Merge pull request #17 from MatBarba/mbarba/no_datadir

Allow test db without schema/data from dump_dir

src/ensembl/utils/plugin.py

@@ -129,15 +129,16 @@ def _db_factory(src: StrPath, name: Optional[str] = None) -> UnitTestDB:
         """Returns a unit test database.
 
         Args:
-            src: Directory path where the test database schema and content files are located.
+            src: Directory path where the test database schema and content files are located, if any.
             name: Name to give to the new database. See `UnitTestDB` for more information.
 
         """
         src_path = Path(src)
         if not src_path.is_absolute():
             src_path = data_dir / src_path
         db_key = name if name else src_path.name
-        return created.setdefault(db_key, UnitTestDB(server_url, dump_dir=src_path, name=name))
+        dump_dir: Path | None = src_path if src_path.exists() else None
+        return created.setdefault(db_key, UnitTestDB(server_url, dump_dir=dump_dir, name=name))
 
     yield _db_factory
     # Drop all unit test databases unless the user has requested to keep them

tests/plugin/test_plugin.py

@@ -18,28 +18,13 @@
 """
 
 from contextlib import nullcontext as does_not_raise
-from dataclasses import dataclass
 from pathlib import Path
 from typing import Callable, ContextManager
-from unittest.mock import patch
 
 import pytest
 from pytest import FixtureRequest, param, raises
 
-from ensembl.utils import StrPath
-from ensembl.utils.database import StrURL
-
-
-@dataclass
-class MockTestDB:
-    """Mocks `UnitTestDB` class by just storing the three arguments provided."""
-
-    server_url: StrURL
-    dump_dir: StrPath
-    name: str
-
-    def drop(self) -> None:
-        """Mocks `UnitTestDB.drop()` method."""
+from ensembl.utils.database import UnitTestDB
 
 
 @pytest.mark.dependency(name="test_data_dir")
@@ -80,27 +65,37 @@ def test_assert_files(
 
 
 @pytest.mark.parametrize(
-    "dump_dir, db_name",
+    "dump_dir, make_absolute, db_name, expected_tables",
     [
-        (Path("dump_dir"), "dump_dir"),
-        (Path("dump_dir").resolve(), "test_db"),
+        param(Path("dump_dir"), False, "relative_dump_db", ["gibberish"], id="Relative dump_dir"),
+        param(Path("dump_dir"), True, "absolute_dump_db", ["gibberish"], id="Absolute dump_dir"),
+        param(Path("not_a_dir"), False, "no_dump_db", [], id="Non-existent dump_dir"),
     ],
 )
-@patch("ensembl.utils.plugin.UnitTestDB", new=MockTestDB)
-def test_db_factory(request: FixtureRequest, db_factory: Callable, dump_dir: Path, db_name: str) -> None:
+def test_db_factory(
+    request: FixtureRequest,
+    db_factory: Callable[[Path, str], UnitTestDB],
+    data_dir: Path,
+    dump_dir: Path,
+    make_absolute: bool,
+    db_name: str,
+    expected_tables: list[str],
+) -> None:
     """Tests the `db_factory` fixture.
 
     Args:
         request: Fixture that provides information of the requesting test function.
         db_factory: Fixture that provides a unit test database factory.
+        data_dir: Directory where this specific test data are stored.
         dump_dir: Directory path where the test database schema and content files are located.
+        make_absolute: change the dump_dir from relative to absolute (based on `data_dir`).
         db_name: Name to give to the new database.
+        expected_tables: List of tables that should be loaded in the test database.
 
     """
-    test_db = db_factory(dump_dir, db_name)
-    assert test_db.server_url == request.config.getoption("server")
-    assert test_db.name == db_name
-    if dump_dir.is_absolute():
-        assert test_db.dump_dir == dump_dir
-    else:
-        assert test_db.dump_dir.stem == str(dump_dir)
+    if make_absolute:
+        dump_dir = Path(data_dir, dump_dir).absolute()
+    test_db: UnitTestDB = db_factory(dump_dir, db_name)
+    assert test_db.dbc.url.startswith(request.config.getoption("server"))
+    assert Path(test_db.dbc.db_name).stem.endswith(db_name)
+    assert set(test_db.dbc.tables.keys()) == set(expected_tables)

tests/plugin/test_plugin/dump_dir/gibberish.txt

@@ -0,0 +1,6 @@
+1	grp1	11
+2	grp1	12
+3	grp2	21
+4	grp2	22
+5	grp2	23
+6	grp3	31

tests/plugin/test_plugin/dump_dir/table.sql

@@ -0,0 +1,7 @@
+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`);