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Hide civic Fix reVUE to fit new genome nexus model Update packages - set cheerio and parse5 version in resolutions, because the 'juice' dependency in cbioportal frontend commons causes some conficts, using older version of cheerio and parse5 is a temp fix.
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200 changes: 100 additions & 100 deletions
200
src/component/variantPage/clinicalImplication/Civic.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,112 +1,112 @@ | ||
| import { observer } from 'mobx-react'; | ||
| // import { observer } from 'mobx-react'; | ||
| import * as React from 'react'; | ||
|
|
||
| import { ICivicEvidenceSummary, ICivicVariantSummary } from 'cbioportal-utils'; | ||
| import { DefaultTooltip } from 'cbioportal-frontend-commons'; | ||
| // import { ICivicEvidenceSummary, ICivicVariantSummary } from 'cbioportal-utils'; | ||
| // import { DefaultTooltip } from 'cbioportal-frontend-commons'; | ||
|
|
||
| import { | ||
| ClinicalSignificance, | ||
| Evidence, | ||
| EvidenceType, | ||
| } from '../../../util/EvidenceUtils'; | ||
| import EvidenceSummary from './EvidenceSummary'; | ||
| import functionalGroupsStyle from '../functionalGroups.module.scss'; | ||
| // import { | ||
| // ClinicalSignificance, | ||
| // Evidence, | ||
| // EvidenceType, | ||
| // } from '../../../util/EvidenceUtils'; | ||
| // import EvidenceSummary from './EvidenceSummary'; | ||
| // import functionalGroupsStyle from '../functionalGroups.module.scss'; | ||
|
|
||
| interface ICivicProps { | ||
| civic?: ICivicVariantSummary; | ||
| isCanonicalTranscriptSelected: boolean; | ||
| } | ||
| // interface ICivicProps { | ||
| // civic?: ICivicVariantSummary; | ||
| // isCanonicalTranscriptSelected: boolean; | ||
| // } | ||
|
|
||
| const DEFAULT_CIVIC_URL = 'https://civicdb.org/'; | ||
| // const DEFAULT_CIVIC_URL = 'https://civicdb.org/'; | ||
|
|
||
| function getEvidenceUrl(civic: ICivicVariantSummary, evidenceId: number) { | ||
| return `https://civicdb.org/events/genes/${civic.geneId}/summary/variants/${civic.id}/summary/evidence/${evidenceId}/summary#evidence`; | ||
| } | ||
| // function getEvidenceUrl(civic: ICivicVariantSummary, evidenceId: number) { | ||
| // return `https://civicdb.org/events/genes/${civic.geneId}/summary/variants/${civic.id}/summary/evidence/${evidenceId}/summary#evidence`; | ||
| // } | ||
|
|
||
| const CivicInfo: React.FunctionComponent<{ | ||
| url: string; | ||
| isCanonicalTranscriptSelected: boolean; | ||
| }> = (props) => { | ||
| return ( | ||
| <DefaultTooltip | ||
| placement="top" | ||
| overlay={ | ||
| <div style={{ maxWidth: 350 }}> | ||
| <a | ||
| href={props.url} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| CIViC | ||
| </a>{' '} | ||
| is a community-edited forum for discussion and | ||
| interpretation of peer-reviewed publications pertaining to | ||
| the clinical relevance of variants (or biomarker | ||
| alterations) in cancer. | ||
| </div> | ||
| } | ||
| > | ||
| <a href={props.url} target="_blank" rel="noopener noreferrer"> | ||
| CIViC <i className="fas fa-external-link-alt" /> | ||
| {!props.isCanonicalTranscriptSelected && `*`} | ||
| </a> | ||
| </DefaultTooltip> | ||
| ); | ||
| }; | ||
| // const CivicInfo: React.FunctionComponent<{ | ||
| // url: string; | ||
| // isCanonicalTranscriptSelected: boolean; | ||
| // }> = (props) => { | ||
| // return ( | ||
| // <DefaultTooltip | ||
| // placement="top" | ||
| // overlay={ | ||
| // <div style={{ maxWidth: 350 }}> | ||
| // <a | ||
| // href={props.url} | ||
| // target="_blank" | ||
| // rel="noopener noreferrer" | ||
| // > | ||
| // CIViC | ||
| // </a>{' '} | ||
| // is a community-edited forum for discussion and | ||
| // interpretation of peer-reviewed publications pertaining to | ||
