problem_validateData.py

[Dr. Avrajit Chakraborty]

OS: Kubuntu 20.04

docker version 28.0.1

cbioportal: 6.0.24

I used docker to install cBioportal and I can see the default page is opening in localhost:8080 in chrom browser. No error. 

 when I am running data validation step

sudo docker compose run cbioportal valdateData.py -s study/lgg_ucsf_2014/ -v  it is showing  error 'ConnectionRefusedError [Error 111]

I checked the connection with curl http://localhost:8080/api/info and didn't get any issue.

I am trying to add -p option for cBioportal info file  but in cBioportal docker folder I didn't get anything like that.  How to resolve this issue?  Please help.

Thanks

[ole...@thehyve.nl]

Dear Avrajit,

The -p option stands for "portal info folder", that can be generated following the "Example 3" on this page: https://docs.cbioportal.org/using-the-dataset-validator/#example-3-validation-with-a-portal-info-folder

Once you have that folder created, you need to place its path in the -p option.

Best regards,

Oleguer Plantalech

Data Engineer & Project Manager

E ole...@thehyve.nl

T +31 30 700 9713

W thehyve.nl

    

Op woensdag 19 maart 2025 om 07:57:17 UTC+1 schreef Dr. Avrajit Chakraborty:

[Dr. Avrajit Chakraborty]

Dear Oleguer,

Thanks for your response. I will try it and update further.

Regards

avrajit chakraborty

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