Added unit test for 'run' main function in 'register_preprocessing_results'

Author: tieneupin

tests/workflows/clem/test_register_preprocessing_results.py

@@ -1,11 +1,96 @@
+from pathlib import Path
+from typing import Any
+from unittest.mock import MagicMock
+
 import pytest
+from pytest_mock import MockerFixture
 
 from murfey.workflows.clem.register_preprocessing_results import (
     _register_clem_image_series,
     _register_dcg_and_atlas,
     _register_grid_square,
     run,
 )
+from tests.conftest import ExampleVisit
+
+visit_name = f"{ExampleVisit.proposal_code}{ExampleVisit.proposal_number}-{ExampleVisit.visit_number}"
+processed_dir_name = "processed"
+grid_name = "Grid_1"
+colors = ("gray", "green", "red")
+
+
+@pytest.fixture
+def preprocessing_messages(tmp_path: Path):
+    # Make directory to where data for current grid is stored
+    visit_dir = tmp_path / "data" / "2020" / visit_name
+    processed_dir = visit_dir / processed_dir_name
+    grid_dir = processed_dir / grid_name
+    grid_dir.mkdir(parents=True, exist_ok=True)
+
+    # Construct all the datasets to be tested
+    datasets: list[tuple[Path, bool, bool, tuple[int, int], float, list[float]]] = [
+        (
+            grid_dir / "Overview_1" / "Image_1",
+            False,
+            True,
+            (2400, 2400),
+            1e-6,
+            [0.002, 0.0044, 0.002, 0.0044],
+        )
+    ]
+    # Add on metadata for a few grid squares
+    datasets.extend(
+        [
+            (
+                grid_dir / "TileScan_1" / f"Position_{n}",
+                True,
+                False,
+                (2048, 2048),
+                1.6e-7,
+                [0.003, 0.00332768, 0.003, 0.00332768],
+            )
+            for n in range(5)
+        ]
+    )
+
+    messages: list[dict[str, Any]] = []
+    for dataset in datasets:
+        # Unpack items from list of dataset parameters
+        series_path = dataset[0]
+        series_name = str(series_path.relative_to(processed_dir)).replace("/", "--")
+        metadata = series_path / "metadata" / f"{series_path.stem}.xml"
+        metadata.parent.mkdir(parents=True, exist_ok=True)
+        metadata.touch(exist_ok=True)
+        output_files = {color: str(series_path / f"{color}.tiff") for color in colors}
+        for output_file in output_files.values():
+            Path(output_file).touch(exist_ok=True)
+        is_stack = dataset[1]
+        is_montage = dataset[2]
+        shape = dataset[3]
+        pixel_size = dataset[4]
+        extent = dataset[5]
+
+        message = {
+            "session_id": ExampleVisit.murfey_session_id,
+            "result": {
+                "series_name": series_name,
+                "number_of_members": 3,
+                "is_stack": is_stack,
+                "is_montage": is_montage,
+                "output_files": output_files,
+                "metadata": str(metadata),
+                "parent_lif": None,
+                "parent_tiffs": {},
+                "pixels_x": shape[0],
+                "pixels_y": shape[1],
+                "units": "m",
+                "pixel_size": pixel_size,
+                "resolution": 1 / pixel_size,
+                "extent": extent,
+            },
+        }
+        messages.append(message)
+    return messages
 
 
 @pytest.mark.skip
@@ -23,6 +108,43 @@ def test_register_grid_square():
     assert _register_grid_square
 
 
-@pytest.mark.skip
-def test_run():
+def test_run(
+    mocker: MockerFixture,
+    preprocessing_messages: list[dict[str, Any]],
+):
+    # Mock the MurfeyDB connection
+    mock_murfey_session_entry = MagicMock()
+    mock_murfey_session_entry.instrument_name = ExampleVisit.instrument_name
+    mock_murfey_session_entry.visit = visit_name
+    mock_murfey_db = MagicMock()
+    mock_murfey_db.exec().return_value.one.return_value = mock_murfey_session_entry
+
+    # 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"
+    )
+
+    for message in preprocessing_messages:
+        result = run(
+            message=message,
+            murfey_db=mock_murfey_db,
+        )
+        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
+    )
     assert run