#!/usr/bin/env python3

"""Module containing the MakeNdx class and the command line interface."""
from typing import Optional
from pathlib import Path
from biobb_common.generic.biobb_object import BiobbObject
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_gromacs.gromacs.common import get_gromacs_version


class MakeNdx(BiobbObject):
    """
    | biobb_gromacs MakeNdx
    | Wrapper of the `GROMACS make_ndx <http://manual.gromacs.org/current/onlinehelp/gmx-make_ndx.html>`_ module.
    | The GROMACS make_ndx module, generates an index file using the atoms of the selection.

    Args:
        input_structure_path (str): Path to the input GRO/PDB/TPR file. File type: input. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/data/gromacs/make_ndx.tpr>`_. Accepted formats: gro (edam:format_2033), pdb (edam:format_1476), tpr (edam:format_2333).
        output_ndx_path (str): Path to the output index NDX file. File type: output. `Sample file <https://github.com/bioexcel/biobb_gromacs/raw/master/biobb_gromacs/test/reference/gromacs/ref_make_ndx.ndx>`_. Accepted formats: ndx (edam:format_2033).
        input_ndx_path (str) (Optional): Path to the input index NDX file. File type: input. Accepted formats: ndx (edam:format_2033).
        properties (dict - Python dictionary object containing the tool parameters, not input/output files):
            * **selection** (*str*) - ("a CA C N O") Heavy atoms. Atom selection string.
            * **gmx_lib** (*str*) - (None) Path set GROMACS GMXLIB environment variable.
            * **binary_path** (*str*) - ("gmx") Path to the GROMACS executable binary.
            * **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.
            * **container_path** (*str*) - (None)  Path to the binary executable of your container.
            * **container_image** (*str*) - ("gromacs/gromacs:latest") Container Image identifier.
            * **container_volume_path** (*str*) - ("/data") Path to an internal directory in the container.
            * **container_working_dir** (*str*) - (None) Path to the internal CWD in the container.
            * **container_user_id** (*str*) - (None) User number id to be mapped inside the container.
            * **container_shell_path** (*str*) - ("/bin/bash") Path to the binary executable of the container shell.

    Examples:
        This is a use example of how to use the building block from Python::

            from biobb_gromacs.gromacs.make_ndx import make_ndx
            prop = { 'selection': 'a CA C N O' }
            make_ndx(input_structure_path='/path/to/myStructure.gro',
                     output_ndx_path='/path/to/newIndex.ndx',
                     properties=prop)

    Info:
        * wrapped_software:
            * name: GROMACS MakeNdx
            * version: 2025.2
            * license: LGPL 2.1
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl
    """

    def __init__(self, input_structure_path: str, output_ndx_path: str, input_ndx_path: Optional[str] = None,
                 properties: Optional[dict] = 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 = {
            "in": {"input_structure_path": input_structure_path, "input_ndx_path": input_ndx_path},
            "out": {"output_ndx_path": output_ndx_path}
        }

        # Properties specific for BB
        self.binary_path = properties.get('binary_path', 'gmx')
        self.selection = properties.get('selection', "a CA C N O")

        # Properties common in all GROMACS BB
        self.gmx_lib = properties.get('gmx_lib', None)
        self.gmx_nobackup = properties.get('gmx_nobackup', True)
        self.gmx_nocopyright = properties.get('gmx_nocopyright', True)
        if self.gmx_nobackup:
            self.binary_path += ' -nobackup'
        if self.gmx_nocopyright:
            self.binary_path += ' -nocopyright'
        if not self.container_path:
            self.gmx_version = get_gromacs_version(self.binary_path)

        # Check the properties
        self.check_properties(properties)
        self.check_arguments()

    @launchlogger
    def launch(self) -> int:
        """Execute the :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` object."""

        # Setup Biobb
        if self.check_restart():
            return 0

        self.selection = self.selection.replace("\\n", "\n")
        self.io_dict['in']['stdin_file_path'] = fu.create_stdin_file(f'{self.selection}\nq\n')
        self.stage_files()

        # Create command line
        self.cmd = [self.binary_path, 'make_ndx',
                    '-f', self.stage_io_dict["in"]["input_structure_path"],
                    '-o', self.stage_io_dict["out"]["output_ndx_path"]]

        if self.stage_io_dict["in"].get("input_ndx_path")\
                and Path(self.stage_io_dict["in"].get("input_ndx_path")).exists():
            self.cmd.append('-n')
            self.cmd.append(self.stage_io_dict["in"].get("input_ndx_path"))

        # Add stdin input file
        self.cmd.append('<')
        self.cmd.append(self.stage_io_dict["in"]["stdin_file_path"])

        if self.gmx_lib:
            self.env_vars_dict['GMXLIB'] = self.gmx_lib

        # create_cmd_line and execute_command
        self.run_biobb()

        # Retrieve results
        self.copy_to_host()

        # Remove temporal files
        self.tmp_files.append(self.io_dict['in'].get("stdin_file_path", ''))
        self.remove_tmp_files()

        self.check_arguments(output_files_created=True, raise_exception=False)
        return self.return_code


def make_ndx(input_structure_path: str, output_ndx_path: str,
             input_ndx_path: Optional[str] = None, properties: Optional[dict] = None, **kwargs) -> int:
    """Create :class:`MakeNdx <gromacs.make_ndx.MakeNdx>` class and
    execute the :meth:`launch() <gromacs.make_ndx.MakeNdx.launch>` method."""
    return MakeNdx(**dict(locals())).launch()


make_ndx.__doc__ = MakeNdx.__doc__
main = MakeNdx.get_main(make_ndx, "Wrapper for the GROMACS make_ndx module.")


if __name__ == '__main__':
    main()
