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Filter SV by custom driver annotations in oncoprint and study page #4552

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merged 1 commit into from
Apr 25, 2023

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BasLee
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@BasLee BasLee commented Mar 20, 2023

Filter structural variants by custom driver annotations in oncoprint and on study page.

Depends on backend PR cBioPortal/cbioportal#10092 for query and es_0 data changes.

Changes

  • Implement custom driver filtering for structural variants in ResultsViewPageStore analogous to CNA and mutations.
  • Fix incomplete filter bug
    • Bug: when changing the tier selection using the annotation menu, the updated filters are not (always) send to backend. This is because the list of tiers first needs to be requested from the backend. When creating the StudyViewPageStore.filters these tiers are requested, but subsequent api calls depending on filters are not waiting for this info.
    • This PR introduces the async initialFiltersRemote and filtersRemote, which allows api calls to wait for a fully loaded filters.
    • There might be a better solution?
  • Test filtering of structural variants by custom driver annotations in oncoprint, in custom-driver-annotations.spec.js

Study View

1 - All tiers selected 2 - Exclude unknown
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3 - Exclude Class 2 and Class 4 4 - Exclude putative drivers
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Oncoprint

1 - Default: Use custom and oncokb drivers 2 - Disable oncokb annotations
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3 - Hide alterations of unknown significance 4 - Disable custom driver tier
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@BasLee BasLee changed the title Sv custom driver annotations Filter SV by custom driver annotations in oncoprint and study page Mar 20, 2023
@inodb inodb requested a review from dippindots March 24, 2023 14:47
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It looks good to me, is there any instructions on how to test this pull request? Also, it's good to get @alisman's opinion too.

@alisman alisman self-requested a review March 27, 2023 14:35
@BasLee BasLee force-pushed the sv-custom-driver-annotations branch from 9b637a2 to 2006e93 Compare April 5, 2023 14:32
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@BasLee It looks good to me now. I wish to get @alisman's comment about the waiting sequence in my comment. If he thinks it's ok, I think this is good to go. And I also noticed that the prettier test is failing. Maybe you can try to run prettier locally again.

If we decide to merge, please make sure we wait until the deployment date (next Tuesday) to release this with the backend together.

@BasLee BasLee force-pushed the sv-custom-driver-annotations branch from 2006e93 to 21bf551 Compare April 17, 2023 08:32
@BasLee BasLee requested review from alisman and dippindots April 17, 2023 09:52
@BasLee BasLee force-pushed the sv-custom-driver-annotations branch from b64b0c0 to b368c3f Compare April 24, 2023 15:02
@BasLee BasLee force-pushed the sv-custom-driver-annotations branch from b368c3f to 4626705 Compare April 25, 2023 08:57
@alisman alisman merged commit de12bed into cBioPortal:master Apr 25, 2023
@dippindots dippindots added the bug label Apr 25, 2023
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3 participants