Coverage for biobb_template / template / template.py: 91%
46 statements
« prev ^ index » next coverage.py v7.13.0, created at 2025-12-22 17:35 +0000
1#!/usr/bin/env python3
3"""Module containing the Template class and the command line interface."""
4import shutil
5from pathlib import PurePath
6from biobb_common.generic.biobb_object import BiobbObject
7from biobb_common.tools import file_utils as fu
8from biobb_common.tools.file_utils import launchlogger
11# 1. Rename class as required
12class Template(BiobbObject):
13 """
14 | biobb_template Template
15 | Short description for the `template <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Mandatory.
16 | Long description for the `template <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 * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
29 Examples:
30 This is a use example of how to use the building block from Python::
32 from biobb_template.template.template import template
34 prop = {
35 'boolean_property': True
36 }
37 template(input_file_path1='/path/to/myTopology.top',
38 output_file_path='/path/to/newCompressedFile.zip',
39 input_file_path2='/path/to/mytrajectory.dcd',
40 properties=prop)
42 Info:
43 * wrapped_software:
44 * name: Zip
45 * version: >=3.0
46 * license: BSD 3-Clause
47 * ontology:
48 * name: EDAM
49 * schema: http://edamontology.org/EDAM.owl
51 """
53 # 2. Adapt input and output file paths as required. Include all files, even optional ones
54 def __init__(self, input_file_path1, output_file_path, input_file_path2=None, properties=None, **kwargs) -> None:
55 properties = properties or {}
57 # 2.0 Call parent class constructor
58 super().__init__(properties)
59 self.locals_var_dict = locals().copy()
61 # 2.1 Modify to match constructor parameters
62 # Input/Output files
63 self.io_dict = {
64 'in': {'input_file_path1': input_file_path1, 'input_file_path2': input_file_path2},
65 'out': {'output_file_path': output_file_path}
66 }
68 # 3. Include all relevant properties here as
69 # self.property_name = properties.get('property_name', property_default_value)
71 # Properties specific for BB
72 self.boolean_property = properties.get('boolean_property', True)
73 self.binary_path = properties.get('binary_path', 'zip')
74 self.properties = properties
76 # Check the properties
77 self.check_properties(properties)
78 # Check the arguments
79 self.check_arguments()
81 @launchlogger
82 def launch(self) -> int:
83 """Execute the :class:`Template <template.template.Template>` object."""
85 # 4. Setup Biobb
86 if self.check_restart():
87 return 0
88 self.stage_files()
90 # Creating temporary folder
91 tmp_folder = fu.create_unique_dir()
92 fu.log('Creating %s temporary folder' % tmp_folder, self.out_log)
94 # 5. Include here all mandatory input files
95 # Copy input_file_path1 to temporary folder
96 shutil.copy(self.io_dict['in']['input_file_path1'], tmp_folder)
98 # 6. Prepare the command line parameters as instructions list
99 instructions = ['-j']
100 if self.boolean_property:
101 instructions.append('-v')
102 fu.log('Appending optional boolean property', self.out_log, self.global_log)
104 # 7. Build the actual command line as a list of items (elements order will be maintained)
105 self.cmd = [self.binary_path,
106 ' '.join(instructions),
107 self.io_dict['out']['output_file_path'],
108 str(PurePath(tmp_folder).joinpath(PurePath(self.io_dict['in']['input_file_path1']).name))]
109 fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
111 # 8. Repeat for optional input files if provided
112 if self.io_dict['in']['input_file_path2']:
113 # Copy input_file_path2 to temporary folder
114 shutil.copy(self.io_dict['in']['input_file_path2'], tmp_folder)
115 # Append optional input_file_path2 to cmd
116 self.cmd.append(str(PurePath(tmp_folder).joinpath(PurePath(self.io_dict['in']['input_file_path2']).name)))
117 fu.log('Appending optional argument to command line', self.out_log, self.global_log)
119 # 9. Uncomment to check the command line
120 # print(' '.join(cmd))
122 # Run Biobb block
123 self.run_biobb()
125 # Copy files to host
126 self.copy_to_host()
128 # Remove temporary file(s)
129 self.tmp_files.append(tmp_folder)
130 self.remove_tmp_files()
132 # Check output arguments
133 self.check_arguments(output_files_created=True, raise_exception=False)
135 return self.return_code
138def template(input_file_path1: str, output_file_path: str, input_file_path2: str = None, properties: dict = None, **kwargs) -> int:
139 """Create :class:`Template <template.template.Template>` class and
140 execute the :meth:`launch() <template.template.Template.launch>` method."""
141 return Template(**dict(locals())).launch()
144template.__doc__ = Template.__doc__
145main = Template.get_main(template, 'Description for the template module.')
148if __name__ == '__main__':
149 main()
151# 12. Complete documentation strings