Merge pull request #449 from Ensembl/jalvarez/testing_alt

Update database.factory.main() function to test all its contents

pyproject.toml

@@ -228,7 +228,6 @@ exclude_lines = [
     "raise NotImplementedError",
     # Do not complain if non-runnable code is not run
     "if __name__ == .__main__.:",
-    "def main",
     # Do not complain about abstract methods, they are not run
     "@(abc\\.)?abstractmethod",
 ]

src/python/ensembl/io/genomio/database/factory.py

@@ -16,10 +16,10 @@
 
 __all__ = ["format_db_data", "get_core_dbs_metadata"]
 
+import argparse
 import json
-from pathlib import Path
-from typing import Dict, List, Optional
 import logging
+from pathlib import Path
 
 from sqlalchemy.engine import URL
 
@@ -29,7 +29,7 @@
 from .dbconnection_lite import DBConnectionLite
 
 
-def format_db_data(server_url: URL, dbs: List[str], brc_mode: bool = False) -> List[Dict]:
+def format_db_data(server_url: URL, dbs: list[str], brc_mode: bool = False) -> list[dict]:
     """Returns a metadata list from the given databases on a server.
 
     Args:
@@ -87,13 +87,14 @@ def format_db_data(server_url: URL, dbs: List[str], brc_mode: bool = False) -> L
 
 def get_core_dbs_metadata(
     server_url: URL,
+    *,
     prefix: str = "",
-    build: Optional[int] = None,
-    version: Optional[int] = None,
+    build: int | None = None,
+    version: int | None = None,
     db_regex: str = "",
-    db_list: Optional[Path] = None,
+    db_list: Path | None = None,
     brc_mode: bool = False,
-) -> List[Dict]:
+) -> list[dict]:
     """Returns all the metadata fetched for the selected core databases.
 
     Args:
@@ -123,8 +124,12 @@ def get_core_dbs_metadata(
     return format_db_data(server_url, databases, brc_mode)
 
 
-def main() -> None:
-    """Main script entry-point."""
+def parse_args(arg_list: list[str] | None) -> argparse.Namespace:
+    """TODO
+
+    Args:
+        arg_list: TODO
+    """
     parser = ArgumentParser(description=__doc__)
     parser.add_server_arguments()
     # Add filter arguments
@@ -140,7 +145,17 @@ def main() -> None:
         help="Enable BRC mode, i.e. use organism_abbrev for species, component for division",
     )
     parser.add_log_arguments()
-    args = parser.parse_args()
+    return parser.parse_args(arg_list)
+
+
+def main(arg_list: list[str] | None = None) -> None:
+    """Main script entry-point.
+
+    Args:
+        arg_list: TODO
+
+    """
+    args = parse_args(arg_list)
     init_logging_with_args(args)
 
     databases_data = get_core_dbs_metadata(

src/python/tests/database/test_factory.py

@@ -20,13 +20,13 @@
 """
 
 from pathlib import Path
-from typing import Dict, List, Optional
 from unittest.mock import call, Mock, patch
 
 from deepdiff import DeepDiff
 import pytest
 from pytest import param
-from sqlalchemy.engine import URL
+from _pytest.capture import CaptureFixture
+from sqlalchemy.engine import make_url, URL
 
 from ensembl.io.genomio.database import factory
 
@@ -115,7 +115,7 @@
     ],
 )
 def test_format_db_data(
-    mock_dbconn: Mock, server_url: URL, dbs: List[str], brc_mode: bool, skip_keys: bool, output: List[Dict]
+    mock_dbconn: Mock, server_url: URL, dbs: list[str], brc_mode: bool, skip_keys: bool, output: list[dict]
 ) -> None:
     """Tests the `factory.format_db_data()` function.
 
@@ -128,7 +128,7 @@ def test_format_db_data(
         output: Expected list of dictionaries with metadata per database.
     """
 
-    def _get_meta_value(meta_key: str) -> Optional[str]:
+    def _get_meta_value(meta_key: str) -> str | None:
         """Return empty string if "species.division" is requested in BRC mode, "Metazoa" otherwise."""
         if (meta_key == "species.division") and brc_mode:
             return ""
@@ -169,7 +169,7 @@ def test_get_core_dbs_metadata(
     mock_format_db_data: Mock,
     data_dir: Path,
     use_db_file: bool,
-    output: List[Dict],
+    output: list[dict],
 ) -> None:
     """Tests the `factory.get_core_dbs_metadata()` function.
 
