sample profile table does not get populated based on sequenced case list

[inodb]

We are currently capturing the difference in the data files between:

1 a sample that has been profiled but has 0 mutations and 2 a sample that has not been profiled for mutations

We are using the sequenced case list to indicate that, e.g.:

https://github.com/cBioPortal/datahub/blob/master/public/acc_tcga_pan_can_atlas_2018/case_lists/cases_sequenced.txt

So if a sample is there and not in the data_mutations_extended.txt file it is considered scenario 1.

If it is not in the sequenced case list it is considered scenario 2.

Some of our localdb tests currently break, because we are not populating the sample_profile table based on the sequenced case list:

reference/filters_mutation_tracks_based_on_gene_filter_setting_element_chrome_1600x1000.png https://7963-32481543-gh.circle-artifacts.com/0/imageCompare.html

We have removed the logic from the API that would check in the sequenced case list, since it caused a lot of performance issues. It would be better to change the importer to properly populate the sample profile table based on the sequenced case list

[stale[bot]]

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