fix: recover from corrupted atlas metadata on initialization

brainglobe_atlasapi/bg_atlas.py

@@ -1,6 +1,8 @@
 """Defines the BrainGlobeAtlas class for accessing brain atlas data."""
 
+import shutil
 import tarfile
+import warnings
 from collections.abc import Callable
 from io import StringIO
 from pathlib import Path
@@ -96,7 +98,24 @@ def __init__(
                 self.download_extract_file()
 
         # Instantiate after eventual download:
-        super().__init__(self.brainglobe_dir / self.local_full_name)
+        for attempt in (0, 1):
+            try:
+                super().__init__(self.brainglobe_dir / self.local_full_name)
+                break
+            except (FileNotFoundError, ValueError):
+                if attempt == 1:
+                    raise
+
+                atlas_path = self.brainglobe_dir / self.local_full_name
+                if atlas_path.exists() and atlas_path.is_dir():
+                    warnings.warn(
+                        "Atlas metadata appears corrupted or incomplete. "
+                        "Re-downloading atlas...",
+                        UserWarning,
+                    )
+                    shutil.rmtree(atlas_path)
+
+                self.download_extract_file()
 
         if check_latest:
             self.check_latest_version()
@@ -155,7 +174,7 @@ def local_full_name(self) -> Optional[str]:
 
     @property
     def remote_url(self) -> Optional[str]:
-        """Format complete url for download."""
+        """Format complete url for download, or None if unavailable."""
         if self.remote_version is not None:
             name = (
                 f"{self.atlas_name}_v{self.remote_version[0]}."

tests/atlasapi/test_recovery.py

@@ -0,0 +1,37 @@
+"""Tests for recovery behavior when atlas metadata is missing."""
+
+from brainglobe_atlasapi.bg_atlas import BrainGlobeAtlas
+
+
+def test_recovers_missing_metadata(mocker):
+    """Test recovery when atlas metadata is missing."""
+    # Mock Atlas.__init__: fail once, succeed second time
+    mock_atlas_init = mocker.patch(
+        "brainglobe_atlasapi.core.Atlas.__init__",
+        side_effect=[FileNotFoundError("Missing metadata"), None],
+        autospec=True,
+    )
+
+    # Mock local_full_name to simulate a valid atlas folder
+    mocker.patch(
+        "brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas.local_full_name",
+        new_callable=mocker.PropertyMock,
+        return_value="example_mouse_100um_v1.0",
+    )
+
+    # Prevent real IO
+    mock_download = mocker.patch(
+        "brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas.download_extract_file"
+    )
+    mocker.patch(
+        "brainglobe_atlasapi.bg_atlas.BrainGlobeAtlas.check_latest_version"
+    )
+
+    mocker.patch("brainglobe_atlasapi.bg_atlas.shutil.rmtree")
+
+    # Act
+    BrainGlobeAtlas("example_mouse_100um", check_latest=False)
+
+    # Assert
+    assert mock_atlas_init.call_count == 2
+    mock_download.assert_called_once()