From 6efbdf7bb073f7cfcc122fe03bd960abfaaf5748 Mon Sep 17 00:00:00 2001
From: Matthijs Pon <matthijs@thehyve.nl>
Date: Wed, 12 Jun 2024 12:01:36 +0200
Subject: [PATCH 1/2] Fix swapping generic assay profiles in comparison view

---
 src/shared/lib/comparison/ComparisonStore.ts | 10 +++++-----
 1 file changed, 5 insertions(+), 5 deletions(-)

diff --git a/src/shared/lib/comparison/ComparisonStore.ts b/src/shared/lib/comparison/ComparisonStore.ts
index 6d24da88278..eccf5b62161 100644
--- a/src/shared/lib/comparison/ComparisonStore.ts
+++ b/src/shared/lib/comparison/ComparisonStore.ts
@@ -1699,14 +1699,14 @@ export default abstract class ComparisonStore extends AnalysisStore
     readonly gaEnrichmentGroupsByAssayType = remoteData({
         await: () => [
             this
-                .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType,
+                .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType,
             this.enrichmentAnalysisGroups,
         ],
         invoke: () => {
             return Promise.resolve(
                 _.mapValues(
                     this
-                        .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
+                        .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
                         .result!,
                     selectedGenericAssayEnrichmentProfileMap => {
                         let studyIds = Object.keys(
@@ -1850,7 +1850,7 @@ export default abstract class ComparisonStore extends AnalysisStore
         await: () => [
             this.gaEnrichmentGroupsByAssayType,
             this
-                .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType,
+                .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType,
         ],
         invoke: () => {
             return Promise.resolve(
@@ -1866,7 +1866,7 @@ export default abstract class ComparisonStore extends AnalysisStore
                                     sample => ({
                                         caseId: sample.sampleId,
                                         molecularProfileId: this
-                                            .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
+                                            .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
                                             .result![genericAssayType][
                                             sample.studyId
                                         ].molecularProfileId,
@@ -1973,7 +1973,7 @@ export default abstract class ComparisonStore extends AnalysisStore
                             await: () => [],
                             getSelectedProfileMap: () =>
                                 this
-                                    .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
+                                    .selectedAllGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
                                     .result![genericAssayType], // returns an empty array if the selected study doesn't have any generic assay profiles
                             fetchData: () => {
                                 if (

From 25fc31cd17f46bd9e9389268433eef2686636799 Mon Sep 17 00:00:00 2001
From: Matthijs Pon <matthijs@thehyve.nl>
Date: Fri, 28 Jun 2024 10:43:58 +0200
Subject: [PATCH 2/2] Remove unused GenericAssayEnrichments.tsx

---
 .../GenericAssayEnrichments.tsx               | 125 ------------------
 1 file changed, 125 deletions(-)
 delete mode 100644 src/pages/groupComparison/GenericAssayEnrichments.tsx

diff --git a/src/pages/groupComparison/GenericAssayEnrichments.tsx b/src/pages/groupComparison/GenericAssayEnrichments.tsx
deleted file mode 100644
index a93e7642074..00000000000
--- a/src/pages/groupComparison/GenericAssayEnrichments.tsx
+++ /dev/null
@@ -1,125 +0,0 @@
-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 GenericAssayEnrichmentsContainer from 'pages/resultsView/enrichments/GenericAssayEnrichmentsContainer';
-import EnrichmentsDataSetDropdown from 'pages/resultsView/enrichments/EnrichmentsDataSetDropdown';
-
-export interface IGenericAssayEnrichmentsProps {
-    store: ComparisonStore;
-    genericAssayType: string;
-    resultsViewMode?: boolean;
-}
-
-@observer
-export default class GenericAssayEnrichments extends React.Component<
-    IGenericAssayEnrichmentsProps,
-    {}
-> {
-    @autobind
-    private onChangeProfile(profileMap: {
-        [studyId: string]: MolecularProfile;
-    }) {
-        this.props.store.setGenericAssayEnrichmentProfileMap(
-            profileMap,
-            this.props.genericAssayType
-        );
-    }
-
-    readonly tabUI = MakeEnrichmentsTabUI(
-        () => this.props.store,
-        () => this.enrichmentsUI,
-        this.props.genericAssayType,
-        true,
-        true,
-        false
-    );
-
-    readonly enrichmentsUI = MakeMobxView({
-        await: () => {
-            const ret: any[] = [
-                this.props.store.gaEnrichmentDataByAssayType,
-                this.props.store
-                    .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType,
-                this.props.store.gaEnrichmentGroupsByAssayType,
-                this.props.store.studies,
-            ];
-            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
-                    .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
-                    .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
-                .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
-                .result![this.props.genericAssayType][studyId];
-            return (
-                <div data-test="GroupComparisonGenericAssayEnrichments">
-                    <EnrichmentsDataSetDropdown
-                        dataSets={
-                            this.props.store
-                                .genericAssayEnrichmentProfilesGroupedByGenericAssayType
-                                .result![this.props.genericAssayType]
-                        }
-                        onChange={this.onChangeProfile}
-                        selectedProfileByStudyId={
-                            this.props.store
-                                .selectedGenericAssayEnrichmentProfileMapGroupedByGenericAssayType
-                                .result![this.props.genericAssayType]
-                        }
-                        alwaysShow={true}
-                        studies={this.props.store.studies.result!}
-                        showDescription={true}
-                    />
-                    <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;
-    }
-}