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src/main/webapp/app/pages/annotationPage/SomaticGermlineAlterationView.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,242 @@ | ||
| import React from 'react'; | ||
| import { observer } from 'mobx-react'; | ||
|
|
||
| import { OncoTreeLink } from 'app/shared/utils/UrlUtils'; | ||
| import { | ||
| ANNOTATION_PAGE_TAB_KEYS, | ||
| DEFAULT_MARGIN_BOTTOM_LG, | ||
| OTHER_BIOMARKERS, | ||
| } from 'app/config/constants'; | ||
| import styles from 'app/pages/alterationPage/AlterationPage.module.scss'; | ||
| import InfoIcon from 'app/shared/icons/InfoIcon'; | ||
| import { Col, Row } from 'react-bootstrap'; | ||
| import classnames from 'classnames'; | ||
| import { action, computed } from 'mobx'; | ||
| import autobind from 'autobind-decorator'; | ||
| import { | ||
| BiologicalVariant, | ||
| VariantAnnotation, | ||
| } from 'app/shared/api/generated/OncoKbPrivateAPI'; | ||
| import { | ||
| FdaImplication, | ||
| TherapeuticImplication, | ||
| } from 'app/store/AnnotationStore'; | ||
| import { isCategoricalAlteration } from 'app/shared/utils/Utils'; | ||
| import CancerTypeSelect from 'app/shared/dropdown/CancerTypeSelect'; | ||
| import AlterationTableTabs from 'app/pages/annotationPage/AlterationTableTabs'; | ||
| import { getSummaries, SummaryKey } from 'app/pages/annotationPage/Utils'; | ||
| import AppStore from 'app/store/AppStore'; | ||
| import { Alteration } from 'app/shared/api/generated/OncoKbAPI'; | ||
|
|
||
| export type IAlterationView = { | ||
| appStore?: AppStore; | ||
| hugoSymbol: string; | ||
| alteration: string; | ||
| matchedAlteration: Alteration | undefined; | ||
| tumorType: string; | ||
| onChangeTumorType: (newTumorType: string) => void; | ||
| annotation: VariantAnnotation; | ||
| biologicalAlterations?: BiologicalVariant[]; | ||
| relevantAlterations?: Alteration[]; | ||
| fdaImplication: FdaImplication[]; | ||
| therapeuticImplications: TherapeuticImplication[]; | ||
| diagnosticImplications: TherapeuticImplication[]; | ||
| prognosticImplications: TherapeuticImplication[]; | ||
| defaultSelectedTab?: ANNOTATION_PAGE_TAB_KEYS; | ||
| onChangeTab?: ( | ||
| selectedTabKey: ANNOTATION_PAGE_TAB_KEYS, | ||
| newTabKey: ANNOTATION_PAGE_TAB_KEYS | ||
| ) => void; | ||
| }; | ||
| @observer | ||
| export default class SomaticGermlineAlterationView extends React.Component< | ||
| IAlterationView, | ||
| {} | ||
| > { | ||
| @autobind | ||
| @action | ||
| updateTumorTypeQuery(selectedOption: any) { | ||
| this.props.onChangeTumorType(selectedOption ? selectedOption.value : ''); | ||
| } | ||
|
|
||
| @computed | ||
| get tumorTypeSummaries() { | ||
| const orderedSummaries = this.props.tumorType | ||
| ? [ | ||
| SummaryKey.TUMOR_TYPE_SUMMARY, | ||
| SummaryKey.DIAGNOSTIC_SUMMARY, | ||
| SummaryKey.PROGNOSTIC_SUMMARY, | ||
| ] | ||
| : []; | ||
| return getSummaries(this.props.annotation, orderedSummaries); | ||
| } | ||
|
|
||
| @computed get isCategoricalAlteration() { | ||
| return isCategoricalAlteration(this.props.alteration); | ||
| } | ||
|
|
||
| @computed | ||
| get showGeneNameLink() { | ||
| const lHugo = this.props.hugoSymbol.toLowerCase(); | ||
| const altNameIncludesGene = this.props.alteration | ||
| .toLowerCase() | ||
| .includes(lHugo); | ||
| const isOtherBiomarkers = lHugo === OTHER_BIOMARKERS.toLowerCase(); | ||
| return !altNameIncludesGene && !isOtherBiomarkers; | ||
| } | ||
|
|
||
| @computed | ||
| get relevantBiologicalVariants(): BiologicalVariant[] { | ||
| if ( | ||
| this.isCategoricalAlteration && | ||
| this.props.biologicalAlterations && | ||
| this.props.relevantAlterations | ||
| ) { | ||
