diff --git a/src/db_utils/config.py b/src/db_utils/config.py index e9fe7185bc59d84334f841b55b1a7d5f7c4fae0b..ed768dad9f88cf4ffb25b579884867efa9808854 100755 --- a/src/db_utils/config.py +++ b/src/db_utils/config.py @@ -16,73 +16,14 @@ class Config: """ A class containing every parameters used in the submodule db_utils """ - db_file = Path(__file__).parents[1] / "db.sqlite3" + db_file = Path(__file__).parents[2] / "results" / 'chia_pet_database.db' tables = ["gin_gene", "gin_exon", "gin_frequency", "gin_interaction"] bed_orf = Path(__file__).parents[1] / "data" / "exon_orf.bed" bed_exon = Path(__file__).parents[1] / "data" / "exon_freq.bed" - output = Path(__file__).parents[1] / "results" + output = Path(__file__).parents[2] / "results" exon_intern = Path(__file__).parents[1] / "data" / "exon_intern.bed" ctrl_exon_file = output / "CTRL_exons.txt" exon_file = output / "exons.txt" gene_file = Path(__file__).parents[1] / "data" / "genes.csv" frequency_file = output / "frequency.txt" - -class LoggingLevelError(Exception): - pass - - -def logging_def(output: Path, level: str = "INFO"): - """ - Define a logging at the current level of the script - - :param output: Folder where the result will be created - :param level: The log level - """ - possible_levels = ["INFO", "DEBUG", "ERROR", "WARNING", "CRITICAL"] - if level in possible_levels: - basename = str(Path(__file__).name).replace(".py", ".log") - LOGGING_CONFIG["handlers"]["file"]["filename"] = output / basename - LOGGING_CONFIG["loggers"][""]["level"] = level - logging.config.dictConfig(LOGGING_CONFIG) - elif level != "DISABLE": - raise LoggingLevelError(f"Logging level unknown : choose from " - f"{possible_levels} or DISABLE to disable the " - f"initialisation of logging in {__file__}") - - -LOGGING_CONFIG = { - 'version': 1, - 'disable_existing_loggers': True, - 'formatters': { - 'complex': { - 'format': '%(filename)s:%(lineno)s:%(funcName)s():%(asctime)s - %(' - 'levelname)s - %(message)s' - }, - "simple": { - 'format': '%(message)s' - } - }, - 'handlers': { - 'default': { - 'level': 'NOTSET', - 'formatter': 'simple', - 'class': 'logging.StreamHandler', - 'stream': 'ext://sys.stdout', # Default is stderr - }, - 'file': { - 'level': 'NOTSET', - 'formatter': 'complex', - 'class': 'logging.FileHandler', - 'filename': 'test.log', - 'mode': 'w', - }, - }, - 'loggers': { - '': { # root logger - 'handlers': ['default', "file"], - 'level': 'NOTSET', - 'propagate': True - }, - } -} # type: Dict[str, Any]