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create react-variant-view package #3459
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| # react-variant-view | ||
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| ## License | ||
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| © [cBioPortal](https://github.com/cBioPortal) |
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| { | ||
| "name": "react-variant-view", | ||
| "version": "0.1.0-beta.0", | ||
| "description": "cBioPortal Variant Viewer", | ||
| "main": "dist/index.js", | ||
| "module": "dist/index.es.js", | ||
| "jsnext:main": "dist/index.es.js", | ||
| "typings": "dist/index.d.ts", | ||
| "styles": "dist/styles.css", | ||
| "engines": { | ||
| "node": ">=8.12.0", | ||
| "yarn": ">=1.22.4" | ||
| }, | ||
| "files": [ | ||
| "dist" | ||
| ], | ||
| "author": "cBioPortal", | ||
| "license": "AGPL-3.0-or-later", | ||
| "repository": "cBioPortal/cbioportal-frontend", | ||
| "scripts": { | ||
| "build": "yarn run tcm && cross-env NODE_ENV=production NODE_OPTIONS=--max-old-space-size=2048 yarn run rollup", | ||
| "start": "yarn run watch", | ||
| "watch": "concurrently \"yarn run tcm:watch\" \"yarn run rollup:watch\"", | ||
| "watchSSL": "yarn run watch", | ||
| "rollup": "rollup -c rollup.config.ts", | ||
| "rollup:watch": "yarn run rollup --watch", | ||
| "tcm": "tcm -p src/**/*.module.scss", | ||
| "tcm:watch": "yarn run tcm --watch", | ||
| "prepare": "yarn run build", | ||
| "test": "cross-env CI=1 react-scripts-ts test --env=jsdom", | ||
| "test:watch": "yarn run test --watch" | ||
| }, | ||
| "peerDependencies": { | ||
| "mobx": "^3.0.0 || ^4.0.0 || ^5.0.0", | ||
| "mobx-react": "^4.0.0 || ^5.0.0", | ||
| "prop-types": "^15.5.4", | ||
| "react": "^15.0.0 || ^16.0.0", | ||
| "react-dom": "^15.0.0 || ^16.0.0", | ||
| "bootstrap": "^3.0.0 || ^4.0.0" | ||
| }, | ||
| "dependencies": { | ||
| "autobind-decorator": "^2.1.0", | ||
| "cbioportal-frontend-commons": "^0.3.9", | ||
| "cbioportal-utils": "^0.2.7", | ||
| "classnames": "^2.2.5", | ||
| "font-awesome": "^4.7.0", | ||
| "genome-nexus-ts-api-client": "^1.1.7", | ||
| "jquery": "^3.2.1", | ||
| "lodash": "^4.17.11", | ||
| "mobxpromise": "github:cbioportal/mobxpromise#v1.0.2", | ||
| "oncokb-styles": "~0.1.2", | ||
| "oncokb-ts-api-client": "^1.1.2", | ||
| "react-bootstrap": "^0.31.5", | ||
| "react-collapse": "4.0.3", | ||
| "react-if": "^2.1.0", | ||
| "react-motion": "^0.5.2", | ||
| "react-mutation-mapper": "^0.6.10", | ||
| "react-rangeslider": "^2.2.0", | ||
| "react-select": "^3.0.4", | ||
| "react-spinkit": "^3.0.0", | ||
| "react-table": "^6.10.0", | ||
| "seamless-immutable": "^7.1.4", | ||
| "superagent": "^3.8.3", | ||
| "typescript": "4.0.3" | ||
| }, | ||
| "devDependencies": { | ||
| "@testing-library/react": "^9.3.2", | ||
| "react-scripts-ts": "^3.1.0" | ||
| } | ||
| } | ||
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| import getRollupOptions from '../config/rollup.config'; | ||
| import pkg from './package.json'; | ||
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| export default getRollupOptions( | ||
| 'src/index.tsx', | ||
| pkg.main, | ||
| pkg.module, | ||
| pkg.styles | ||
| ); |
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packages/react-variant-view/src/component/biologicalFunction/BiologicalFunction.tsx
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| import { observer } from 'mobx-react'; | ||
| import * as React from 'react'; | ||
