diff fetch_latest_pangolearn.py @ 6:437e28791761 draft

"planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/pangolin commit f53dc92d3cf6997da9ad21f01ad3fd3477aae068"

--- a/fetch_latest_pangolearn.py	Mon Jun 21 16:14:55 2021 +0000
+++ b/fetch_latest_pangolearn.py	Wed Jul 07 09:24:31 2021 +0000
@@ -1,27 +1,42 @@
 #!/usr/bin/env python
 
+import argparse
 import json
 import os
+import sys
 import tarfile
 
 # rely on the fact that pangolin itself uses the requests module
 import requests
+from requests.adapters import HTTPAdapter
 
-response = requests.get(
-    "https://api.github.com/repos/cov-lineages/pangoLEARN/releases/latest"
-)
-if response.status_code == 200:
-    details = json.loads(response.text)
-    response = requests.get(details["tarball_url"])
+parser = argparse.ArgumentParser(description='download latest pangoLEARN database')
+parser.add_argument('--timeout', type=float, default=60.0, help="Timeout for connecting or downloading the pangoLEARN database (in seconds)")
+parser.add_argument('--max_retries', type=int, default=5, help="How many times to retry fetching the pangoLEARN database")
+args = parser.parse_args()
+
+try:
+    s = requests.Session()
+    s.mount('https://', HTTPAdapter(max_retries=args.max_retries))
+    response = s.get(
+        "https://api.github.com/repos/cov-lineages/pangoLEARN/releases/latest"
+    )
     if response.status_code == 200:
-        with open("pangolearn.tgz", "wb") as handle:
-            handle.write(response.content)
-        tf = tarfile.open("pangolearn.tgz")
-        pl_path = tf.next().name
-        tf.extractall()
-        tf.close()
-        os.rename(os.path.join(pl_path, "pangoLEARN"), "datadir")
+        details = json.loads(response.text)
+        response = s.get(details["tarball_url"], timeout=args.timeout)
+        if response.status_code == 200:
+            with open("pangolearn.tgz", "wb") as handle:
+                handle.write(response.content)
+            tf = tarfile.open("pangolearn.tgz")
+            pl_path = tf.next().name
+            tf.extractall()
+            tf.close()
+            os.rename(os.path.join(pl_path, "pangoLEARN"), "datadir")
+        else:
+            response.raise_for_status()
     else:
         response.raise_for_status()
-else:
-    response.raise_for_status()
+except (requests.ConnectionError, requests.HTTPError, requests.TooManyRedirects) as e:
+    sys.exit('Failed to download pangoLEARN database: {}'.format(e))
+except requests.Timeout:
+    sys.exit('Timeout while trying to download pangoLEARN database')