Change log level for duplicate data table entries to warning

Fixes https://github.com/galaxyproject/galaxy/issues/16987,
though there's probably something to be done for loc files
being loaded from tools. At the minimum this is a versioning
issue, if a new version of featureCounts comes with a new
built-in reference then an old version shouldn't use it,
and vice-versa. Seems like a hard problem to solve.

lib/galaxy/tool_util/data/__init__.py

@@ -250,6 +250,11 @@ class ToolDataTable(Dictifiable):
                 self.add_entry(
                     entry, allow_duplicates=allow_duplicates, persist=persist, entry_source=entry_source, **kwd
                 )
+            except MessageException as e:
+                if e.type == "warning":
+                    log.warning(str(e))
+                else:
+                    log.error(str(e))
             except Exception as e:
                 log.error(str(e))
         return self._loaded_content_version
@@ -686,7 +691,8 @@ class TabularToolDataTable(ToolDataTable):
                 self.data.append(fields)
             else:
                 raise MessageException(
-                    f"Attempted to add fields ({fields}) to data table '{self.name}', but this entry already exists and allow_duplicates is False."
+                    f"Attempted to add fields ({fields}) to data table '{self.name}', but this entry already exists and allow_duplicates is False.",
+                    type="warning",
                 )
         else:
             raise MessageException(