Coverage for biobb_io/api/drugbank.py: 76%

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 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory. 

24 

25 Examples: 

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

27 

28 from biobb_io.api.drugbank import drugbank 

29 prop = { 

30 'drugbank_id': 'DB00530' 

31 } 

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

33 properties=prop) 

34 

35 Info: 

36 * wrapped_software: 

37 * name: Drugbank 

38 * license: Creative Commons 

39 * ontology: 

40 * name: EDAM 

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

42 

43 """ 

44 

45 def __init__(self, output_sdf_path, 

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

47 properties = properties or {} 

48 

49 # Call parent class constructor 

50 super().__init__(properties) 

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

52 

53 # Input/Output files 

54 self.io_dict = { 

55 "out": {"output_sdf_path": output_sdf_path} 

56 } 

57 

58 # Properties specific for BB 

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

60 self.properties = properties 

61 

62 # Check the properties 

63 self.check_properties(properties) 

64 self.check_arguments() 

65 

66 def check_data_params(self, out_log, err_log): 

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

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

69 

70 @launchlogger 

71 def launch(self) -> int: 

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

73 

74 # check input/output paths and parameters 

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

76 

77 # Setup Biobb 

78 if self.check_restart(): 

79 return 0 

80 

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

82 

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

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

85 

86 # Downloading SDF file 

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

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

89 

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

91 

92 return 0 

93 

94 

95def drugbank(output_sdf_path: str, properties: dict = None, **kwargs) -> int: 

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

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

98 

99 return Drugbank(output_sdf_path=output_sdf_path, 

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

101 

102 

103def main(): 

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

105 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)) 

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

107 

108 # Specific args of each building block 

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

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

111 

112 args = parser.parse_args() 

113 config = args.config if args.config else None 

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

115 

116 # Specific call of each building block 

117 drugbank(output_sdf_path=args.output_sdf_path, 

118 properties=properties) 

119 

120 

121if __name__ == '__main__': 

122 main()