Coverage for src/ensembl/utils/logging.py: 100%

1# See the NOTICE file distributed with this work for additional information 

2# regarding copyright ownership. 

3# 

4# Licensed under the Apache License, Version 2.0 (the "License"); 

5# you may not use this file except in compliance with the License. 

6# You may obtain a copy of the License at 

7# 

8# http://www.apache.org/licenses/LICENSE-2.0 

9# 

10# Unless required by applicable law or agreed to in writing, software 

11# distributed under the License is distributed on an "AS IS" BASIS, 

12# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. 

13# See the License for the specific language governing permissions and 

14# limitations under the License. 

15"""Easy initialisation functionality to set an event logging system. 

16 

17Examples: 

18 

19 >>> import logging, pathlib 

20 >>> from ensembl.utils.logging import init_logging 

21 >>> logfile = pathlib.Path("test.log") 

22 >>> init_logging("INFO", logfile, "DEBUG") 

23 >>> logging.info("This message is written in both stderr and the log file") 

24 >>> logging.debug("This message is only written in the log file") 

25 

26""" 

27 

28from __future__ import annotations 

29 

30__all__ = [ 

31 "LogLevel", 

32 "init_logging", 

33 "init_logging_with_args", 

34] 

35 

36import argparse 

37import logging 

38from typing import Optional, Union 

39 

40from ensembl.utils import StrPath 

41 

42 

43LogLevel = Union[int, str] 

44 

45 

46def init_logging( 

47 log_level: LogLevel = "WARNING", 

48 log_file: Optional[StrPath] = None, 

49 log_file_level: LogLevel = "DEBUG", 

50 msg_format: str = "%(asctime)s\t%(levelname)s\t%(message)s", 

51 date_format: str = r"%Y-%m-%d_%H:%M:%S", 

52) -> None: 

53 """Initialises the logging system. 

54 

55 By default, all the log messages corresponding to `log_level` (and above) will be printed in the 

56 standard error. If `log_file` is provided, all messages of `log_file_level` level (and above) will 

57 be written into the provided file. 

58 

59 Args: 

60 log_level: Minimum logging level for the standard error. 

61 log_file: Logging file where to write logging messages besides the standard error. 

62 log_file_level: Minimum logging level for the logging file. 

63 msg_format: A format string for the logged output as a whole. More information: 

64 https://docs.python.org/3/library/logging.html#logrecord-attributes 

65 date_format: A format string for the date/time portion of the logged output. More information: 

66 https://docs.python.org/3/library/logging.html#logging.Formatter.formatTime 

67 

68 """ 

69 # Configure the basic logging system, setting the root logger to the minimum log level available 

70 # to avoid filtering messages in any handler due to "parent delegation". Also close and remove any 

71 # existing handlers before setting this configuration. 

72 logging.basicConfig(format=msg_format, datefmt=date_format, level="DEBUG", force=True) 

73 # Set the correct log level of the new StreamHandler (by default it is set to NOTSET) 

74 logging.root.handlers[0].setLevel(log_level) 

75 if log_file: 

76 # Create the log file handler and add it to the root logger 

77 formatter = logging.Formatter(msg_format, datefmt=date_format) 

78 file_handler = logging.FileHandler(log_file) 

79 file_handler.setLevel(log_file_level) 

80 file_handler.setFormatter(formatter) 

81 logging.root.addHandler(file_handler) 

82 

83 

84def init_logging_with_args(args: argparse.Namespace) -> None: 

85 """Processes the Namespace object provided to call `init_logging()` with the correct arguments. 

86 

87 Args: 

88 args: Namespace populated by an argument parser. 

89 

90 """ 

91 args_dict = vars(args) 

92 log_args = {x: args_dict[x] for x in ["log_level", "log_file", "log_file_level"] if x in args_dict} 

93 init_logging(**log_args)