Coverage for biobb_io/api/drugbank.py: 77%

43 statements  

« prev     ^ index     » next       coverage.py v7.3.1, created at 2023-09-07 10:41 +0000

1#!/usr/bin/env python 

2 

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

4import argparse 

5from biobb_common.generic.biobb_object import BiobbObject 

6from biobb_common.configuration import settings 

7from biobb_common.tools.file_utils import launchlogger 

8from biobb_io.api.common import check_output_path, check_mandatory_property, download_drugbank, write_sdf 

9 

10 

11class Drugbank(BiobbObject): 

12 """ 

13 | biobb_io Drugbank 

14 | This class is a wrapper for the `Drugbank <https://www.drugbank.ca/>`_ REST API. 

15 | Download a single component in SDF format from the `Drugbank <https://www.drugbank.ca/>`_ REST API. 

16 

17 Args: 

18 output_sdf_path (str): Path to the output SDF component file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_drugbank.sdf>`_. Accepted formats: sdf (edam:format_3814). 

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

20 * **drugbank_id** (*str*) - (None) Drugbank component id. 

21 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files. 

22 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist. 

23 

24 Examples: 

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

26 

27 from biobb_io.api.drugbank import drugbank 

28 prop = { 

29 'drugbank_id': 'DB00530' 

30 } 

31 drugbank(output_sdf_path='/path/to/newComponent.sdf', 

32 properties=prop) 

33 

34 Info: 

35 * wrapped_software: 

36 * name: Drugbank 

37 * license: Creative Commons 

38 * ontology: 

39 * name: EDAM 

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

41 

42 """ 

43 

44 def __init__(self, output_sdf_path, 

45 properties=None, **kwargs) -> None: 

46 properties = properties or {} 

47 

48 # Call parent class constructor 

49 super().__init__(properties) 

50 self.locals_var_dict = locals().copy() 

51 

52 # Input/Output files 

53 self.io_dict = { 

54 "out": {"output_sdf_path": output_sdf_path} 

55 } 

56 

57 # Properties specific for BB 

58 self.drugbank_id = properties.get('drugbank_id', None) 

59 self.properties = properties 

60 

61 # Check the properties 

62 self.check_properties(properties) 

63 self.check_arguments() 

64 

65 def check_data_params(self, out_log, err_log): 

66 """ Checks all the input/output paths and parameters """ 

67 self.output_sdf_path = check_output_path(self.io_dict["out"]["output_sdf_path"], "output_sdf_path", False, out_log, self.__class__.__name__) 

68 

69 @launchlogger 

70 def launch(self) -> int: 

71 """Execute the :class:`Drugbank <api.drugbank.Drugbank>` api.drugbank.Drugbank object.""" 

72 

73 # check input/output paths and parameters 

74 self.check_data_params(self.out_log, self.err_log) 

75 

76 # Setup Biobb 

77 if self.check_restart(): 

78 return 0 

79 

80 check_mandatory_property(self.drugbank_id, 'drugbank_id', self.out_log, self.__class__.__name__) 

81 

82 self.drugbank_id = self.drugbank_id.strip().lower() 

83 url = "https://www.drugbank.ca/structures/small_molecule_drugs/%s.sdf?type=3d" 

84 

85 # Downloading SDF file 

86 sdf_string = download_drugbank(self.drugbank_id, url, self.out_log, self.global_log) 

87 write_sdf(sdf_string, self.output_sdf_path, self.out_log, self.global_log) 

88 

89 self.check_arguments(output_files_created=True, raise_exception=False) 

90 

91 return 0 

92 

93 

94def drugbank(output_sdf_path: str, properties: dict = None, **kwargs) -> int: 

95 """Execute the :class:`Drugbank <api.drugbank.Drugbank>` class and 

96 execute the :meth:`launch() <api.drugbank.Drugbank.launch>` method.""" 

97 

98 return Drugbank(output_sdf_path=output_sdf_path, 

99 properties=properties, **kwargs).launch() 

100 

101 

102def main(): 

103 """Command line execution of this building block. Please check the command line documentation.""" 

104 parser = argparse.ArgumentParser(description="Download a component in SDF format from the Drugbank (https://www.drugbank.ca/).", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

105 parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string") 

106 

107 # Specific args of each building block 

108 required_args = parser.add_argument_group('required arguments') 

109 required_args.add_argument('-o', '--output_sdf_path', required=True, help="Path to the output SDF component file. Accepted formats: sdf.") 

110 

111 args = parser.parse_args() 

112 config = args.config if args.config else None 

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

114 

115 # Specific call of each building block 

116 drugbank(output_sdf_path=args.output_sdf_path, 

117 properties=properties) 

118 

119 

120if __name__ == '__main__': 

121 main()