#!/usr/bin/env python3

"""Module containing the Cpptraj Rgyr class and the command line interface."""
import argparse
from biobb_common.configuration import  settings
from biobb_common.tools import file_utils as fu
from biobb_common.tools.file_utils import launchlogger
from biobb_common.command_wrapper import cmd_wrapper
from biobb_analysis.ambertools.common import *


class CpptrajRgyr():
    """Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.
    Wrapper of the Ambertools Cpptraj module.
    Cpptraj (the successor to ptraj) is the main program in Ambertools for processing coordinate trajectories and data files.
    The parameter names and defaults are the same as the ones in the official `Cpptraj manual <https://amber-md.github.io/cpptraj/CPPTRAJ.xhtml>`_.

   Args:
        input_top_path (str): Path to the input structure or topology file. File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.parm.top>`_. Accepted formats: top, pdb, prmtop, parmtop, zip.
        input_traj_path (str): Path to the input trajectory to be processed.  File type: input. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/data/ambertools/cpptraj.traj.dcd>`_. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.
        output_cpptraj_path (str): Path to the output analysis. File type: output. `Sample file <https://github.com/bioexcel/biobb_analysis/raw/master/biobb_analysis/test/reference/ambertools/ref_cpptraj.rgyr.dat>`_. Accepted formats: dat, agr, xmgr, gnu.
        properties (dic):
            * **in_parameters** (*dic*) - (None) Parameters for input trajectory.
                * **start** (*int*) - (1) Starting frame for slicing
                * **end** (*int*) - (-1) Ending frame for slicing
                * **step** (*int*) - (1) Step for slicing
                * **mask** (*str*) - ("all-atoms") Mask definition. Values: c-alpha, backbone, all-atoms, heavy-atoms, side-chain, solute, ions, solvent.
            * **cpptraj_path** (*str*) - ("cpptraj") Path to the cpptraj executable binary.
            * **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*) - ('afandiadib/ambertools:serial') 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.
    """

    def __init__(self, input_top_path, input_traj_path,
                 output_cpptraj_path, properties=None, **kwargs) -> None:
        properties = properties or {}

        # Input/Output files
        self.io_dict = { 
            "in": { "input_top_path": input_top_path, "input_traj_path": input_traj_path }, 
            "out": { "output_cpptraj_path": output_cpptraj_path } 
        }

        # Properties specific for BB
        self.instructions_file = get_default_value('instructions_file')
        self.properties = properties
        self.cpptraj_path = get_binary_path(properties, 'cpptraj_path')

        # container Specific
        self.container_path = properties.get('container_path')
        self.container_image = properties.get('container_image', 'afandiadib/ambertools:serial')
        self.container_volume_path = properties.get('container_volume_path', '/tmp')
        self.container_working_dir = properties.get('container_working_dir')
        self.container_user_id = properties.get('container_user_id')
        self.container_shell_path = properties.get('container_shell_path', '/bin/bash')

        # Properties common in all BB
        self.can_write_console_log = properties.get('can_write_console_log', True)
        self.global_log = properties.get('global_log', None)
        self.prefix = properties.get('prefix', None)
        self.step = properties.get('step', None)
        self.path = properties.get('path', '')
        self.remove_tmp = properties.get('remove_tmp', True)
        self.restart = properties.get('restart', False)

    def check_data_params(self, out_log, err_log):
        """ Checks all the input/output paths and parameters """
        self.io_dict["in"]["input_top_path"], self.input_top_path_orig = check_top_path(self.io_dict["in"]["input_top_path"], out_log, self.__class__.__name__)
        self.io_dict["in"]["input_traj_path"] = check_traj_path(self.io_dict["in"]["input_traj_path"], out_log, self.__class__.__name__)
        self.io_dict["out"]["output_cpptraj_path"] = check_out_path(self.io_dict["out"]["output_cpptraj_path"], out_log, self.__class__.__name__)
        self.in_parameters = get_parameters(self.properties, 'in_parameters', self.__class__.__name__, out_log)

    def create_instructions_file(self, container_io_dict, out_log, err_log):
        """Creates an input file using the properties file settings"""
        instructions_list = []
        # different path if container execution or not
        if self.container_path:
            self.instructions_file = str(PurePath(self.container_volume_path).joinpath(self.instructions_file))
        else:
            self.instructions_file = str(PurePath(fu.create_unique_dir()).joinpath(self.instructions_file))
        fu.create_name(prefix=self.prefix, step=self.step, name=self.instructions_file)

