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EGA-archive / ega-download-client

A Python-based EGA download client
Apache License 2.0
94 stars 52 forks source link

filaled to download #145

Closed JianGuoZhou3 closed 2 years ago

JianGuoZhou3 commented 2 years ago 
(pyega3) [zhou@localhost EGA]$ pyega3 -cf ~/raid/EGA/zjg.zmu_credential_file.json files EGAD00001007575
[2022-03-11 05:04:48 +0800] 
[2022-03-11 05:04:48 +0800] pyEGA3 - EGA python client version 4.0.0 (https://github.com/EGA-archive/ega-download-client)
[2022-03-11 05:04:48 +0800] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly
[2022-03-11 05:04:48 +0800] Python version : 3.8.12
[2022-03-11 05:04:48 +0800] OS version : Linux #1 SMP Fri Jan 14 13:59:45 UTC 2022
[2022-03-11 05:04:48 +0800] Server URL: https://ega.ebi.ac.uk:8052/elixir/data
[2022-03-11 05:04:48 +0800] Session-Id: 3070537591

[2022-03-11 05:20:16 +0800] Invalid username, password or secret key - please check and retry. If problem persists contact helpdesk on helpdesk@ega-archive.org
Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 703, in urlopen
    httplib_response = self._make_request(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 386, in _make_request
    self._validate_conn(conn)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 1040, in _validate_conn
    conn.connect()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connection.py", line 416, in connect
    self.sock = ssl_wrap_socket(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
    ssl_sock = _ssl_wrap_socket_impl(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 500, in wrap_socket
    return self.sslsocket_class._create(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 1040, in _create
    self.do_handshake()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 1309, in do_handshake
    self._sslobj.do_handshake()
TimeoutError: [Errno 110] Connection timed out

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/adapters.py", line 440, in send
    resp = conn.urlopen(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 785, in urlopen
    retries = retries.increment(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/util/retry.py", line 550, in increment
    raise six.reraise(type(error), error, _stacktrace)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/packages/six.py", line 769, in reraise
    raise value.with_traceback(tb)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 703, in urlopen
    httplib_response = self._make_request(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 386, in _make_request
    self._validate_conn(conn)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connectionpool.py", line 1040, in _validate_conn
    conn.connect()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/connection.py", line 416, in connect
    self.sock = ssl_wrap_socket(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/util/ssl_.py", line 449, in ssl_wrap_socket
    ssl_sock = _ssl_wrap_socket_impl(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/urllib3/util/ssl_.py", line 493, in _ssl_wrap_socket_impl
    return ssl_context.wrap_socket(sock, server_hostname=server_hostname)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 500, in wrap_socket
    return self.sslsocket_class._create(
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 1040, in _create
    self.do_handshake()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/ssl.py", line 1309, in do_handshake
    self._sslobj.do_handshake()
urllib3.exceptions.ProtocolError: ('Connection aborted.', TimeoutError(110, 'Connection timed out'))

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/pyega3/libs/auth_client.py", line 35, in token
    r = requests.post(self.url, headers=headers, data=data)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/api.py", line 117, in post
    return request('post', url, data=data, json=json, **kwargs)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/api.py", line 61, in request
    return session.request(method=method, url=url, **kwargs)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/sessions.py", line 529, in request
    resp = self.send(prep, **send_kwargs)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/sessions.py", line 645, in send
    r = adapter.send(request, **kwargs)
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/adapters.py", line 501, in send
    raise ConnectionError(err, request=request)
requests.exceptions.ConnectionError: ('Connection aborted.', TimeoutError(110, 'Connection timed out'))

I confirmed my password and id are correlated, but still showed errors.

(pyega3) [zhou@localhost ~]$  openssl s_client -connect ega.ebi.ac.uk:8443
CONNECTED(00000003)

but 8052 is not working.....

openssl s_client -connect ega.ebi.ac.uk:8052

write:errno=110
---
no peer certificate available
---
No client certificate CA names sent
---
SSL handshake has read 0 bytes and written 315 bytes
Verification: OK
---
New, (NONE), Cipher is (NONE)
Secure Renegotiation IS NOT supported
alxm0182 commented 2 years ago

Hello,

I'm having a similar problem and receiving the same error:

