Overview grouping error: Unsuccessful HTTP response (mouse cbio)

[Niklas de Andrade Krätzig]

Dear cbioportal team,

first of all thank you for the amazing analysis platform you provide. 

We are running a mouse cbioportal version on a local server, but now we encountered a severe issue: we can not define groups in the overview page (see attached images, "Error: Unsuccessful HTTP response").

The first image is from our first server with cbioportal v3.7.1, the second image is from another server I deployed today using v5.4.10. 

We are using docker-compose with:

cdgs.sql: Schema 2.3.1, SQL file with create table statements for portal release 1.7.3

seed: seed-cbioportal_mm10_v2.3.1.sql.gz

This is not the "newest" available version for mouse, however this is the only combination of versions which is actually usable, as I already described here: https://github.com/cBioPortal/cbioportal/issues/8544

We also have a local human version using docker-compose but we do not see this issue there. Therefore I assume the error has something to do with the mouse seed and cdgs. 

We urgently need the instance (with groups) and would be very happy about any help. 

Thank you very much.

Best wishes,

Niklas

[Aaron L]

Hi Nikas, from what you sent it seems there is a problem with the session service.  This is indeed necessary for the groups feature to work.   The browser error console you sent shows 503 which is kind of a general server error.  We need to get to the bottom of what is causing that.  The best way is to access the logs of the web server.   If you're using docker, you need to look up how to access the logs inside a running container.  It's not hard.  Once you do that, let us know what errors you find, specifically when the session service is called.  If you need help, we could jump on a Zoom and help debug.

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[Niklas de Andrade Krätzig]

Dear Aaron,

I just wanted to kindly follow up to check if my last email has arrived (regarding zoom and details) or if you’ve had a chance to review the issue I mentioned.

Again, thank you very much for your help.

Best,

Niklas

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Von: Niklas de Andrade Krätzig
Gesendet: Montag, 11. November 2024 09:48
An: Aaron L
Betreff: AW: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

Dear Aaron, 

Thank you very much for your reply, I really appreciate it!

Attached you can find the different logs. 

I checked the logs using docker logs -f -t ID for all 4 containers (cbioportal/cbioportal:5.4.10, cbioportal/session-service:0.6.1, mongo:4.2, mysql:5.7), however I do not see any new log entries when I generate the 503 error.

A Zoom call would be amazing. I am available any day at any time between 9am-1pm New York time (i.e. Europe: 2pm - 6pm).

In the meantime, if it helps you could also have a look at this (dev) instance: (see mail)
This is based on a newer version of cbio as compared to our main instance, however the error is identical (pressing on the groups tab = crash).

For testing, I modified the default dataset lgg_ucsf_2014 to be mouse as follows:

- add "reference_genome: mm10" to meta_study.txt

- sed -i 's/GRCh37/GRCm38/g' data_mutations.txt

Thanks again.

Best,

Niklas

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Von: Aaron L <lisman...@gmail.com>
Gesendet: Freitag, 8. November 2024 16:09:44
An: Niklas de Andrade Krätzig
Cc: cbiop...@googlegroups.com
Betreff: Re: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

[Aaron L]

Hi Nikas, 

So sorry I missed this.  Are you available at 12 noon today EST?

[Aaron L]

Glad to hear it's fixed Niklas!

On Thu, Nov 21, 2024 at 12:21 PM Niklas de Andrade Krätzig <niklas.andr...@tum.de> wrote:

Dear Aaron,

I think you managed to fix the issue! 

Everything is now working as expected on the test server and I will confirm it on the main server soon. 

I tracked down this yml file and found the very first commit to have the problematic line of code ("-Dauthenticate=noauthsessionservice"): 

https://github.com/cBioPortal/cbioportal-docker-compose/blob/015aee86358abbe105178bc372d589887185b96f/docker-compose.yml

I guess I pulled that one a while ago and did not use the most recent one, or the old yml is connected to a specific (older) docker-compose/cbio version that I am using.

Again thank you very much for your help!

Best,

Niklas

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Von: Niklas de Andrade Krätzig

Gesendet: Donnerstag, 21. November 2024 16:12:35

An: Aaron L
Betreff: AW: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

Hi,

yes, today 11:30 EST is perfect.

Thank you very much!

This is the zoom link: https://tum-conf.zoom-x.de/j/68675321636?pwd=TmpyUlArNWk1UlpBSjZkRFdKS05GQT09

Best,

Niklas

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Von: Aaron L <lisman...@gmail.com>
Gesendet: Donnerstag, 21. November 2024 15:59:45

An: Niklas de Andrade Krätzig

Betreff: Re: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

Hi Niklas, not sure what 11 noon means!     Could we meet at 11:30 eST today?

On Thu, Nov 21, 2024 at 8:22 AM Niklas de Andrade Krätzig <niklas.andr...@tum.de> wrote:

Hi Aaron, 

for some reason weird your second answer was in my spam folder, sorry for missing it. 

Thank you very much for the offer to help.

I am available today from now until 11 noon EST.
Alternatively, I am available on a very flexible date/time next week. 

Best,

Niklas

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Von: Aaron L <lisman...@gmail.com>
Gesendet: Freitag, 15. November 2024 15:08