simplify validation function (#113)

* simplify validation function

- all validation functions just take an atlas object
- means we don't need a parameters list
- also simplify output list to be dicts of lists mapping the atlas name to values

- another advantage of this is that it simplifies mocking of atlas functions in the tests

* [pre-commit.ci] auto fixes from pre-commit.com hooks

for more information, see https://pre-commit.ci

* Fix bug found in code review

---------

Co-authored-by: pre-commit-ci[bot] <66853113+pre-commit-ci[bot]@users.noreply.github.com>

bg_atlasgen/validate_atlases.py

@@ -10,13 +10,18 @@
 from bg_atlasapi.list_atlases import (
     get_all_atlases_lastversions,
     get_atlases_lastversions,
+    get_local_atlas_version,
 )
 from bg_atlasapi.update_atlases import update_atlas
 
 
-def validate_atlas_files(atlas_path: Path):
+def validate_atlas_files(atlas: BrainGlobeAtlas):
     """Checks if basic files exist in the atlas folder"""
 
+    atlas_path = (
+        Path(get_brainglobe_dir())
+        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    )
     assert atlas_path.is_dir(), f"Atlas path {atlas_path} not found"
     expected_files = [
         "annotation.tiff",
@@ -90,28 +95,31 @@ def validate_mesh_matches_image_extents(atlas: BrainGlobeAtlas):
     return True
 
 
-def open_for_visual_check():
+def open_for_visual_check(atlas: BrainGlobeAtlas):
     # implement visual checks later
     pass
 
 
-def validate_checksum():
+def validate_checksum(atlas: BrainGlobeAtlas):
     # implement later
     pass
 
 
-def check_additional_references():
+def check_additional_references(atlas: BrainGlobeAtlas):
     # check additional references are different, but have same dimensions
     pass
 
 
-def validate_mesh_structure_pairs(atlas_name: str, atlas_path: Path):
-    # json_path = Path(atlas_path / "structures.json")
-    atlas = BrainGlobeAtlas(atlas_name)
+def validate_mesh_structure_pairs(atlas: BrainGlobeAtlas):
+    """Ensure mesh files (.obj) exist for each expected structure in the atlas."""
+    ids_from_bg_atlas_api = list(atlas.structures.keys())
 
+    atlas_path = (
+        Path(get_brainglobe_dir())
+        / f"{atlas.atlas_name}_v{get_local_atlas_version(atlas.atlas_name)}"
+    )
     obj_path = Path(atlas_path / "meshes")
 
-    ids_from_bg_atlas_api = list(atlas.structures.keys())
     ids_from_mesh_files = [
         int(Path(file).stem)
         for file in os.listdir(obj_path)
@@ -135,7 +143,7 @@ def validate_mesh_structure_pairs(atlas_name: str, atlas_path: Path):
         )
 
 
-def validate_atlas(atlas_name, version, all_validation_functions):
+def validate_atlas(atlas_name, version, validation_functions):
     """Validates the latest version of a given atlas"""
 
     print(atlas_name, version)
@@ -144,34 +152,16 @@ def validate_atlas(atlas_name, version, all_validation_functions):
     if not updated:
         update_atlas(atlas_name)
 
-    validation_function_parameters = [
-        # validate_atlas_files(atlas_path: Path)
-        (Path(get_brainglobe_dir() / f"{atlas_name}_v{version}"),),
-        # validate_mesh_matches_image_extents(atlas: BrainGlobeAtlas)
-        (BrainGlobeAtlas(atlas_name),),
-        # open_for_visual_check()
-        (),
-        # validate_checksum()
-        (),
-        # check_additional_references()
-        (),
-        # validate_mesh_structure_pairs(atlas_name: str, atlas_path: Path):
-        (
-            atlas_name,
-            Path(get_brainglobe_dir() / f"{atlas_name}_v{version}"),
-        ),
-    ]
-
     # list to store the errors of the failed validations
-    failed_validations = []
-    successful_validations = []
+    failed_validations = {atlas_name: []}
+    successful_validations = {atlas_name: []}
 
-    for i, validation_function in enumerate(all_validation_functions):
+    for i, validation_function in enumerate(validation_functions):
         try:
-            validation_function(*validation_function_parameters[i])
-            successful_validations.append((atlas_name, validation_function))
+            validation_function(BrainGlobeAtlas(atlas_name))
+            successful_validations[atlas_name].append(validation_function)
         except AssertionError as error:
-            failed_validations.append((atlas_name, validation_function, error))
+            failed_validations[atlas_name].append((validation_function, error))
 
     return successful_validations, failed_validations
 

tests/test_unit/test_validation.py

@@ -1,4 +1,4 @@
-from pathlib import Path
+import os
 
 import numpy as np
 import pytest
@@ -12,13 +12,33 @@
 )
 
 
-def test_validate_mesh_matches_image_extents():
-    atlas = BrainGlobeAtlas("allen_mouse_100um")
+@pytest.fixture
+def atlas():
+    """A fixture providing a low-res Allen Mouse atlas for testing.
+    Tests assume this atlas is valid"""
+    return BrainGlobeAtlas("allen_mouse_100um")
+
+
+@pytest.fixture
+def atlas_with_bad_reference_file():
+    """A fixture providing an invalid version of Allen Mouse atlas for testing.
+    The atlas will have a misnamed template file that won't be found by the API
+    This fixture also does the clean-up after the test has run
+    """
+    good_name = get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference.tiff"
+    bad_name = (
+        get_brainglobe_dir() / "allen_mouse_100um_v1.2/reference_bad.tiff"
+    )
+    os.rename(good_name, bad_name)
+    yield BrainGlobeAtlas("allen_mouse_100um")
+    os.rename(bad_name, good_name)
+
+
+def test_validate_mesh_matches_image_extents(atlas):
     assert validate_mesh_matches_image_extents(atlas)
 
 
-def test_validate_mesh_matches_image_extents_negative(mocker):
-    atlas = BrainGlobeAtlas("allen_mouse_100um")
+def test_validate_mesh_matches_image_extents_negative(mocker, atlas):
     flipped_annotation_image = np.transpose(atlas.annotation)
     mocker.patch(
         "bg_atlasapi.BrainGlobeAtlas.annotation",
@@ -31,16 +51,13 @@ def test_validate_mesh_matches_image_extents_negative(mocker):
         validate_mesh_matches_image_extents(atlas)
 
 
-def test_valid_atlas_files():
-    _ = BrainGlobeAtlas("allen_mouse_100um")
-    atlas_path = Path(get_brainglobe_dir()) / "allen_mouse_100um_v1.2"
-    assert validate_atlas_files(atlas_path)
+def test_valid_atlas_files(atlas):
+    assert validate_atlas_files(atlas)
 
 
-def test_invalid_atlas_path():
-    atlas_path = Path.home()
+def test_invalid_atlas_path(atlas_with_bad_reference_file):
     with pytest.raises(AssertionError, match="Expected file not found"):
-        validate_atlas_files(atlas_path)
+        validate_atlas_files(atlas_with_bad_reference_file)
 
 
 def test_assert_close():