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| import Oncokb from './Oncokb'; | ||
| import { IndicatorQueryResp } from 'oncokb-ts-api-client'; | ||
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| interface IBiologicalFunctionProps { | ||
| oncokb: IndicatorQueryResp | undefined; | ||
| isCanonicalTranscriptSelected: boolean; | ||
| } | ||
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| @observer | ||
| class BiologicalFunction extends React.Component<IBiologicalFunctionProps> { | ||
| public render() { | ||
| return ( | ||
| <Oncokb | ||
| oncokb={this.props.oncokb} | ||
| isCanonicalTranscriptSelected={ | ||
| this.props.isCanonicalTranscriptSelected | ||
| } | ||
| /> | ||
| ); | ||
| } | ||
| } | ||
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| export default BiologicalFunction; |
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packages/react-variant-view/src/component/biologicalFunction/Oncokb.tsx
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| import { observer } from 'mobx-react'; | ||
| import * as React from 'react'; | ||
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| import { DefaultTooltip } from 'cbioportal-frontend-commons'; | ||
| import { IndicatorQueryResp } from 'oncokb-ts-api-client'; | ||
| import featureTableStyle from '../featureTable/FeatureTable.module.scss'; | ||
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| interface IOncokbProps { | ||
| oncokb: IndicatorQueryResp | undefined; | ||
| isCanonicalTranscriptSelected: boolean; | ||
| } | ||
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| export enum ONCOGENICITY { | ||
| ONCOGENIC = 'Oncogenic', | ||
| LIKELY_ONCOGENIC = 'Likely Oncogenic', | ||
| PREDICTED_ONCOGENIC = 'Predicted Oncogenic', | ||
| NEUTRAL = 'Neutral', | ||
| LIKELY_NEUTRAL = 'Likely Neutral', | ||
| INCONCLUSIVE = 'Inconclusive', | ||
| VUS = 'vus', | ||
| UNKNOWN = 'Unknown', | ||
| } | ||
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| export const ONCOGENICITY_CLASS_NAMES: { [oncogenic: string]: string } = { | ||
| [ONCOGENICITY.ONCOGENIC]: 'oncogenic', | ||
| [ONCOGENICITY.LIKELY_ONCOGENIC]: 'oncogenic', | ||
| [ONCOGENICITY.PREDICTED_ONCOGENIC]: 'oncogenic', | ||
| [ONCOGENICITY.NEUTRAL]: 'neutral', | ||
| [ONCOGENICITY.LIKELY_NEUTRAL]: 'neutral', | ||
| [ONCOGENICITY.INCONCLUSIVE]: 'inconclusive', | ||
| [ONCOGENICITY.VUS]: 'vus', | ||
| [ONCOGENICITY.UNKNOWN]: 'unknown', | ||
| }; | ||
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| export enum MUTATION_EFFECT { | ||
| GAIN_OF_FUNCTION = 'Gain-of-function', | ||
| LIKELY_GAIN_OF_FUNCTION = 'Likely Gain-of-function', | ||
| LOSS_OF_FUNCTION = 'Loss-of-function', | ||
| LIKELY_LOSS_OF_FUNCTION = 'Likely Loss-of-function', | ||
| SWITCH_OF_FUNCTION = 'Switch-of-function', | ||
| LIKELY_SWITCH_OF_FUNCTION = 'Likely Switch-of-function', | ||
| NEUTRAL = 'Neutral', | ||
| LIKELY_NEUTRAL = 'Likely Neutral', | ||
| INCONCLUSIVE = 'Inconclusive', | ||
| UNKNOWN = 'Unknown', | ||
| } | ||
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| export const MUTATION_EFFECT_CLASS_NAMES: { | ||
| [mutationEffect: string]: string; | ||
| } = { | ||
| [MUTATION_EFFECT.GAIN_OF_FUNCTION]: 'gain', | ||
| [MUTATION_EFFECT.LIKELY_GAIN_OF_FUNCTION]: 'gain', | ||
| [MUTATION_EFFECT.LOSS_OF_FUNCTION]: 'loss', | ||
| [MUTATION_EFFECT.LIKELY_LOSS_OF_FUNCTION]: 'loss', | ||
| [MUTATION_EFFECT.SWITCH_OF_FUNCTION]: 'switch', | ||
