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Merge pull request #4686 from Djokovic0311/GenericAssay-Jiahang
(GSoC) Generic Assay Categorical/Binary data implementation Frontend
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src/pages/groupComparison/GenericAssayEnrichmentCollections.tsx
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,263 @@ | ||
| import * as React from 'react'; | ||
| import { observer } from 'mobx-react'; | ||
| import autobind from 'autobind-decorator'; | ||
| import { MolecularProfile } from 'cbioportal-ts-api-client'; | ||
| import { MakeMobxView } from '../../shared/components/MobxView'; | ||
| import Loader from '../../shared/components/loadingIndicator/LoadingIndicator'; | ||
| import ErrorMessage from '../../shared/components/ErrorMessage'; | ||
| import { MakeEnrichmentsTabUI } from './GroupComparisonUtils'; | ||
| import _ from 'lodash'; | ||
| import ComparisonStore from '../../shared/lib/comparison/ComparisonStore'; | ||
| import GenericAssayBinaryEnrichmentsContainer from 'pages/resultsView/enrichments/GenericAssayBinaryEnrichmentsContainer'; | ||
| import EnrichmentsDataSetDropdown from 'pages/resultsView/enrichments/EnrichmentsDataSetDropdown'; | ||
| import { makeObservable, observable } from 'mobx'; | ||
| import GenericAssayEnrichmentsContainer from 'pages/resultsView/enrichments/GenericAssayEnrichmentsContainer'; | ||
| import GenericAssayCategoricalEnrichmentsContainer from 'pages/resultsView/enrichments/GenericAssayCategoricalEnrichmentsContainer'; | ||
|
|
||
| export interface IGenericAssayEnrichmentCollectionsProps { | ||
| store: ComparisonStore; | ||
| genericAssayType: string; | ||
| resultsViewMode?: boolean; | ||
| } | ||
|
|
||
| @observer | ||
| export default class GenericAssayEnrichmentCollections extends React.Component< | ||
| IGenericAssayEnrichmentCollectionsProps, | ||
| {} | ||
| > { | ||
| constructor(props: IGenericAssayEnrichmentCollectionsProps) { | ||
| super(props); | ||
| makeObservable(this); | ||
| } | ||
|
|
||
| @observable isBinary: boolean | undefined = false; | ||
| @observable isCategorical: boolean | undefined = false; | ||
| @observable isNumerical: boolean | undefined = false; | ||
|
|
||
| @autobind | ||
| private onChangeProfile(profileMap: { | ||
| [studyId: string]: MolecularProfile; | ||
| }) { | ||
| const type = Object.values(profileMap)[0].datatype; | ||
| this.props.store.setAllGenericAssayEnrichmentProfileMap( | ||
| profileMap, | ||
| this.props.genericAssayType | ||
| ); | ||
| if (type === 'BINARY') { | ||
| this.isBinary = true; | ||
| this.isCategorical = false; | ||
| this.isNumerical = false; | ||
| } else if (type === 'CATEGORICAL') { | ||
| this.isBinary = false; | ||
| this.isCategorical = true; | ||
| this.isNumerical = false; | ||
| } else { | ||
| this.isBinary = false; | ||
| this.isCategorical = false; | ||
| this.isNumerical = true; | ||
| } | ||
| } | ||
|
|
||
| readonly tabUI = MakeEnrichmentsTabUI( | ||
| () => this.props.store, | ||
| () => this.enrichmentsUI, | ||
| this.props.genericAssayType, | ||
| true, | ||
| true, | ||
| false | ||
| ); | ||
|
|
||
| readonly enrichmentsUI = MakeMobxView({ | ||
| await: () => { | ||
| const ret: any[] = [ | ||
| this.props.store.gaBinaryEnrichmentDataByAssayType, | ||
| this.props.store | ||
| .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType, | ||
| this.props.store.gaBinaryEnrichmentGroupsByAssayType, | ||
| this.props.store.gaCategoricalEnrichmentDataByAssayType, | ||
| this.props.store.gaCategoricalEnrichmentGroupsByAssayType, | ||
| this.props.store.gaEnrichmentDataByAssayType, | ||
| this.props.store.gaEnrichmentGroupsByAssayType, | ||
| this.props.store.studies, | ||
| ]; | ||
| if ( | ||
| this.props.store.gaBinaryEnrichmentDataByAssayType.isComplete && | ||
| this.props.store.gaBinaryEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ] | ||
| ) { | ||
| ret.push( | ||
| this.props.store.gaBinaryEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ] | ||
| ); | ||
| } | ||
|
|
||
| if ( | ||
| this.props.store.gaCategoricalEnrichmentDataByAssayType | ||
| .isComplete && | ||
| this.props.store.gaCategoricalEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ] | ||
| ) { | ||
| ret.push( | ||
| this.props.store.gaCategoricalEnrichmentDataByAssayType | ||
| .result![this.props.genericAssayType] | ||
| ); | ||
| } | ||
| if ( | ||
| this.props.store.gaEnrichmentDataByAssayType.isComplete && | ||
| this.props.store.gaEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ] | ||
| ) { | ||
| ret.push( | ||
| this.props.store.gaEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ] | ||
| ); | ||
| } | ||
| return ret; | ||
| }, | ||