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ pyega3 -cf APM_Credentials.json datasets [2022-03-14 10:51:18 -0500] [2022-03-14 10:51:18 -0500] pyEGA3 - EGA python client version 3.4.1 (https://github.com/EGA-archive/ega-download-client) [2022-03-14 10:51:18 -0500] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly [2022-03-14 10:51:18 -0500] Python version : 3.6.13 [2022-03-14 10:51:18 -0500] OS version : Linux #1 SMP Wed Jun 3 14:28:03 UTC 2020 [2022-03-14 10:51:18 -0500] Server URL: https://ega.ebi.ac.uk:8052/elixir/data [2022-03-14 10:51:18 -0500] Session-Id: 2968141525

Traceback (most recent call last):

File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 175, in _new_conn (self._dns_host, self.port), self.timeout, **extra_kw File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/connection.py", line 96, in create_connection raise err File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/connection.py", line 86, in create_connection sock.connect(sa) ConnectionRefusedError:` [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen chunked=chunked, File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 382, in _make_request self._validate_conn(conn) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn conn.connect() File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 358, in connect conn = self._new_conn() File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 187, in _new_conn self, "Failed to establish a new connection: %s" % e urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/adapters.py", line 449, in send timeout=timeout File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/retry.py", line 574, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8443): Max retries exceeded with url: /ega-openid-connect-server/token (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/bin/pyega3", line 8, in sys.exit(main()) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/pyega3/pyega3.py", line 646, in main token = get_token(credentials) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/pyega3/pyega3.py", line 140, in get_token r = requests.post(URL_AUTH, headers=headers, data=data) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/api.py", line 117, in post return request('post', url, data=data, json=json, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/sessions.py", line 542, in request resp = self.send(prep, send_kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/sessions.py", line 655, in send r = adapter.send(request, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8443): Max retries exceeded with url: /ega-openid-connect-server/token (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused',))

But instead of 8052 not working, 8443 is not working for me.

8052 ...

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ openssl s_client -connect ega.ebi.ac.uk:8052

CONNECTED(00000003)

8443 ...

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ openssl s_client -connect ega.ebi.ac.uk:8443

46912496921600:error:0200206F:system library:connect:Connection refused:crypto/bio/b_sock2.c:110: 46912496921600:error:2008A067:BIO routines:BIO_connect:connect error:crypto/bio/b_sock2.c:111: connect:errno=111

Any help would be greatly appreciated! Thank you!

JianGuoZhou3 commented 2 years ago

Hello,

I'm having a similar problem and receiving the same error:

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ pyega3 -cf APM_Credentials.json datasets [2022-03-14 10:51:18 -0500] [2022-03-14 10:51:18 -0500] pyEGA3 - EGA python client version 3.4.1 (https://github.com/EGA-archive/ega-download-client) [2022-03-14 10:51:18 -0500] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly [2022-03-14 10:51:18 -0500] Python version : 3.6.13 [2022-03-14 10:51:18 -0500] OS version : Linux #1 SMP Wed Jun 3 14:28:03 UTC 2020 [2022-03-14 10:51:18 -0500] Server URL: https://ega.ebi.ac.uk:8052/elixir/data [2022-03-14 10:51:18 -0500] Session-Id: 2968141525

Traceback (most recent call last):

File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 175, in _new_conn (self._dns_host, self.port), self.timeout, **extra_kw File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/connection.py", line 96, in create_connection raise err File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/connection.py", line 86, in create_connection sock.connect(sa) ConnectionRefusedError:` [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 706, in urlopen chunked=chunked, File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 382, in _make_request self._validate_conn(conn) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 1010, in _validate_conn conn.connect() File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 358, in connect conn = self._new_conn() File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connection.py", line 187, in _new_conn self, "Failed to establish a new connection: %s" % e urllib3.exceptions.NewConnectionError: <urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/adapters.py", line 449, in send timeout=timeout File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/connectionpool.py", line 756, in urlopen method, url, error=e, _pool=self, _stacktrace=sys.exc_info()[2] File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/urllib3/util/retry.py", line 574, in increment raise MaxRetryError(_pool, url, error or ResponseError(cause)) urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8443): Max retries exceeded with url: /ega-openid-connect-server/token (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused',))

During handling of the above exception, another exception occurred:

