Add tests for '_get_source' and '_file_transferred_to' for the CLEMContext

Author: tieneupin

tests/client/contexts/test_clem.py

@@ -1,14 +1,141 @@
-def test_post_transfer_lif_data():
-    pass
+from pathlib import Path
+from unittest.mock import MagicMock
 
+import pytest
 
-def test_post_transfer_tiff_data():
-    pass
+from murfey.client.context import _file_transferred_to, _get_source
+
+visit_name = "cm12345-6"
+project_name = "2025_06_30_10_00_00--grid_1001"
+example_file_paths = [
+    f"{project_name}{path}"
+    for path in [
+        # TIFF files
+        "/TileScan 1/Position 1--Z00.tif",
+        "/TileScan 1/Position 1--C00.tif",
+        "/TileScan 1/Position 1--Stage00.tif",
+        "/TileScan 1/Position 1--Z00--C00.tif",
+        "/TileScan 1/Position 1--Stage00--C00.tif",
+        "/TileScan 1/Position 1--Stage00--Z00.tif",
+        "/TileScan 1/Position 1--Stage00--Z00--C00.tif",
+        "/TileScan 1/Position 1_ICC--Z00.tif",
+        "/TileScan 1/Position 1_Lng_LVCC--C00.tif",
+        "/TileScan 1/Position 1_Lng_SVCC--Stage00.tif",
+        "/TileScan 1/Position 1_ICC--Z00--C00.tif",
+        "/TileScan 1/Position 1_Lng_LVCC--Stage00--C00.tif",
+        "/TileScan 1/Position 1_Lng_SVCC--Stage00--Z00.tif",
+        "/TileScan 1/Metadata/Position 1.xlif",
+        "/Series001--Z00--C00.tif",
+        "/Series001--Stage00--C00.tif",
+        "/Series001--Stage00--Z00.tif",
+        "/Series001--Stage00--Z00--C00.tif",
+        "/Series001_ICC--Z00.tif",
+        "/Series001_Lng_LVCC--C00.tif",
+        "/Series001_Lng_SVCC--Stage00.tif",
+        "/Metadata/Series001_Lng_LVCC.xlif",
+        "/Image 1_ICC--Z00--C00.tif",
+        "/Image 1_Lng_LVCC--Stage00--C00.tif",
+        "/Image 1_Lng_SVCC--Stage00--Z00.tif",
+        "/Image 1--Z00.tif",
+        "/Image 1--C00.tif",
+        "/Image 1--Stage00.tif",
+        "/Image 1--Stage00--Z00--C00.tif",
+        "/Metadata/Image 1_ICC.xlif",
+        # LIF file
+        ".lif",
+    ]
+]
+
+
+def create_tiff_dataset(
+    visit_dir: Path,
+    series_name: str,
+    num_tiles: int | None = None,
+    num_frames: int | None = None,
+    num_channels: int | None = None,
+):
+    """
+    Creates mock files mimicking the folder structure and naming pattern of actual
+    CLEM TIFF datasets.
+    """
+
+    # Construct the TIFF files
+    tiff_files = []
+    for c in range(num_channels or 1):
+        for t in range(num_tiles or 1):
+            for z in range(num_frames or 1):
+                # Construct name of file based on the presence of tiles, frames, and channels
+                file_name = series_name
+                if num_tiles is not None:
+                    file_name += f"--Stage{str(t).zfill(2)}"
+                if num_frames is not None:
+                    file_name += f"--Z{str(z).zfill(2)}"
+                if num_channels is not None:
+                    file_name += f"--C{str(c).zfill(2)}"
+                file_name += ".tif"
+                file = visit_dir / "images" / file_name
+                file.touch(exist_ok=True)
+                tiff_files.append(file)
+
+    # Construct the metadata file
+    file_name = f"{series_name}.xlif"
+    metadata_file = visit_dir / "images" / file_name
+    # Insert "Metadata" before the file name
+    metadata_file = metadata_file.parent / "Metadata" / metadata_file.name
+    metadata_file.touch(exist_ok=True)
+
+    return tiff_files, metadata_file
 
 
-def test_process_lif_file():
+@pytest.fixture
+def visit_dir(
+    tmp_path: Path,
+):
+    visit_dir = tmp_path / visit_name
+    visit_dir.mkdir(parents=True, exist_ok=True)
+    return visit_dir
+
+
+@pytest.mark.parametrize("file_path", example_file_paths)
+def test_get_source(
+    tmp_path: Path,
+    visit_dir: Path,
+    file_path: str,
+):
+    # Mock the MurfeyInstanceEnvironment
+    mock_environment = MagicMock()
+    mock_environment.sources = [
+        visit_dir,
+        tmp_path / "another_dir",
+    ]
+    # Check that the correct source directory is found
+    assert _get_source(visit_dir / "images" / file_path, mock_environment) == visit_dir
+
+
+@pytest.mark.parametrize("file_path", example_file_paths)
+def test_file_transferred_to(tmp_path: Path, visit_dir: Path, file_path: str):
+    # Create the client-side file
+    file = visit_dir / "images" / file_path
+
+    # Mock the environment
+    mock_environment = MagicMock()
+    mock_environment.default_destinations = {visit_dir: "current_year"}
+    mock_environment.visit = visit_name
+
+    # Iterate across the FIB files to compare against
+    destination_dir = tmp_path / "clem" / "data" / "current_year" / visit_name
+    # Work out what the expected destination will be
+    assert _file_transferred_to(
+        environment=mock_environment,
+        source=visit_dir,
+        file_path=file,
+        rsync_basepath=tmp_path / "clem" / "data",
+    ) == destination_dir / file.relative_to(visit_dir)
+
+
+def test_post_transfer_lif_data():
     pass
 
 
-def test_process_tiff_file():
+def test_post_transfer_tiff_data():
     pass