printing data frames with validation function information

bg_atlasgen/validate_atlases.py

@@ -1,6 +1,7 @@
 """Script to validate atlases"""
 
 
+import json
 import os
 from pathlib import Path
 
@@ -15,10 +16,10 @@
 from bg_atlasapi.update_atlases import update_atlas
 
 
 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)}"
     )
@@ -95,26 +96,26 @@
     return True
 
 
 def open_for_visual_check(atlas: BrainGlobeAtlas):
     # implement visual checks later
     pass
 
 
 def validate_checksum(atlas: BrainGlobeAtlas):
     # implement later
     pass
 
 
 def check_additional_references(atlas: BrainGlobeAtlas):
     # check additional references are different, but have same dimensions
     pass
 
 
 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)}"
     )
@@ -143,7 +144,7 @@
         )
 
 
 def validate_atlas(atlas_name, version, validation_functions):
     """Validates the latest version of a given atlas"""
 
     print(atlas_name, version)
@@ -152,16 +153,20 @@
     if not updated:
         update_atlas(atlas_name)
 
-    # list to store the errors of the failed validations
+    # dictionary of lists to store the errors of the failed validations
     failed_validations = {atlas_name: []}
     successful_validations = {atlas_name: []}
 
     for i, validation_function in enumerate(validation_functions):
         try:
             validation_function(BrainGlobeAtlas(atlas_name))
-            successful_validations[atlas_name].append(validation_function)
+            successful_validations[atlas_name].append(
+                validation_function.__name__
+            )
         except AssertionError as error:
-            failed_validations[atlas_name].append((validation_function, error))
+            failed_validations[atlas_name].append(
+                (validation_function.__name__, str(error))
+            )
 
     return successful_validations, failed_validations
 
@@ -179,17 +184,50 @@
 
     valid_atlases = []
     invalid_atlases = []
+    successful_validations = {}
+    failed_validations = {}
+
     for atlas_name, version in get_all_atlases_lastversions().items():
-        successful_validations, failed_validations = validate_atlas(
+        temp_successful_validations, temp_failed_validations = validate_atlas(
             atlas_name, version, all_validation_functions
         )
+
+        successful_validations.update(temp_successful_validations)
+        failed_validations.update(temp_failed_validations)
+
         for item in successful_validations:
             valid_atlases.append(item)
         for item in failed_validations:
             invalid_atlases.append(item)
 
-    print("Summary")
-    print("### Valid atlases ###")
-    print(valid_atlases)
-    print("### Invalid atlases ###")
-    print(invalid_atlases)
+    print("Validation has been completed")
+    print(
+        "Find successful_validations.json and failed_validations.json in ~/.brainglobe/atlases/validation/"
+    )
+
+    # Get the directory path
+    output_dir_path = str(get_brainglobe_dir() / "atlases/validation")
+
+    # Create the directory if it doesn't exist
+    if not os.path.exists(output_dir_path):
+        os.makedirs(output_dir_path)
+
+    # Open a file for writing
+    with open(
+        str(
+            get_brainglobe_dir() / "atlases/validation/failed_validations.json"
+        ),
+        "w",
+    ) as file:
+        # Write the dictionary to the file in JSON format
+        json.dump(failed_validations, file)
+
+    with open(
+        str(
+            get_brainglobe_dir()
+            / "atlases/validation/successful_validations.json"
+        ),
+        "w",
+    ) as file:
+        # Write the dictionary to the file in JSON format
+        json.dump(successful_validations, file)