Added unit test for 'align_and_merge' workflow

Author: tieneupin

tests/workflows/clem/test_align_and_merge.py

@@ -0,0 +1,129 @@
+from pathlib import Path
+from unittest.mock import MagicMock, patch
+
+import pytest
+
+from murfey.server.ispyb import TransportManager
+from murfey.util.config import MachineConfig
+from murfey.workflows.clem.align_and_merge import submit_cluster_request
+
+# Folder and file settings
+session_id = 0
+instrument_name = "clem"
+raw_folder = "images"
+processed_folder = "processed"
+visit_name = "cm12345-6"
+area_name = "test_area"
+series_name = "test_series"
+colors = [
+    "gray",
+    "green",
+    "red",
+]
+feedback_queue = "murfey_feedback"
+
+# Align and merge settings
+crop_to_n_frames = 20
+align_self = "enabled"
+flatten = "max"
+align_across = "enabled"
+
+
+@pytest.fixture
+def processed_dir(tmp_path: Path):
+    processed_dir = tmp_path / visit_name / processed_folder
+    processed_dir.mkdir(parents=True, exist_ok=True)
+    return processed_dir
+
+
+@pytest.fixture
+def image_stacks(processed_dir: Path):
+
+    image_dir = processed_dir / area_name / series_name
+    image_dir.mkdir(parents=True, exist_ok=True)
+
+    images = [image_dir / f"{color}.tiff" for color in colors]
+    for image in images:
+        if not image.exists():
+            image.touch()
+
+    return images
+
+
+@pytest.fixture
+def metadata(processed_dir: Path):
+
+    metadata_dir = processed_dir / area_name / series_name / "metadata"
+    metadata_dir.mkdir(parents=True, exist_ok=True)
+
+    metadata = metadata_dir / f"{series_name}.xml"
+    if not metadata.exists():
+        metadata.touch()
+
+    return metadata
+
+
+@patch("murfey.workflows.clem.align_and_merge.get_machine_config")
+def test_submit_cluster_request(
+    image_stacks: list[Path],
+    metadata: Path,
+    processed_dir: Path,
+    mock_get_machine_config,
+):
+
+    # Construct the long series name
+    series_name_long = "--".join(
+        image_stacks[0].parent.relative_to(processed_dir).parts
+    )
+
+    # Create a mock tranpsort object
+    mock_transport = MagicMock(spec=TransportManager)
+    mock_transport.feedback_queue = feedback_queue
+
+    # Construct a mock MachineConfig object for use within the function
+    mock_machine_config = MagicMock(spec=MachineConfig)
+    mock_machine_config.return_value.processed_directory_name = processed_folder
+    mock_get_machine_config.return_value = {
+        instrument_name: mock_machine_config,
+    }
+
+    # Run the function
+    submit_cluster_request(
+        session_id=session_id,
+        instrument_name=instrument_name,
+        series_name=series_name_long,
+        images=image_stacks,
+        metadata=metadata,
+        crop_to_n_frames=crop_to_n_frames,
+        align_self=align_self,
+        flatten=flatten,
+        align_across=align_across,
+        messenger=mock_transport,
+    )
+
+    # Construct expected recipe to be sent
+    sent_recipe = {
+        "recipes": ["clem-align-and-merge"],
+        "parameters": {
+            # Job parameters
+            "series_name": series_name_long,
+            "images": [str(file) for file in image_stacks],
+            "metadata": str(metadata),
+            "crop_to_n_frames": crop_to_n_frames,
+            "align_self": align_self,
+            "flatten": flatten,
+            "align_across": align_across,
+            # Other recipe parameters
+            "session_dir": str(processed_dir.parent),
+            "session_id": session_id,
+            "job_name": series_name,
+            "feedback_queue": feedback_queue,
+        },
+    }
+
+    # Check that it sends the expected recipe
+    mock_transport.send.assert_called_once_with(
+        "processing_recipe",
+        sent_recipe,
+        new_connection=True,
+    )