Merge branch 'master' into add-clinical-attributes-mutations-tab

packages/react-mutation-mapper/src/component/filter/ProteinImpactTypeBadgeSelector.tsx

@@ -66,7 +66,7 @@ export class ProteinImpactTypeBadgeSelector<
     public static defaultProps: Partial<ProteinImpactTypeBadgeSelectorProps> = {
         colors: DEFAULT_PROTEIN_IMPACT_TYPE_COLORS,
         alignColumns: true,
-        unselectOthersWhenAllSelected: true,
+        unselectOthersWhenAllSelected: false,
         numberOfColumnsPerRow: 2,
     };
 

packages/react-mutation-mapper/src/index.tsx

@@ -152,7 +152,6 @@ export { SequenceSpec } from './model/SequenceSpec';
 
 export * from './util/DataFetcherUtils';
 export * from './util/FilterUtils';
-export * from 'cbioportal-utils';
 export {
     MUTATION_TYPE_PRIORITY,
     mutationTypeSort,
@@ -163,6 +162,7 @@ export {
     defaultOncoKbFilter,
     groupOncoKbIndicatorDataByMutations,
 } from './util/OncoKbUtils';
+export * from './util/SelectorUtils';
 export * from './util/TrackUtils';
 
 export { default as DefaultMutationMapperDataFetcher } from './store/DefaultMutationMapperDataFetcher';

src/pages/patientView/structuralVariant/column/AnnotationColumnFormatter.tsx

@@ -7,7 +7,6 @@ import {
     IAnnotation,
     USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB,
     oncoKbAnnotationSortValue,
-    calculateOncoKbAvailableDataType,
 } from 'react-mutation-mapper';
 import { CancerStudy, StructuralVariant } from 'cbioportal-ts-api-client';
 import { IAnnotationColumnProps } from 'shared/components/mutationTable/column/AnnotationColumnFormatter';
@@ -17,6 +16,7 @@ import {
     IOncoKbData,
     generateQueryStructuralVariantId,
     OncoKbCardDataType,
+    calculateOncoKbAvailableDataType,
 } from 'cbioportal-utils';
 
 export default class AnnotationColumnFormatter {

src/pages/resultsView/mutation/DriverAnnotationProteinImpactTypeBadgeSelector.tsx

@@ -3,8 +3,11 @@ import {
     ProteinImpactTypeBadgeSelectorProps,
     DEFAULT_PROTEIN_IMPACT_TYPE_COLORS,
     BadgeSelector,
+    getAllOptionValues,
+    getSelectedOptionValues,
     getProteinImpactTypeOptionLabel,
     getProteinImpactTypeBadgeLabel,
+    DataFilter,
 } from 'react-mutation-mapper';
 import * as React from 'react';
 import {
@@ -20,7 +23,7 @@ import {
 } from 'cbioportal-frontend-commons';
 import _ from 'lodash';
 import { observer } from 'mobx-react';
-import { action, makeObservable, observable } from 'mobx';
+import { action, computed, makeObservable, observable } from 'mobx';
 import './mutations.scss';
 import styles from './badgeSelector.module.scss';
 
@@ -51,6 +54,32 @@ export interface IDriverAnnotationProteinImpactTypeBadgeSelectorProps
         allValuesSelected?: boolean
     ) => void;
     onClickSettingMenu?: (visible: boolean) => void;
+    annotatedProteinImpactTypeFilter?: DataFilter<string>;
+}
+
+function findSelectedDriverVsVus(
+    type: DriverVsVusType,
+    selectedOption: string[],
+    alreadySelectedValues: { value: string }[],
+    allTypes: ProteinImpactType[]
+): string[] {
+    let toSelect: string[] = [];
+
+    // If "type" is selected then also select all of corresponding mutation types
+    if (selectedOption.includes(type)) {
+        toSelect = allTypes;
+    }
+    // If "type" is not selected, decide whether we unselect all mutations corresponding to that type as well
+    else {
+        // if selected mutation types already includes ALL of the mutations corresponding to the given type
+        // then it means "type" is just UNSELECTED,
+        // we should not add "type" mutations back in the selected in that case
+        if (alreadySelectedValues.length !== allTypes.length) {
+            toSelect = alreadySelectedValues.map(v => v.value);
+        }
+    }
+
+    return toSelect;
 }
 
 @observer
@@ -62,18 +91,59 @@ export default class DriverAnnotationProteinImpactTypeBadgeSelector extends Prot
         makeObservable(this);
     }
 
-    @observable selectedDriverVsVusValues: string[] = [
-        DriverVsVusType.DRIVER,
-        DriverVsVusType.VUS,
-    ];
     @observable settingMenuVisible = false;
 
