1 files changed, 75 insertions, 0 deletions
diff --git a/clnindexdl.py b/clnindexdl.py
new file mode 100755
index 0000000..5b1f537
--- /dev/null
+++ b/clnindexdl.py
@@ -0,0 +1,75 @@
+#!/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
+
+	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'[{filepath}] : 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()