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. I could also provide you the access/link to our cbio instance if this would help.

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

Thank you very much.

Best wishes,

Niklas

[Benjamin Gross]

Hi Niklas,

Thanks for your patience.  Running the cBioPortal with mouse data is not a common use case for our community, so we don’t have a readily available installation to help troubleshoot this configuration.   Perhaps we can use your setup to provide more insight.

Did you deploy your instance using docker?  If so, I’m wondering if you can provide additional information from the session service logs.  The container name would be “cbioportal-session”  (https://github.com/cBioPortal/cbioportal-docker-compose/blob/master/docker-compose.yml#L39)

Can you view the logs while you generate the 503 error in the browser?   Perhaps there is an incompatibility between mouse data and the session service.

Best,

-Benjamin

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[Niklas de Andrade Krätzig]

Hi Benjamin,

thank you very much for your help.

I checked the session service (see attached log), however nothing happens when I encounter the error. I also attached the docker-compose log. 

Previously it was very tedious to get the mouse version running, but with docker it is actually pretty straight forward. 

The only real change is required for data/init.sh to:

wget -O cgds.sql "https://raw.githubusercontent.com/cBioPortal/cbioportal/v1.7.3/db-scripts/src/main/resources/cgds.sql"
wget -O seed.sql.gz "https://github.com/cBioPortal/datahub/raw/master/seedDB_mouse/seed-cbioportal_mm10_v2.3.1.sql.gz"

# newer but not working at all, see github issue
#wget -O cgds.sql "https://raw.githubusercontent.com/cBioPortal/cbioportal/v1.9.0/db-scripts/src/main/resources/cgds.sql"
#wget -O seed.sql.gz "https://github.com/cBioPortal/datahub/raw/master/seedDB_mouse/seed-cbioportal_mm10_v2.12.3.sql.gz"

I also changed this in the portal.properties, but I don't feel like this does anything: 

species=mouse
ncbi.build=38
ucsc.build=mm10

For testing, the default dataset lgg_ucsf_2014 can be modified as follows:

- add "reference_genome: mm10" to meta_study.txt

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

Best,

Niklas

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Von: Benjamin Gross <benjami...@gmail.com>
Gesendet: Dienstag, 18. Juni 2024 21:10:53
An: Niklas de Andrade Krätzig
Cc: cbiop...@googlegroups.com; Sebastian Müller
Betreff: Re: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

[Benjamin Gross]

Hi Niklas,

Thanks for the information below.  I may end up setting up an instance to troubleshoot.  In the meantime, I was looking through the source code and I noticed that the cBioPortal website backend is a proxy to the session service.  That is the web application/browser doesn’t speak to it directly.

Can you view the logs of the “cbioportal" service docker container while you generate the 503 error in the browser.  This could shed light on a communications error between the cBioPortal backend and the cBioPortal session service.

Best,

-Benjamin

<session_service.log><dockercompose-build.log>

[Niklas de Andrade Krätzig]

Hi Benjamin,

again thank you very much for your help.

So 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.

I attached the last few lines for you. 

Best,

Niklas

---

Von: Benjamin Gross <benjami...@gmail.com>
Gesendet: Donnerstag, 20. Juni 2024 16:33:17

[Benjamin Gross]

Hi Niklas,

Thanks for your patience.  I was able to setup a test environment and I’m now trying to recreate the issue you are having.  Can you provide me with the steps you are executing to cause this exception?

Best,

-Benjamin

<cbio_logs>

[Niklas de Andrade Krätzig]

Hi Benjamin,

are there any news regarding this issue?

Thank you!

Best,

Niklas

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Von: Niklas de Andrade Krätzig
Gesendet: Mittwoch, 26. Juni 2024 13:45:07
An: Benjamin Gross
Cc: Sebastian Müller
Betreff: AW: [cbioportal] Overview grouping error: Unsuccessful HTTP response (mouse cbio)

 

Hi Benjamin,

thank you very much for your help!

After loading any study and opening the overview page, as soon as I press on the "Groups" tab on the right side I get the error. 

For testing, the default dataset lgg_ucsf_2014 can be modified as follows:

- add "reference_genome: mm10" to meta_study.txt

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

Alternatively, you can have a look here: http://138.246.225.206:8080/study/summary?id=lgg_ucsf_2014

Best,

Niklas

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Von: Benjamin Gross <benjami...@gmail.com>
Gesendet: Dienstag, 25. Juni 2024 21:41:23

[Niklas de Andrade Krätzig]

Dear Benjamin and the cbioportal team,

sorry for bothering you again. 

Our mouse cbio instance will be part of a publication that we will be submitting shortly. Therefore we would be very grateful for any help to resolve this critical error. 

Again thank you very much!

Kind regards,

Niklas

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Von: Niklas de Andrade Krätzig

Gesendet: Dienstag, 16. Juli 2024 11:00:27
An: Benjamin Gross
Cc: Sebastian Müller; cbiop...@googlegroups.com