Fix incorrect oncokb data and cancer type label used in mutations table #4758
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| if (this.getSameTumorTypeAttribute(data) === 'CANCER_TYPE_DETAILED') { | ||
| return this.resolveTumorType; | ||
| } | ||
| if (this.getSameTumorTypeAttribute(data) === 'CANCER_TYPE') { | ||
| return this.resolveCancerType; | ||
| } |
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this resolveTumorType vs resolveCancerType naming feels a little weird, tho i guess it was already there. Not super clear what the difference between those is
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yea, I wasn't sure what to name it but resolveTumorType already exists and typically gets the Cancer Type Detailed from a mutation while the newly added resolveCancerType will retrieve the Cancer Type. any ideas on name changes? throughout the codebase, the term Tumor Type is used but mostly just for Cancer Type Detailed and I didn't want to change that.
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I see - yeah as long as it is consistent that's fine by me. If we were to change it throughout the code I'd prolly be explicit and just say resolveCancerType vs resolveCancerTypeDetailed
src/shared/lib/StoreUtils.ts
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| // // first priority is CANCER_TYPE_DETAILED in clinical data | ||
| // _.each(clinicalDataForSamples.result, (clinicalData: ClinicalData) => { | ||
| // if (clinicalData.clinicalAttributeId === 'CANCER_TYPE_DETAILED') { | ||
| // map[clinicalData.uniqueSampleKey] = clinicalData.value; | ||
| // } | ||
| // }); |
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maybe good to remove commented out code?
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@gblaih did you respond to Ino's comments? |
…le (#4758) * fix incorrect cancer type and oncokb levels in mutations table --------- Co-authored-by: Bryan Lai <laib1@mskcc.org>
Fixes cBioPortal/cbioportal#10421
Currently, when
CANCER_TYPE_DETAILEDis the same for all mutations of a row in the table, it uses this to fetch the oncoKb data; otherwise, it uses "Cancer of Unknown Primary".This fixes it so that if there are multiple
CANCER_TYPE_DETAILEDfor mutations of a row, it checks ifCANCER_TYPEis the same and if so, uses that to fetch the oncoKb data. If there are multipleCANCER_TYPEas well, then it uses "Cancer of Unknown Primary".