mcb-update-actions - Improve error handling

.github/scripts/request_validation.py

@@ -2,33 +2,29 @@
 import os
 import sys
 
-from utils.json_validation import request_validation, \
-    get_errors_response
+from utils.json_validation import request_validation, get_errors_response
 
-# --------- #
 # Handling arguments
-# --------- #
 dirname = sys.argv[1]
 curl_URL = sys.argv[2]
 
-# - #
 # Hardcoded values
-# - #
 extension = ".json"
 
-# --------- #
 # Running validations
-# --------- #
 error_dict = {}
-# We iterate over the JSON documents to validate
+validated_files = []
+total_files = 0
+files_with_errors = 0
+
+# Iterate over the JSON documents to validate
 for file in os.scandir(dirname):
     if not file.path.endswith(extension):
         continue
 
-    #!
-    print(f"----Validation attempt for file '{file}'")
-    #!
-
+    total_files += 1
+    validated_files.append(file.name)
+
     request = request_validation(
         data_filepath=file,
         validator_url=curl_URL
@@ -40,7 +36,17 @@
     )
     if val_error:
         error_dict[file.name] = val_error
+        files_with_errors += 1
 
 # If the dictionary is not empty, fail the script returning it
+summary = {
+    "n_total_files": total_files,
+    "n_files_with_errors": files_with_errors,
+    "error_files": error_dict,
+    "all_files": validated_files
+}
+
 if error_dict:
-    sys.exit(json.dumps(error_dict, sort_keys=True, indent=4))
+    sys.exit(json.dumps(summary, sort_keys=True, indent=4))
+else:
+    print(json.dumps(summary, sort_keys=True, indent=4))

.github/scripts/utils/json_validation.py

@@ -49,8 +49,8 @@ def get_errors_response(
     if not response.status_code == requests.codes.ok:
         error_message = (
             f"The POST response was not successful: instead of {requests.codes.ok},"
-            f" the status code was '{response.status_code}' when validating file '{filename}'.\n"
-            f"Response content: {response.content.decode('utf-8')}"
+            f" the status code was '{response.status_code}' when validating file '{filename}'."
+            f" Response content: {response.content.decode('utf-8')}"
         )
         return error_message
 

.github/workflows/json_validation_deploying_biovalidator.yml

@@ -76,12 +76,6 @@ jobs:
           # We want to specify the JSON schemas and documents with the new 
           #   changes. Therefore we specify the schemas at deployment level (-r)
         run: |
-          #!
-          echo "--- Listing files:"
-          pwd
-          ls
-          ls ./schemas
-          #!
           schemas_dir="./schemas"
           node biovalidator/src/biovalidator -r "$schemas_dir/*.json" > biovalidator.log 2>&1 &
           
@@ -116,7 +110,3 @@ jobs:
           #   Biovalidator
           url="http://localhost:3020/validate"
           python3 ./.github/scripts/request_validation.py "$json_ex_dir" "$url"
-          #!
-          echo "Biovalidator log:\n"
-          cat biovalidator.log
-          #!