Coverage for biobb_io/api/memprotmd_sim.py: 74%

1#!/usr/bin/env python 

2 

3"""Module containing the MemProtMDSim 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, get_memprotmd_sim 

9 

10 

11class MemProtMDSim(BiobbObject): 

12 """ 

13 | biobb_io MemProtMDSim 

14 | This class is a wrapper of the MemProtMD to download a simulation using its REST API. 

15 | Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to download a simulation. 

16 

17 Args: 

18 output_simulation (str): Path to the output simulation in a ZIP file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim.zip>`_. Accepted formats: zip (edam:format_3987). 

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

20 * **pdb_code** (*str*) - (None) RSCB PDB code. 

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.memprotmd_sim import memprotmd_sim 

29 prop = { 

30 'pdb_code': '2VGB' 

31 } 

32 memprotmd_sim(output_simulation='/path/to/newSimulation.zip', 

33 properties=prop) 

34 

35 Info: 

36 * wrapped_software: 

37 * name: MemProtMD DB 

38 * license: Creative Commons 

39 * ontology: 

40 * name: EDAM 

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

42 

43 """ 

44 

45 def __init__(self, output_simulation, 

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_simulation": output_simulation} 

56 } 

57 

58 # Properties specific for BB 

59 self.pdb_code = properties.get('pdb_code', 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_simulation = check_output_path(self.io_dict["out"]["output_simulation"], "output_simulation", False, out_log, self.__class__.__name__) 

69 

70 @launchlogger 

71 def launch(self) -> int: 

72 """Execute the :class:`MemProtMDSim <api.memprotmd_sim.MemProtMDSim>` api.memprotmd_sim.MemProtMDSim 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.pdb_code, 'pdb_code', self.out_log, self.__class__.__name__) 

82 

83 # get simulation files and save to output 

84 get_memprotmd_sim(self.pdb_code, self.output_simulation, self.out_log, self.global_log) 

85 

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

87 

88 return 0 

89 

90 

91def memprotmd_sim(output_simulation: str, properties: dict = None, **kwargs) -> int: 

92 """Execute the :class:`MemProtMDSim <api.memprotmd_sim.MemProtMDSim>` class and 

93 execute the :meth:`launch() <api.memprotmd_sim.MemProtMDSim.launch>` method.""" 

94 

95 return MemProtMDSim(output_simulation=output_simulation, 

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

97 

98 

99def main(): 

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

101 parser = argparse.ArgumentParser(description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to download a simulation.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999)) 

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

103 

104 # Specific args of each building block 

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

106 required_args.add_argument('-o', '--output_simulation', required=True, help="Path to the output simulation in a ZIP file. Accepted formats: zip.") 

107 

108 args = parser.parse_args() 

109 config = args.config if args.config else None 

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

111 

112 # Specific call of each building block 

113 memprotmd_sim(output_simulation=args.output_simulation, 

114 properties=properties) 

115 

116 

117if __name__ == '__main__': 

118 main()