#!/usr/bin/env python

import argparse
import importlib.util
import logging
import os
from pathlib import Path
import sys
import time
import types

import pandas as pd
import requests


def main(username: str, password: str):
    dataset_root_dir = Path(__file__).resolve().parent.parent

    # import dataset loader script to access its functions
    phytozome_genomes_spec = importlib.util.spec_from_file_location('phytozome_genomes', dataset_root_dir / 'phytozome_genomes.py')
    phytozome_genomes = importlib.util.module_from_spec(phytozome_genomes_spec)
    sys.modules['phytozome_genomes'] = phytozome_genomes
    phytozome_genomes_spec.loader.exec_module(phytozome_genomes)

    genomes = pd.read_table(
        dataset_root_dir / 'genomes.tsv',
        index_col = 'id'
    )
    
    jgi_session = phytozome_genomes.create_JGI_session(username = username, password = password)
    for jamo_id in genomes.index.to_list():
        time.sleep(0.5)
        with jgi_session.get(f"https://files.jgi.doe.gov/download_files/{jamo_id}", stream = True) as response:
            if response.status_code == requests.codes.conflict:
                print(f"File '{jamo_id}' has been requested from the tape archive; please check again in 24 hours.")
            else:
                print(f"File '{jamo_id}' is already restored, nothing to be done.")
    jgi_session.close()


if __name__ == '__main__':
    parser = argparse.ArgumentParser(
        description = 'Requests all files in dataset to be pulled from Phytozome tape archives if they are not already restored'
    )

    parser.add_argument(
        '--username',
        help = 'JGI username (overrides JGI_USERNAME environment variable)'
    )

    parser.add_argument(
        '--password',
        help = 'JGI password (overrides JGI_PASSWORD environment variable)'
    )

    args = parser.parse_args()

    if args.username is None:
        if 'JGI_USERNAME' in os.environ:
            args.username = os.environ['JGI_USERNAME']
        else:
            logging.error('Either pass a JGI username with --username or by setting the JGI_USERNAME environment variable')
            parser.print_usage(sys.stderr)
            sys.exit(1)

    if args.password is None:
        if 'JGI_PASSWORD' in os.environ:
            args.password = os.environ['JGI_PASSWORD']
        else:
            logging.error('Either set the JGI_PASSWORD environment variable or pass a JGI password using --password (not recommended)')
            parser.print_usage(sys.stderr)
            sys.exit(1)

    main(username = args.username, password = args.password)