Coverage for biobb_haddock/haddock/folder_test.py: 0%

1#!/usr/bin/env python3 

2 

3"""Module containing the haddock class and the command line interface.""" 

4 

5import os 

6import argparse 

7from typing import Optional 

8 

9from biobb_common.configuration import settings 

10from biobb_common.generic.biobb_object import BiobbObject 

11# from biobb_common.tools import file_utils as fu 

12from biobb_common.tools.file_utils import launchlogger 

13 

14 

15class FolderTest(BiobbObject): 

16 """ 

17 | biobb_haddock FolderTest 

18 | Wrapper class for the FolderTest module. 

19 | The FolderTest module. 

20 

21 Args: 

22 output_folder (dir): Path of the output folder. File type: output. `Sample file <https://raw.githubusercontent.com/bioexcel/biobb_haddock/master/biobb_haddock/test/reference/haddock/ref_caprieval.zip>`_. Accepted formats: format (edam:format_1915). 

23 properties (dict - Python dictionary object containing the tool parameters, not input/output files): 

24 * **n** (*int*) - (4) Number of files create. 

25 

26 Examples: 

27 This is a use example of how to use the building block from Python:: 

28 

29 from biobb_haddock.haddock.folder_test import folder_test 

30 folder_test(output_folder='/path/to/myfiles', 

31 properties={'n': 4}) 

32 

33 Info: 

34 * wrapped_software: 

35 * name: None 

36 * version: None 

37 * license: Apache-2.0 

38 * ontology: 

39 * name: EDAM 

40 * schema: http://edamontology.org/EDAM.owl 

41 """ 

42 

43 def __init__( 

44 self, 

45 output_folder: str, 

46 properties: Optional[dict] = None, 

47 **kwargs, 

48 ) -> None: 

49 properties = properties or {} 

50 

51 # Call parent class constructor 

52 super().__init__(properties) 

53 

54 # Input/Output files 

55 self.io_dict = { 

56 "out": {"output_folder": output_folder}, 

57 } 

58 

59 self.n = properties.get('n', 4) 

60 # Check the properties 

61 self.check_properties(properties) 

62 self.check_arguments() 

63 

64 @launchlogger 

65 def launch(self) -> int: 

66 """Execute the :class:`FolderTest <biobb_haddock.haddock.folder_test>` object.""" 

67 # tmp_files = [] 

68 

69 # Setup Biobb 

70 if self.check_restart(): 

71 return 0 

72 self.stage_files() 

73 

74 # Create n files in the output folder 

75 sandbox_output_folder = f'{self.stage_io_dict["unique_dir"]}/{self.io_dict["out"]["output_folder"]}' 

76 os.makedirs(sandbox_output_folder, exist_ok=True) 

77 for i in range(1, self.n + 1): 

78 with open(f'{sandbox_output_folder}/file_{i}.txt', 'w') as f: 

79 f.write(f"This is file number {i}") 

80 

81 # Copy files to host 

82 self.copy_to_host() 

83 

84 # Remove temporal files 

85 # self.tmp_files.extend([]) 

86 self.remove_tmp_files() 

87 

88 return self.return_code 

89 

90 

91def folder_test( 

92 output_folder: str, 

93 properties: Optional[dict] = None, 

94 **kwargs, 

95) -> int: 

96 """Create :class:`FolderTest <biobb_haddock.haddock.folder_test>` class and 

97 execute the :meth:`launch() <biobb_haddock.haddock.folder_test.launch>` method.""" 

98 

99 return FolderTest( 

100 output_folder=output_folder, 

101 properties=properties, 

102 **kwargs, 

103 ).launch() 

104 

105 

106folder_test.__doc__ = FolderTest.__doc__ 

107 

108 

109def main(): 

110 parser = argparse.ArgumentParser( 

111 description="Wrapper of the haddock FolderTest module.", 

112 formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999), 

113 ) 

114 parser.add_argument( 

115 "-c", 

116 "--config", 

117 required=False, 

118 help="This file can be a YAML file, JSON file or JSON string", 

119 ) 

120 

121 # Specific args of each building block 

122 required_args = parser.add_argument_group("required arguments") 

123 required_args.add_argument("--output_folder", required=True) 

124 

125 args = parser.parse_args() 

126 config = args.config if args.config else None 

127 properties = settings.ConfReader(config=config).get_prop_dic() 

128 

129 # Specific call of each building block 

130 folder_test( 

131 output_folder=args.output_folder, 

132 properties=properties, 

133 ) 

134 

135 

136if __name__ == "__main__": 

137 main()