Run test workflow with Murfey and ISPyB databases

Author: tieneupin

tests/workflows/clem/test_register_preprocessing_results.py

@@ -4,6 +4,8 @@
 
 import pytest
 from pytest_mock import MockerFixture
+from sqlalchemy.orm.session import Session as SQLAlchemySession
+from sqlmodel.orm.session import Session as SQLModelSession
 
 from murfey.workflows.clem.register_preprocessing_results import (
     _register_clem_image_series,
@@ -20,9 +22,14 @@
 
 
 @pytest.fixture
-def preprocessing_messages(tmp_path: Path):
+def rsync_basepath(tmp_path: Path):
+    return tmp_path / "data"
+
+
+@pytest.fixture
+def preprocessing_messages(rsync_basepath: Path):
     # Make directory to where data for current grid is stored
-    visit_dir = tmp_path / "data" / "2020" / visit_name
+    visit_dir = rsync_basepath / "2020" / visit_name
     processed_dir = visit_dir / processed_dir_name
     grid_dir = processed_dir / grid_name
     grid_dir.mkdir(parents=True, exist_ok=True)
@@ -147,4 +154,65 @@ def test_run(
     assert mock_align_and_merge_call.call_count == len(preprocessing_messages) * len(
         colors
     )
-    assert run
+
+
+def test_run_with_db(
+    mocker: MockerFixture,
+    preprocessing_messages: list[dict[str, Any]],
+    rsync_basepath: Path,
+    mock_ispyb_credentials,
+    murfey_db_session: SQLModelSession,
+    seed_murfey_db,
+    ispyb_db_session: SQLAlchemySession,
+    seed_ispyb_db,
+):
+    # Mock out module-level functions
+    mock_security_config = MagicMock()
+    mock_security_config.ispyb_credentials = mock_ispyb_credentials
+    mock_get_security_config = mocker.patch("murfey.server.ispyb.get_security_config")
+    mock_get_security_config.return_value = mock_security_config
+
+    # Mock the ISPyB connection
+    mock_ispyb_sessionmaker = mocker.patch("murfey.server.ispyb.sessionmaker")
+    mock_ispyb_sessionmaker.return_value.return_value = ispyb_db_session
+
+    # Mock out the machine config used in the helper sanitisation function
+    mock_get_machine_config = mocker.patch("murfey.workflows.clem.get_machine_config")
+    mock_machine_config = MagicMock()
+    mock_machine_config.rsync_basepath = rsync_basepath
+    mock_get_machine_config.return_value = {
+        "": mock_machine_config,
+    }
+
+    # Mock the align and merge workflow call
+    mock_align_and_merge_call = mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results.submit_cluster_request"
+    )
+
+    # Patch the TransportManager object in the workflows called
+    from murfey.server.ispyb import TransportManager
+
+    mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results._transport_object",
+        new=TransportManager("PikaTransport"),
+    )
+    mocker.patch(
+        "murfey.workflows.register_data_collection_group._transport_object",
+        new=TransportManager("PikaTransport"),
+    )
+    mocker.patch(
+        "murfey.workflows.register_atlas_update._transport_object",
+        new=TransportManager("PikaTransport"),
+    )
+
+    # Run the function
+    for message in preprocessing_messages:
+        result = run(
+            message=message,
+            murfey_db=murfey_db_session,
+        )
+        assert result == {"success": True}
+    assert mock_align_and_merge_call.call_count == len(preprocessing_messages) * len(
+        colors
+    )
+    murfey_db_session.close()