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(GSoC) Generic Assay Categorical/Binary data implementation Frontend #4686

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merged 3 commits into from
Sep 21, 2023
Merged

(GSoC) Generic Assay Categorical/Binary data implementation Frontend #4686

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19546b3
add new endpoints
Djokovic0311 Aug 7, 2023
ca43da7
Update feature flag
dippindots Sep 20, 2023
dd772da
Update screenshots
dippindots Sep 21, 2023
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3 changes: 3 additions & 0 deletions packages/cbioportal-ts-api-client/src/index.tsx
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Expand Up @@ -36,6 +36,9 @@ export {
GenericAssayDataBinFilter,
GenericAssayDataCountFilter,
GenericAssayDataCountItem,
GenericAssayCountSummary,
GenericAssayBinaryEnrichment,
GenericAssayCategoricalEnrichment,
GenericAssayEnrichment,
Geneset,
GenesetCorrelation,
Expand Down
263 changes: 263 additions & 0 deletions src/pages/groupComparison/GenericAssayEnrichmentCollections.tsx
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@@ -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;
}
}
29 changes: 18 additions & 11 deletions src/pages/groupComparison/GroupComparisonPage.tsx
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Expand Up @@ -36,7 +36,6 @@ import styles from './styles.module.scss';
import { OverlapStrategy } from '../../shared/lib/comparison/ComparisonStore';
import { buildCBioPortalPageUrl } from 'shared/api/urls';
import MethylationEnrichments from './MethylationEnrichments';
import GenericAssayEnrichments from './GenericAssayEnrichments';
import _ from 'lodash';
import AlterationEnrichments from './AlterationEnrichments';
import AlterationEnrichmentTypeSelector from '../../shared/lib/comparison/AlterationEnrichmentTypeSelector';
Expand All @@ -46,12 +45,13 @@ import {
buildCustomTabs,
prepareCustomTabConfigurations,
} from 'shared/lib/customTabs/customTabHelpers';
import { getSortedGenericAssayTabSpecs } from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
import { getSortedGenericAssayAllTabSpecs } from 'shared/lib/GenericAssayUtils/GenericAssayCommonUtils';
import { HelpWidget } from 'shared/components/HelpWidget/HelpWidget';
import GroupComparisonPathwayMapper from './pathwayMapper/GroupComparisonPathwayMapper';
import GroupComparisonMutationsTab from './GroupComparisonMutationsTab';
import GroupComparisonPathwayMapperUserSelectionStore from './pathwayMapper/GroupComparisonPathwayMapperUserSelectionStore';
import { Tour } from 'tours';
import GenericAssayEnrichmentCollections from './GenericAssayEnrichmentCollections';

export interface IGroupComparisonPageProps {
routing: any;
Expand Down Expand Up @@ -135,6 +135,8 @@ export default class GroupComparisonPage extends React.Component<
this.store.methylationEnrichmentProfiles,
this.store.survivalClinicalDataExists,
this.store.genericAssayEnrichmentProfilesGroupedByGenericAssayType,
this.store
.genericAssayBinaryEnrichmentProfilesGroupedByGenericAssayType,
this.store.alterationsEnrichmentData,
this.store.alterationsEnrichmentAnalysisGroups,
this.store.genesSortedByMutationFrequency,
Expand Down Expand Up @@ -313,34 +315,39 @@ export default class GroupComparisonPage extends React.Component<
<MethylationEnrichments store={this.store} />
</MSKTab>
)}
{this.store.showGenericAssayTab &&
getSortedGenericAssayTabSpecs(
{(this.store.showGenericAssayCategoricalTab ||
this.store.showGenericAssayBinaryTab ||
this.store.showGenericAssayTab) &&
getSortedGenericAssayAllTabSpecs(
this.store
.genericAssayEnrichmentProfilesGroupedByGenericAssayType
.genericAssayAllEnrichmentProfilesGroupedByGenericAssayType
.result
).map(genericAssayTabSpecs => {
).map(genericAssayAllTabSpecs => {
return (
<MSKTab
id={`${
GroupComparisonTab.GENERIC_ASSAY_PREFIX
}_${genericAssayTabSpecs.genericAssayType.toLowerCase()}`}
linkText={genericAssayTabSpecs.linkText}
}_${genericAssayAllTabSpecs.genericAssayType.toLowerCase()}`}
linkText={genericAssayAllTabSpecs.linkText}
anchorClassName={
this.store
.genericAssayCategoricalTabUnavailable &&
this.store
.genericAssayBinaryTabUnavailable &&
this.store.genericAssayTabUnavailable
? 'greyedOut'
: ''
}
>
<GenericAssayEnrichments
<GenericAssayEnrichmentCollections
store={this.store}
genericAssayType={
genericAssayTabSpecs.genericAssayType
genericAssayAllTabSpecs.genericAssayType
}
/>
</MSKTab>
);
})}

{buildCustomTabs(this.customTabs)}
</MSKTabs>
);
Expand Down
2 changes: 2 additions & 0 deletions src/pages/groupComparison/GroupComparisonTabs.ts
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Expand Up @@ -7,6 +7,8 @@ export enum GroupComparisonTab {
DNAMETHYLATION = 'dna_methylation',
ALTERATIONS = 'alterations',
GENERIC_ASSAY_PREFIX = 'generic_assay',
GENERIC_ASSAY_BINARY_PREFIX = 'generic_assay_binary',
GENERIC_ASSAY_CATEGORICAL_PREFIX = 'generic_assay_categorical',
MUTATIONS = 'mutations',
PATHWAYS = 'pathways',
}
Expand Down
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