+    @computed get selectedMutationTypeValues() {
+        return getSelectedOptionValues(
+            getAllOptionValues(this.options),
+            this.props.filter
+        );
+    }
+
+    @computed get selectedDriverMutationTypeValues() {
+        return this.selectedMutationTypeValues.filter(v =>
+            (PUTATIVE_DRIVER_TYPE as string[]).includes(v.value)
+        );
+    }
+
+    @computed get selectedVUSMutationTypeValues() {
+        return this.selectedMutationTypeValues.filter(v =>
+            (UNKNOWN_SIGNIFICANCE_TYPE as string[]).includes(v.value)
+        );
+    }
+
+    @computed get selectedDriverVsVusValues() {
+        if (this.props.annotatedProteinImpactTypeFilter) {
+            // If all driver(vus) mutation types are selected, select "Driver"("VUS") button
+            let driverVsVusValues = [];
+            if (
+                _.intersection(
+                    this.props.annotatedProteinImpactTypeFilter.values,
+                    PUTATIVE_DRIVER_TYPE
+                ).length === PUTATIVE_DRIVER_TYPE.length
+            ) {
+                driverVsVusValues.push(DriverVsVusType.DRIVER);
+            }
+            if (
+                _.intersection(
+                    this.props.annotatedProteinImpactTypeFilter.values,
+                    UNKNOWN_SIGNIFICANCE_TYPE
+                ).length === UNKNOWN_SIGNIFICANCE_TYPE.length
+            ) {
+                driverVsVusValues.push(DriverVsVusType.VUS);
+            }
+            return driverVsVusValues;
+        } else {
+            return [DriverVsVusType.DRIVER, DriverVsVusType.VUS];
+        }
+    }
+
     public static defaultProps: Partial<
         IDriverAnnotationProteinImpactTypeBadgeSelectorProps
     > = {
         colors: DEFAULT_PROTEIN_IMPACT_TYPE_COLORS,
         alignColumns: true,
-        unselectOthersWhenAllSelected: true,
+        unselectOthersWhenAllSelected: false,
         numberOfColumnsPerRow: 2,
     };
 
@@ -198,42 +268,25 @@ export default class DriverAnnotationProteinImpactTypeBadgeSelector extends Prot
         selectedOption: string[],
         allValuesSelected: boolean
     ) {
-        let selected: string[] = [];
-        // If select "Driver" or "VUS", then also select corresponding mutation types
-        _.forEach(selectedOption, option => {
-            if (option === DriverVsVusType.DRIVER) {
-                selected = _.union(selected, PUTATIVE_DRIVER_TYPE);
-            }
-            if (option === DriverVsVusType.VUS) {
-                selected = _.union(selected, UNKNOWN_SIGNIFICANCE_TYPE);
-            }
-        });
-        this.props.onSelect && this.props.onSelect(selected, allValuesSelected);
-        this.selectedDriverVsVusValues = selectedOption;
-    }
+        const selectedDriver = findSelectedDriverVsVus(
+            DriverVsVusType.DRIVER,
+            selectedOption,
+            this.selectedDriverMutationTypeValues,
+            PUTATIVE_DRIVER_TYPE
+        );
+
+        const selectedVus = findSelectedDriverVsVus(
+            DriverVsVusType.VUS,
+            selectedOption,
+            this.selectedVUSMutationTypeValues,
+            UNKNOWN_SIGNIFICANCE_TYPE
+        );
 
-    @action.bound
-    protected onMutationTypeSelect(
-        selectedOption: string[],
-        allValuesSelected: boolean
-    ) {
-        // If all driver(vus) mutation types are selected, select "Driver"("VUS") button
-        let updatedDriverVsVusValues = [];
-        if (
-            _.intersection(selectedOption, PUTATIVE_DRIVER_TYPE).length ===
-            PUTATIVE_DRIVER_TYPE.length
-        ) {
-            updatedDriverVsVusValues.push(DriverVsVusType.DRIVER);
-        }
-        if (
-            _.intersection(selectedOption, UNKNOWN_SIGNIFICANCE_TYPE).length ===
-            UNKNOWN_SIGNIFICANCE_TYPE.length
-        ) {
-            updatedDriverVsVusValues.push(DriverVsVusType.VUS);
-        }
-        this.selectedDriverVsVusValues = updatedDriverVsVusValues;
         this.props.onSelect &&
-            this.props.onSelect(selectedOption, allValuesSelected);
+            this.props.onSelect(
+                selectedDriver.concat(selectedVus),
+                allValuesSelected
+            );
     }
 
     @action.bound
@@ -263,7 +316,7 @@ export default class DriverAnnotationProteinImpactTypeBadgeSelector extends Prot
                     getOptionLabel={getProteinImpactTypeOptionLabel}
                     getBadgeLabel={getProteinImpactTypeBadgeLabel}
                     {...this.props}
-                    onSelect={this.onMutationTypeSelect}
+                    onSelect={this.props.onSelect}
                 />
             </div>
         );

src/shared/components/mutationMapper/MutationMapper.tsx

@@ -333,6 +333,12 @@ export default class MutationMapper<
         return findProteinImpactTypeFilter(this.store.dataStore.dataFilters);
     }
 
+    @computed get annotatedProteinImpactTypeFilter() {
+        return this.store.dataStore.dataFilters.find(
+            filter => filter.type === ANNOTATED_PROTEIN_IMPACT_FILTER_TYPE
+        );
+    }
+
     /**
      * Overriding the parent method to have a customized filter panel.
      */
@@ -350,6 +356,9 @@ export default class MutationMapper<
                             counts={this.mutationCountsByProteinImpactType}
                             onSelect={this.onProteinImpactTypeSelect}
                             onClickSettingMenu={this.props.onClickSettingMenu}
+                            annotatedProteinImpactTypeFilter={
+                                this.annotatedProteinImpactTypeFilter
+                            }
                         />
                     </div>
                 ) : (