From 4c9891b3242f87c38e6d67613067ea17242d76a3 Mon Sep 17 00:00:00 2001 From: Khoroshevskyi Date: Thu, 19 Dec 2024 12:50:45 -0500 Subject: [PATCH] Fixed Donald comments for PR --- bbconf/config_parser/bedbaseconfig.py | 4 ++-- bbconf/modules/bedfiles.py | 8 ++++++-- 2 files changed, 8 insertions(+), 4 deletions(-) diff --git a/bbconf/config_parser/bedbaseconfig.py b/bbconf/config_parser/bedbaseconfig.py index 64b2200..204af1a 100644 --- a/bbconf/config_parser/bedbaseconfig.py +++ b/bbconf/config_parser/bedbaseconfig.py @@ -253,8 +253,8 @@ def _init_qdrant_text_backend(self) -> Union[QdrantBackend, None]: qdrant_host=self.config.qdrant.host, qdrant_api_key=self.config.qdrant.api_key, ) - except Exception as _: - _LOGGER.error("Error in Connection to qdrant text! skipping...") + except Exception as e: + _LOGGER.error(f"Error in Connection to qdrant text! skipping {e}") warnings.warn( "Error in Connection to qdrant text! skipping...", UserWarning ) diff --git a/bbconf/modules/bedfiles.py b/bbconf/modules/bedfiles.py index 9cef005..c04a547 100644 --- a/bbconf/modules/bedfiles.py +++ b/bbconf/modules/bedfiles.py @@ -947,6 +947,8 @@ def _update_ref_validation( """ Update reference validation data + ! This function won't update the reference validation data, if it exists, it will skip it. + :param sa_session: sqlalchemy session :param bed_object: bed sqlalchemy object :param ref_validation: bed file metadata @@ -1018,11 +1020,13 @@ def upload_pephub(self, identifier: str, metadata: dict, overwrite: bool = False overwrite=overwrite, ) - def update_pephub(self, identifier: str, metadata: dict, overwrite: bool = False): + def update_pephub( + self, identifier: str, metadata: dict, overwrite: bool = False + ) -> None: try: if not metadata: _LOGGER.warning("No metadata provided. Skipping pephub upload..") - return False + return None self._config.phc.sample.update( namespace=self._config.config.phc.namespace, name=self._config.config.phc.name,