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cBioPortal / icebox

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Remove retrieval of gene sets when no gene set data in study #91

Open sandertan opened 6 years ago

sandertan commented 6 years ago

Currently, the seed database (on database schema 2.6.0), contains the MSigDB gene sets. This is useful for testing validation and loading of test study study_es_0, as well as potentially loading any gene set scoring data in cBioPortal. The downside is that validation is a couple seconds slower because all gene sets are requested and downloaded using the API.

It would be nice if the retrieval of gene sets is only done if the study contains gene set scoring data.

This will require refactoring of the validator, because the retrieval of cancer types, genes, gene aliases and gene sets is done at the start of validation, before data types are identified.

jjgao commented 6 years ago

Yes, please :)

Can we also remove the geneset_list parameter from url when no genesets were queried?

stale[bot] commented 4 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.

stale[bot] commented 4 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.

jjgao commented 4 years ago

unstale

stale[bot] commented 4 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.