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cBioPortal / datahub

A centralized location for storing curated data from cBioPortal
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Data issue for study: coadread_cass_2020 #2081

Open jmtang2018 opened 1 month ago

jmtang2018 commented 1 month ago

We are trying to import coadread_cass_2020 into our 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']

Column 18 and 19 on data_clinical_sample.txt are defined as NUMBER but column 18 contains [<0.5, > 1500] and column 19 contains [<2, <2.0, >1200]. Maybe consider changing to a STRING? Let us know if we should open a PR instead?

Thanks, Jeff

rmadupuri commented 1 month ago

Hi @jmtang2018, thank you for reporting this. The same issue has been addressed in the discussion: https://github.com/cBioPortal/datahub/issues/2054

jmtang2018 commented 1 month ago

I just imported again. I don't think the issue have been resolved. https://media.githubusercontent.com/media/cBioPortal/datahub/refs/heads/master/public/coadread_cass_2020/data_clinical_patient.txt