Merge pull request #1426 from sorgerlab/robust-pubmed-client

Add more robust retry to the pubmed client's send_request

indra/literature/pubmed_client.py

@@ -2,6 +2,8 @@
 Search and get metadata for articles in Pubmed.
 """
 import logging
+import random
+
 import requests
 from time import sleep
 from typing import List
@@ -19,7 +21,7 @@
 
 # Send request can't be cached by lru_cache because it takes a dict
 # (a mutable/unhashable type) as an argument. We cache the callers instead.
-def send_request(url, data):
+def send_request(url, data, retry_pause=0.5, max_tries=3):
     try:
         res = requests.get(url, params=data)
     except requests.exceptions.Timeout as e:
@@ -32,9 +34,12 @@ def send_request(url, data):
         logger.error('url: %s, data: %s' % (url, data))
         logger.error(e)
         return None
-    if res.status_code == 429:
-        sleep(0.5)
-        res = requests.get(url, params=data)
+    if res.status_code in {429, 502, 503} and max_tries > 0:
+        sleep(retry_pause)
+        # Increase the sleep time at random to avoid multiple clients
+        # retrying at the same time for e.g. tests
+        retry_pause += 1 + random.random()
+        return send_request(url, data, retry_pause, max_tries - 1)
     if not res.status_code == 200:
         logger.error('Got return code %d from pubmed client.'
                      % res.status_code)

indra/tests/test_db_rest.py

@@ -1,4 +1,3 @@
-import random
 import unittest
 from datetime import datetime
 from time import sleep
@@ -58,23 +57,19 @@ def test_bigger_request():
 
 
 @pytest.mark.nonpublic
-def test_timeout_no_persist_agent():
-    candidates = ['TP53', 'NFkappaB@FPLX', 'AKT@FPLX']
-    agent = random.choice(candidates)
-    print(agent)
-    resp = dbr.get_statements(agents=[agent], persist=False, timeout=0)
+def test_timeout_no_persist_nfkb():
+    resp = dbr.get_statements(agents=["NFkappaB@FPLX"], persist=False, timeout=0)
     assert resp.is_working(), "Lookup resolved too fast."
     resp.wait_until_done(70)
     assert len(resp.statements) > 0.9*EXPECTED_BATCH_SIZE, len(resp.statements)
 
 
 @pytest.mark.nonpublic
 def test_timeout_no_persist_type_object():
-    candidates = ['TP53', 'NFkappaB@FPLX', 'AKT@FPLX']
-    agent = random.choice(candidates)
-    print(agent)
-    resp = dbr.get_statements(stmt_type='phosphorylation', object=agent,
-                              persist=False, timeout=0)
+    resp = dbr.get_statements(stmt_type='phosphorylation',
+                              object="NFkappaB@FPLX",
+                              persist=False,
+                              timeout=0)
     assert resp.is_working(), "Lookup resolved too fast."
     resp.wait_until_done(70)
     assert len(resp.statements) > 0.9*EXPECTED_BATCH_SIZE, len(resp.statements)