Scout: Unable to create General report (dowloading of PDF)

[KickiLagerstedt]

I tried yesterday and today and I get the same error message:

"Internal Server Error

The server encountered an internal error and was unable to complete your request. Either the server is overloaded or there is an error in the application."

Something wrong with my computer or something general??

[northwestwitch]

We've received some error messages from the server at this regard, I'll take a look as soon as I'm at the office.

[northwestwitch]

@ingkebil we are having some problems with scout that might be due to server settings, here's the error:

Traceback (most recent call last):
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/connectionpool.py", line 603, in urlopen
chunked=chunked)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/connectionpool.py", line 344, in _make_request
self._validate_conn(conn)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/connectionpool.py", line 843, in _validate_conn
conn.connect()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/connection.py", line 370, in connect
ssl_context=context)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/util/ssl_.py", line 355, in ssl_wrap_socket
return context.wrap_socket(sock, server_hostname=server_hostname)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/ssl.py", line 401, in wrap_socket
_context=self, _session=session)
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/ssl.py", line 808, in __init__
self.do_handshake()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/ssl.py", line 1061, in do_handshake
self._sslobj.do_handshake()
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/ssl.py", line 683, in do_handshake
self._sslobj.do_handshake()
ssl.SSLError: [SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:748)

During handling of the above exception, another exception occurred:

Traceback (most recent call last):
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/requests/adapters.py", line 449, in send
timeout=timeout
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/connectionpool.py", line 641, in urlopen
_stacktrace=sys.exc_info()[2])
File "/home/hiseq.clinical/miniconda/envs/prod/lib/python3.6/site-packages/urllib3/util/retry.py", line 399, in increment
raise MaxRetryError(_pool, url, error or ResponseError(cause))
urllib3.exceptions.MaxRetryError: HTTPSConnectionPool(host='scout.scilifelab.se', port=443): Max retries exceeded with url: /reports/report?level=10&panel_name=OMIM-AUTO+%284.0%29&sample_id=ACC4407A1&sample_id=ACC5556A3&sample_id=ACC5556A4 (Caused by SSLError(SSLError(1, '[SSL: CERTIFICATE_VERIFY_FAILED] certificate verify failed (_ssl.c:748)'),))

How do we fix it?

[dnil]

Perhaps call FL/file an issue with scilifelab IT again; pretty sure this is related to the certificate update issues Friday afternoon! 😊

[northwestwitch]

It's definitely a server settings issue and I've been looking into the settings we have for scout and scout stage in the servers. I'm moving this issue there but I'll notify here when it is fixed.

[northwestwitch]

Moved it here: https://github.com/Clinical-Genomics/servers/issues/179

[northwestwitch]

Perhaps call FL/file an issue with scilifelab IT again; pretty sure this is related to the certificate update issues Friday afternoon!

@ingkebil says we should disable the SSL certificates for scout and the settings are probably on our servers and we should be able to modify them

[ingkebil]

yes, exactly. This way, IT can update the certificates without being dependent on an application. There is no need to encrypt traffic between localhost.

[northwestwitch]

We are trying to fix it with the IT, I'll let you know as soon as we have news

[1ctw]

I see you are working to solve this. Just want to tell you that we at CMMS have the same problem...

[northwestwitch]

I see you are working to solve this. Just want to tell you that we at CMMS have the same problem...

Sorry for the inconvenience, hopefully we'll fix it soon

[ingkebil]

Alright. We have now fixed the problem. Download ahead!

[dnil]

Works!

[northwestwitch]

Nice! Thanks @ingkebil !