fix: remove silent failures and redundant checks

Critical fixes for code quality (Robert C. Martin standards):

1. Replace ignore_errors=True with explicit exception handling
- pipeline.py: staging cleanup now logs failures
- adapter.py: temp dir cleanup now logs failures
- app.py: results cleanup now logs failures

2. Fix redundant truthy check on prediction_mask
- prediction_mask is typed as Path (not Optional)
- Changed misleading `x and x.exists()` to just `x.exists()`
- Added clarifying comment about defense-in-depth

3. Fix outdated docstring in create_niivue_html
- Changed "Data URL or URL" to "Gradio file URL"
- Fixed reference from NIIVUE_JS_ON_LOAD to NIIVUE_ON_LOAD_JS

4. Update test to match new cleanup behavior
- test_pipeline_cleanup now expects rmtree without ignore_errors

All 134 tests pass, mypy strict passes.

src/stroke_deepisles_demo/data/adapter.py

@@ -326,9 +326,12 @@ class HuggingFaceDataset:
 
     def cleanup(self) -> None:
         """Remove temp directory and clear cache."""
-        if self._temp_dir and self._temp_dir.exists():
-            shutil.rmtree(self._temp_dir, ignore_errors=True)
-            logger.debug("Cleaned up temp directory: %s", self._temp_dir)
+        if self._temp_dir is not None and self._temp_dir.exists():
+            try:
+                shutil.rmtree(self._temp_dir)
+                logger.debug("Cleaned up temp directory: %s", self._temp_dir)
+            except OSError as e:
+                logger.warning("Failed to cleanup temp directory %s: %s", self._temp_dir, e)
         self._temp_dir = None
         self._cached_cases.clear()
 

src/stroke_deepisles_demo/pipeline.py

@@ -162,7 +162,10 @@ def run_pipeline_on_case(
 
     # 5. Cleanup (Optional)
     if cleanup_staging:
-        shutil.rmtree(staging_root, ignore_errors=True)
+        try:
+            shutil.rmtree(staging_root)
+        except OSError as e:
+            logger.warning("Failed to cleanup staging directory %s: %s", staging_root, e)
 
     elapsed = time.time() - start_time
 

src/stroke_deepisles_demo/ui/app.py

@@ -84,9 +84,13 @@ def run_segmentation(
         global _previous_results_dir
 
         # Clean up previous results to prevent disk accumulation on HF Spaces
-        if _previous_results_dir and _previous_results_dir.exists():
-            shutil.rmtree(_previous_results_dir, ignore_errors=True)
-            logger.debug("Cleaned up previous results: %s", _previous_results_dir)
+        if _previous_results_dir is not None and _previous_results_dir.exists():
+            try:
+                shutil.rmtree(_previous_results_dir)
+                logger.debug("Cleaned up previous results: %s", _previous_results_dir)
+            except OSError as e:
+                # Log but don't fail - cleanup is best-effort
+                logger.warning("Failed to cleanup %s: %s", _previous_results_dir, e)
 
         logger.info("Running segmentation for %s", case_id)
         result = run_pipeline_on_case(
@@ -106,8 +110,10 @@ def run_segmentation(
         dwi_path = result.input_files["dwi"]
         dwi_url = nifti_to_gradio_url(dwi_path)
 
+        # prediction_mask is always a valid Path from the pipeline (not Optional)
+        # The .exists() check is defense-in-depth only
         mask_url = None
-        if result.prediction_mask and result.prediction_mask.exists():
+        if result.prediction_mask.exists():
             mask_url = nifti_to_gradio_url(result.prediction_mask)
 
         niivue_html = create_niivue_html(

src/stroke_deepisles_demo/ui/viewer.py

@@ -298,14 +298,14 @@ def create_niivue_html(
 
     This function generates an HTML snippet with data attributes containing
     volume URLs. The actual NiiVue initialization is handled by js_on_load
-    in the gr.HTML component (see NIIVUE_JS_ON_LOAD).
+    in the gr.HTML component (see NIIVUE_ON_LOAD_JS).
 
     IMPORTANT: Gradio's gr.HTML strips <script> tags for security.
     JavaScript must be passed via the js_on_load parameter instead.
 
     Args:
-        volume_url: Data URL or URL to volume NIfTI file
-        mask_url: Optional data URL or URL to mask NIfTI file
+        volume_url: Gradio file URL (e.g., /gradio_api/file=/path/to/file.nii.gz)
+        mask_url: Optional Gradio file URL to mask NIfTI file
         height: Viewer height in pixels
 
     Returns:

tests/test_pipeline_cleanup.py

@@ -50,4 +50,5 @@ def test_pipeline_cleanup_default(temp_dir: Path) -> None:
         staging_root_passed = args[1]
 
         # Verify rmtree was called with that same path
-        mock_rmtree.assert_called_with(staging_root_passed, ignore_errors=True)
+        # Note: We no longer use ignore_errors=True; failures are logged instead
+        mock_rmtree.assert_called_with(staging_root_passed)