Traceback (most recent call last): File "/storage/hpc/data/apmfz5/Dissertation/EGA/bin/pyega3", line 8, in sys.exit(main()) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/pyega3/pyega3.py", line 646, in main token = get_token(credentials) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/pyega3/pyega3.py", line 140, in get_token r = requests.post(URL_AUTH, headers=headers, data=data) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/api.py", line 117, in post return request('post', url, data=data, json=json, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/api.py", line 61, in request return session.request(method=method, url=url, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/sessions.py", line 542, in request resp = self.send(prep, send_kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/sessions.py", line 655, in send r = adapter.send(request, kwargs) File "/storage/hpc/data/apmfz5/Dissertation/EGA/lib/python3.6/site-packages/requests/adapters.py", line 516, in send raise ConnectionError(e, request=request) requests.exceptions.ConnectionError: HTTPSConnectionPool(host='ega.ebi.ac.uk', port=8443): Max retries exceeded with url: /ega-openid-connect-server/token (Caused by NewConnectionError('<urllib3.connection.HTTPSConnection object at 0x2aaab3540588>: Failed to establish a new connection: [Errno 111] Connection refused',))

But instead of 8052 not working, 8443 is not working for me.

8052 ...

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ openssl s_client -connect ega.ebi.ac.uk:8052

CONNECTED(00000003)

8443 ...

(EGA)[apmfz5@lewis4-r630-login-node675 EGA_dc]$ openssl s_client -connect ega.ebi.ac.uk:8443

46912496921600:error:0200206F:system library:connect:Connection refused:crypto/bio/b_sock2.c:110: 46912496921600:error:2008A067:BIO routines:BIO_connect:connect error:crypto/bio/b_sock2.c:111: connect:errno=111

Any help would be greatly appreciated! Thank you!

Hi @alxm0182 I found the official web shared the news: "Our download client is currently down and we are working as hard as possible to resolve the issue. Please refrain from creating tickets for download issues at this time. When this banner is removed, normal download services will be resumed.

Thank you for patience and understanding. EGA Team.” So please waiting for the EGA Team!

alxm0182 commented 2 years ago

@jianguozhouzunyimedicaluniversity ah, thank you for the update! Hopefully it will be back online soon!

malloryfreeberg commented 2 years ago

Hi @jianguozhouzunyimedicaluniversity . Thank you for reporting this issue. Indeed, our service has been down recently. You should be able to try again now. If you continue to experience this - or another issue - please email the EGA Helpdesk at helpdesk@ega-archive.org with this issue and attach the output log produced by pyega3 (pyega3_output.log). The Helpdesk team can then provide further assistance. Thank you.

JianGuoZhou3 commented 2 years ago

Hi @malloryfreeberg still error....

(base) [zhou@localhost ~]$ conda activate pyega3 
(pyega3) [zhou@localhost ~]$  openssl s_client -connect ega.ebi.ac.uk:8443
CONNECTED(00000003)
depth=2 C = BM, O = QuoVadis Limited, CN = QuoVadis Root CA 2 G3
verify return:1
depth=1 C = NL, O = QuoVadis Trustlink B.V., CN = QuoVadis Europe EV SSL CA G1
verify return:1
depth=0 jurisdictionC = GB, businessCategory = Government Entity, serialNumber = Government Entity, C = GB, ST = Essex, L = Saffron Walden, O = European Bioinformatics Institute, CN = ega.ebi.ac.uk
verify return:1
---
Certificate chain
 0 s:jurisdictionC = GB, businessCategory = Government Entity, serialNumber = Government Entity, C = GB, ST = Essex, L = Saffron Walden, O = European Bioinformatics Institute, CN = ega.ebi.ac.uk
   i:C = NL, O = QuoVadis Trustlink B.V., CN = QuoVadis Europe EV SSL CA G1
 1 s:C = NL, O = QuoVadis Trustlink B.V., CN = QuoVadis Europe EV SSL CA G1
   i:C = BM, O = QuoVadis Limited, CN = QuoVadis Root CA 2 G3
 2 s:C = BM, O = QuoVadis Limited, CN = QuoVadis Root CA 2 G3
   i:C = BM, O = QuoVadis Limited, CN = QuoVadis Root CA 2 G3
---
Server certificate
-----BEGIN CERTIFICATE-----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-----END CERTIFICATE-----
subject=jurisdictionC = GB, businessCategory = Government Entity, serialNumber = Government Entity, C = GB, ST = Essex, L = Saffron Walden, O = European Bioinformatics Institute, CN = ega.ebi.ac.uk

