Mercurial > repos > iuc > pangolin

comparison fetch_latest_pangolearn.py @ 6:437e28791761 draft

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"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f53dc92d3cf6997da9ad21f01ad3fd3477aae068"
author iuc
date Wed, 07 Jul 2021 09:24:31 +0000
parents f557122d379e
children
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equal deleted inserted replaced
5:42a174224817 6:437e28791761
1 #!/usr/bin/env python 1 #!/usr/bin/env python
2 2
3 import argparse
3 import json 4 import json
4 import os 5 import os
6 import sys
5 import tarfile 7 import tarfile
6 8
7 # rely on the fact that pangolin itself uses the requests module 9 # rely on the fact that pangolin itself uses the requests module
8 import requests 10 import requests
11 from requests.adapters import HTTPAdapter
9 12
10 response = requests.get( 13 parser = argparse.ArgumentParser(description='download latest pangoLEARN database')
11 "https://api.github.com/repos/cov-lineages/pangoLEARN/releases/latest" 14 parser.add_argument('--timeout', type=float, default=60.0, help="Timeout for connecting or downloading the pangoLEARN database (in seconds)")
12 ) 15 parser.add_argument('--max_retries', type=int, default=5, help="How many times to retry fetching the pangoLEARN database")
13 if response.status_code == 200: 16 args = parser.parse_args()
14 details = json.loads(response.text) 17
15 response = requests.get(details["tarball_url"]) 18 try:
19 s = requests.Session()
20 s.mount('https://', HTTPAdapter(max_retries=args.max_retries))
21 response = s.get(
22 "https://api.github.com/repos/cov-lineages/pangoLEARN/releases/latest"
23 )
16 if response.status_code == 200: 24 if response.status_code == 200:
17 with open("pangolearn.tgz", "wb") as handle: 25 details = json.loads(response.text)
18 handle.write(response.content) 26 response = s.get(details["tarball_url"], timeout=args.timeout)
19 tf = tarfile.open("pangolearn.tgz") 27 if response.status_code == 200:
20 pl_path = tf.next().name 28 with open("pangolearn.tgz", "wb") as handle:
21 tf.extractall() 29 handle.write(response.content)
22 tf.close() 30 tf = tarfile.open("pangolearn.tgz")
23 os.rename(os.path.join(pl_path, "pangoLEARN"), "datadir") 31 pl_path = tf.next().name
32 tf.extractall()
33 tf.close()
34 os.rename(os.path.join(pl_path, "pangoLEARN"), "datadir")
35 else:
36 response.raise_for_status()
24 else: 37 else:
25 response.raise_for_status() 38 response.raise_for_status()
26 else: 39 except (requests.ConnectionError, requests.HTTPError, requests.TooManyRedirects) as e:
27 response.raise_for_status() 40 sys.exit('Failed to download pangoLEARN database: {}'.format(e))
41 except requests.Timeout:
42 sys.exit('Timeout while trying to download pangoLEARN database')