Parametrised test to further improve coverage

Author: tieneupin

tests/workflows/spa/test_atlas_workflow.py

@@ -2,14 +2,29 @@
 from unittest.mock import MagicMock
 
 import numpy as np
+import pytest
 from pytest_mock import MockerFixture
+from werkzeug.utils import secure_filename
 
 from murfey.workflows.spa.atlas import atlas_jpg_from_mrc
 
+atlas_jpg_from_mrc_test_matrix = (
+    ("Atlas1.mrc",),
+    ("Sample1/Atlas1.mrc",),
+)
 
-def test_atlas_jpg_from_mrc(mocker: MockerFixture, tmp_path: Path):
+
+@pytest.mark.parametrize("test_params", atlas_jpg_from_mrc_test_matrix)
+def test_atlas_jpg_from_mrc(
+    mocker: MockerFixture, tmp_path: Path, test_params: tuple[str]
+):
+    # Unpack test params
+    (file_name_stub,) = test_params
+
+    # Set up mock session params
     visit_name = "test_visit"
     instrument_name = "test"
+    processed_dir_name = "processed"
 
     # Create a 16-bit grayscale image
     shape = (64, 64)
@@ -23,17 +38,32 @@ def test_atlas_jpg_from_mrc(mocker: MockerFixture, tmp_path: Path):
 
     # Mock the return result of 'get_machine_config()'
     mock_machine_config = MagicMock()
-    mock_machine_config.processed_directory_name = "processed"
+    mock_machine_config.processed_directory_name = processed_dir_name
     mocker.patch(
         "murfey.workflows.spa.atlas.get_machine_config",
         return_value={"test": mock_machine_config},
     )
 
     # Create a test file
-    test_dir = tmp_path / instrument_name / "data" / visit_name / "atlas"
-    test_dir.mkdir(parents=True, exist_ok=True)
-    test_file = test_dir / "Atlas1.mrc"
+    test_file = (
+        tmp_path / instrument_name / "data" / visit_name / "atlas" / file_name_stub
+    )
+    test_file.parent.mkdir(parents=True, exist_ok=True)
     test_file.touch(exist_ok=True)
 
-    # Run the function
+    # Create the expected destination directory and file
+    processed_dir = (
+        tmp_path / instrument_name / "data" / visit_name / processed_dir_name / "atlas"
+    )
+    sample_id = "Sample"
+    for part in file_name_stub.split("/"):
+        if part.startswith("Sample"):
+            sample_id = part
+            break
+    processed_file_name = processed_dir / secure_filename(
+        f"{sample_id}_{test_file.stem}_fullres.jpg"
+    )
+
+    # Run the function and check that the expected calls are made
     atlas_jpg_from_mrc(instrument_name, visit_name, test_file)
+    assert processed_file_name.exists()