Attempt to run test on this workflow with the Murfey and ISPyB databases

Author: tieneupin

tests/workflows/clem/test_register_preprocessing_results.py

@@ -147,4 +147,61 @@ 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]],
+    murfey_db_session,
+    seed_murfey_db,
+    ispyb_db_session_factory,
+    ispyb_db_session,
+    seed_ispyb_db,
+):
+    # Mock out module-level functions
+    mock_get_security_config = mocker.patch("murfey.server.ispyb.get_security_config")
+    mock_get_security_config.return_value = MagicMock()
+    mock_url = mocker.patch("murfey.server.ispyb.url")
+    mock_url.return_value = MagicMock()
+    mock_create_engine = mocker.patch("murfey.server.ispyb.create_engine")
+    mock_create_engine.return_value = MagicMock()
+
+    # Mock the ISPyB connection
+    mock_ispyb_sessionmaker = mocker.patch("murfey.server.ispyb.sessionmaker")
+    mock_ispyb_sessionmaker.return_value = ispyb_db_session_factory
+    mock_ispyb_sessionmaker.return_value.return_value = ispyb_db_session
+
+    # Mock the registration helper functions
+    mock_register_clem_series = mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results._register_clem_image_series"
+    )
+    mock_register_dcg_and_atlas = mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results._register_dcg_and_atlas"
+    )
+    mock_register_grid_square = mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results._register_grid_square"
+    )
+
+    # Mock the align and merge workflow call
+    mock_align_and_merge_call = mocker.patch(
+        "murfey.workflows.clem.register_preprocessing_results.submit_cluster_request"
+    )
+
+    # Import and set up the TransportManager only after mocking
+    import murfey.server
+    from murfey.server.ispyb import TransportManager
+
+    murfey.server._transport_object = TransportManager("PikaTransport")
+
+    for message in preprocessing_messages:
+        result = run(
+            message=message,
+            murfey_db=murfey_db_session,
+        )
+        assert result == {"success": True}
+    assert mock_register_clem_series.call_count == len(preprocessing_messages)
+    assert mock_register_dcg_and_atlas.call_count == len(preprocessing_messages)
+    assert mock_register_grid_square.call_count == len(preprocessing_messages) - 1
+    assert mock_align_and_merge_call.call_count == len(preprocessing_messages) * len(
+        colors
+    )