Merge pull request #4201 from leexgh/genie-na

Customize "NA" category on GENIE comparison clinical tab
cBioPortal · Mar 22, 2022 · 468491c · 468491c
2 parents fdd45cd + e5fc6c6
commit 468491c
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Showing 9 changed files with 17 additions and 2 deletions.
diff --git a/...rison_page_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png b/...rison_page_clinical_tab_bar_chart_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png b/...chart_exclude_overlapping_samples_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...ge_clinical_tab_stacked_bar_chart_chi_squared_test_element_chrome_1600x1000.png b/...ge_clinical_tab_stacked_bar_chart_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png b/...stacked_bar_chart_horizontal_bars_chi_squared_test_element_chrome_1600x1000.png
diff --git a/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png b/...tab_stacked_bar_chart_swaped_axes_chi_squared_test_element_chrome_1600x1000.png
diff --git a/src/config/IAppConfig.ts b/src/config/IAppConfig.ts
@@ -157,4 +157,5 @@ export interface IServerConfig {
     skin_home_page_show_unauthorized_studies: boolean;
     skin_home_page_unauthorized_studies_global_message: string;
     skin_mutation_table_namespace_column_show_by_default: boolean;
+    comparison_categorical_na_values: string;
 }
diff --git a/src/config/serverConfigDefaults.ts b/src/config/serverConfigDefaults.ts
@@ -194,6 +194,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
 
     skin_home_page_unauthorized_studies_global_message:
         'The study is unauthorized. You need to request access.',
+    comparison_categorical_na_values: 'NA',
 };
 
 export default ServerConfigDefaults;
diff --git a/src/pages/groupComparison/ClinicalData.tsx b/src/pages/groupComparison/ClinicalData.tsx
@@ -48,6 +48,7 @@ import ComplexKeyMap from 'shared/lib/complexKeyDataStructures/ComplexKeyMap';
 import { Sample } from 'cbioportal-ts-api-client';
 import ComparisonStore from '../../shared/lib/comparison/ComparisonStore';
 import { createSurvivalAttributeIdsDict } from 'pages/resultsView/survival/SurvivalUtil';
+import { getComparisonCategoricalNaValue } from './ClinicalDataUtils';
 
 export interface IClinicalDataProps {
     store: ComparisonStore;
@@ -246,7 +247,7 @@ export default class ClinicalData extends React.Component<
     @observable logScaleFunction: IAxisLogScaleParams | undefined;
     @observable swapAxes = false;
     @observable horizontalBars = false;
-    @observable showNA = false;
+    @observable showNA = true;
 
     @action.bound
     private onClickLogScale() {
@@ -314,7 +315,12 @@ export default class ClinicalData extends React.Component<
                     data: axisData.data.filter(
                         x =>
                             typeof x.value !== 'string' ||
-                            x.value.toLowerCase() !== 'unknown'
+                            _.every(
+                                getComparisonCategoricalNaValue(),
+                                naValue =>
+                                    naValue.toLowerCase() !==
+                                    (x.value as string).toLowerCase()
+                            )
                     ),
                 });
             }

diff --git a/src/pages/groupComparison/ClinicalDataUtils.ts b/src/pages/groupComparison/ClinicalDataUtils.ts
@@ -0,0 +1,7 @@
+import { getServerConfig } from 'config/config';
+
+export function getComparisonCategoricalNaValue(): string[] {
+    const rawString = getServerConfig().comparison_categorical_na_values;
+    const naValues = rawString.split(',');
+    return naValues;
+}