Question (maybe) related to Session service

[Wen Ting Bian - Network]

Hi all,

 

We built an internal version of cbioportal on AWS with keycloak authentication. The database is based on RDS and all other services (cbioportal-container, cbioportal-session-container, cbioportal-session-database-container) are on an EC2 instance.

 

Currently, we encountered a strange issue:

The first user, who is the first to login after restarting, can use "Query by Gene" as expected. All of the afterwards users will get "Oops. There was an error retrieving data." when use "Query by Gene" (detailed error are attached). If that first user log out, he/she cannot use it any more.

Based on this phenomena, we suspected whether it is associated with the session service. But it is started via docker-compose. The only difference is that we move the mysql server into RDS.

 

More strangely, only "Query by Gene" caused error, but "Explore selected Studies" worked normally. If use "Quick Search", study or sample worked find, but gene caused error.

Maybe it suggested that issues related with GENE? But I have no idea why it worked for the first user.

 

Thanks,

Wenting

 

 

[Benjamin Gross]

Hi Wenting,

Thank you for your email and sorry you are having troubles with your instance of cBioPortal.  It's difficult to identify the cause of the issue based on the error log you have provided (is it permission or an issue calling /api/reference-genome-genes?).

For starters, have you tried to turn off authentication and access the cBioPortal?  Does that work without any problems?  If so, that would indicate an issue with your Keycloak configuration (and eliminate session service as a potential cause).

If it is a problem with your Keycloak configuration, I would turn on logging in the security library and see if that sheds light on the issue.  You can do that by following the docs here:

https://docs.cbioportal.org/2.2-authorization-and-authentication/authenticating-users-via-saml#troubleshooting-tips

If you provide me the log with additional info, I can help you troubleshoot.

Regards,

Benjamin

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[Wen Ting Bian - Network]

Hi Benjamin,

 

Thanks for your reply. This error has been fixed after I changed the database from Aurora MySQL to RDS MySQL.

I am unsure how the database is related with it. The error is related with “GeneMemoizerServiceImpl.allTablesUpToDate”, so I guess the Aurora MySQL is not compatible to standard MySQL on some timestamp-related function.

 

Thanks,

Wenting

 

 

From: Benjamin Gross <benjami...@gmail.com>
Sent: 2021年4月14日 21:31
To: Wen Ting Bian - Network <bian_w...@network.lilly.com>
Cc: cbiop...@googlegroups.com
Subject: [EXTERNAL] Re: [cbioportal] Question (maybe) related to Session service

 

EXTERNAL EMAIL: Use caution before replying, clicking links, and opening attachments.

[Benjamin Gross]

Thanks for the follow-up Wenting.  Interesting, we’ve talked about looking at Aurora as a potential dbms platform.  Its good to know we may have some problems to address.

Regards,

Benjamin