#!/bin/env python3

import csv
import subprocess
import sys
from pathlib import Path
from multiprocessing import Pool
import time

def md5sum(path):
	'''
		Compute MD5 message digest and return hex digest
	'''
	res = subprocess.run(['md5sum', path], capture_output=True, check=True)
	sums = str(res.stdout, encoding='ascii')

	if sums != '':
		return sums.split()[0]

def flatten_filename(ftp_url):
	'''
		Transform URL into a unique filename:

		ftp://domain.ext/some/path/read_file.gz -> some__path__read_file.gz
	'''
	_, ext = ftp_url.split('//')
	_, *path = ext.split('/')
	return '__'.join(path)

def wget_and_verify( ftp_url, md5, output_dir ):
	basename = flatten_filename(ftp_url)

	filename = output_dir / basename

	q = Path(filename)

	if q.exists():

		sums = md5sum(filename)

		if sums == md5:
			print(f'[{filename}] skipping already exists')
			return

	print(f'[{filename}] : starting download')

	retry = 0
	while retry < 3:
		out = subprocess.run(['curl', ftp_url, '--output', filename], capture_output=True)

		if out.returncode != 0:
			print(f'[{filename}] ERR: curl failed')

		sums = md5sum(filename)

		if sums != md5:
			retry += 1
			print(f'RETRY {retry}: ERR: checksum mismatch {sums} != {md5}', file=sys.stderr)
		else:
			print(f'[{filename}] : completed download')
			return

	print(f'ERR: MAXIMUM RETRIES EXCEEDED', file=sys.stderr)

def download_all_from_index( index, output_dir, threads ):

	reader = csv.DictReader( index, delimiter='\t' )

	with Pool(threads) as pool:
		res = []

		for files in reader:
			r = pool.apply_async(wget_and_verify, (files['FASTQ'], files['FASTQ_MD5'], output_dir))
			res.append(r)
			r = pool.apply_async(wget_and_verify, (files['PAIRED_FASTQ'], files['PAIRED_FASTQ_MD5'], output_dir))
			res.append(r)

		for r in res:
			r.get()