From 6ae51d39b072b1814c6a1465d2cc4cf029ce1cd4 Mon Sep 17 00:00:00 2001
From: Bas Leenknegt <basleenknegt@thehyve.nl>
Date: Wed, 2 Aug 2023 15:42:53 +0200
Subject: [PATCH] Add defaults for mutation heatmap and line chart checkboxes

---
 src/config/IAppConfig.ts                                 | 3 +++
 .../patientView/mutation/oncoprint/MutationOncoprint.tsx | 9 +++++++--
 src/pages/patientView/timeline/VAFChartWrapperStore.tsx  | 8 ++++++--
 3 files changed, 16 insertions(+), 4 deletions(-)

diff --git a/src/config/IAppConfig.ts b/src/config/IAppConfig.ts
index 0531719af6b..b342ea4d558 100644
--- a/src/config/IAppConfig.ts
+++ b/src/config/IAppConfig.ts
@@ -168,7 +168,10 @@ export interface IServerConfig {
     skin_patient_view_structural_variant_table_columns_show_on_init: string;
     comparison_categorical_na_values: string;
     oncoprint_clinical_tracks_config_json: string;
+    oncoprint_clustered_default: boolean;
     enable_cross_study_expression: string;
     studyview_max_samples_selected: number;
     study_download_url: string;
+    vaf_sequential_mode_default: boolean;
+    vaf_log_scale_default: boolean;
 }
diff --git a/src/pages/patientView/mutation/oncoprint/MutationOncoprint.tsx b/src/pages/patientView/mutation/oncoprint/MutationOncoprint.tsx
index 4fa6468df3a..b5bbc948272 100644
--- a/src/pages/patientView/mutation/oncoprint/MutationOncoprint.tsx
+++ b/src/pages/patientView/mutation/oncoprint/MutationOncoprint.tsx
@@ -44,6 +44,7 @@ import { Mutation } from 'cbioportal-ts-api-client';
 import ReactDOM from 'react-dom';
 import PatientViewUrlWrapper from '../../PatientViewUrlWrapper';
 import { getVariantAlleleFrequency } from 'shared/lib/MutationUtils';
+import { getServerConfig } from 'config/config';
 
 export interface IMutationOncoprintProps {
     store: PatientViewPageStore;
@@ -84,11 +85,15 @@ export default class MutationOncoprint extends React.Component<
         });
     }
 
-    private get clustered() {
+    private get clustered(): boolean {
         const urlValue = this.props.urlWrapper.query.genomicEvolutionSettings
             .clusterHeatmap;
-        return !urlValue || urlValue === 'true'; // default true
+        if (urlValue) {
+            return urlValue === 'true';
+        }
+        return getServerConfig().oncoprint_clustered_default;
     }
+
     private set clustered(o: boolean) {
         this.props.urlWrapper.updateURL(currentParams => {
             currentParams.genomicEvolutionSettings.clusterHeatmap = o.toString();
diff --git a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
index 923f0795130..b045955019c 100644
--- a/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
+++ b/src/pages/patientView/timeline/VAFChartWrapperStore.tsx
@@ -1,9 +1,12 @@
 import { action, computed, observable, makeObservable } from 'mobx';
+import { getServerConfig } from 'config/config';
 
 export default class VAFChartWrapperStore {
     @observable groupByOption: string | null = null;
 
-    @observable _showSequentialMode: boolean | undefined = undefined;
+    @observable _showSequentialMode: boolean = getServerConfig()
+        .vaf_sequential_mode_default;
+
     @computed
     get showSequentialMode() {
         return this.isOnlySequentialModePossible || this._showSequentialMode;
@@ -11,7 +14,8 @@ export default class VAFChartWrapperStore {
 
     @observable onlyShowSelectedInVAFChart: boolean | undefined = undefined;
 
-    @observable vafChartLogScale: boolean | undefined = undefined;
+    @observable vafChartLogScale: boolean = getServerConfig()
+        .vaf_log_scale_default;
 
     @observable vafChartYAxisToDataRange: boolean | undefined = undefined;