#!/usr/bin/env python3
"""Module containing the TemplateContainer class and the command line interface."""
import argparse
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.configuration import settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
# 1. Rename class as required
[docs]class TemplateContainer(BiobbObject):
"""
| biobb_template TemplateContainer
| Short description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Mandatory.
| Long description for the `template container <http://templatedocumentation.org>`_ module in Restructured Text (reST) syntax. Optional.
Args:
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).
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).
output_file_path (str): Description for the output file path. File type: output. `Sample file <https://urlto.sample>`_. Accepted formats: zip (edam:format_3987).
properties (dic):
* **boolean_property** (*bool*) - (True) Example of boolean property.
* **binary_path** (*str*) - ("zip") Example of executable binary property.
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
* **container_path** (*str*) - (None) Container path definition.
* **container_image** (*str*) - ('mmbirb/zip:latest') Container image definition.
* **container_volume_path** (*str*) - ('/tmp') Container volume path definition.
* **container_working_dir** (*str*) - (None) Container working directory definition.
* **container_user_id** (*str*) - (None) Container user_id definition.
* **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.
Examples:
This is a use example of how to use the building block from Python::
from biobb_template.template.template_container import template_container
prop = {
'boolean_property': True,
'container_path': 'docker',
'container_image': 'mmbirb/zip:latest',
'container_volume_path': '/tmp'
}
template_container(input_file_path1='/path/to/myTopology.top',
output_file_path='/path/to/newCompressedFile.zip',
input_file_path2='/path/to/mytrajectory.dcd',
properties=prop)
Info:
* wrapped_software:
* name: Zip
* version: >=3.0
* license: BSD 3-Clause
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
# 2. Adapt input and output file paths as required. Include all files, even optional ones
def __init__(self, input_file_path1, output_file_path, input_file_path2=None, properties=None, **kwargs) -> None:
properties = properties or {}
# 2.0 Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# 2.1 Modify to match constructor parameters
# Input/Output files
self.io_dict = {
'in': {'input_file_path1': input_file_path1, 'input_file_path2': input_file_path2},
'out': {'output_file_path': output_file_path}
}
# 3. Include all relevant properties here as
# self.property_name = properties.get('property_name', property_default_value)
# Properties specific for BB
self.boolean_property = properties.get('boolean_property', True)
self.binary_path = properties.get('binary_path', 'zip')
self.properties = properties
# Check the properties
self.check_properties(properties)
# Check the arguments
self.check_arguments()
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`TemplateContainer <template.template_container.TemplateContainer>` object."""
# 4. Setup Biobb
if self.check_restart():
return 0
self.stage_files()
# Creating temporary folder
self.tmp_folder = fu.create_unique_dir()
fu.log('Creating %s temporary folder' % self.tmp_folder, self.out_log)
# 5. Prepare the command line parameters as instructions list
instructions = ['-j']
if self.boolean_property:
instructions.append('-v')
fu.log('Appending optional boolean property', self.out_log, self.global_log)
# 6. Build the actual command line as a list of items (elements order will be maintained)
self.cmd = [self.binary_path,
' '.join(instructions),
self.stage_io_dict['out']['output_file_path'],
self.stage_io_dict['in']['input_file_path1']]
fu.log('Creating command line with instructions and required arguments', self.out_log, self.global_log)
# 7. Repeat for optional input files if provided
if self.stage_io_dict['in']['input_file_path2']:
# Append optional input_file_path2 to cmd
self.cmd.append(self.stage_io_dict['in']['input_file_path2'])
fu.log('Appending optional argument to command line', self.out_log, self.global_log)
# 8. Uncomment to check the command line
# print(' '.join(cmd))
# Run Biobb block
self.run_biobb()
# Copy files to host
self.copy_to_host()
# Remove temporary file(s)
self.tmp_files.extend([
self.stage_io_dict.get("unique_dir"),
self.tmp_folder
])
self.remove_tmp_files()
# Check output arguments
self.check_arguments(output_files_created=True, raise_exception=False)
return self.return_code
[docs]def template_container(input_file_path1: str, output_file_path: str, input_file_path2: str = None, properties: dict = None, **kwargs) -> int:
"""Create :class:`TemplateContainer <template.template_container.TemplateContainer>` class and
execute the :meth:`launch() <template.template_container.TemplateContainer.launch>` method."""
return TemplateContainer(input_file_path1=input_file_path1,
output_file_path=output_file_path,
input_file_path2=input_file_path2,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description='Description for the template container module.', formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('--config', required=False, help='Configuration file')
# 10. Include specific args of each building block following the examples. They should match step 2
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('--input_file_path1', required=True, help='Description for the first input file path. Accepted formats: top.')
parser.add_argument('--input_file_path2', required=False, help='Description for the second input file path (optional). Accepted formats: dcd.')
required_args.add_argument('--output_file_path', required=True, help='Description for the output file path. Accepted formats: zip.')
args = parser.parse_args()
args.config = args.config or "{}"
properties = settings.ConfReader(config=args.config).get_prop_dic()
# 11. Adapt to match Class constructor (step 2)
# Specific call of each building block
template_container(input_file_path1=args.input_file_path1,
output_file_path=args.output_file_path,
input_file_path2=args.input_file_path2,
properties=properties)
if __name__ == '__main__':
main()
# 13. Complete documentation strings