#!/usr/bin/env python
"""Module containing the MemProtMDSimList 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.file_utils import launchlogger
from biobb_io.api.common import check_output_path, get_memprotmd_sim_list, write_json
[docs]class MemProtMDSimList(BiobbObject):
"""
| biobb_io MemProtMDSimList
| This class is a wrapper of the MemProtMD to get all available membrane-protein systems from its REST API.
| Wrapper for the `MemProtMD DB REST API <http://memprotmd.bioch.ox.ac.uk/>`_ to get all available membrane-protein systems (simulations).
Args:
output_simulations (str): Path to the output JSON file. File type: output. `Sample file <https://github.com/bioexcel/biobb_io/raw/master/biobb_io/test/reference/api/output_sim_list.json>`_. Accepted formats: json (edam:format_3464).
properties (dic - Python dictionary object containing the tool parameters, not input/output files):
* **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.
* **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.
Examples:
This is a use example of how to use the building block from Python::
from biobb_io.api.memprotmd_sim_list import memprotmd_sim_list
prop = { }
memprotmd_sim_list(output_simulations='/path/to/newSimulationList.json',
properties=prop)
Info:
* wrapped_software:
* name: MemProtMD DB
* license: Creative Commons
* ontology:
* name: EDAM
* schema: http://edamontology.org/EDAM.owl
"""
def __init__(self, output_simulations,
properties=None, **kwargs) -> None:
properties = properties or {}
# Call parent class constructor
super().__init__(properties)
self.locals_var_dict = locals().copy()
# Input/Output files
self.io_dict = {
"out": {"output_simulations": output_simulations}
}
# Properties specific for BB
self.properties = properties
# Check the properties
self.check_properties(properties)
self.check_arguments()
[docs] def check_data_params(self, out_log, err_log):
""" Checks all the input/output paths and parameters """
self.output_simulations = check_output_path(self.io_dict["out"]["output_simulations"], "output_simulations", False, out_log, self.__class__.__name__)
[docs] @launchlogger
def launch(self) -> int:
"""Execute the :class:`MemProtMDSimList <api.memprotmd_sim_list.MemProtMDSimList>` api.memprotmd_sim_list.MemProtMDSimList object."""
# check input/output paths and parameters
self.check_data_params(self.out_log, self.err_log)
# Setup Biobb
if self.check_restart():
return 0
# get JSON object
json_string = get_memprotmd_sim_list(self.out_log, self.global_log)
# write JSON file
write_json(json_string, self.output_simulations, self.out_log, self.global_log)
self.check_arguments(output_files_created=True, raise_exception=False)
return 0
[docs]def memprotmd_sim_list(output_simulations: str, properties: dict = None, **kwargs) -> int:
"""Execute the :class:`MemProtMDSimList <api.memprotmd_sim_list.MemProtMDSimList>` class and
execute the :meth:`launch() <api.memprotmd_sim_list.MemProtMDSimList.launch>` method."""
return MemProtMDSimList(output_simulations=output_simulations,
properties=properties, **kwargs).launch()
[docs]def main():
"""Command line execution of this building block. Please check the command line documentation."""
parser = argparse.ArgumentParser(description="Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
parser.add_argument('-c', '--config', required=False, help="This file can be a YAML file, JSON file or JSON string")
# Specific args of each building block
required_args = parser.add_argument_group('required arguments')
required_args.add_argument('-o', '--output_simulations', required=True, help="Path to the output JSON file. Accepted formats: json.")
args = parser.parse_args()
config = args.config if args.config else None
properties = settings.ConfReader(config=config).get_prop_dic()
# Specific call of each building block
memprotmd_sim_list(output_simulations=args.output_simulations, properties=properties)
if __name__ == '__main__':
main()