| render: () => { | ||
| // since generic assay enrichments tab is enabled only for one study, selectedGenericAssayEnrichmentProfileMap | ||
| // would contain only one key. | ||
| const studyId = Object.keys( | ||
| this.props.store | ||
| .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType] | ||
| )[0]; | ||
|
|
||
| // select the first found profile in the study as the default selection for selected genericAssayType | ||
| const selectedProfile = this.props.store | ||
| .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType][studyId]; | ||
|
|
||
| let profileList: MolecularProfile[] = []; | ||
| const genericAssayBinaryEnrichmentProfiles = this.props.store | ||
| .genericAssayBinaryEnrichmentProfilesGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType]; | ||
| const genericAssayCategoricalEnrichmentProfiles = this.props.store | ||
| .genericAssayCategoricalEnrichmentProfilesGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType]; | ||
| const genericAssayEnrichmentProfiles = this.props.store | ||
| .genericAssayEnrichmentProfilesGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType]; | ||
|
|
||
| if (genericAssayBinaryEnrichmentProfiles !== undefined) { | ||
| profileList = profileList.concat( | ||
| genericAssayBinaryEnrichmentProfiles | ||
| ); | ||
| } | ||
| if (genericAssayCategoricalEnrichmentProfiles !== undefined) { | ||
| profileList = profileList.concat( | ||
| genericAssayCategoricalEnrichmentProfiles | ||
| ); | ||
| } | ||
| if (genericAssayEnrichmentProfiles !== undefined) { | ||
| profileList = profileList.concat( | ||
| genericAssayEnrichmentProfiles | ||
| ); | ||
| } | ||
|
|
||
| if (selectedProfile.datatype == 'BINARY') { | ||
| this.isBinary = true; | ||
| this.isCategorical = false; | ||
| this.isNumerical = false; | ||
| } else if (selectedProfile.datatype == 'CATEGORICAL') { | ||
| this.isBinary = false; | ||
| this.isCategorical = true; | ||
| this.isNumerical = false; | ||
| } else { | ||
| this.isBinary = false; | ||
| this.isCategorical = false; | ||
| this.isNumerical = true; | ||
| } | ||
|
|
||
| return ( | ||
| <div data-test="GroupComparisonGenericAssayEnrichments"> | ||
| <EnrichmentsDataSetDropdown | ||
| dataSets={profileList} | ||
| onChange={this.onChangeProfile} | ||
| selectedProfileByStudyId={ | ||
| this.props.store | ||
| .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType | ||
| .result![this.props.genericAssayType] | ||
| } | ||
| alwaysShow={true} | ||
| studies={this.props.store.studies.result!} | ||
| showDescription={true} | ||
| /> | ||
| {this.isBinary && ( | ||
| <GenericAssayBinaryEnrichmentsContainer | ||
| data={ | ||
| this.props.store | ||
| .gaBinaryEnrichmentDataByAssayType.result![ | ||
| this.props.genericAssayType | ||
| ].result | ||
| } | ||
| groups={ | ||
| this.props.store | ||
| .gaBinaryEnrichmentGroupsByAssayType | ||
| .result![this.props.genericAssayType] | ||
| } | ||
| selectedProfile={selectedProfile} | ||
| alteredVsUnalteredMode={false} | ||
| sampleKeyToSample={ | ||
| this.props.store.sampleKeyToSample.result! | ||
| } | ||
| genericAssayType={this.props.genericAssayType} | ||
| /> | ||
| )} | ||
| {this.isCategorical && ( | ||
| <GenericAssayCategoricalEnrichmentsContainer | ||
| data={ | ||
| this.props.store | ||
| .gaCategoricalEnrichmentDataByAssayType | ||
| .result![this.props.genericAssayType].result | ||
| } | ||
| groups={ | ||
| this.props.store | ||
| .gaCategoricalEnrichmentGroupsByAssayType | ||
| .result![this.props.genericAssayType] | ||
| } | ||
| selectedProfile={selectedProfile} | ||
| alteredVsUnalteredMode={false} | ||
| sampleKeyToSample={ | ||
| this.props.store.sampleKeyToSample.result! | ||
| } | ||
| genericAssayType={this.props.genericAssayType} | ||
| dataStore={this.props.store} | ||
| /> | ||
| )} | ||
| {this.isNumerical && ( | ||
| <GenericAssayEnrichmentsContainer | ||
| data={ | ||
| this.props.store.gaEnrichmentDataByAssayType | ||
| .result![this.props.genericAssayType].result | ||
| } | ||
| groups={ | ||
| this.props.store.gaEnrichmentGroupsByAssayType | ||
| .result![this.props.genericAssayType] | ||
| } | ||
| selectedProfile={selectedProfile} | ||
| alteredVsUnalteredMode={false} | ||
| sampleKeyToSample={ | ||
| this.props.store.sampleKeyToSample.result! | ||
| } | ||
| genericAssayType={this.props.genericAssayType} | ||
| /> | ||
| )} | ||
| </div> | ||
| ); | ||
| }, | ||
| renderPending: () => ( | ||
| <Loader center={true} isLoading={true} size={'big'} /> | ||
| ), | ||
| renderError: () => <ErrorMessage />, | ||
| }); | ||
|
|
||
| render() { | ||
| return this.tabUI.component; | ||
| } | ||
| } |
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