Specify unprofiled in any or unprofiled in every for results view fil…

…tering

Signed-off-by: Adam Abeshouse <abeshoua@mskcc.org>

src/pages/resultsView/ResultsViewPageStore.ts

@@ -521,7 +521,9 @@ export type ModifyQueryParams = {
 
 interface IResultsViewExclusionSettings {
     setExcludeGermlineMutations: (value: boolean) => void;
-    setHideUnprofiledSamples: (value: boolean) => void;
+    setHideUnprofiledSamples: (
+        value: IAnnotationFilterSettings['hideUnprofiledSamples']
+    ) => void;
 }
 
 /* fields and methods in the class below are ordered based on roughly
@@ -701,17 +703,24 @@ export class ResultsViewPageStore
 
     @computed
     public get hideUnprofiledSamples() {
-        return this.urlWrapper.query.hide_unprofiled_samples === 'true';
+        const value = this.urlWrapper.query.hide_unprofiled_samples;
+        if (value === 'any' || value === 'totally') {
+            return value;
+        } else {
+            return false;
+        }
     }
 
     @action.bound
-    public setHideUnprofiledSamples(e: boolean) {
+    public setHideUnprofiledSamples(
+        e: IAnnotationFilterSettings['hideUnprofiledSamples']
+    ) {
         this.urlWrapper.updateURL({
-            hide_unprofiled_samples: e.toString(),
+            hide_unprofiled_samples: (e || false).toString(),
         });
     }
 
-    public set hideUnprofiledSamples(include: boolean) {
+    public set hideUnprofiledSamples(include: 'any' | 'totally' | false) {
         this.setHideUnprofiledSamples(include);
     }
 
@@ -3810,11 +3819,23 @@ export class ResultsViewPageStore
     });
 
     readonly filteredSamples = remoteData({
-        await: () => [this.samples, this.unprofiledSampleKeyToSample],
+        await: () => [
+            this.samples,
+            this.unprofiledSampleKeyToSample,
+            this.totallyUnprofiledSamples,
+        ],
         invoke: () => {
             if (this.hideUnprofiledSamples) {
-                const unprofiledSampleKeys = this.unprofiledSampleKeyToSample
-                    .result!;
+                let unprofiledSampleKeys: { [key: string]: Sample };
+                if (this.hideUnprofiledSamples === 'any') {
+                    unprofiledSampleKeys = this.unprofiledSampleKeyToSample
+                        .result!;
+                } else if (this.hideUnprofiledSamples === 'totally') {
+                    unprofiledSampleKeys = _.keyBy(
+                        this.totallyUnprofiledSamples.result!,
+                        s => s.uniqueSampleKey
+                    );
+                }
                 return Promise.resolve(
                     this.samples.result!.filter(
                         s => !(s.uniqueSampleKey in unprofiledSampleKeys)
@@ -3837,19 +3858,29 @@ export class ResultsViewPageStore
             // Samples that are unprofiled for at least one (gene, profile)
             const genes = this.genes.result!;
             const coverageInfo = this.coverageInformation.result!;
-            const queryProfileIds = this.selectedMolecularProfiles.result!.map(
-                p => p.molecularProfileId
+            const studyToSelectedMolecularProfileIds = _.mapValues(
+                _.groupBy(
+                    this.selectedMolecularProfiles.result!,
+                    p => p.studyId
+                ),
+                profiles => profiles.map(p => p.molecularProfileId)
             );
 
             return Promise.resolve(
                 this.samples.result!.filter(sample => {
+                    // Only look at profiles for this sample's study - doesn't
+                    //  make sense to look at profiles for other studies, which
+                    //  the sample certainly is not part of.
+                    const profileIds =
+                        studyToSelectedMolecularProfileIds[sample.studyId];
+
                     // Sample that is unprofiled for some gene
                     return _.some(genes, gene => {
                         // for some profile
                         return !_.every(
                             isSampleProfiledInMultiple(
                                 sample.uniqueSampleKey,
-                                queryProfileIds,
+                                profileIds,
                                 coverageInfo,
                                 gene.hugoGeneSymbol
                             )
@@ -3870,19 +3901,29 @@ export class ResultsViewPageStore
         invoke: () => {
             const genes = this.genes.result!;
             const coverageInfo = this.coverageInformation.result!;
-            const queryProfileIds = this.selectedMolecularProfiles.result!.map(
-                p => p.molecularProfileId
+            const studyToSelectedMolecularProfileIds = _.mapValues(
+                _.groupBy(
+                    this.selectedMolecularProfiles.result!,
+                    p => p.studyId
+                ),
+                profiles => profiles.map(p => p.molecularProfileId)
             );
 
             return Promise.resolve(
                 this.unprofiledSamples.result!.filter(sample => {
+                    // Only look at profiles for this sample's study - doesn't
+                    //  make sense to look at profiles for other studies, which
+                    //  the sample certainly is not part of.
+                    const profileIds =
+                        studyToSelectedMolecularProfileIds[sample.studyId];
+
                     // Among unprofiled samples, pick out samples that are unprofiled for EVERY gene ...(gene x profile)
                     return _.every(genes, gene => {
                         // for EVERY profile
                         return !_.some(
                             isSampleProfiledInMultiple(
                                 sample.uniqueSampleKey,
-                                queryProfileIds,
+                                profileIds,
                                 coverageInfo,
                                 gene.hugoGeneSymbol
                             )

