import argparse

import os

import subprocess

import sys

import yaml

import papermill as pm

sys.path.append('.')

sys.path.append('..')

from pyMultiOmics.common import create_if_not_exist

def load_config_file(config_file):

    with open(config_file) as f:

        config = yaml.safe_load(f)

    return config

def main(args):

    # input excel

    input_excel = os.path.abspath(args.input_excel)

    print('Input Excel:', input_excel)

    # annotation CSV

    annot_csv = os.path.abspath(args.annot_csv)

    print('Annotation CSV:', annot_csv)

    # config file

    config_file = os.path.abspath(args.config_file)

    print('Config file:', config_file)

    processing_params = load_config_file(config_file)

    print('Pre-processing parameters:')

    print(yaml.dump(processing_params, indent=4))

    params = {}

    params['file_name'] = input_excel

    params['annot_csv'] = annot_csv

    params.update(processing_params)

    # output dir

    output_dir = os.path.abspath(args.output_dir)

    print('Output Directory:', output_dir)

    # Check if template file exists in parent directory

    template_parent_dir = os.path.abspath(os.path.join(os.path.dirname(__file__), '..'))

    template_file = os.path.abspath(

        os.path.join(template_parent_dir, 'templates', 'cic_template.ipynb'))

    if os.path.isfile(template_file):

        print('Template Notebook:', template_file)

    else:

        # Check if template file exists in current directory

        template_file = os.path.abspath(os.path.join('.', 'templates', 'cic_template.ipynb'))

        if os.path.isfile(template_file):

            print('Template Notebook:', template_file)

        else:

            print('Error: template notebook not found')

            return

    output_notebook = os.path.abspath(os.path.join(output_dir, 'cic_analysis.ipynb'))

    output_pdf = os.path.abspath(os.path.join(output_dir, 'cic_analysis.pdf'))

    print('Output Notebook:', output_notebook)

    print('Output PDF:', output_pdf)

    create_if_not_exist(output_dir)

    _ = pm.execute_notebook(template_file, output_notebook, report_mode=True, parameters=params)

    command = ['jupyter', 'nbconvert', '--TemplateExporter.exclude_input=True', '--output',

               output_pdf,

               '--to', 'pdf', output_notebook]

    result = subprocess.run(command, capture_output=True, text=True)

    if result.returncode == 0:

        print(f'\nPDF output saved to {output_pdf}\n')

    else:

        print(f'\nFailed to create PDF: {result.stderr}\n')

if __name__ == '__main__':

    print('***********************************')

    print('* CIC Analysis                    *')

    print('***********************************')

    print()

    parser = argparse.ArgumentParser(

        description='Runs a notebook-based analysis on input data and saves the results as a PDF.')

    parser.add_argument('--input_excel', required=True, help='Path to the input Excel file.')

    parser.add_argument('--annot_csv', required=True, help='Path to the annotation CSV file.')

    parser.add_argument('--output_dir', required=True, help='Path to the output directory.')

    parser.add_argument('--config_file', required=True, help='Path to the YAML configuration file.')

    args = parser.parse_args()

    main(args)