Authorized to see the study but error retrieving data

[Yuki]

Hello, 

I've set a cbioportal with keycloak authentication. I uploaded some of our own data, and encountered a very strange problem: users can see the studies on the main page,  but immediately when I click the study or tick the checkbox the following error occurs. However, with almost the same setting, this error does not happen for study_es_0 .

Please see the following screenshots:

users can see both studies (including study_es_0 ) 

o

but when click anywhere for the first study (data prepared by ourselves), we got the following error:

From the error log, I can only see that the error occurred when it's trying to GET some content from my/url/studies/mystudy/molecular-profiles

and that returned "Access to the specified resource has been forbidden" message.

-----------------------------------------------

I have the following set up:

I used groups for authorization. 

1. I assign the users 'PUBLIC' group in keycloak

2. changed portal.properties: always_show_study_group=PUBLIC

3. then update the database to add PUBLIC for test_data_set

+-----------------+-------------------------+-----------------------+

| CANCER_STUDY_ID | CANCER_STUDY_IDENTIFIER | GROUPS                |

+-----------------+-------------------------+-----------------------+

|               1 | study_es_0              | SU2C-PI3K;PUBLIC;GDAC |

|               6 | mystudy                | PUBLIC                |

+-----------------+-------------------------+-----------------------+

I didn't add anything to authorities or users table for either study,  study_es_0 works perfectly, but mystudy had the problem.

I tried to load the study from another testing cbioportal server which does not require authentication or authorization, and it works fine on that server. 

Did I miss any configurations?

Thanks very much

 

[Benjamin Gross]

Hi Yuki,

Sorry for the delayed response.   As a quick check, can you turn off authentication and confirm that you can access the study?

Best

Benjamin

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[Yuki]

Hi Benjamin, Thanks for looking into this. 

I'm not sure how to turn off authentication, but I have a parallel cbioportal server,  which does not has authentication but connected to exactly the same database. With this server (no-auth), I can view the data without any problem.  

I also have study_es_0 which has almost the same set-up, but both server works fine with  study_es_0.

Can you spot what when wrong?  Let me know if you need more details.

Thanks

Yuki

[Benjamin Gross]

Ok, thats good - wanted to make sure the data was imported properly.  Can you see an exception in the backend server (tomcat) log when attempting to fetch the study (in docker I think you can do docker logs -f cbioportal_container .  If running tomcat natively, its where your log file location is set In your log4j.properties file https://github.com/cBioPortal/cbioportal/blob/master/src/main/resources/log4j.properties.EXAMPLE)?

To view this discussion on the web visit https://groups.google.com/d/msgid/cbioportal/13b67949-695e-492f-ac54-082a5afcaea1n%40googlegroups.com.

[Yuki]

Thanks so much, Benjamin.

I found the exception which seems to be related to session service ("exception":"org.cbioportal.session_service.service.exception.SessionNotFoundException"). And the problem disappeared once I restarted the session service. 

Best regards. 

Yuki