@@ -181,7 +181,7 @@ def test_get_core_dbs_metadata(
         output: Expected list of dictionaries with some metadata for each selected database.
     """
 
-    def _format_db_data(server_url: URL, dbs: List[str], brc_mode: bool = False) -> List[Dict]:
+    def _format_db_data(server_url: URL, dbs: list[str], brc_mode: bool = False) -> list[dict]:
         """Returns metadata from a list of databases."""
         _ = (server_url, brc_mode)  # Unused by mock
         return [{"database": db, "species": "dog"} for db in dbs]
@@ -196,3 +196,106 @@ def _format_db_data(server_url: URL, dbs: List[str], brc_mode: bool = False) ->
     db_list = data_dir / "databases.txt" if use_db_file else None
     result = factory.get_core_dbs_metadata(URL.create("mysql"), db_list=db_list)
     assert not DeepDiff(result, output)
+
+
+@pytest.mark.parametrize(
+    "arg_list, expected",
+    [
+        param(
+            ["--host", "localhost", "--port", "42", "--user", "me"],
+            {
+                "host": "localhost",
+                "port": 42,
+                "user": "me",
+                "password": None,
+                "url": make_url("mysql://me@localhost:42"),
+                "prefix": "",
+                "build": None,
+                "version": None,
+                "db_regex": "",
+                "db_list": None,
+                "brc_mode": False,
+                "log_level": "WARNING",
+            },
+            id="Default args",
+        ),
+        param(
+            [
+                "--host",
+                "localhost",
+                "--port",
+                "42",
+                "--user",
+                "me",
+                "--password",
+                "secret",
+                "--prefix",
+                "pre",
+                "--build",
+                "70",
+                "--version",
+                "114",
+                "--db_regex",
+                "%_core_%",
+                "--db_list",
+                __file__,
+                "--brc_mode",
+            ],
+            {
+                "host": "localhost",
+                "port": 42,
+                "user": "me",
+                "password": "secret",
+                "url": make_url("mysql://me:secret@localhost:42"),
+                "prefix": "pre",
+                "build": 70,
+                "version": 114,
+                "db_regex": "%_core_%",
+                "db_list": __file__,
+                "brc_mode": True,
+                "log_level": "WARNING",
+            },
+            id="New arg values",
+        ),
+    ],
+)
+def test_parse_args(arg_list: list[str], expected: dict) -> None:
+    """Tests the `factory.parse_args()` function."""
+    args = factory.parse_args(arg_list)
+    if args.db_list:
+        # DeepDiff is not able to compare two objects of Path type, so convert it to string
+        setattr(args, "db_list", str(args.db_list))
+    assert not DeepDiff(vars(args), expected)
+
+
+@pytest.mark.parametrize(
+    "arg_list, server_url, stdout",
+    [
+        (
+            ["--host", "localhost", "--port", "42", "--user", "me"],
+            make_url("mysql://me@localhost:42"),
+            '{\n    "test": "output"\n}\n',
+        ),
+    ],
+)
+@patch("ensembl.io.genomio.database.factory.get_core_dbs_metadata")
+def test_main(
+    mock_get_core_dbs_metadata: Mock,
+    capsys: CaptureFixture[str],
+    arg_list: list[str],
+    server_url: URL,
+    stdout: str,
+) -> None:
+    """Tests the `factory.main()` function (entry point).
+
+    Fixtures: capsys
+    """
+    mock_get_core_dbs_metadata.return_value = {"test": "output"}
+    factory.main(arg_list)
+    # Check that we have called the mocked function once with the expected parameters
+    mock_get_core_dbs_metadata.assert_called_once_with(
+        server_url=server_url, prefix="", build=None, version=None, db_regex="", db_list=None, brc_mode=False
+    )
+    # Check that the stdout is as expected
+    captured = capsys.readouterr()
+    assert captured.out == stdout