#!/usr/bin/env python3

"""Module containing the Dendrogram class and the command line interface."""
import argparse
import pandas as pd
import matplotlib.pyplot as plt
import seaborn as sns
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
from biobb_ml.utils.common import check_input_path, check_output_path, getHeader, getIndependentVars


class Dendrogram(BiobbObject):
    """
    | biobb_ml Dendrogram
    | Generates a dendrogram from a given dataset.

    Args:
        input_dataset_path (str): Path to the input dataset. File type: input. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/data/utils/dataset_dendrogram.csv>`_. Accepted formats: csv (edam:format_3752).
        output_plot_path (str): Path to the dendrogram plot. File type: output. `Sample file <https://github.com/bioexcel/biobb_ml/raw/master/biobb_ml/test/reference/utils/ref_output_plot_dendrogram.png>`_. Accepted formats: png (edam:format_3603).
        properties (dic):
            * **features** (*dict*) - ({}) Independent variables or columns from your dataset you want to compare. You can specify either a list of columns names from your input dataset, a list of columns indexes or a range of columns indexes. Formats: { "columns": ["column1", "column2"] } or { "indexes": [0, 2, 3, 10, 11, 17] } or { "range": [[0, 20], [50, 102]] }. In case of mulitple formats, the first one will be picked.
            * **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_ml.utils.dendrogram import dendrogram
            prop = {
                'features': {
                    'columns': [ 'column1', 'column2', 'column3' ]
                }
            }
            dendrogram(input_dataset_path='/path/to/myDataset.csv',
                            output_plot_path='/path/to/newPlot.png',
                            properties=prop)

    Info:
        * wrapped_software:
            * name: In house
            * license: Apache-2.0
        * ontology:
            * name: EDAM
            * schema: http://edamontology.org/EDAM.owl

    """

    def __init__(self, input_dataset_path, output_plot_path,
                 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 = {
            "in": {"input_dataset_path": input_dataset_path},
            "out": {"output_plot_path": output_plot_path}
        }

        # Properties specific for BB
        self.features = properties.get('features', {})
        self.properties = properties

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

    def check_data_params(self, out_log, err_log):
        """ Checks all the input/output paths and parameters """
        self.io_dict["in"]["input_dataset_path"] = check_input_path(self.io_dict["in"]["input_dataset_path"], "input_dataset_path", out_log, self.__class__.__name__)
        self.io_dict["out"]["output_plot_path"] = check_output_path(self.io_dict["out"]["output_plot_path"], "output_plot_path", False, out_log, self.__class__.__name__)

    @launchlogger
    def launch(self) -> int:
        """Execute the :class:`Dendrogram <utils.dendrogram.Dendrogram>` utils.dendrogram.Dendrogram 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
        self.stage_files()

        # load dataset
        fu.log('Getting dataset from %s' % self.io_dict["in"]["input_dataset_path"], self.out_log, self.global_log)
        if 'columns' in self.features:
            labels = getHeader(self.io_dict["in"]["input_dataset_path"])
            skiprows = 1
        else:
            labels = None
            skiprows = None
        data = pd.read_csv(self.io_dict["in"]["input_dataset_path"], header=None, sep="\\s+|;|:|,|\t", engine="python", skiprows=skiprows, names=labels)

        if self.features:
            data = getIndependentVars(self.features, data, self.out_log, self.__class__.__name__)

        fu.log('Generating dendrogram', self.out_log, self.global_log)

        sns.clustermap(data, cmap='Blues')

        plt.savefig(self.io_dict["out"]["output_plot_path"], dpi=150)
        fu.log('Saving Dendrogram Plot to %s' % self.io_dict["out"]["output_plot_path"], self.out_log, self.global_log)

        # Copy files to host
        self.copy_to_host()

        self.tmp_files.extend([
            self.stage_io_dict.get("unique_dir")
        ])
        self.remove_tmp_files()

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

        return 0


def dendrogram(input_dataset_path: str, output_plot_path: str, properties: dict = None, **kwargs) -> int:
    """Execute the :class:`Dendrogram <utils.dendrogram.Dendrogram>` class and
    execute the :meth:`launch() <utils.dendrogram.Dendrogram.launch>` method."""

    return Dendrogram(input_dataset_path=input_dataset_path,
                      output_plot_path=output_plot_path,
                      properties=properties, **kwargs).launch()


def main():
    """Command line execution of this building block. Please check the command line documentation."""
    parser = argparse.ArgumentParser(description="Generates a dendrogram from a given dataset", 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_dataset_path', required=True, help='Path to the input dataset. Accepted formats: csv.')
    required_args.add_argument('--output_plot_path', required=True, help='Path to the dendrogram plot. Accepted formats: png.')

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

    # Specific call of each building block
    dendrogram(input_dataset_path=args.input_dataset_path,
               output_plot_path=args.output_plot_path,
               properties=properties)


if __name__ == '__main__':
    main()
