Describe the bug
When I download a GEO data, I find the Openssl issue, how to fix it? thanks
Traceback (most recent call last):
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request
self._validate_conn(conn)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1096, in _validate_conn
conn.connect()
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connection.py", line 642, in connect
sock_and_verified = _ssl_wrap_socket_and_match_hostname(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connection.py", line 782, in _ssl_wrap_socket_and_match_hostname
ssl_sock = ssl_wrap_socket(
File "/home/sheep_1217/miniconda3/envs/10xenv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 470, in ssl_wrap_socket
ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname)
File "/home/sheep_1217/miniconda3/envs/10xenv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 514, in _ssl_wrap_socket_impl
return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 513, in wrap_socket
return self.sslsocket_class._create(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 1104, in _create
self.do_handshake()
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 1375, in do_handshake
self._sslobj.do_handshake()
ssl.SSLEOFError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 790, in urlopen
response = self._make_request(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request
raise new_e
urllib3.exceptions.SSLError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/adapters.py", line 486, in send
resp = conn.urlopen(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 844, in urlopen
retries = retries.increment(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/util/retry.py", line 515, in increment
raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type]
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/esummary.fcgi?db=sra&usehistory=n&retmode=json&query_key=1&WebEnv=MCID_65a1f2ca2e77e108540d52bb&retstart=0&retmax=500 (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/sheep_1217/miniconda3/envs/10x_env/bin/pysradb", line 10, in
sys.exit(parse_args())
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/cli.py", line 1181, in parse_args
download(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/cli.py", line 114, in download
metadata = sradb.sra_metadata(srp_x, detailed=True)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/sraweb.py", line 415, in sra_metadata
esummary_result = self.get_esummary_response("sra", srp)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/sraweb.py", line 298, in get_esummary_response
request = requests.get(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, send_kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/esummary.fcgi?db=sra&usehistory=n&retmode=json&query_key=1&WebEnv=MCID_65a1f2ca2e77e108540d52bb&retstart=0&retmax=500 (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)')))
To Reproduce
Steps to reproduce the behavior:
pysradb download -y -t 8 --out-dir /home/sheep_1217/SRP363708/1.sra -p SRP363708
Desktop (please complete the following information):
Describe the bug When I download a GEO data, I find the Openssl issue, how to fix it? thanks Traceback (most recent call last): File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 467, in _make_request self._validate_conn(conn) File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 1096, in _validate_conn conn.connect() File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connection.py", line 642, in connect sock_and_verified = _ssl_wrap_socket_and_match_hostname( File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connection.py", line 782, in _ssl_wrap_socket_and_match_hostname ssl_sock = ssl_wrap_socket( File "/home/sheep_1217/miniconda3/envs/10xenv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 470, in ssl_wrap_socket ssl_sock = _ssl_wrap_socket_impl(sock, context, tls_in_tls, server_hostname) File "/home/sheep_1217/miniconda3/envs/10xenv/lib/python3.10/site-packages/urllib3/util/ssl.py", line 514, in _ssl_wrap_socket_impl return ssl_context.wrap_socket(sock, server_hostname=server_hostname) File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 513, in wrap_socket return self.sslsocket_class._create( File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 1104, in _create self.do_handshake() File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/ssl.py", line 1375, in do_handshake self._sslobj.do_handshake() ssl.SSLEOFError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 790, in urlopen response = self._make_request( File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 491, in _make_request raise new_e urllib3.exceptions.SSLError: [SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/adapters.py", line 486, in send resp = conn.urlopen( File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/connectionpool.py", line 844, in urlopen retries = retries.increment( File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/urllib3/util/retry.py", line 515, in increment raise MaxRetryError(_pool, url, reason) from reason # type: ignore[arg-type] urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/esummary.fcgi?db=sra&usehistory=n&retmode=json&query_key=1&WebEnv=MCID_65a1f2ca2e77e108540d52bb&retstart=0&retmax=500 (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)')))
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/home/sheep_1217/miniconda3/envs/10x_env/bin/pysradb", line 10, in
sys.exit(parse_args())
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/cli.py", line 1181, in parse_args
download(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/cli.py", line 114, in download
metadata = sradb.sra_metadata(srp_x, detailed=True)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/sraweb.py", line 415, in sra_metadata
esummary_result = self.get_esummary_response("sra", srp)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/pysradb/sraweb.py", line 298, in get_esummary_response
request = requests.get(
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/api.py", line 73, in get
return request("get", url, params=params, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/api.py", line 59, in request
return session.request(method=method, url=url, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/sessions.py", line 589, in request
resp = self.send(prep, send_kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/sessions.py", line 703, in send
r = adapter.send(request, kwargs)
File "/home/sheep_1217/miniconda3/envs/10x_env/lib/python3.10/site-packages/requests/adapters.py", line 517, in send
raise SSLError(e, request=request)
requests.exceptions.SSLError: HTTPSConnectionPool(host='eutils.ncbi.nlm.nih.gov', port=443): Max retries exceeded with url: /entrez/eutils/esummary.fcgi?db=sra&usehistory=n&retmode=json&query_key=1&WebEnv=MCID_65a1f2ca2e77e108540d52bb&retstart=0&retmax=500 (Caused by SSLError(SSLEOFError(8, '[SSL: UNEXPECTED_EOF_WHILE_READING] EOF occurred in violation of protocol (_ssl.c:1007)')))
To Reproduce Steps to reproduce the behavior: pysradb download -y -t 8 --out-dir /home/sheep_1217/SRP363708/1.sra -p SRP363708
Desktop (please complete the following information):