fix: Copy filtered submission files before converting notebooks

This ensures that all the files that should be included in the submission
are copied. The original notebooks, which are to be autograded, are
later overwritten with their converted versions, which is fine.

Author: natkam

grader_service/convert/converters/base.py

@@ -264,10 +264,6 @@ def matches_allowed_patterns(file_path):
             """
             Check if a file matches any of the allowed glob patterns.
             """
-            # Note: ignoring notebooks is needed to not overwrite converted notebooks
-            # with the original ones as currently the copying process is done after the conversion
-            if file_path.endswith(".ipynb"):
-                return False
             return any(fnmatch.fnmatch(file_path, pattern) for pattern in files_patterns)
 
         def is_ignored(file_path):
@@ -289,6 +285,9 @@ def is_ignored(file_path):
             ]  # Modify dirs in-place to ignore unwanted dirs
 
             for file in files:
+                if file == "gradebook.json":
+                    continue
+
                 abs_file_path = os.path.join(root, file)
                 rel_file_path = os.path.relpath(abs_file_path, src)
 
@@ -345,6 +344,10 @@ def _handle_failure(exception) -> None:
             if not should_process:
                 return
 
+            json_path = os.path.join(self._output_directory, "gradebook.json")
+            with Gradebook(json_path) as gb:
+                self.copy_unmatched_files(gb)
+
             self.run_pre_convert_hook()
 
             # convert all the notebooks
@@ -355,10 +358,6 @@ def _handle_failure(exception) -> None:
             self.set_permissions()
             self.run_post_convert_hook()
 
-            json_path = os.path.join(self._output_directory, "gradebook.json")
-            with Gradebook(json_path) as gb:
-                self.copy_unmatched_files(gb)
-
         except UnresponsiveKernelError as e:
             self.log.error(
                 "While processing files %s, the kernel became "