issuer=C = NL, O = QuoVadis Trustlink B.V., CN = QuoVadis Europe EV SSL CA G1

---
No client certificate CA names sent
Peer signing digest: SHA256
Peer signature type: RSA
Server Temp Key: ECDH, P-256, 256 bits
---
SSL handshake has read 5659 bytes and written 441 bytes
Verification: OK
---
New, TLSv1.2, Cipher is ECDHE-RSA-AES128-GCM-SHA256
Server public key is 2048 bit
Secure Renegotiation IS supported
Compression: NONE
Expansion: NONE
No ALPN negotiated
SSL-Session:
    Protocol  : TLSv1.2
    Cipher    : ECDHE-RSA-AES128-GCM-SHA256
    Session-ID: 7A90BCEB4E54B04E62586673B49D58D04ECE30A3068B360770CD0661862DA8E7
    Session-ID-ctx: 
    Master-Key: 8D8E37C75F68B474610A15009D8A4D0461A616E189579198A64857B28D645043AD58FE276A49DB580505CA14F0297DF5
    PSK identity: None
    PSK identity hint: None
    SRP username: None
    Start Time: 1647449650
    Timeout   : 7200 (sec)
    Verify return code: 0 (ok)
    Extended master secret: yes
---
openssl s_client -connect ega.ebi.ac.uk:8052
HTTP/1.1 400 Bad Request
Server: nginx/1.17.10
Date: Wed, 16 Mar 2022 16:56:16 GMT
Content-Type: text/html
Content-Length: 158
Connection: close

<html>
<head><title>400 Bad Request</title></head>
<body>
<center><h1>400 Bad Request</h1></center>
<hr><center>nginx/1.17.10</center>
</body>
</html>
read:errno=0
(pyega3) [zhou@localhost ~]$ 
(pyega3) [zhou@localhost ~]$ 
(pyega3) [zhou@localhost ~]$ 
(pyega3) [zhou@localhost ~]$ 
(pyega3) [zhou@localhost ~]$  pyega3 -cf ~/raid/EGA/zjg.zmu_credential_file.json datasets
[2022-03-17 00:56:35 +0800] 
[2022-03-17 00:56:35 +0800] pyEGA3 - EGA python client version 4.0.0 (https://github.com/EGA-archive/ega-download-client)
[2022-03-17 00:56:35 +0800] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly
[2022-03-17 00:56:35 +0800] Python version : 3.8.12
[2022-03-17 00:56:35 +0800] OS version : Linux #1 SMP Fri Jan 14 13:59:45 UTC 2022
[2022-03-17 00:56:35 +0800] Server URL: https://ega.ebi.ac.uk:8052/elixir/data
[2022-03-17 00:56:35 +0800] Session-Id: 1880068365

[2022-03-17 00:56:37 +0800] 
[2022-03-17 00:56:37 +0800] Invalid username, password or secret key - please check and retry. If problem persists contact helpdesk on helpdesk@ega-archive.org
Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/pyega3/libs/auth_client.py", line 38, in token
    r.raise_for_status()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/models.py", line 960, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error:  for url: https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token
malloryfreeberg commented 2 years ago

Hi @jianguozhouzunyimedicaluniversity

Are you able to run pyega3 with the test credentials: pyega3 -t datasets?

JianGuoZhou3 commented 2 years ago

@malloryfreeberg That's crazing....

(pyega3) [zhou@localhost ~]$  pyega3 -cf ~/raid/EGA/zjg.zmu_credential_file.json datasets
[2022-03-17 00:56:35 +0800] 
[2022-03-17 00:56:35 +0800] pyEGA3 - EGA python client version 4.0.0 (https://github.com/EGA-archive/ega-download-client)
[2022-03-17 00:56:35 +0800] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly
[2022-03-17 00:56:35 +0800] Python version : 3.8.12
[2022-03-17 00:56:35 +0800] OS version : Linux #1 SMP Fri Jan 14 13:59:45 UTC 2022
[2022-03-17 00:56:35 +0800] Server URL: https://ega.ebi.ac.uk:8052/elixir/data
[2022-03-17 00:56:35 +0800] Session-Id: 1880068365