| // the clinical relevance of variants (or biomarker | ||
| // alterations) in cancer. | ||
| // </div> | ||
| // } | ||
| // > | ||
| // <a href={props.url} target="_blank" rel="noopener noreferrer"> | ||
| // CIViC <i className="fas fa-external-link-alt" /> | ||
| // {!props.isCanonicalTranscriptSelected && `*`} | ||
| // </a> | ||
| // </DefaultTooltip> | ||
| // ); | ||
| // }; | ||
|
|
||
| function civicEvidenceToEvidence( | ||
| civicEvidence: ICivicEvidenceSummary | ||
| ): Evidence { | ||
| return { | ||
| ...civicEvidence, | ||
| clinicalSignificance: civicEvidence.clinicalSignificance.includes( | ||
| ClinicalSignificance.Sensitivity | ||
| ) | ||
| ? ClinicalSignificance.Sensitivity | ||
| : civicEvidence.clinicalSignificance, | ||
| } as Evidence; | ||
| } | ||
| // function civicEvidenceToEvidence( | ||
| // civicEvidence: ICivicEvidenceSummary | ||
| // ): Evidence { | ||
| // return { | ||
| // ...civicEvidence, | ||
| // clinicalSignificance: civicEvidence.clinicalSignificance.includes( | ||
| // ClinicalSignificance.Sensitivity | ||
| // ) | ||
| // ? ClinicalSignificance.Sensitivity | ||
| // : civicEvidence.clinicalSignificance, | ||
| // } as Evidence; | ||
| // } | ||
|
|
||
| @observer | ||
| export default class Civic extends React.Component<ICivicProps> { | ||
| get clinicalEvidences() { | ||
| return ( | ||
| this.props.civic?.evidences | ||
| .map(civicEvidenceToEvidence) | ||
| .filter( | ||
| (e) => | ||
| e.type === EvidenceType.Predictive || | ||
| e.type === EvidenceType.Prognostic || | ||
| e.type === EvidenceType.Diagnostic | ||
| ) || [] | ||
| ); | ||
| } | ||
| // @observer | ||
| // export default class Civic extends React.Component<ICivicProps> { | ||
| // get clinicalEvidences() { | ||
| // return ( | ||
| // this.props.civic?.evidences | ||
| // .map(civicEvidenceToEvidence) | ||
| // .filter( | ||
| // (e) => | ||
| // e.type === EvidenceType.Predictive || | ||
| // e.type === EvidenceType.Prognostic || | ||
| // e.type === EvidenceType.Diagnostic | ||
| // ) || [] | ||
| // ); | ||
| // } | ||
|
|
||
| public render() { | ||
| const url = this.props.civic ? this.props.civic.url : DEFAULT_CIVIC_URL; | ||
| // public render() { | ||
| // const url = this.props.civic ? this.props.civic.url : DEFAULT_CIVIC_URL; | ||
|
|
||
| return ( | ||
| <div className={functionalGroupsStyle['functional-group']}> | ||
| <div className={functionalGroupsStyle['data-source']}> | ||
| <CivicInfo | ||
| url={url} | ||
| isCanonicalTranscriptSelected={ | ||
| this.props.isCanonicalTranscriptSelected | ||
| } | ||
| /> | ||
| </div> | ||
| <EvidenceSummary | ||
| url={url} | ||
| evidences={this.clinicalEvidences} | ||
| getEvidenceUrl={this.getEvidenceUrl} | ||
| /> | ||
| </div> | ||
| ); | ||
| } | ||
| // return ( | ||
| // <div className={functionalGroupsStyle['functional-group']}> | ||
| // <div className={functionalGroupsStyle['data-source']}> | ||
| // <CivicInfo | ||
| // url={url} | ||
| // isCanonicalTranscriptSelected={ | ||
| // this.props.isCanonicalTranscriptSelected | ||
| // } | ||
| // /> | ||
| // </div> | ||
| // <EvidenceSummary | ||
| // url={url} | ||
| // evidences={this.clinicalEvidences} | ||
| // getEvidenceUrl={this.getEvidenceUrl} | ||
| // /> | ||
| // </div> | ||
| // ); | ||
| // } | ||
|
|
||
| private getEvidenceUrl = (evidence: ICivicEvidenceSummary) => { | ||
| return this.props.civic | ||
| ? getEvidenceUrl(this.props.civic, evidence.id) | ||
| : DEFAULT_CIVIC_URL; | ||
| }; | ||
| } | ||
| // private getEvidenceUrl = (evidence: ICivicEvidenceSummary) => { | ||
| // return this.props.civic | ||
| // ? getEvidenceUrl(this.props.civic, evidence.id) | ||
| // : DEFAULT_CIVIC_URL; | ||
| // }; | ||
| // } |
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