warn for merged span fragments only if it contains real content

brat.py

@@ -87,10 +87,16 @@ def example_to_document(
             )
         if merge_non_contiguous_spans:
             if len(starts) > 1:
-                logger.warning(
-                    f"document '{doc.id}' contains a non-contiguous span (will be merged into a single span): "
-                    f"{span_dict}, text parts: {span_text_parts}"
-                )
+                # check if the text in between the fragments holds only space
+                merged_content_spans = list(zip(ends[:-1],starts[1:]))
+                merged_content_spans_filtered = [s.trim() for s in merged_content_spans if s.trim() != ""]
+                if len(merged_content_spans_filtered) > 0:
+                    logger.warning(
+                        f"document '{doc.id}' contains a non-contiguous span (will be merged into a single span): "
+                        f"newly covered text parts: {merged_content_spans_filtered}, "
+                        f"merged span text: '{doc.text[starts[0]:ends[-1]]}', "
+                        f"annotation: {span_dict}"
+                    )
             # just take everything
             start = min(starts)
             end = max(ends)