Coverage for biobb_template/template/template.py: 76%
58 statements
« prev ^ index » next coverage.py v7.3.2, created at 2023-11-30 16:51 +0000
« prev ^ index » next coverage.py v7.3.2, created at 2023-11-30 16:51 +0000
1#!/usr/bin/env python3
3"""Module containing the Template class and the command line interface."""
4import argparse
5import shutil
6from pathlib import PurePath
7from biobb_common.generic.biobb_object import BiobbObject
8from biobb_common.configuration import settings
9from biobb_common.tools import file_utils as fu
10from biobb_common.tools.file_utils import launchlogger
13# 1. Rename class as required
14class Template(BiobbObject):
15 """
16 | biobb_template Template
17 | Short description for the `template <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Mandatory.
18 | Long description for the `template <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Optional.
20 Args:
21 input_file_path1 (str): Description for the first input file path. File type: input. `Sample file <https://urlto.sample>`_. Accepted formats: top (edam:format_3881).
22 input_file_path2 (str) (Optional): Description for the second input file path (optional). File type: input. `Sample file <https://urlto.sample>`_. Accepted formats: dcd (edam:format_3878).
23 output_file_path (str): Description for the output file path. File type: output. `Sample file <https://urlto.sample>`_. Accepted formats: zip (edam:format_3987).
24 properties (dic):
25 * **boolean_property** (*bool*) - (True) Example of boolean property.
26 * **binary_path** (*str*) - ("zip") Example of executable binary property.
27 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
28 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
30 Examples:
31 This is a use example of how to use the building block from Python::
33 from biobb_template.template.template import template
35 prop = {
36 'boolean_property': True
37 }
38 template(input_file_path1='/path/to/myTopology.top',
39 output_file_path='/path/to/newCompressedFile.zip',
40 input_file_path2='/path/to/mytrajectory.dcd',
41 properties=prop)
43 Info:
44 * wrapped_software:
45 * name: Zip
46 * version: >=3.0
47 * license: BSD 3-Clause
48 * ontology:
49 * name: EDAM
50 * schema: http://edamontology.org/EDAM.owl
52 """
54 # 2. Adapt input and output file paths as required. Include all files, even optional ones
55 def __init__(self, input_file_path1, output_file_path, input_file_path2=None, properties=None, **kwargs) -> None:
56 properties = properties or {}
58 # 2.0 Call parent class constructor
59 super().__init__(properties)
60 self.locals_var_dict = locals().copy()
62 # 2.1 Modify to match constructor parameters
63 # Input/Output files
64 self.io_dict = {
65 'in': {'input_file_path1': input_file_path1, 'input_file_path2': input_file_path2},
66 'out': {'output_file_path': output_file_path}
67 }
69 # 3. Include all relevant properties here as
70 # self.property_name = properties.get('property_name', property_default_value)
72 # Properties specific for BB
73 self.boolean_property = properties.get('boolean_property', True)
74 self.binary_path = properties.get('binary_path', 'zip')
75 self.properties = properties
77 # Check the properties
78 self.check_properties(properties)
79 # Check the arguments
80 self.check_arguments()
82 @launchlogger
83 def launch(self) -> int:
84 """Execute the :class:`Template <template.template.Template>` object."""
86 # 4. Setup Biobb
87 if self.check_restart():
88 return 0
89 self.stage_files()
91 # Creating temporary folder
92 self.tmp_folder = fu.create_unique_dir()
93 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
95 # 5. Include here all mandatory input files
96 # Copy input_file_path1 to temporary folder
97 shutil.copy(self.io_dict['in']['input_file_path1'], self.tmp_folder)
99 # 6. Prepare the command line parameters as instructions list
100 instructions = ['-j']
101 if self.boolean_property:
102 instructions.append('-v')
103 fu.log('Appending optional boolean property', self.out_log, self.global_log)
105 # 7. Build the actual command line as a list of items (elements order will be maintained)
106 self.cmd = [self.binary_path,
107 ' '.join(instructions),
108 self.io_dict['out']['output_file_path'],
109 str(PurePath(self.tmp_folder).joinpath(PurePath(self.io_dict['in']['input_file_path1']).name))]
110 fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
112 # 8. Repeat for optional input files if provided
113 if self.io_dict['in']['input_file_path2']:
114 # Copy input_file_path2 to temporary folder
115 shutil.copy(self.io_dict['in']['input_file_path2'], self.tmp_folder)
116 # Append optional input_file_path2 to cmd
117 self.cmd.append(str(PurePath(self.tmp_folder).joinpath(PurePath(self.io_dict['in']['input_file_path2']).name)))
118 fu.log('Appending optional argument to command line', self.out_log, self.global_log)
120 # 9. Uncomment to check the command line
121 # print(' '.join(cmd))
123 # Run Biobb block
124 self.run_biobb()
126 # Copy files to host
127 self.copy_to_host()
129 # Remove temporary file(s)
130 self.tmp_files.extend([
131 self.stage_io_dict.get("unique_dir"),
132 self.tmp_folder
133 ])
134 self.remove_tmp_files()
136 # Check output arguments
137 self.check_arguments(output_files_created=True, raise_exception=False)
139 return self.return_code
142def template(input_file_path1: str, output_file_path: str, input_file_path2: str = None, properties: dict = None, **kwargs) -> int:
143 """Create :class:`Template <template.template.Template>` class and
144 execute the :meth:`launch() <template.template.Template.launch>` method."""
146 return Template(input_file_path1=input_file_path1,
147 output_file_path=output_file_path,
148 input_file_path2=input_file_path2,
149 properties=properties, **kwargs).launch()
152def main():
153 """Command line execution of this building block. Please check the command line documentation."""
154 parser = argparse.ArgumentParser(description='Description for the template module.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
155 parser.add_argument('--config', required=False, help='Configuration file')
157 # 10. Include specific args of each building block following the examples. They should match step 2
158 required_args = parser.add_argument_group('required arguments')
159 required_args.add_argument('--input_file_path1', required=True, help='Description for the first input file path. Accepted formats: top.')
160 parser.add_argument('--input_file_path2', required=False, help='Description for the second input file path (optional). Accepted formats: dcd.')
161 required_args.add_argument('--output_file_path', required=True, help='Description for the output file path. Accepted formats: zip.')
163 args = parser.parse_args()
164 args.config = args.config or "{}"
165 properties = settings.ConfReader(config=args.config).get_prop_dic()
167 # 11. Adapt to match Class constructor (step 2)
168 # Specific call of each building block
169 template(input_file_path1=args.input_file_path1,
170 output_file_path=args.output_file_path,
171 input_file_path2=args.input_file_path2,
172 properties=properties)
175if __name__ == '__main__':
176 main()
178# 12. Complete documentation strings