| [MUTATION_EFFECT.LIKELY_SWITCH_OF_FUNCTION]: 'switch', | ||
| [MUTATION_EFFECT.NEUTRAL]: 'neutral', | ||
| [MUTATION_EFFECT.LIKELY_NEUTRAL]: 'neutral', | ||
| [MUTATION_EFFECT.INCONCLUSIVE]: 'inconclusive', | ||
| [MUTATION_EFFECT.UNKNOWN]: 'unknown', | ||
| }; | ||
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| export const ONCOKB_URL = 'https://www.oncokb.org'; | ||
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| @observer | ||
| export default class Oncokb extends React.Component<IOncokbProps> { | ||
| public oncogenicity(oncokb: IndicatorQueryResp) { | ||
| if (oncokb.oncogenic && oncokb.oncogenic !== '') { | ||
| return oncokb.oncogenic; | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
| public oncokbTooltip(oncokbUrl: string) { | ||
| return ( | ||
| <DefaultTooltip | ||
| placement="top" | ||
| overlay={ | ||
| <span> | ||
| <a | ||
| href={oncokbUrl} | ||
| target="_blank" | ||
| rel="noopener noreferrer" | ||
| > | ||
| OncoKB | ||
| </a>{' '} | ||
| is a precision oncology knowledge base and contains | ||
| <br /> | ||
| information about the effects and treatment implications | ||
| <br /> | ||
| of specific cancer gene alterations. <br /> | ||
| </span> | ||
| } | ||
| > | ||
| <a href={oncokbUrl} target="_blank" rel="noopener noreferrer"> | ||
| OncoKB | ||
| <i className="fas fa-external-link-alt" /> | ||
| {!this.props.isCanonicalTranscriptSelected && ( | ||
| <span> *</span> | ||
| )} | ||
| </a> | ||
| </DefaultTooltip> | ||
| ); | ||
| } | ||
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| public mutationEffect(oncokb: IndicatorQueryResp) { | ||
| if (oncokb.mutationEffect && oncokb.mutationEffect.knownEffect !== '') { | ||
| return oncokb.mutationEffect.knownEffect; | ||
| } else { | ||
| return null; | ||
| } | ||
| } | ||
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| public render() { | ||
| const oncokbUrl = generateOncokbLink(ONCOKB_URL, this.props.oncokb); | ||
| return this.props.oncokb ? ( | ||
| <div className={featureTableStyle['functional-group']}> | ||
| <div className={featureTableStyle['data-source']}> | ||
| {this.oncokbTooltip(oncokbUrl)} | ||
| </div> | ||
| <div className={featureTableStyle['data-with-link']}> | ||
| {this.biologicalFunctionData( | ||
| this.mutationEffect(this.props.oncokb), | ||
| this.oncogenicity(this.props.oncokb), | ||
| oncokbUrl | ||
| )} | ||
| </div> | ||
| </div> | ||
| ) : ( | ||
| <div className={featureTableStyle['functional-group']}> | ||
| <div className={featureTableStyle['data-source']}> | ||
| {this.oncokbTooltip(oncokbUrl)} | ||
| </div> | ||
| <div>N/A</div> | ||
| </div> | ||
| ); | ||
| } | ||
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| private biologicalFunctionData( | ||
| mutationEffect: string | null, | ||
| oncogenicity: string | null, | ||
| oncokbUrl: string | ||
| ) { | ||
| let biologicalFunctionData: string | null = null; | ||
| if (mutationEffect && oncogenicity) { | ||
| biologicalFunctionData = `${mutationEffect}, ${oncogenicity}`; | ||
| } else if (mutationEffect) { | ||
| biologicalFunctionData = oncogenicity; | ||
| } else if (oncogenicity) { | ||
| biologicalFunctionData = mutationEffect; | ||
| } else { | ||
| biologicalFunctionData = 'N/A'; | ||
| } | ||
| return ( | ||
| <a href={oncokbUrl} target="_blank" rel="noopener noreferrer"> | ||
| <p>{biologicalFunctionData}</p> | ||
| </a> | ||
| ); | ||
| } | ||
| } | ||
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| export function generateOncokbLink( | ||
