Geneset version issue

[Mohammedhusen]

Hi Team,

We are getting below error, even though the same geneset_version present in DB as below. DB_SCHEMA_VERSION, GENESET_VERSION '2.12.3', 'Bindea_ORIG'

Error: geneset_def_version is different from the geneset_version in the database; value encountered: 'Bindea_ORIG'

GSV metafile:

cancer_study_identifier: study_id genetic_alteration_type: GENESET_SCORE datatype: GSVA-SCORE stable_id: gsva_scores source_stable_id: rna_seq_mrna profile_name: GSVA scores on oncogenic signatures gene sets profile_description: GSVA scores on oncogenic signatures gene sets using mRNA expression data calculated with GSVA version x with parameters x and y. data_filename: data_gsva_bindea_scores.txt show_profile_in_analysis_tab: true geneset_def_version: Bindea_ORIG

[dianab0]

Hello Mohammed,

How do you call the import script?

• If you pass a portalinfo folder path, could you please check the /portalinfo/genesets_version.json file to see if you have the correct version there? If not, the portalinfo may need to be updated for the new DB.
• If you pass the cBioPortal URL, then you can check what the https://cbioportal-URL/api/genesets/version returns.

Please let me know.

[Mohammedhusen]

Hi @dianab0 ,

Thanks for your reply.

I have used the below command to import the gene set.

./importGenesetData.pl --data /dataload/coad_lusi_2020/Bindea_ORIG.gmt --new-version Bindea_ORIG

And also below URL gives the same version. https://localhost/api/genesets/version "Bindea_ORIG"

But still, it shows an error: geneset_def_version is different from the geneset_version in the database; value encountered: 'Bindea_ORIG'

[oplantalech]

Hi @Mohammedhusen,

I don't think the problem is related to the importGenesetData.pl command, but on the metaImport.py command used to load the study, as my colleague @dianab0 mentioned. Can you please share this command with us?

[Mohammedhusen]

Hi @oplantalech ,

Thanks for your reply.

I am running a validate script as below and getting this error.

./validateData.py -s /dataload/studyfolder/ -n

[oplantalech]

Hi @Mohammedhusen,

I found the cause of the problem. There is a bug in the -n parameter that caused to check the geneset_version (in the database). I have created a pull request to fix the bug.

Meanwhile, you can use the -u parameter or generate the cached-portal side data, as explained in here: https://github.com/cBioPortal/cbioportal/blob/master/docs/docker/example_commands.md#importing-data

[Mohammedhusen]

Hello @oplantalech ,

Thanks a lot for your quick support really appreciated. Now I could load the study successfully. However, in the portal, it doesn't show up GSVA profile in the analysis tab any idea why is it so? but I can see it in the database profile being created.

[oplantalech]

Hi @Mohammedhusen,

Can you select the GSVA profile in the query page, under the area "Select Genomic Profiles"? If that is not the case, check if your portal.properties has skin.show_gsva=true commented out (GSVA is disabled by default).

[Mohammedhusen]

Hi @oplantalech ,

Thanks a lot, now I can see the option after adding the line skin.show_gsva=true.