Coverage for biobb_flexserv / pcasuite / pcz_stiffness.py: 97%

1#!/usr/bin/env python3 

2 

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

4from typing import Optional 

5import shutil 

6import json 

7import math 

8from pathlib import PurePath 

9from biobb_common.tools import file_utils as fu 

10from biobb_common.generic.biobb_object import BiobbObject 

11from biobb_common.tools.file_utils import launchlogger 

12 

13 

14class PCZstiffness(BiobbObject): 

15 """ 

16 | biobb_flexserv PCZstiffness 

17 | Extract PCA stiffness from a compressed PCZ file. 

18 | Wrapper of the pczdump tool from the PCAsuite FlexServ module. 

19 

20 Args: 

21 input_pcz_path (str): Input compressed trajectory file. File type: input. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/data/pcasuite/pcazip.pcz>`_. Accepted formats: pcz (edam:format_3874). 

22 output_json_path (str): Output json file with PCA Stiffness. File type: output. `Sample file <https://github.com/bioexcel/biobb_flexserv/raw/master/biobb_flexserv/test/reference/pcasuite/pcz_stiffness.json>`_. Accepted formats: json (edam:format_3464). 

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

24 * **binary_path** (*str*) - ("pczdump") pczdump binary path to be used. 

25 * **eigenvector** (*int*) - (0) PCA mode (eigenvector) from which to extract stiffness. 

26 * **temperature** (*int*) - (300) Temperature with which compute the apparent stiffness. 

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

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

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

30 

31 Examples: 

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

33 

34 from biobb_flexserv.pcasuite.pcz_stiffness import pcz_stiffness 

35 

36 prop = { 

37 'eigenvector': 1 

38 } 

39 

40 pcz_stiffness( input_pcz_path='/path/to/pcazip_input.pcz', 

41 output_json_path='/path/to/pcz_stiffness.json', 

42 properties=prop) 

43 

44 Info: 

45 * wrapped_software: 

46 * name: FlexServ PCAsuite 

47 * version: >=1.0 

48 * license: Apache-2.0 

49 * ontology: 

50 * name: EDAM 

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

52 

53 """ 

54 

55 def __init__(self, input_pcz_path: str, 

56 output_json_path: str, properties: Optional[dict] = None, **kwargs) -> None: 

57 

58 properties = properties or {} 

59 

60 # Call parent class constructor 

61 super().__init__(properties) 

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

63 

64 # Input/Output files 

65 self.io_dict = { 

66 'in': {'input_pcz_path': input_pcz_path}, 

67 'out': {'output_json_path': output_json_path} 

68 } 

69 

70 # Properties specific for BB 

71 self.properties = properties 

72 self.binary_path = properties.get('binary_path', 'pczdump') 

73 self.eigenvector = properties.get('eigenvector', 0) 

74 self.temperature = properties.get('temperature', 300) 

75 

76 # Check the properties 

77 self.check_properties(properties) 

78 self.check_arguments() 

79 

80 @launchlogger 

81 def launch(self): 

82 """Launches the execution of the FlexServ pcz_stiffness module.""" 

83 

84 # Setup Biobb 

85 if self.check_restart(): 

86 return 0 

87 # self.stage_files() 

88 

89 # Internal file paths 

90 # try: 

91 # # Using rel paths to shorten the amount of characters due to fortran path length limitations 

92 # input_pcz = str(Path(self.stage_io_dict["in"]["input_pcz_path"]).relative_to(Path.cwd())) 

93 # output_json = str(Path(self.stage_io_dict["out"]["output_json_path"]).relative_to(Path.cwd())) 

94 # except ValueError: 

95 # # Container or remote case 

96 # input_pcz = self.stage_io_dict["in"]["input_pcz_path"] 

97 # output_json = self.stage_io_dict["out"]["output_json_path"] 

98 

99 # Manually creating a Sandbox to avoid issues with input parameters buffer overflow: 

100 # Long strings defining a file path makes Fortran or C compiled programs crash if the string 

101 # declared is shorter than the input parameter path (string) length. 

