Geneset database error when importing gsva data

[sstein93]

Hello,

I have docker version of cBioPortal v6.0.20. I updated the geneset version to msigdb.v2024.1.Hs using the gmt file from msigdb:https://www.gsea-msigdb.org/gsea/msigdb/human/collections.jsp. I used the following code to import this geneset, which seemed to work without any errors:

docker-compose run -v /path/to/genesets/msigdb.v2024.1.Hs.entrez.gmt:/genesets/msigdb.v2024.1.Hs.entrez.gmt:ro \
cbioportal bash -c 'cd /core/scripts/ && ./importGenesetData.pl \
--data /genesets/msigdb.v2024.1.Hs.entrez.gmt --new-version msigdb.v2024.1.Hs'

I have geneset_def_version: msigdb.v2024.1.Hs in both meta_ssgsea_scores.txt and meta_ssgsea_pvalues.txt. I get this error during the validation step of the importer

ERROR: meta_ssgsea_pvalues.txt: geneset_def_version is different from the geneset_version in the database; value encountered: 'msigdb.v2024.1.Hs'
ERROR: meta_ssgsea_scores.txt: geneset_def_version is different from the geneset_version in the database; value encountered: 'msigdb.v2024.1.Hs'
I think this suggests that the geneset_version in the database was not updated to 'msigdb.v2024.1.Hs' even though I ran the ./importGenesetData.pl and restarted the portal.

I then tried running the importer with 'geneset_def_version: msigdb_7.5.1' in both the scores and pvalues meta files, and was able to get past the data validation step (i.e. I did not get the above error). However, the importer threw an error during the data loading step complaining that the 'geneset_def_version' property (msigdb_7.5.1) in 'study/depmap_23q4/meta_ssgsea_scores.txt' differs from database version (msigdb.v2024.1.Hs).

It seems like during the validation step, maybe the script is comparing the geneset_def_version from the meta file to a geneset_version variable that is still set to msigdb_7.5.1. However, during the data load step of the importer, the script is (correctly) expecting geneset_def_version = msigdb.v2024.1.Hs. I am wondering if there is a bug in either the importGenesetData.pl or metaImport.py scripts where geneset_def_version or geneset_version isn't getting properly updated or referred to?

Thanks!
Shayna