diff --git a/htsinfer/htsinfer.py b/htsinfer/htsinfer.py index 4967a4d..d29c89a 100755 --- a/htsinfer/htsinfer.py +++ b/htsinfer/htsinfer.py @@ -85,7 +85,7 @@ def evaluate(self): self.get_library_stats() LOGGER.info( "Library stats determined: " - f"{self.config.results.library_stats.json()}" + f"{self.config.results.library_stats.model_dump_json()}" ) # determine library source @@ -93,7 +93,7 @@ def evaluate(self): self.config.results.library_source = self.get_library_source() LOGGER.info( "Library source determined: " - f"{self.config.results.library_source.json()}" + f"{self.config.results.library_source.model_dump_json()}" ) # determine library type @@ -106,7 +106,7 @@ def evaluate(self): LOGGER.warning(f"{type(exc).__name__}: {str(exc)}") LOGGER.info( "Library type determined: " - f"{self.config.results.library_type.json()}" + f"{self.config.results.library_type.model_dump_json()}" ) # determine read orientation @@ -119,7 +119,7 @@ def evaluate(self): LOGGER.warning(f"{type(exc).__name__}: {str(exc)}") LOGGER.info( "Read orientation determined: " - f"{self.config.results.read_orientation.json()}" + f"{self.config.results.read_orientation.model_dump_json()}" ) # determine read layout @@ -132,7 +132,7 @@ def evaluate(self): LOGGER.warning(f"{type(exc).__name__}: {str(exc)}") LOGGER.info( "Read layout determined: " - f"{self.config.results.read_layout.json()}" + f"{self.config.results.read_layout.model_dump_json()}" ) except FileProblem as exc: @@ -148,7 +148,7 @@ def evaluate(self): LOGGER.error(f"{type(exc).__name__}: {str(exc)}") # log results - LOGGER.info(f"Results: {self.config.results.json()}") + LOGGER.info(f"Results: {self.config.results.model_dump_json()}") def prepare_env(self): """Set up work environment."""