Coverage for biobb_template/template/template_container.py: 24%
54 statements
« 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 TemplateContainer 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 import file_utils as fu
8from biobb_common.tools.file_utils import launchlogger
11# 1. Rename class as required
12class TemplateContainer(BiobbObject):
13 """
14 | biobb_template TemplateContainer
15 | Short description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Mandatory.
16 | Long description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Optional.
18 Args:
19 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).
20 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).
21 output_file_path (str): Description for the output file path. File type: output. `Sample file <https://urlto.sample>`_. Accepted formats: zip (edam:format_3987).
22 properties (dic):
23 * **boolean_property** (*bool*) - (True) Example of boolean property.
24 * **binary_path** (*str*) - ("zip") Example of executable binary property.
25 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
26 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
27 * **container_path** (*str*) - (None) Container path definition.
28 * **container_image** (*str*) - ('mmbirb/zip:latest') Container image definition.
29 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
30 * **container_working_dir** (*str*) - (None) Container working directory definition.
31 * **container_user_id** (*str*) - (None) Container user_id definition.
32 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
34 Examples:
35 This is a use example of how to use the building block from Python::
37 from biobb_template.template.template_container import template_container
39 prop = {
40 'boolean_property': True,
41 'container_path': 'docker',
42 'container_image': 'mmbirb/zip:latest',
43 'container_volume_path': '/tmp'
44 }
45 template_container(input_file_path1='/path/to/myTopology.top',
46 output_file_path='/path/to/newCompressedFile.zip',
47 input_file_path2='/path/to/mytrajectory.dcd',
48 properties=prop)
50 Info:
51 * wrapped_software:
52 * name: Zip
53 * version: >=3.0
54 * license: BSD 3-Clause
55 * ontology:
56 * name: EDAM
57 * schema: http://edamontology.org/EDAM.owl
59 """
61 # 2. Adapt input and output file paths as required. Include all files, even optional ones
62 def __init__(self, input_file_path1, output_file_path, input_file_path2=None, properties=None, **kwargs) -> None:
63 properties = properties or {}
65 # 2.0 Call parent class constructor
66 super().__init__(properties)
67 self.locals_var_dict = locals().copy()
69 # 2.1 Modify to match constructor parameters
70 # Input/Output files
71 self.io_dict = {
72 'in': {'input_file_path1': input_file_path1, 'input_file_path2': input_file_path2},
73 'out': {'output_file_path': output_file_path}
74 }
76 # 3. Include all relevant properties here as
77 # self.property_name = properties.get('property_name', property_default_value)
79 # Properties specific for BB
80 self.boolean_property = properties.get('boolean_property', True)
81 self.binary_path = properties.get('binary_path', 'zip')
82 self.properties = properties
84 # Check the properties
85 self.check_properties(properties)
86 # Check the arguments
87 self.check_arguments()
89 @launchlogger
90 def launch(self) -> int:
91 """Execute the :class:`TemplateContainer <template.template_container.TemplateContainer>` object."""
93 # 4. Setup Biobb
94 if self.check_restart():
95 return 0
96 self.stage_files()
98 # Creating temporary folder
99 self.tmp_folder = fu.create_unique_dir()
100 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
102 # 5. Prepare the command line parameters as instructions list
103 instructions = ['-j']
104 if self.boolean_property:
105 instructions.append('-v')
106 fu.log('Appending optional boolean property', self.out_log, self.global_log)
108 # 6. Build the actual command line as a list of items (elements order will be maintained)
109 self.cmd = [self.binary_path,
110 ' '.join(instructions),
111 self.stage_io_dict['out']['output_file_path'],
112 self.stage_io_dict['in']['input_file_path1']]
113 fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
115 # 7. Repeat for optional input files if provided
116 if self.stage_io_dict['in']['input_file_path2']:
117 # Append optional input_file_path2 to cmd
118 self.cmd.append(self.stage_io_dict['in']['input_file_path2'])
119 fu.log('Appending optional argument to command line', self.out_log, self.global_log)
121 # 8. Uncomment to check the command line
122 # print(' '.join(cmd))
124 # Run Biobb block
125 self.run_biobb()
127 # Copy files to host
128 self.copy_to_host()
130 # Remove temporary file(s)
131 self.tmp_files.extend([
132 self.stage_io_dict.get("unique_dir"),
133 self.tmp_folder
134 ])
135 self.remove_tmp_files()
137 # Check output arguments
138 self.check_arguments(output_files_created=True, raise_exception=False)
140 return self.return_code
143def template_container(input_file_path1: str, output_file_path: str, input_file_path2: str = None, properties: dict = None, **kwargs) -> int:
144 """Create :class:`TemplateContainer <template.template_container.TemplateContainer>` class and
145 execute the :meth:`launch() <template.template_container.TemplateContainer.launch>` method."""
147 return TemplateContainer(input_file_path1=input_file_path1,
148 output_file_path=output_file_path,
149 input_file_path2=input_file_path2,
150 properties=properties, **kwargs).launch()
153def main():
154 """Command line execution of this building block. Please check the command line documentation."""
155 parser = argparse.ArgumentParser(description='Description for the template container module.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
156 parser.add_argument('--config', required=False, help='Configuration file')
158 # 10. Include specific args of each building block following the examples. They should match step 2
159 required_args = parser.add_argument_group('required arguments')
160 required_args.add_argument('--input_file_path1', required=True, help='Description for the first input file path. Accepted formats: top.')
161 parser.add_argument('--input_file_path2', required=False, help='Description for the second input file path (optional). Accepted formats: dcd.')
162 required_args.add_argument('--output_file_path', required=True, help='Description for the output file path. Accepted formats: zip.')
164 args = parser.parse_args()
165 args.config = args.config or "{}"
166 properties = settings.ConfReader(config=args.config).get_prop_dic()
168 # 11. Adapt to match Class constructor (step 2)
169 # Specific call of each building block
170 template_container(input_file_path1=args.input_file_path1,
171 output_file_path=args.output_file_path,
172 input_file_path2=args.input_file_path2,
173 properties=properties)
176if __name__ == '__main__':
177 main()
179# 13. Complete documentation strings