src/pages/resultsView/comparison/ResultsViewComparisonUtils.ts

@@ -74,7 +74,7 @@ export function getAlteredVsUnalteredGroups(
     unalteredAndProfiledSamples: Sample[],
     totallyUnprofiledSamples: Sample[],
     queryContainsOql: boolean,
-    hideUnprofiledSamples: boolean
+    hideUnprofiledSamples: 'any' | 'totally' | false
 ): SessionGroupData[] {
     const ret = [];
     if (alteredSamples.length > 0) {
@@ -106,7 +106,10 @@ export function getAlteredVsUnalteredGroups(
             color: UNALTERED_COLOR,
         });
     }
-    if (totallyUnprofiledSamples.length > 0 && !hideUnprofiledSamples) {
+    if (
+        totallyUnprofiledSamples.length > 0 &&
+        hideUnprofiledSamples !== 'totally'
+    ) {
         ret.push({
             name: UNPROFILED_GROUP_NAME,
             description: `${

src/pages/resultsView/settings/SettingsMenu.tsx

@@ -19,6 +19,8 @@ enum EVENT_KEY {
     hidePutativePassengers = '0',
     showGermlineMutations = '1',
     hideUnprofiledSamples = '1.1',
+    hideAnyUnprofiledSamples = '1.2',
+    hideTotallyUnprofiledSamples = '1.3',
 
     dataTypeSample = '2',
     dataTypePatient = '3',
@@ -63,8 +65,17 @@ export default class SettingsMenu extends React.Component<
                     .props.store.driverAnnotationSettings.includeVUS;
                 break;
             case EVENT_KEY.hideUnprofiledSamples:
-                this.props.store.hideUnprofiledSamples = !this.props.store
-                    .hideUnprofiledSamples;
+                if (!this.props.store.hideUnprofiledSamples) {
+                    this.props.store.hideUnprofiledSamples = 'any';
+                } else {
+                    this.props.store.hideUnprofiledSamples = false;
+                }
+                break;
+            case EVENT_KEY.hideAnyUnprofiledSamples:
+                this.props.store.hideUnprofiledSamples = 'any';
+                break;
+            case EVENT_KEY.hideTotallyUnprofiledSamples:
+                this.props.store.hideUnprofiledSamples = 'totally';
                 break;
             case EVENT_KEY.showGermlineMutations:
                 this.props.store.includeGermlineMutations = !this.props.store
@@ -161,20 +172,58 @@ export default class SettingsMenu extends React.Component<
                         </label>
                     </div>
                     {this.props.resultsView && (
-                        <div className="checkbox">
-                            <label>
-                                <input
-                                    data-test="HideUnprofiled"
-                                    type="checkbox"
-                                    value={EVENT_KEY.hideUnprofiledSamples}
-                                    checked={
-                                        this.props.store.hideUnprofiledSamples
-                                    }
-                                    onClick={this.onInputClick}
-                                />{' '}
-                                Exclude samples that are not profiled for all
-                                queried genes in all queried profiles
-                            </label>
+                        <div>
+                            <div className="checkbox">
+                                <label>
+                                    <input
+                                        data-test="HideUnprofiled"
+                                        type="checkbox"
+                                        value={EVENT_KEY.hideUnprofiledSamples}
+                                        checked={
+                                            this.props.store
+                                                .hideUnprofiledSamples !== false
+                                        }
+                                        onClick={this.onInputClick}
+                                    />{' '}
+                                    Exclude unprofiled samples
+                                </label>
+                            </div>
+                            <div style={{ marginLeft: 10 }}>
+                                <div className="radio">
+                                    <label>
+                                        <input
+                                            type="radio"
+                                            checked={
+                                                this.props.store
+                                                    .hideUnprofiledSamples ===
+                                                'any'
+                                            }
+                                            value={
+                                                EVENT_KEY.hideAnyUnprofiledSamples
+                                            }
+                                            onClick={this.onInputClick}
+                                        />
+                                        Exclude samples that are unprofiled in
+                                        any queried gene or profile
+                                    </label>
+                                    <label>
+                                        <input
+                                            type="radio"
+                                            checked={
+                                                this.props.store
+                                                    .hideUnprofiledSamples ===
+                                                'totally'
+                                            }
+                                            value={
+                                                EVENT_KEY.hideTotallyUnprofiledSamples
+                                            }
+                                            onClick={this.onInputClick}
+                                        />
+                                        Exclude samples that are unprofiled in
+                                        every queried gene and profile.
+                                    </label>
+                                </div>
+                            </div>
                         </div>
                     )}
                 </div>

src/shared/alterationFiltering/AnnotationFilteringSettings.ts

@@ -18,7 +18,7 @@ export interface IExclusionSettings {
     includeGermlineMutations: boolean;
     includeSomaticMutations: boolean;
     includeUnknownStatusMutations: boolean;
-    hideUnprofiledSamples?: boolean;
+    hideUnprofiledSamples?: 'any' | 'totally' | false;
 }
 
 export interface DriverAnnotationSettings {

src/shared/components/driverAnnotations/SettingsMenu.tsx

@@ -22,7 +22,6 @@ enum EVENT_KEY {
     showSomaticMutations = '4',
     showUnknownStatusMutations = '5',
     showUnknownTier = '6',
-    hideUnprofiledSamples = '7',
     toggleAllMutationStatus = '8',
     toggleAllDriverAnnotation = '9',
     toggleAllDriverTiers = '10',
@@ -82,10 +81,6 @@ export default class SettingsMenu extends React.Component<
                     .props.store.driverAnnotationSettings
                     .includeUnknownOncogenicity;
                 break;
-            case EVENT_KEY.hideUnprofiledSamples:
-                this.props.store.hideUnprofiledSamples = !this.props.store
-                    .hideUnprofiledSamples;
-                break;
             case EVENT_KEY.showGermlineMutations:
                 this.props.store.includeGermlineMutations = !this.props.store
                     .includeGermlineMutations;