search

cBioPortal / icebox

very low priority issues
0 stars 0 forks source link

Namespace not upload in cBioPortal docker image #312

Open sungyoonkimb opened 2 years ago

sungyoonkimb commented 2 years ago

I want to upload my own column to cbioportal docker image. So, referring to the link[https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#mutation-data], I wrote the input files according to the format and checked the screen. However, unlike the git image you uploaded[https://github.com/cBioPortal/cbioportal-frontend/pull/4070], the column I uploaded does not appear, so I am registering an issue to ask if there is a wrong way.

show my input data

-meta_mutation_extended.txt- cancer_study_identifier: ctDNA_amc_SeraSEQ2 genetic_alteration_type: MUTATION_EXTENDED datatype: MAF stable_id: mutations show_profile_in_analysis_tab: true profile_description: Somatic mutations from targeted sequencing. profile_name: Somatic mutations data_filename: data_mutations_extended.csv namespaces: ngs variant_classification_filter: variant_classification_filter.txt

-data_mutation_extended.txt-

NGS.Tier | NGS.Report | NGS.Warning | NGS.FALSE | Hugo_Symbol | Entrez_Gene_Id | Center | NCBI_Build | Chromosome T1 | Y | . | N | AKT1 | 207 | . | GRCh37 | chr14

upload that data. my cBioPortal mutation sheet unchanged thank you.

inodb commented 2 years ago

@sungyoonkimb Thanks for filing this! Apologies for the delay. I believe the data imports now into the database but it does not appear yet in the mutations table. I think the open PR you referenced should address this: https://github.com/cBioPortal/cbioportal-frontend/pull/4070. CC @pvannierop: do you see something wrong with this input data?

@sungyoonkimb Note: to use this feature one would have to build a docker image of the PR first and use that in your cbioportal-docker-compose setup. Otherwise it would not work, since the code has not been merged to the main branch yet

inodb commented 2 years ago

See also related user mailing list discussion: https://groups.google.com/g/cbioportal/c/9HmiNFCfnxY/m/PpxoPn7_BQAJ

pvannierop commented 2 years ago

@sungyoonkimb @inodb I have been working on the namespace import indeed. There seems nothing wrong with the input data. The data will not appear until PR cBioPortal/cbioportal-frontend#4070 has been merged.

stale[bot] commented 2 years ago

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.