authorities table

[Lloyd Gill]

Hi there,

I have created authorities and groups. I have this value set-

always_show_study_group=PUBLIC

I have admin users set as - cbioportal:ALL (should be able to see all studies, public and private)

some users are set as cbioportal:PUBLIC (can see only public studies)

then other users in private studies are set as cbioportal:PUBLIC;Lung (can see public and Lung study)

What I have from this configuration is that I have the cbioportal:ALL authority, but I only see the public studies. My expectation is that I would be able to see all studies. Do I also need to be in the specific private study group?

This is the docker deployment version.

thanks,

Lloyd

[Benjamin Gross]

Hi Lloyd,

I’m sorry for the delayed response.  Your’e expectations are correct.  With cbioportal:ALL, you should see all studies in the cancer study table (assuming your app.name is cbioportal).  What authentication method are you using?  Are you sure you are authenticating properly and using the correct email that you have set in the user/authorities table?  Also, I’ve never used the always_show_study_group feature.  I’m curious. If you turn off that setting, do you end up seeing both public/private studies?

Let us know how it goes.

-Benjamin

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[Lloyd Gill]

Hi Ben,

thank you for the response. I set that value based on the recommendation here - https://docs.cbioportal.org/2.2-authorization-and-authentication/user-authorization

The recommendation was for authenticated users to always see PUBLIC studies.

Lloyd

[Lloyd Gill]

I am configured in authorities table as - | myemail@domain   | cbioportal:ALL        |

and of the 13 studies, i can only see 9. I also set the PUBLIC column to '0' and that did not seem to have any effect.

+-----------------+-----------------------------------+--------+------------+--------+
| CANCER_STUDY_ID | CANCER_STUDY_IDENTIFIER           | PUBLIC | GROUPS     | STATUS |
+-----------------+-----------------------------------+--------+------------+--------+
|               2 | lgg_ucsf_2014                     |      0 | PUBLIC     |      1 |
|               4 | nsclc_tcga_broad_2016             |      0 | LungCOE    |      1 |
|               5 | study_es_0                        |      0 | PUBLIC     |      1 |
|               6 | acbc_mskcc_2015                   |      0 | PUBLIC     |      1 |
|               7 | all_phase2_target_2018_pub        |      0 | PUBLIC     |      1 |
|               8 | blca_tcga_pan_can_atlas_2018      |      0 | BladderCOE |      1 |
|               9 | blca_tcga_pub_2017                |      0 | BladderCOE |      1 |
|              10 | nbl_target_2018_pub               |      0 | PUBLIC     |      1 |
|              11 | wt_target_2018_pub                |      0 | PUBLIC     |      1 |
|              12 | msk_ch_2020                       |      0 | PUBLIC     |      1 |
|              13 | pancan_pcawg_2020                 |      0 | PUBLIC     |      1 |
|              14 | metastatic_solid_tumors_mich_2017 |      0 | PUBLIC     |      1 |
|              15 | mixed_allen_2018                  |      0 | PUBLIC     |      1 |
+-----------------+-----------------------------------+--------+------------+--------+

[Lloyd Gill]

I set all studies back to PUBLIC, and now i see 12 of 13. Seems my value of cbioportal:ALL is not being honored when i have some studies part of a non-public group.

[Lloyd Gill]

Just want to update this in case someone else has similar issue where groups are not being honored. In my case, the cancer_study table and authorities table appeared correct, so I went and reviewed all values in portal.properties. It turned out to be filter_groups_by_appname=true (was set to false). Now everything is working as expected. Thanks.

[debr...@mskcc.org]

Great! Thanks so much for sharing your solution!

Best wishes,

Ino

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From: cbiop...@googlegroups.com <cbiop...@googlegroups.com> on behalf of Lloyd Gill <lloyd....@gmail.com>
Sent: Thursday, February 24, 2022 7:39:03 AM
To: cBioPortal for Cancer Genomics Discussion Group <cbiop...@googlegroups.com>
Subject: [EXTERNAL] [cbioportal] Re: authorities table

 

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