Coverage for biobb_template / template / template_container.py: 26%
42 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-10 14:44 +0000
1#!/usr/bin/env python3
3"""Module containing the TemplateContainer class and the command line interface."""
4from biobb_common.generic.biobb_object import BiobbObject
5from biobb_common.tools import file_utils as fu
6from biobb_common.tools.file_utils import launchlogger
9# 1. Rename class as required
10class TemplateContainer(BiobbObject):
11 """
12 | biobb_template TemplateContainer
13 | Short description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Mandatory.
14 | Long description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Optional.
16 Args:
17 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).
18 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).
19 output_file_path (str): Description for the output file path. File type: output. `Sample file <https://urlto.sample>`_. Accepted formats: zip (edam:format_3987).
20 properties (dic):
21 * **boolean_property** (*bool*) - (True) Example of boolean property.
22 * **binary_path** (*str*) - ("zip") Example of executable binary property.
23 * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
24 * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
25 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
26 * **container_path** (*str*) - (None) Container path definition.
27 * **container_image** (*str*) - ('mmbirb/zip:latest') Container image definition.
28 * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
29 * **container_working_dir** (*str*) - (None) Container working directory definition.
30 * **container_user_id** (*str*) - (None) Container user_id definition.
31 * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
33 Examples:
34 This is a use example of how to use the building block from Python::
36 from biobb_template.template.template_container import template_container
38 prop = {
39 'boolean_property': True,
40 'container_path': 'docker',
41 'container_image': 'mmbirb/zip:latest',
42 'container_volume_path': '/tmp'
43 }
44 template_container(input_file_path1='/path/to/myTopology.top',
45 output_file_path='/path/to/newCompressedFile.zip',
46 input_file_path2='/path/to/mytrajectory.dcd',
47 properties=prop)
49 Info:
50 * wrapped_software:
51 * name: Zip
52 * version: >=3.0
53 * license: BSD 3-Clause
54 * ontology:
55 * name: EDAM
56 * schema: http://edamontology.org/EDAM.owl
58 """
60 # 2. Adapt input and output file paths as required. Include all files, even optional ones
61 def __init__(self, input_file_path1, output_file_path, input_file_path2=None, properties=None, **kwargs) -> None:
62 properties = properties or {}
64 # 2.0 Call parent class constructor
65 super().__init__(properties)
66 self.locals_var_dict = locals().copy()
68 # 2.1 Modify to match constructor parameters
69 # Input/Output files
70 self.io_dict = {
71 'in': {'input_file_path1': input_file_path1, 'input_file_path2': input_file_path2},
72 'out': {'output_file_path': output_file_path}
73 }
75 # 3. Include all relevant properties here as
76 # self.property_name = properties.get('property_name', property_default_value)
78 # Properties specific for BB
79 self.boolean_property = properties.get('boolean_property', True)
80 self.binary_path = properties.get('binary_path', 'zip')
81 self.properties = properties
83 # Check the properties
84 self.check_properties(properties)
85 # Check the arguments
86 self.check_arguments()
88 @launchlogger
89 def launch(self) -> int:
90 """Execute the :class:`TemplateContainer <template.template_container.TemplateContainer>` object."""
92 # 4. Setup Biobb
93 if self.check_restart():
94 return 0
95 self.stage_files()
97 # Creating temporary folder
98 self.tmp_folder = fu.create_unique_dir()
99 fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
101 # 5. Prepare the command line parameters as instructions list
102 instructions = ['-j']
103 if self.boolean_property:
104 instructions.append('-v')
105 fu.log('Appending optional boolean property', self.out_log, self.global_log)
107 # 6. Build the actual command line as a list of items (elements order will be maintained)
108 self.cmd = [self.binary_path,
109 ' '.join(instructions),
110 self.stage_io_dict['out']['output_file_path'],
111 self.stage_io_dict['in']['input_file_path1']]
112 fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
114 # 7. Repeat for optional input files if provided
115 if self.stage_io_dict['in']['input_file_path2']:
116 # Append optional input_file_path2 to cmd
117 self.cmd.append(self.stage_io_dict['in']['input_file_path2'])
118 fu.log('Appending optional argument to command line', self.out_log, self.global_log)
120 # 8. 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.append(self.tmp_folder)
131 self.remove_tmp_files()
133 # Check output arguments
134 self.check_arguments(output_files_created=True, raise_exception=False)
136 return self.return_code
139def template_container(input_file_path1: str, output_file_path: str, input_file_path2: str = None, properties: dict = None, **kwargs) -> int:
140 """Create :class:`TemplateContainer <template.template_container.TemplateContainer>` class and
141 execute the :meth:`launch() <template.template_container.TemplateContainer.launch>` method."""
142 return TemplateContainer(**dict(locals())).launch()
145template_container.__doc__ = TemplateContainer.__doc__
146main = TemplateContainer.get_main(template_container, 'Description for the template container module.')
149if __name__ == '__main__':
150 main()
152# 13. Complete documentation strings