| const relevantAltNames = this.props.relevantAlterations.map( | ||
| alt => alt.alteration | ||
| ); | ||
| return this.props.biologicalAlterations.filter(variant => | ||
| relevantAltNames.includes(variant.variant.alteration) | ||
| ); | ||
| } else { | ||
| return []; | ||
| } | ||
| } | ||
|
|
||
| render() { | ||
| const dropdownColor = '#0968C3'; | ||
| return ( | ||
| <> | ||
| <Row className="mt-4"> | ||
| <Col> | ||
| <div | ||
| className={classnames( | ||
| 'd-flex', | ||
| 'align-items-center', | ||
| 'justify-content-left', | ||
| 'flex-wrap', | ||
| DEFAULT_MARGIN_BOTTOM_LG | ||
| )} | ||
| > | ||
| <span className={classnames('mr-3', 'h6')}> | ||
| Filter this list by: | ||
| </span> | ||
| <span | ||
| className={classnames(styles.headerTumorTypeSelection, 'mr-2')} | ||
| > | ||
| <span> | ||
| <CancerTypeSelect | ||
| styles={{ | ||
| control: base => ({ | ||
| ...base, | ||
| height: '30px', | ||
| minHeight: '30px', | ||
| borderBottomWidth: '1px', | ||
| borderBottomColor: dropdownColor, | ||
| borderStyle: 'none', | ||
| borderBottomStyle: 'solid', | ||
| borderRadius: '0px', | ||
| '&:hover': { | ||
| borderBottomColor: dropdownColor, | ||
| }, | ||
| }), | ||
| indicatorsContainer: base => ({ | ||
| ...base, | ||
| '& div': { | ||
| color: dropdownColor, | ||
| }, | ||
| '& div:hover': { | ||
| color: dropdownColor, | ||
| }, | ||
| }), | ||
| indicatorSeparator: base => ({ | ||
| ...base, | ||
| width: '0px', | ||
| }), | ||
| dropdownIndicator: base => ({ | ||
| ...base, | ||
| padding: 4, | ||
| }), | ||
| clearIndicator: base => ({ | ||
| ...base, | ||
| padding: 4, | ||
| }), | ||
| valueContainer: base => ({ | ||
| ...base, | ||
| padding: '0px 6px', | ||
| }), | ||
| input: base => ({ | ||
| ...base, | ||
| margin: 0, | ||
| padding: 0, | ||
| }), | ||
| menu: base => ({ ...base, zIndex: 10 }), | ||
| }} | ||
| cancerType={this.props.tumorType} | ||
| onChange={(selectedOption: any) => | ||
| this.updateTumorTypeQuery(selectedOption) | ||
| } | ||
| /> | ||
| </span> | ||
| </span> | ||
| <InfoIcon | ||
| overlay={ | ||
| <span> | ||
| For cancer type specific information, please select a cancer | ||
| type from the dropdown. The cancer type is curated using{' '} | ||
| <OncoTreeLink /> | ||
| </span> | ||
| } | ||
| placement="top" | ||
| /> | ||
| </div> | ||
| </Col> | ||
| </Row> | ||
| {this.props.tumorType && !this.isCategoricalAlteration ? ( | ||
| <Row> | ||
| <Col> | ||
| {this.tumorTypeSummaries.map((summary, index) => { | ||
| return ( | ||
| <div | ||
| className={DEFAULT_MARGIN_BOTTOM_LG} | ||
| key={`summary-${index}`} | ||
| > | ||
| <h6 className={'mb-0'}>{summary.title}</h6> | ||
| {summary.content} | ||
| </div> | ||
| ); | ||
| })} | ||
| </Col> | ||
| </Row> | ||
| ) : null} | ||
| <Row className="mt-2"> | ||
| <Col> | ||
| <AlterationTableTabs | ||
| selectedTab={this.props.defaultSelectedTab} | ||
| appStore={this.props.appStore} | ||
| hugoSymbol={this.props.hugoSymbol} | ||
| alteration={ | ||
| this.props.matchedAlteration | ||
| ? { | ||
| alteration: this.props.matchedAlteration.alteration, | ||
| name: this.props.matchedAlteration.name, | ||
| } | ||
| : { | ||
| alteration: this.props.alteration, | ||
| name: this.props.alteration, | ||
| } | ||
| } | ||
| cancerType={this.props.tumorType} | ||
| biological={[]} | ||
| tx={this.props.therapeuticImplications} | ||
| dx={this.props.diagnosticImplications} | ||
| px={this.props.prognosticImplications} | ||
| fda={this.props.fdaImplication} | ||
| onChangeTab={this.props.onChangeTab} | ||
| /> | ||
| </Col> | ||
| </Row> | ||
| </> | ||
| ); | ||
| } | ||
| } |
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