From ec32669cf51bea5882316d84657fc2224a5976c5 Mon Sep 17 00:00:00 2001 From: mvdbeek Date: Wed, 8 Nov 2023 10:38:42 +0100 Subject: [PATCH] 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 | 8 +++++++- 1 file changed, 7 insertions(+), 1 deletion(-) diff --git a/lib/galaxy/tool_util/data/__init__.py b/lib/galaxy/tool_util/data/__init__.py index 5e2fdfb7908b..927841d9004c 100644 --- a/lib/galaxy/tool_util/data/__init__.py +++ b/lib/galaxy/tool_util/data/__init__.py @@ -250,6 +250,11 @@ def add_entries( 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 @@ def _add_entry( 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(