Data issue for study: coadread_cass_2020

[saxenanurag]

I am trying to import coadread_cass_2020 into a private installation of cbioportal and getting this error:

ERROR: data_clinical_patient.txt: lines [74, 108]: columns [18, 19]: Value of numeric attribute is not a real number; values encountered: ['<0.5', '<2.0']

I downloaded the files directly from cbioportal.org as well and got the same error.

[alexsigaras]

Thanks @saxenanurag. I can confirm we are having the same issue on our end. This refers to values of the columns CEA Biomarker and CA19-9 Antigen.

The issue is that <0.5 is not a NUMBER but a STRING instead and could be changed at line 3 at the respective columns.

Looking at https://www.cbioportal.org/study/clinicalData?id=coadread_cass_2020 it seems that the data are imported with the < and > symbols so perhaps a fix would be to change the data_clinical_patient.txt problematic definitions from NUMBER to STRING.

Kindly let us know if you would like us to open a PR instead.

[rmadupuri]

Hi @saxenanurag @alexsigaras, thank you for bringing this issue to our attention. I have updated the validator to accept >,< and float values as numbers (see PR #58). However, this update will be available in the next release. In the meantime, please feel free to update the column on your side to string to bypass the validator check.

[alexsigaras]

Thank you for your response @rmadupuri . Indeed as suggested changing NUMBER to STRING solves the issue but your solution above is a much better approach. I suggest keeping this open until the PR is part of a release