[2022-03-17 00:56:37 +0800] 
[2022-03-17 00:56:37 +0800] Invalid username, password or secret key - please check and retry. If problem persists contact helpdesk on helpdesk@ega-archive.org
Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/pyega3/libs/auth_client.py", line 38, in token
    r.raise_for_status()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/models.py", line 960, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error:  for url: https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token
(pyega3) [zhou@localhost ~]$ 
(pyega3) [zhou@localhost ~]$ pyega3 -d -t datasets
[2022-03-17 01:40:30 +0800] 
[2022-03-17 01:40:30 +0800] pyEGA3 - EGA python client version 4.0.0 (https://github.com/EGA-archive/ega-download-client)
[2022-03-17 01:40:30 +0800] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly
[2022-03-17 01:40:30 +0800] Python version : 3.8.12
[2022-03-17 01:40:30 +0800] OS version : Linux #1 SMP Fri Jan 14 13:59:45 UTC 2022
[2022-03-17 01:40:30 +0800] Server URL: https://ega.ebi.ac.uk:8052/elixir/data
[2022-03-17 01:40:30 +0800] Session-Id: 2405447546
[2022-03-17 01:40:30 +0800] Starting new HTTPS connection (1): ipinfo.io:443
[2022-03-17 01:40:30 +0800] https://ipinfo.io:443 "GET /json HTTP/1.1" 200 None
[2022-03-17 01:40:30 +0800] Starting new HTTPS connection (1): ega.ebi.ac.uk:8443
[2022-03-17 01:40:34 +0800] https://ega.ebi.ac.uk:8443 "POST /ega-openid-connect-server/token HTTP/1.1" 200 None
[2022-03-17 01:40:34 +0800] 
[2022-03-17 01:40:34 +0800] Authentication success for user 'ega-test-data@ebi.ac.uk'
[2022-03-17 01:40:34 +0800] Starting new HTTPS connection (1): ega.ebi.ac.uk:8052
[2022-03-17 01:40:38 +0800] https://ega.ebi.ac.uk:8052 "GET /elixir/data/metadata/datasets HTTP/1.1" 200 None
[2022-03-17 01:40:38 +0800] Request URL : https://ega.ebi.ac.uk:8052/elixir/data/metadata/datasets
[2022-03-17 01:40:38 +0800] Response    :
 [
    "EGAD00001003338",
    "EGAD00001006673"
]
[2022-03-17 01:40:38 +0800] Dataset ID
[2022-03-17 01:40:38 +0800] -----------------
[2022-03-17 01:40:38 +0800] EGAD00001003338
[2022-03-17 01:40:38 +0800] EGAD00001006673

BUT my password and id did not change anymore.

JianGuoZhou3 commented 2 years ago 
(pyega3) [zhou@localhost STAR]$ pyega3 -cf ~/raid/EGA/zjg.zmu_credential_file.json datasets
[2022-03-18 04:30:29 +0800] 
[2022-03-18 04:30:29 +0800] pyEGA3 - EGA python client version 4.0.0 (https://github.com/EGA-archive/ega-download-client)
[2022-03-18 04:30:29 +0800] Parts of this software are derived from pyEGA (https://github.com/blachlylab/pyega) by James Blachly
[2022-03-18 04:30:29 +0800] Python version : 3.8.12
[2022-03-18 04:30:29 +0800] OS version : Linux #1 SMP Fri Jan 14 13:59:45 UTC 2022
[2022-03-18 04:30:29 +0800] Server URL: https://ega.ebi.ac.uk:8052/elixir/data
[2022-03-18 04:30:29 +0800] Session-Id: 1207189894
[2022-03-18 04:30:30 +0800] 
[2022-03-18 04:30:30 +0800] Invalid username, password or secret key - please check and retry. If problem persists contact helpdesk on helpdesk@ega-archive.org
Traceback (most recent call last):
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/pyega3/libs/auth_client.py", line 38, in token
    r.raise_for_status()
  File "/home/zhou/miniconda2/envs/pyega3/lib/python3.8/site-packages/requests/models.py", line 960, in raise_for_status
    raise HTTPError(http_error_msg, response=self)
requests.exceptions.HTTPError: 500 Server Error:  for url: https://ega.ebi.ac.uk:8443/ega-openid-connect-server/token
malloryfreeberg commented 2 years ago

Hi @jianguozhouzunyimedicaluniversity. Please email the EGA Helpdesk at helpdesk@ega-archive.org with this issue and attach the output log produced by pyega3 (pyega3_output.log). The Helpdesk team can then provide further assistance for your specific account. Thank you.