Add reVUE revised effect for one KIT variant#139
Add reVUE revised effect for one KIT variant#139inodb wants to merge 5 commits intogenome-nexus:masterfrom
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This uses some of the old "curious cases" infrastructure but replaces it by directly using the VUE data from the revue-website repo. This still needs to be fully refactored to lose all references to "curious cases".
leexgh
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leexgh
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Looks great! Should we change protein change in transcript table too?
Probably also need to make some changes to OncoKB in the Clinical implication and Biological function
| style={{ textDecoration: 'none' }} | ||
| > | ||
| <img | ||
| src="https://www.cancerrevue.org/static/media/vue_logo.f7904d3925e95ec147ad.png" |
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Can we store the icon somewhere locally in case the URL changes? E.g. we have oncokb logo here https://github.com/genome-nexus/genome-nexus-frontend/blob/master/src/component/variantPage/biologicalFunction/oncokb.png
| <span> | ||
| {props.vue.comment}{' '} | ||
| <a | ||
| href={`https://pubmed.ncbi.nlm.nih.gov/${props.vue.pubmedIds[0]}/`} |
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I guess in the future we would show all PubMed ids, right?
| renderData = renderData.filter((data) => data.value != null); // remove null fields | ||
| } | ||
| let basicInfoList = _.map(renderData, (data) => { | ||
| let basicInfoBeforeVUE = _.map(renderData.slice(0, 2), (data) => { |
| data.category | ||
| ); | ||
| }); | ||
| let basicInfoAfterVUE = _.map(renderData.slice(2), (data) => { |
| category: getMutationTypeClassName(transcript), | ||
| }); | ||
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| // Check if variant is a VUE |
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As far as I understand, the logic here is trying to say, check if this variant is VUE, if it's VUE, don't add protein change and variant classification, and read from VUE component instead. If it's not VUE, add default protein change and variant classification.
So better to change the comment to indicate this is the situation that "add default protein change and variant classification when it is not VUE"
| style={{ | ||
| paddingLeft: 3, | ||
| paddingTop: 2, | ||
| paddingBottom: 2, | ||
| paddingRight: 0, | ||
| marginLeft: -2, | ||
| marginRight: 4, | ||
| }} |
| import * as React from 'react'; | ||
| import functionalGroupsStyle from '../functionalGroups.module.scss'; | ||
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| export declare type RevisedProteinEffectRecord = { |
| [TrackName.UniprotTopology]: 'visible', | ||
| }} | ||
| hugoSymbol={mutation[0].gene.hugoGeneSymbol} | ||
| hugoSymbol={mutation[0]?.gene?.hugoGeneSymbol} |
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Not harmful, but we already have undefined checks above. https://github.com/genome-nexus/genome-nexus-frontend/blob/master/src/page/Variant.tsx#L154-L157
| import { getTranscriptConsequenceSummary } from '../util/AnnotationSummaryUtil'; | ||
| import { getDataFetcher } from '../util/ApiUtils'; | ||
| import genomeNexusInternalClient from '../util/genomeNexusClientInternalInstance'; | ||
| //import genomeNexusInternalClient from '../util/genomeNexusClientInternalInstance'; |
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If it's not being used, we can remove this
| import oncoKbClient from '../util/oncokbClientInstance'; | ||
| import { | ||
| variantToGenomicLocationString, | ||
| //variantToGenomicLocationString, |
3 participants
This uses some of the old "curious cases" infrastructure but replaces it by directly using the VUE data from the revue-website repo. This still needs to be fully refactored to lose all references to "curious cases".
Works for: https://deploy-preview-139--genome-nexus-frontend.netlify.app/variant/4:g.55593576_55593606del
This introduces quite some frontend logic to manage the revising of the protein effect. Eventually we can hopefully move this to the server side instead