        # parm
        instructions_list.append('parm ' + container_io_dict["in"]["input_top_path"])

        # trajin
        in_params = get_in_parameters(self.in_parameters, out_log)
        instructions_list.append('trajin ' + container_io_dict["in"]["input_traj_path"] + ' ' + in_params)

        # Set up
        instructions_list += setup_structure(self)

        # mask
        mask = self.in_parameters.get('mask', '')
        if mask:
            strip_mask = get_negative_mask(mask, out_log)
            instructions_list.append('strip ' + strip_mask)

        # output
        instructions_list.append('radgyr time 1 out ' + container_io_dict["out"]["output_cpptraj_path"])

        # create .in file
        with open(self.instructions_file, 'w') as mdp:
            for line in instructions_list:
                mdp.write(line.strip() + '\n')

        return self.instructions_file

    @launchlogger
    def launch(self) -> int:
        """Launches the execution of the Ambertools cpptraj module."""
        
        # Get local loggers from launchlogger decorator
        out_log = getattr(self, 'out_log', None)
        err_log = getattr(self, 'err_log', None)

        # check input/output paths and parameters
        self.check_data_params(out_log, err_log)

        # Check the properties
        fu.check_properties(self, self.properties)

        if self.restart:
            output_file_list = [self.io_dict["out"]["output_cpptraj_path"]]
            if fu.check_complete_files(output_file_list):
                fu.log('Restart is enabled, this step: %s will the skipped' % self.step, out_log, self.global_log)
                return 0

        # copy inputs to container
        container_io_dict = fu.copy_to_container(self.container_path, self.container_volume_path, self.io_dict)

        # create instructions file
        self.create_instructions_file(container_io_dict, out_log, err_log) 

        # if container execution, copy intructions file to container
        if self.container_path:
            copy_instructions_file_to_container(self.instructions_file, container_io_dict['unique_dir'])

        # create cmd and launch execution
        cmd = [self.cpptraj_path, '-i', self.instructions_file]
        cmd = fu.create_cmd_line(cmd, container_path=self.container_path, 
                                 host_volume=container_io_dict.get("unique_dir"), 
                                 container_volume=self.container_volume_path, 
                                 container_working_dir=self.container_working_dir, 
                                 container_user_uid=self.container_user_id, 
                                 container_image=self.container_image, 
                                 container_shell_path=self.container_shell_path, 
                                 out_log=out_log, global_log=self.global_log)
        returncode = cmd_wrapper.CmdWrapper(cmd, out_log, err_log, self.global_log).launch()

        # copy output(s) to output(s) path(s) in case of container execution
        fu.copy_to_host(self.container_path, container_io_dict, self.io_dict)

        # remove temporary folder(s)
        tmp_files = [PurePath(self.instructions_file).parent]
        if self.container_path: tmp_files.append(container_io_dict['unique_dir'])
        remove_tmp_files(tmp_files, self.remove_tmp, out_log, self.input_top_path_orig, self.io_dict["in"]["input_top_path"])

        return returncode

def main():
    parser = argparse.ArgumentParser(description="Computes the radius of gyration (Rgyr) from a given cpptraj compatible trajectory.", formatter_class=lambda prog: argparse.RawTextHelpFormatter(prog, width=99999))
    parser.add_argument('--config', required=False, help='Configuration file')

    # Specific args of each building block
    required_args = parser.add_argument_group('required arguments')
    required_args.add_argument('--input_top_path', required=True, help='Path to the input structure or topology file. Accepted formats: top, pdb, prmtop, parmtop, zip.')
    required_args.add_argument('--input_traj_path', required=True, help='Path to the input trajectory to be processed. Accepted formats: crd, cdf, netcdf, restart, ncrestart, restartnc, dcd, charmm, cor, pdb, mol2, trr, gro, binpos, xtc, cif, arc, sqm, sdf, conflib.')
    required_args.add_argument('--output_cpptraj_path', required=True, help='Path to the output analysis.')

    args = parser.parse_args()
    args.config = args.config or "{}"
    properties = settings.ConfReader(config=args.config).get_prop_dic()

    # Specific call of each building block
    CpptrajRgyr(input_top_path=args.input_top_path, input_traj_path=args.input_traj_path, 
                output_cpptraj_path=args.output_cpptraj_path, 
                properties=properties).launch()

if __name__ == '__main__':
    main()