src/db_utils/config.py: modification of Config.db_file and Config.output +...

src/db_utils/config.py: modification of Config.db_file and Config.output + deletion of LOGGING_CONFIG, logging_def and LoggingLevelError

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]