Coverage for anonymise/demo_config.py: 61%

1#!/usr/bin/env python 

2 

3""" 

4crate_anon/anonymise/demo_config.py 

5 

6=============================================================================== 

7 

8 Copyright (C) 2015, University of Cambridge, Department of Psychiatry. 

9 Created by Rudolf Cardinal (rnc1001@cam.ac.uk). 

10 

11 This file is part of CRATE. 

12 

13 CRATE is free software: you can redistribute it and/or modify 

14 it under the terms of the GNU General Public License as published by 

15 the Free Software Foundation, either version 3 of the License, or 

16 (at your option) any later version. 

17 

18 CRATE is distributed in the hope that it will be useful, 

19 but WITHOUT ANY WARRANTY; without even the implied warranty of 

20 MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the 

21 GNU General Public License for more details. 

22 

23 You should have received a copy of the GNU General Public License 

24 along with CRATE. If not, see <https://www.gnu.org/licenses/>. 

25 

26=============================================================================== 

27 

28**Print a demonstration config file for the anonymiser.** 

29 

30""" 

31 

32import argparse 

33import pprint 

34import re 

35import sys 

36from typing import Dict 

37 

38from cardinal_pythonlib.file_io import smart_open 

39from rich_argparse import ArgumentDefaultsRichHelpFormatter 

40 

41from crate_anon.anonymise.constants import DEMO_CONFIG 

42from crate_anon.common.constants import EXIT_FAILURE 

43from crate_anon.version import CRATE_VERSION_PRETTY 

44 

45 

46# ============================================================================= 

47# Get a demo config, with placeholders replaced 

48# ============================================================================= 

49 

50 

51def search_replace_text(text: str, replace_dict: Dict[str, str]) -> str: 

52 for search, replace in replace_dict.items(): 

53 if replace is None: 

54 print(f"Can't replace '{search}' with None") 

55 sys.exit(EXIT_FAILURE) 

56 

57 text = text.replace(f"@@{search}@@", replace) 

58 

59 return text 

60 

61 

62def get_demo_config() -> str: 

63 replace_dict = { 

64 "admin_db_url": "mysql+mysqldb://username:password@127.0.0.1:3306/admin_databasename?charset=utf8", # noqa: E501 

65 "change_detection_encryption_phrase": "YETANOTHER", 

66 "data_dictionary_filename": "testdd.tsv", 

67 "dest_db_url": "mysql+mysqldb://username:password@127.0.0.1:3306/output_databasename?charset=utf8", # noqa: E501 

68 "master_patient_id_encryption_phrase": "SOME_OTHER_PASSPHRASE_REPLACE_ME", # noqa: E501 

69 "per_table_patient_id_encryption_phrase": "SOME_PASSPHRASE_REPLACE_ME", 

70 "source_db1_ddgen_include_fields": "", 

71 "source_db1_ddgen_scrubsrc_patient_fields": "", 

72 "source_db1_url": "mysql+mysqldb://username:password@127.0.0.1:3306/source_databasename?charset=utf8", # noqa: E501 

73 } 

74 

75 config = search_replace_text(DEMO_CONFIG, replace_dict) 

76 

77 missing_dict = {} 

78 

79 regex = r"@@([^@]*)@@" 

80 for match in re.finditer(regex, config): 

81 missing_dict[f"{match.group(1)}"] = "" 

82 

83 if missing_dict: 

84 print( 

85 "@@ Placeholders not substituted in DEMO_CONFIG:", file=sys.stderr 

86 ) 

87 pprint.pprint(missing_dict, stream=sys.stderr) 

88 sys.exit(EXIT_FAILURE) 

89 

90 return config.strip() 

91 

92 

93# ============================================================================= 

94# Main 

95# ============================================================================= 

96 

97 

98def main() -> None: 

99 """ 

100 Command-line entry point. 

101 """ 

102 # noinspection PyTypeChecker 

103 parser = argparse.ArgumentParser( 

104 description=f"Print a demo config file for the CRATE anonymiser. " 

105 f"({CRATE_VERSION_PRETTY})", 

106 formatter_class=ArgumentDefaultsRichHelpFormatter, 

107 ) 

108 

109 parser.add_argument( 

110 "--output", default="-", help="File for output; use '-' for stdout." 

111 ) 

112 parser.add_argument( 

113 "--leave_placeholders", 

114 action="store_true", 

115 help="Don't substitute @@ placeholders with examples", 

116 ) 

117 

118 args = parser.parse_args() 

119 

120 # ------------------------------------------------------------------------- 

121 # Print demo config 

122 # ------------------------------------------------------------------------- 

123 

124 with smart_open(args.output, "w") as f: 

125 if args.leave_placeholders: 

126 contents = DEMO_CONFIG.strip() 

127 else: 

128 contents = get_demo_config() 

129 print(contents, file=f) 

130 

131 

132if __name__ == "__main__": 

133 main()