102 # Generating a temporary folder and working inside this folder (sandbox) fixes this problem. 

103 # The problem was found in Galaxy executions, launching Singularity containers (May 2023). 

104 

105 # Creating temporary folder 

106 tmp_folder = fu.create_unique_dir() 

107 fu.log('Creating %s temporary folder' % tmp_folder, self.out_log) 

108 

109 shutil.copy2(self.io_dict["in"]["input_pcz_path"], tmp_folder) 

110 

111 # Temporary output 

112 # temp_out = str(Path(self.stage_io_dict.get("unique_dir", "")).joinpath("output.dat")) 

113 temp_out = "output.dat" 

114 temp_json = "output.json" 

115 

116 # Command line 

117 # pczdump -i structure.ca.std.pcz --stiffness -o pcz.stiffness 

118 # self.cmd = [self.binary_path, 

119 # "-i", input_pcz, 

120 # "-o", temp_out, 

121 # "--stiffness={}".format(self.eigenvector), 

122 # "--temperature={}".format(self.temperature) 

123 # ] 

124 

125 self.cmd = ['cd', tmp_folder, ';', 

126 self.binary_path, 

127 "-i", PurePath(self.io_dict["in"]["input_pcz_path"]).name, 

128 "-o", temp_out, 

129 "--stiff={}".format(self.eigenvector), 

130 "--temperature={}".format(self.temperature) 

131 ] 

132 

133 # Run Biobb block 

134 self.run_biobb() 

135 

136 # Parse output stiffness 

137 info_dict = {} 

138 info_dict['stiffness'] = [] 

139 info_dict['stiffness_log'] = [] 

140 row = 0 

141 with open(PurePath(tmp_folder).joinpath(temp_out), 'r') as file: 

142 for line in file: 

143 info = line.strip().split(',') 

144 line_array = [] 

145 line_array_log = [] 

146 for nums in info: 

147 if nums: 

148 line_array.append(float(nums)) 

149 if float(nums) != 0: 

150 line_array_log.append(math.log10(float(nums))) 

151 else: 

152 line_array_log.append(float(nums)) 

153 

154 info_dict['stiffness'].append(line_array) 

155 info_dict['stiffness'][row][row] = float('inf') 

156 info_dict['stiffness_log'].append(line_array_log) 

157 info_dict['stiffness_log'][row][row] = float('inf') 

158 row += 1 

159 

160 with open(PurePath(tmp_folder).joinpath(temp_json), 'w') as out_file: 

161 out_file.write(json.dumps(info_dict, indent=4)) 

162 

163 # Copy outputs from temporary folder to output path 

164 shutil.copy2(PurePath(tmp_folder).joinpath(temp_json), PurePath(self.io_dict["out"]["output_json_path"])) 

165 

166 # Copy files to host 

167 # self.copy_to_host() 

168 

169 # Remove temporary folder(s) 

170 self.tmp_files.append(tmp_folder) 

171 self.remove_tmp_files() 

172 

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

174 

175 return self.return_code 

176 

177 

178def pcz_stiffness(input_pcz_path: str, output_json_path: str, 

179 properties: Optional[dict] = None, **kwargs) -> int: 

180 """Create :class:`PCZstiffness <flexserv.pcasuite.pcz_stiffness>`flexserv.pcasuite.PCZstiffness class and 

181 execute :meth:`launch() <flexserv.pcasuite.pcz_stiffness.launch>` method""" 

182 return PCZstiffness(**dict(locals())).launch() 

183 

184 

185pcz_stiffness.__doc__ = PCZstiffness.__doc__ 

186main = PCZstiffness.get_main(pcz_stiffness, "Extract PCA Stiffness from a compressed PCZ file.") 

187 

188if __name__ == '__main__': 

189 main()