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import pandas as pd
import numpy as np
from chembl_webresource_client.new_client import new_client
from rdkit import Chem
from rdkit.Chem import Draw
from time import sleep
[...]
for smile in SMILES:
tmp = pd.DataFrame()
tmp['SMILES'] = smile
records = similarity.filter(smiles=smile, similarity=70)
[...]
hmp2_hmdb_chembl = pd.concat([hmp2_hmdb_chembl, tmp]
sleep(10)
Unfortunately I ran across the dreaded urllib3 error SSLError: HTTPSConnectionPool. Now I cannot even run from chembl_webresource_client.new_client import new_client that I got this error thrown.
Error Traceback (most recent call last)
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py in wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname)
484 try:
--> 485 cnx.do_handshake()
486 except OpenSSL.SSL.WantReadError:
/home/cdsw/.local/lib/python3.6/site-packages/OpenSSL/SSL.py in do_handshake(self)
1914 result = _lib.SSL_do_handshake(self._ssl)
-> 1915 self._raise_ssl_error(self._ssl, result)
1916
/home/cdsw/.local/lib/python3.6/site-packages/OpenSSL/SSL.py in _raise_ssl_error(self, ssl, result)
1646 else:
-> 1647 _raise_current_error()
1648
/home/cdsw/.local/lib/python3.6/site-packages/OpenSSL/_util.py in exception_from_error_queue(exception_type)
53
---> 54 raise exception_type(errors)
55
Error: [('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')]
During handling of the above exception, another exception occurred:
SSLError Traceback (most recent call last)
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
661 if is_new_proxy_conn:
--> 662 self._prepare_proxy(conn)
663
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/connectionpool.py in _prepare_proxy(self, conn)
947 conn.set_tunnel(self._proxy_host, self.port, self.proxy_headers)
--> 948 conn.connect()
949
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/connection.py in connect(self)
393 server_hostname=server_hostname,
--> 394 ssl_context=context,
395 )
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/util/ssl_.py in ssl_wrap_socket(sock, keyfile, certfile, cert_reqs, ca_certs, server_hostname, ssl_version, ciphers, ssl_context, ca_cert_dir, key_password)
369 if HAS_SNI and server_hostname is not None:
--> 370 return context.wrap_socket(sock, server_hostname=server_hostname)
371
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/contrib/pyopenssl.py in wrap_socket(self, sock, server_side, do_handshake_on_connect, suppress_ragged_eofs, server_hostname)
490 except OpenSSL.SSL.Error as e:
--> 491 raise ssl.SSLError("bad handshake: %r" % e)
492 break
SSLError: ("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",)
During handling of the above exception, another exception occurred:
MaxRetryError Traceback (most recent call last)
/home/cdsw/.local/lib/python3.6/site-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
448 retries=self.max_retries,
--> 449 timeout=timeout
450 )
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/connectionpool.py in urlopen(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)
719 retries = retries.increment(
--> 720 method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2]
721 )
/home/cdsw/.local/lib/python3.6/site-packages/urllib3/util/retry.py in increment(self, method, url, response, error, _pool, _stacktrace)
435 if new_retry.is_exhausted():
--> 436 raise MaxRetryError(_pool, url, error or ResponseError(cause))
437
MaxRetryError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /chembl/api/data/spore (Caused by SSLError(SSLError("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",),))
During handling of the above exception, another exception occurred:
SSLError Traceback (most recent call last)
in engine
----> 1 from chembl_webresource_client.new_client import new_client
/home/cdsw/.local/lib/python3.6/site-packages/chembl_webresource_client/new_client.py in <module>()
65 #-----------------------------------------------------------------------------------------------------------------------
66
---> 67 new_client = client_from_url(Settings.Instance().NEW_CLIENT_URL + '/spore')
68
69 #-----------------------------------------------------------------------------------------------------------------------
/home/cdsw/.local/lib/python3.6/site-packages/chembl_webresource_client/new_client.py in client_from_url(url, base_url)
25
26 """
---> 27 res = requests.get(url)
28 if not res.ok:
29 raise Exception('Error getting schema from url {0} with status {1} and msg {2}'.format(url, res.status_code, res.text))
/home/cdsw/.local/lib/python3.6/site-packages/requests/api.py in get(url, params, **kwargs)
73
74 kwargs.setdefault('allow_redirects', True)
---> 75 return request('get', url, params=params, **kwargs)
76
77
/home/cdsw/.local/lib/python3.6/site-packages/requests/api.py in request(method, url, **kwargs)
58 # cases, and look like a memory leak in others.
59 with sessions.Session() as session:
---> 60 return session.request(method=method, url=url, **kwargs)
61
62
/home/cdsw/.local/lib/python3.6/site-packages/requests/sessions.py in request(self, method, url, params, data, headers, cookies, files, auth, timeout, allow_redirects, proxies, hooks, stream, verify, cert, json)
531 }
532 send_kwargs.update(settings)
--> 533 resp = self.send(prep, **send_kwargs)
534
535 return resp
/home/cdsw/.local/lib/python3.6/site-packages/requests/sessions.py in send(self, request, **kwargs)
644
645 # Send the request
--> 646 r = adapter.send(request, **kwargs)
647
648 # Total elapsed time of the request (approximately)
/home/cdsw/.local/lib/python3.6/site-packages/requests/adapters.py in send(self, request, stream, timeout, verify, cert, proxies)
512 if isinstance(e.reason, _SSLError):
513 # This branch is for urllib3 v1.22 and later.
--> 514 raise SSLError(e, request=request)
515
516 raise ConnectionError(e, request=request)
SSLError: HTTPSConnectionPool(host='www.ebi.ac.uk', port=443): Max retries exceeded with url: /chembl/api/data/spore (Caused by SSLError(SSLError("bad handshake: Error([('SSL routines', 'tls_process_server_certificate', 'certificate verify failed')],)",),))
I have used the same script months ago but without the similarity search (only identity search via SMILES string). Any idea on how to fix it? Rebooting, spawn new sessions or reinstalling urllib3 did not help. Similar to another thread I saw here, but in my case just waiting for a couple of days did not solve either.
Thanks
The text was updated successfully, but these errors were encountered:
Discovered some temporary files in the /home folder from sqlite. Deleting them solves mitigates the issue. I am able to rerun the script and import the web service, but I still get the error after a while. What is the limit of requests?
Hello,
I was trying to run similarity searches by using:
Unfortunately I ran across the dreaded urllib3 error
SSLError: HTTPSConnectionPool
. Now I cannot even runfrom chembl_webresource_client.new_client import new_client
that I got this error thrown.I have used the same script months ago but without the similarity search (only identity search via SMILES string). Any idea on how to fix it? Rebooting, spawn new sessions or reinstalling urllib3 did not help. Similar to another thread I saw here, but in my case just waiting for a couple of days did not solve either.
Thanks
The text was updated successfully, but these errors were encountered: