils/__init__.py

@@ -14,7 +14,7 @@
 # limitations under the License.
 """Ensembl Python general-purpose utils library."""
 
-__version__ = "0.3.0"
+__version__ = "0.4.0"
 
 __all__ = [
     "StrPath",

src/ensembl/utils/database/dbconnection.py

@@ -41,7 +41,7 @@
 from typing import ContextManager, Generator, Optional, TypeVar
 
 import sqlalchemy
-from sqlalchemy import create_engine, event, text
+from sqlalchemy import create_engine, event
 from sqlalchemy.orm import sessionmaker
 from sqlalchemy.schema import MetaData, Table
 
@@ -152,25 +152,6 @@ def dispose(self) -> None:
         """Disposes of the connection pool."""
         self._engine.dispose()
 
-    def execute(self, statement: Query, parameters=None, execution_options=None) -> sqlalchemy.engine.Result:
-        """Executes the given SQL query and returns its result.
-
-        See `sqlalchemy.engine.Connection.execute()` method for more information about the
-        additional arguments.
-
-        Args:
-            statement: SQL query to execute.
-            parameters: Parameters which will be bound into the statement.
-            execution_options: Optional dictionary of execution options, which will be associated
-                with the statement execution.
-
-        """
-        if isinstance(statement, str):
-            statement = text(statement)  # type: ignore[assignment]
-        return self.connect().execute(
-            statement=statement, parameters=parameters, execution_options=execution_options
-        )  # type: ignore[call-overload]
-
     def _enable_sqlite_savepoints(self, engine: sqlalchemy.engine.Engine) -> None:
         """Enables SQLite SAVEPOINTS to allow session rollbacks."""
 

tests/database/test_dbconnection.py

@@ -14,21 +14,19 @@
 # limitations under the License.
 """Unit testing of `ensembl.utils.database.dbconnection` module."""
 
-from contextlib import nullcontext as does_not_raise
 import os
 from pathlib import Path
-from typing import ContextManager
 
 import pytest
-from pytest import FixtureRequest, param, raises
+from pytest import FixtureRequest, param
 from sqlalchemy import text, VARCHAR
 from sqlalchemy.orm import DeclarativeBase, Mapped, mapped_column
 from sqlalchemy.engine.url import make_url
-from sqlalchemy.exc import IntegrityError, SQLAlchemyError
+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, Query, UnitTestDB
+from ensembl.utils.database import DBConnection, UnitTestDB
 
 
 class MockBase(DeclarativeBase):
@@ -157,34 +155,7 @@ def test_dispose(self) -> None:
             num_conn = self.dbc._engine.pool.checkedin()  # pylint: disable=protected-access
             assert num_conn == 0, "A new pool should have 0 checked-in connections"
 
-    @pytest.mark.dependency(name="test_exec", depends=["test_init"], scope="class")
-    @pytest.mark.parametrize(
-        "query, nrows, expectation",
-        [
-            param("SELECT * FROM gibberish", 6, does_not_raise(), id="Valid string query"),
-            param(text("SELECT * FROM gibberish"), 6, does_not_raise(), id="Valid text query"),
-            param(
-                "SELECT * FROM my_table",
-                0,
-                raises(SQLAlchemyError, match=r"(my_table.* doesn't exist|no such table: my_table)"),
-                id="Querying an unexistent table",
-            ),
-        ],
-    )
-    def test_execute(self, query: Query, nrows: int, expectation: ContextManager) -> None:
-        """Tests `DBConnection.execute()` method.
-
-        Args:
-            query: SQL query.
-            nrows: Number of rows expected to be returned from the query.
-            expectation: Context manager for the expected exception.
-
-        """
-        with expectation:
-            result = self.dbc.execute(query)
-            assert len(result.fetchall()) == nrows, "Unexpected number of rows returned"
-
-    @pytest.mark.dependency(depends=["test_init", "test_connect", "test_exec"], scope="class")
+    @pytest.mark.dependency(depends=["test_init", "test_connect"], scope="class")
     @pytest.mark.parametrize(
         "identifier, rows_to_add, before, after",
         [
@@ -232,7 +203,7 @@ def test_session_scope(
             results = session.execute(query)
             assert len(results.fetchall()) == after
 
-    @pytest.mark.dependency(depends=["test_init", "test_connect", "test_exec"], scope="class")
+    @pytest.mark.dependency(depends=["test_init", "test_connect"], scope="class")
     def test_test_session_scope(self) -> None:
         """Tests `DBConnection.test_session_scope()` method."""
         # Session requires mapped classes to interact with the database