#!/usr/bin/env python
"""Module containing the MemProtMDSimList class and the command line interface."""
from typing import Optional
from biobb_common.generic.biobb_object import BiobbObject
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_schema_validator.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.
* **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.
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: Optional[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(**dict(locals())).launch()
memprotmd_sim_list.__doc__ = MemProtMDSimList.__doc__
main = MemProtMDSimList.get_main(memprotmd_sim_list, "Wrapper for the MemProtMD DB REST API (http://memprotmd.bioch.ox.ac.uk/) to get all available membrane-protein systems (simulations).")
if __name__ == "__main__":
main()