| link: string, | ||
| oncokb: IndicatorQueryResp | undefined | ||
| ): string { | ||
| let url = link; | ||
| const hugoSymbol = oncokb && oncokb.query && oncokb.query.hugoSymbol; | ||
| const alteration = oncokb && oncokb.query && oncokb.query.alteration; | ||
| if (hugoSymbol && alteration) { | ||
| url = `${url}/gene/${hugoSymbol}/${alteration}`; | ||
| } | ||
| return url; | ||
| } |
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96
packages/react-variant-view/src/component/featureTable/FeatureTable.module.scss
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| .group-name { | ||
| background-color: #f2f2f2; | ||
| font-size: 0.875rem; | ||
| font-weight: bold; | ||
| margin-top: 3px; | ||
| margin-bottom: 3px; | ||
| padding-bottom: 4px; | ||
| padding-top: 4px; | ||
| max-width: 27%; | ||
| display: flex; | ||
| align-items: center; | ||
| } | ||
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| .group-content { | ||
| display: flex; | ||
| align-items: center; | ||
| } | ||
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| .data-content { | ||
| margin-top: 3px; | ||
| margin-bottom: 3px; | ||
| padding-bottom: 4px; | ||
| padding-top: 4px; | ||
| } | ||
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| .data-group-gap { | ||
| display: block; | ||
| } | ||
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| .no-data { | ||
| font-size: 1rem; | ||
| margin-left: 15px; | ||
| color: black; | ||
| } | ||
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| /* gnomad */ | ||
| .gnomad { | ||
| font-size: 1rem; | ||
| font-weight: bold; | ||
| } | ||
|
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| /* dbsnp */ | ||
| .dbsnp { | ||
| font-size: 1rem; | ||
| font-weight: bold; | ||
| } | ||
|
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| /* functional prediction */ | ||
| .functional-prediction-data { | ||
| display: flex; | ||
| align-items: center; | ||
| font-size: 1rem; | ||
| } | ||
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| .functional-prediction-no-data { | ||
| font-size: 1rem; | ||
| font-weight: bold; | ||
| } | ||
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| // oncokb | ||
| .oncokb { | ||
| font-size: 1rem; | ||
| font-weight: bold; | ||
| } | ||
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| // redesign from here. remove some of classes above after complete | ||
| .feature-table { | ||
| padding-top: 10px; | ||
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| p { | ||
| margin-bottom: 5px; | ||
| } | ||
| p:last-child { | ||
| margin-bottom: 0; | ||
| } | ||
| } | ||
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| .data-source { | ||
| min-width: 200px; | ||
| } | ||
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| .functional-group { | ||
| display: flex; | ||
| } | ||
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| .data-with-link { | ||
| a { | ||
| color: black; | ||
| &:hover, | ||
| &:focus, | ||
| &:active, | ||
| &:visited { | ||
| color: black; | ||
| } | ||
| } | ||
| } |
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We need to make sure that these dependencies are complete. This package may still work inside the monorepo even if some dependencies are not listed here. But when we include the package in another project we may get missing dependency errors. For now we can test it with signal to see if it works fine (after publishing the beta version to npm).