Add reVUE revised effect for one KIT variant #139
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
|
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@@ -20,6 +20,8 @@ import basicInfo from './BasicInfo.module.scss'; | |
| import { Link } from 'react-router-dom'; | ||
| import { annotationQueryFields } from '../../config/configDefaults'; | ||
| import Toggle from '../Toggle'; | ||
| import { RevisedProteinEffectRecord, VUE } from './biologicalFunction/ReVUE'; | ||
| import { ReVUEContent } from './biologicalFunction/ReVUE'; | ||
|
|
||
| interface IBasicInfoProps { | ||
| annotation: VariantAnnotationSummary | undefined; | ||
|
|
@@ -31,6 +33,8 @@ interface IBasicInfoProps { | |
| isCanonicalTranscriptSelected?: boolean | undefined; | ||
| allValidTranscripts: string[]; | ||
| onTranscriptSelect(transcriptId: string): void; | ||
| vue: VUE | undefined; | ||
| revisedProteinEffectRecord: RevisedProteinEffectRecord | undefined; | ||
| } | ||
|
|
||
| type MutationTypeFormat = { | ||
|
|
@@ -141,15 +145,23 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> { | |
| if (this.props.annotation) { | ||
| let renderData: BasicInfoData[] | null = | ||
| this.getDataFromTranscriptConsequenceSummary( | ||
| selectedTranscript || canonicalTranscript, | ||
| this.props.variant | ||
| ); | ||
| if (renderData === null) { | ||
| return null; | ||
| } | ||
| if (renderData) { | ||
| renderData = renderData.filter((data) => data.value != null); // remove null fields | ||
| } | ||
| let basicInfoBeforeVUE = _.map(renderData.slice(0, 2), (data) => { | ||
| return this.generateBasicInfoPills( | ||
| data.value, | ||
| data.key, | ||
| data.category | ||
| ); | ||
| }); | ||
| let basicInfoAfterVUE = _.map(renderData.slice(2), (data) => { | ||
|
|
||
| return this.generateBasicInfoPills( | ||
| data.value, | ||
| data.key, | ||
|
|
@@ -160,7 +172,14 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> { | |
| return ( | ||
| <div className={basicInfo['basic-info-container']}> | ||
| <span className={basicInfo['basic-info-pills']}> | ||
| {basicInfoBeforeVUE} | ||
| {this.props.revisedProteinEffectRecord && | ||
| this.props.vue && | ||
| this.generateBasicInfoReVUE( | ||
| this.props.vue, | ||
| this.props.revisedProteinEffectRecord | ||
| )} | ||
| {basicInfoAfterVUE} | ||
| {this.jsonButton()} | ||
| {haveTranscriptTable && | ||
| this.transcriptsButton(this.showAllTranscripts)} | ||
|
|
@@ -204,7 +223,8 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> { | |
| } | ||
|
|
||
| public getDataFromTranscriptConsequenceSummary( | ||
| transcript: TranscriptConsequenceSummary | undefined, | ||
| variant: string | ||
| ): BasicInfoData[] | null { | ||
| // no canonical transcript, return null | ||
| if (transcript === undefined) { | ||
|
|
@@ -235,18 +255,23 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> { | |
| key: 'tsg', | ||
| category: 'tsg', | ||
| }); | ||
|
|
||
| // Check if variant is a VUE | ||
|
There was a problem hiding this comment. 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" |
||
| if (!this.props.revisedProteinEffectRecord) { | ||
| // protein change | ||
| parsedData.push({ | ||
| value: transcript.hgvspShort, | ||
| key: 'hgvsShort', | ||
| category: 'default', | ||
| }); | ||
| // variant classification | ||
| parsedData.push({ | ||
| value: transcript.variantClassification, | ||
| key: 'variantClassification', | ||
| category: getMutationTypeClassName(transcript), | ||
| }); | ||
| } | ||
|
|
||
| // variant type | ||
| parsedData.push({ | ||
| value: this.props.annotation!.variantType, | ||
|
|
@@ -342,6 +367,72 @@ export default class BasicInfo extends React.Component<IBasicInfoProps> { | |
| ); | ||
| } | ||
|
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||
| public generateBasicInfoReVUE( | ||
| vue: VUE, | ||
| revisedProteinEffectRecord: RevisedProteinEffectRecord | ||
| ) { | ||
| return ( | ||
| <DefaultTooltip | ||
| placement="bottom" | ||
| overlay={ | ||
| <span> | ||
| <ReVUEContent vue={vue} /> | Source:{' '} | ||
| <a | ||
| href="https://cancerrevue.org" | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| reVUE <i className="fa fa-external-link" /> | ||
| </a> | ||
| </span> | ||
| } | ||
| > | ||
| <span | ||
| className={classNames(basicInfo[`vue-wrapper`])} | ||
| style={{ | ||
| paddingLeft: 3, | ||
| paddingTop: 2, | ||
| paddingBottom: 2, | ||
| paddingRight: 0, | ||
| marginLeft: -2, | ||
| marginRight: 4, | ||
| }} | ||
|
Comment on lines
+392
to
+399
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||
| > | ||
| <a | ||
| href="https://cancerrevue.org" | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| style={{ textDecoration: 'none' }} | ||
| > | ||
| <img | ||
| src="https://www.cancerrevue.org/static/media/vue_logo.f7904d3925e95ec147ad.png" | ||
|
There was a problem hiding this comment. 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 |
||
| alt="reVUE logo" | ||
| width={22} | ||
| style={{ paddingRight: 5, marginTop: -2 }} | ||
| /> | ||
| <span | ||
| style={{ color: '#8e7cc3' }} | ||
| className={classNames(basicInfo[`data-pills`])} | ||
| > | ||
| VUE | ||
| </span> | ||
| <span className={classNames(basicInfo[`data-pills`])}> | ||
| {revisedProteinEffectRecord.revisedProteinEffect} | ||
| </span> | ||
| <span | ||
| className={classNames( | ||
| basicInfo[`data-pills`], | ||
| basicInfo[`inframe-mutation`] | ||
| )} | ||
| > | ||
| {revisedProteinEffectRecord.variantClassification} | ||
| </span> | ||
| </a> | ||
| </span> | ||
| </DefaultTooltip> | ||
| ); | ||
| } | ||
|
|
||
| public generateBasicInfoPills( | ||
| value: string | null, | ||
| key: string, | ||
|
|
||
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Better to find by name or id