cBioPortal v6.4.1 and SAML

[Oliver Stolpe]

Dear all,

I'm trying to set up cBioPortal v6.4.1 (latest stable version) with a keycloak v26.6.1 running on the same server using the Docker setup. I was following the cBioPortal documentation as far as possible. Both are behind a traefik reverse proxy. Each service is running fine and is reachable. However, when I want to connect the cBioPortal instance to the keycloak by enabling SAML by switching from --authenticate=false to --authenticate=saml and restart the cBioPortal container, the container keeps restarting with the error displayed below. No matter the settings in the application.settings file, I always get this error. Any ideas of where to look at?

Thanks in advance,

  Oliver

```
cbioportal-container  | ***************************
cbioportal-container  | APPLICATION FAILED TO START
cbioportal-container  | ***************************
cbioportal-container  |
cbioportal-container  | Description:
cbioportal-container  |
cbioportal-container  | Parameter 1 of method samlFilterChain in org.cbioportal.application.security.config.Saml2SecurityConfig required a bean of type 'org.springframework.security.saml2.provider.service.registration.RelyingPartyRegistrationRepository' that could not be found.
cbioportal-container  |
cbioportal-container  |
cbioportal-container  | Action:
cbioportal-container  |
cbioportal-container  | Consider defining a bean of type 'org.springframework.security.saml2.provider.service.registration.RelyingPartyRegistrationRepository' in your configuration.
cbioportal-container  |
```

[Ruslan Forostianov]

Hi Oliver,

It looks like RelyingPartyRegistrationRepository bean is not being created.

In Spring Boot, this bean is usually created automatically from the correct SAML properties. Please check that you are using the spring.security.saml2.relyingparty.registration.* properties and that cBioPortal is actually loading them.

See the cBioPortal docs here https://docs.cbioportal.org/deployment/customization/security.properties-reference/#saml-configuration

If that does not help, try enabling more detailed Spring Security logs:

logging.level.org.springframework.security=TRACE

This should give more information about why the SAML registration is not being created.

I hope this helps.

Regards,

Ruslan,

SE4BIO

[Oliver Stolpe]

Dear Ruslan,

thank you, I got it working in the meantime by setting those properties with help of ChatGPT. I was following the instructions under https://docs.cbioportal.org/deployment/authorization-and-authentication/authenticating-and-authorizing-users-via-keycloak/#modifying-configuration as I'm using (the latest version of) keycloak. The instructions appear to be a bit outdated and I wasn't aware of the ones you just provided. Sorry for not searching more thoroughly in the manual.

Best,

  Oliver

[elias]

Hi Oliver,

I have also enountered this problem a view Months ago and also updated the cBioPortal Docs with a Pullrequest. Sadly this was not included in the official docs till now. 

If there are more proplems with the set up you might look at https://github.com/eliaslautensack/cbioportal/tree/patch-1 in the docs directory should be my updated version. 

In most cases it is just the Keycloak UI that Updated and things might be at slightly different places. 

Maybe this helps.

Best regards 

Elias

[de Bruijn, Ino]

Hi Elias,

Apologies about the delay on this. Just merged it

Thank you again for making the fixes to the docs!

@Oliver - hope Elias's fixes help! Let us know if you run into any issues

Best wishes,

Ino

---

De: cbiop...@googlegroups.com <cbiop...@googlegroups.com> en nombre de elias <elias.la...@med.uni-goettingen.de>
Enviado: miércoles, mayo 20, 2026 8:41:57 a.m.
Para: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Asunto: [EXTERNAL] [cbioportal] Re: cBioPortal v6.4.1 and SAML

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