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add hgvsg column in mutation table and link out to genome nexus
- hgvsg is shown by default - the hgvsg will be shorted with ... if the ref or var is too long
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107 changes: 107 additions & 0 deletions
107
src/shared/components/mutationTable/column/HgvsgColumnFormatter.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,107 @@ | ||
| import * as React from 'react'; | ||
| import {Circle} from "better-react-spinkit"; | ||
| import 'rc-tooltip/assets/bootstrap_white.css'; | ||
| import {Mutation} from "shared/api/generated/CBioPortalAPI"; | ||
| import { | ||
| TableCellStatusIndicator, | ||
| TableCellStatus, | ||
| VariantAnnotation | ||
| } from "cbioportal-frontend-commons"; | ||
| import GenomeNexusCache, { GenomeNexusCacheDataType } from "shared/cache/GenomeNexusCache"; | ||
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| import hgvsgStyles from "./hgvsg.module.scss"; | ||
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| export default class HgvsgColumnFormatter { | ||
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| public static renderFunction(data:Mutation[], | ||
| genomeNexusCache:GenomeNexusCache|undefined) { | ||
| const genomeNexusCacheData = HgvsgColumnFormatter.getGenomeNexusDataFromCache(data, genomeNexusCache); | ||
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| return <span className={hgvsgStyles["hgvsg-data"]}>{HgvsgColumnFormatter.getHgvsgDataViz(genomeNexusCacheData)}</span>; | ||
| } | ||
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| private static getGenomeNexusDataFromCache(data:Mutation[], cache:GenomeNexusCache|undefined):GenomeNexusCacheDataType | null { | ||
| if (data.length === 0 || !cache) { | ||
| return null; | ||
| } | ||
| return cache.get(data[0]); | ||
| } | ||
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| private static getHgvsgDataViz(genomeNexusCacheData:GenomeNexusCacheDataType|null) { | ||
| let status:TableCellStatus | null = null; | ||
| if (genomeNexusCacheData === null) { | ||
| status = TableCellStatus.LOADING; | ||
| } else if (genomeNexusCacheData.status === "error") { | ||
| status = TableCellStatus.ERROR; | ||
| } else if (genomeNexusCacheData.data === null) { | ||
| status = TableCellStatus.NA; | ||
| } else { | ||
| let hgvsgData = HgvsgColumnFormatter.getData(genomeNexusCacheData.data); | ||
| if (hgvsgData == null) { | ||
| return null; | ||
| } | ||
| else { | ||
| return ( | ||
| <a href={`https://www.genomenexus.org/variant/${hgvsgData}`} target="_blank" rel="noopener noreferrer"> | ||
| {hgvsgData} | ||
| <img | ||
| height='16' | ||
| width='16' | ||
| src={require("./GenomeNexusLogo.png")} | ||
| alt='Genome Nexus' | ||
| /> | ||
| </a> | ||
| ); | ||
| } | ||
| } | ||
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| if (status !== null) { | ||
| // show loading circle | ||
| if (status === TableCellStatus.LOADING) { | ||
| return <Circle size={18} scaleEnd={0.5} scaleStart={0.2} color="#aaa" className="pull-left"/>; | ||
| } | ||
| else { | ||
| return <TableCellStatusIndicator status={status}/>; | ||
| } | ||
| } | ||
| } | ||
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| public static getData(genomeNexusData: VariantAnnotation | null): string | null | ||
| { | ||
| if (!genomeNexusData) | ||
| { | ||
| return null; | ||
| } | ||
| return genomeNexusData.hgvsg; | ||
| } | ||
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| public static download(data:Mutation[], genomeNexusCache:GenomeNexusCache): string | ||
| { | ||
| const genomeNexusData = HgvsgColumnFormatter.getGenomeNexusDataFromCache(data, genomeNexusCache); | ||
| const hgvsgData = genomeNexusData && HgvsgColumnFormatter.getData(genomeNexusData.data); | ||
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| if (!hgvsgData) { | ||
| return ""; | ||
| } | ||
| else { | ||
| return hgvsgData; | ||
| } | ||
| } | ||
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| public static getSortValue(data:Mutation[], genomeNexusCache:GenomeNexusCache): string|null { | ||
| const genomeNexusCacheData = HgvsgColumnFormatter.getGenomeNexusDataFromCache(data, genomeNexusCache); | ||
| if (genomeNexusCacheData) { | ||
| let hgvsgData = HgvsgColumnFormatter.getData(genomeNexusCacheData.data); | ||
| if (hgvsgData == null) { | ||
| return null | ||
| } | ||
| else { | ||
| return hgvsgData; | ||
| } | ||
| } | ||
| else { | ||
| return null; | ||
| } | ||
| } | ||
| } |
22 changes: 22 additions & 0 deletions
22
src/shared/components/mutationTable/column/hgvsg.module.scss
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,22 @@ | ||
| .hgvsg-data a, | ||
| .hgvsg-data a:hover, | ||
| .hgvsg-data a:focus, | ||
| .hgvsg-data a:active, | ||
| .hgvsg-data a:visited { | ||
| color: black; | ||
| } | ||
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| .hgvsg-data { | ||
| white-space: nowrap; | ||
| max-width: 300px; | ||
| overflow: hidden; | ||
| text-overflow: ellipsis; | ||
| display:block; | ||
| } | ||
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| .hgvsg-data:hover { | ||
| text-overflow: clip; | ||
| word-break: break-all; | ||
| overflow: visible; | ||
| white-space: normal; | ||
| } |
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