Assembly.download module and Events.dump logging updated #203
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Example output when called with --verbose: 11/09/2023_02:07:40(PM) - INFO - Download the files |
| parser.add_argument("-v", "--verbose", action="store_true", required=False, | ||
| help="Verbose level logging") | ||
| parser.add_argument("-d", "--debug", action="store_true", required=False, | ||
| help="Debug level logging") |
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Maybe we should place these after the mandatory arguments ?
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Sure I can do, only reason I put them there was I thought it was needed given they are optional flag not positional args
"The add_argument() method must know whether an optional argument, like -f or --foo, or a positional argument, like a list of filenames, is expected. The first arguments passed to add_argument() must therefore be either a series of flags, or a simple argument name."
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I believe that sentence refers to the first arguments passed to the function add_argument(), i.e. add_argument("-f", "--foo", ...), and not to the parser.
| if args.verbose: | ||
| logging.basicConfig( | ||
| filename=log_file, format=logging_format, datefmt=date_format, | ||
| filemode="w", level=logging.INFO | ||
| ) | ||
| elif args.debug: | ||
| logging.basicConfig( | ||
| filename=log_file, format=logging_format, datefmt=date_format, | ||
| filemode="w", level=logging.DEBUG | ||
| ) | ||
| else: | ||
| logging.basicConfig( | ||
| filename=log_file, format=logging_format, datefmt=date_format, | ||
| filemode="w", level=logging.WARNING | ||
| ) |
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We can factorize this further with something like:
| if args.verbose: | |
| logging.basicConfig( | |
| filename=log_file, format=logging_format, datefmt=date_format, | |
| filemode="w", level=logging.INFO | |
| ) | |
| elif args.debug: | |
| logging.basicConfig( | |
| filename=log_file, format=logging_format, datefmt=date_format, | |
| filemode="w", level=logging.DEBUG | |
| ) | |
| else: | |
| logging.basicConfig( | |
| filename=log_file, format=logging_format, datefmt=date_format, | |
| filemode="w", level=logging.WARNING | |
| ) | |
| log_level = None | |
| if args.debug: | |
| log_level = logging.DEBUG | |
| elif args.verbose: | |
| log_level = logging.INFO | |
| logging.basicConfig( | |
| filename=log_file, format=logging_format, datefmt=date_format, | |
| filemode="w", level=log_level | |
| ) |
Note that I've put debug before verbose: assuming we get the 2 params, I suppose debug should take priority.
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This is actually better handled by the add_mutually_exclusive_group() when adding the parameters to the parser [link].
ens-LCampbell
changed the title
| self._connector.database = db_name | ||
| try: | ||
| self._connector.database = db_name | ||
| except: | ||
| logging.critical(f"Unknown database: '{db_name}' - Not located on host !") |
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I don't think this is needed: if there is an exception here, it should be allowed to be raised and the script should stop anyway
| parser.add_argument("-v", "--verbose", action="store_true", required=False, | ||
| help="Verbose level logging") | ||
| parser.add_argument("-d", "--debug", action="store_true", required=False, | ||
| help="Debug level logging") | ||
| args = parser.parse_args() | ||
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| retrieve_assembly_data(**vars(args)) | ||
| # Configure logging | ||
| date_format='%Y/%m/%d_%I:%M:%S(%p)' | ||
| logging_format='%(asctime)s - %(levelname)s - %(message)s' | ||
| reload(logging) | ||
| log_level = None | ||
| if args.debug: | ||
| log_level = logging.DEBUG | ||
| elif args.verbose: | ||
| log_level = logging.INFO | ||
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| logging.basicConfig( | ||
| format=logging_format, datefmt=date_format, | ||
| filemode="w", level=log_level | ||
| ) | ||
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| retrieve_assembly_data(args.accession, args.download_dir) |
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This should be rewritten with the new argparse and init_logging from ensembl-py
| parser.add_argument("-v", "--verbose", action="store_true", required=False, | ||
| help="Verbose level logging") | ||
| parser.add_argument("-d", "--debug", action="store_true", required=False, | ||
| help="Debug level logging") | ||
| args = parser.parse_args() | ||
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| # Configure logging | ||
| date_format='%Y/%m/%d_%I:%M:%S(%p)' | ||
| logging_format='%(asctime)s - %(levelname)s - %(message)s' | ||
| reload(logging) | ||
| log_level = None | ||
| if args.debug: | ||
| log_level = logging.DEBUG | ||
| elif args.verbose: | ||
| log_level = logging.INFO | ||
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| logging.basicConfig( | ||
| format=logging_format, datefmt=date_format, | ||
| filemode="w", level=log_level | ||
| ) | ||
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Likewise, rewrite with new system
| parser.add_argument("-v", "--verbose", action="store_true", required=False, | ||
| help="Verbose level logging") | ||
| parser.add_argument("-d", "--debug", action="store_true", required=False, | ||
| help="Debug level logging") | ||
| args = parser.parse_args() | ||
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| # Configure logging | ||
| date_format='%Y/%m/%d_%I:%M:%S(%p)' | ||
| logging_format='%(asctime)s - %(levelname)s - %(message)s' | ||
| reload(logging) | ||
| log_level = None | ||
| if args.debug: | ||
| log_level = logging.DEBUG | ||
| elif args.verbose: | ||
| log_level = logging.INFO | ||
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| logging.basicConfig( | ||
| format=logging_format, datefmt=date_format, | ||
| filemode="w", level=log_level | ||
| ) | ||
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Simple implementation of logging to file :
With log level dictated via command line args (flag).
If not defined default is set to WARNING, and file created with or without WARN level events being triggered.