oncoprint - fix bugs with removing tracks arising from putting more o…

…ncoprint state in URL

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <[email protected]>

end-to-end-test/remote/specs/core/oncoprint.screenshot.spec.js

@@ -11,6 +11,20 @@ const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, "");
 
 const ONCOPRINT_TIMEOUT = 60000;
 
+function getNthTrackOptionsElements(n) {
+    // n is one-indexed
+
+    const button_selector = "#oncoprintDiv .oncoprintjs__track_options__toggle_btn_img.nth-"+n;
+    const dropdown_selector = "#oncoprintDiv .oncoprintjs__track_options__dropdown.nth-"+n;
+
+    return {
+        button: $(button_selector),
+        button_selector,
+        dropdown: $(dropdown_selector),
+        dropdown_selector
+    };
+}
+
 describe("oncoprint screenshot tests", function() {
     it("coadread_tcga_pub with clinical and heatmap tracks", function(){
         var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=coadread_tcga_pub&Z_SCORE_THRESHOLD=1&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS%20NRAS%20BRAF&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=coadread_tcga_pub_rna_seq_mrna_median_Zscores&show_samples=false&clinicallist=0%2C2%2CMETHYLATION_SUBTYPE&heatmap_track_groups=coadread_tcga_pub_rna_seq_mrna_median_Zscores%2CKRAS%2CNRAS%2CBRAF&`;
@@ -93,6 +107,18 @@ describe("oncoprint screenshot tests", function() {
         var res = checkOncoprintElement('.oncoprintContainer');
         assertScreenShotMatch(res);
     });
+    it("removes top treatment track successfully", function() {
+        goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=ccle_broad_2019&case_set_id=ccle_broad_2019_cnaseq&data_priority=0&gene_list=TP53&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=ccle_broad_2019_cna&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=ccle_broad_2019_mutations&profileFilter=0&tab_index=tab_visualize&heatmap_track_groups=ccle_broad_2019_CCLE_drug_treatment_IC50%2CAfatinib-2%2CAKTinhibitorVIII-1&treatment_list=Afatinib-2%3BAKTinhibitorVIII-1`);
+        waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+        const elements = getNthTrackOptionsElements(2);
+        setDropdownOpen(true, elements.button_selector, elements.dropdown_selector, "Couldnt open top treatment track options");
+        browser.click(elements.dropdown_selector + ' li:nth-child(3)'); // Click Remove
+        waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+        var res = checkOncoprintElement('.oncoprintContainer');
+        assertScreenShotMatch(res);
+    });
 });
 
 describe("track group headers", function() {
@@ -153,21 +179,6 @@ describe("track group headers", function() {
 });
 
 describe("sorting", function(){
-
-    function getNthTrackOptionsElements(n) {
-        // n is one-indexed
-
-        const button_selector = "#oncoprintDiv .oncoprintjs__track_options__toggle_btn_img.nth-"+n;
-        const dropdown_selector = "#oncoprintDiv .oncoprintjs__track_options__dropdown.nth-"+n;
-
-        return {
-            button: $(button_selector),
-            button_selector,
-            dropdown: $(dropdown_selector),
-            dropdown_selector
-        };
-    }
-
     it("oncoprint should sort patients correctly in coadread_tcga_pub", function(){
         goToUrlAndSetLocalStorage(CBIOPORTAL_URL);
 

src/shared/components/oncoprint/DeltaUtils.ts

@@ -653,7 +653,9 @@ function tryRemoveTrack(
         // removeCallback to forget its track ID
         const trackId = trackSpecKeyToTrackId[prevSpec.key];
         if (typeof trackId !== "undefined") {
-            oncoprint.removeTrack(trackId);
+            if (oncoprint.getTracks().includes(trackId)) {
+                oncoprint.removeTrack(trackId);
+            }
             delete trackSpecKeyToTrackId[prevSpec.key];
         }
         return true;
@@ -864,8 +866,10 @@ function transitionClinicalTrack(
             label: nextSpec.label,
             description: ((nextSpec.label || "").trim() === (nextSpec.description || "").trim()) ? undefined : nextSpec.description,
             removable: true,
-            removeCallback: ()=>{
+            removeCallback: () => {
                 delete getTrackSpecKeyToTrackId()[nextSpec.key];
+            },
+            onClickRemoveInTrackMenu: ()=>{
                 nextProps.onDeleteClinicalTrack && nextProps.onDeleteClinicalTrack(nextSpec.key);
             },
             sort_direction_changeable: true,
@@ -1010,12 +1014,15 @@ export function transitionHeatmapTrack(
             track_label_font_weight: nextSpec.labelFontWeight,
             track_label_left_padding: nextSpec.labelLeftPadding,
             target_group: nextSpec.trackGroupIndex,
-            removable: !!nextSpec.onRemove,
+            removable: !!nextSpec.onRemove || !!nextSpec.onClickRemoveInTrackMenu,
             movable: nextSpec.movable,
             na_legend_label: nextSpec.naLegendLabel,
             removeCallback: ()=>{
                 delete getTrackSpecKeyToTrackId()[nextSpec.key];
-                if (nextSpec.onRemove) nextSpec.onRemove();
+                nextSpec.onRemove && nextSpec.onRemove();
+            },
+            onClickRemoveInTrackMenu:()=>{
+                nextSpec.onClickRemoveInTrackMenu && nextSpec.onClickRemoveInTrackMenu();
             },
             sort_direction_changeable: ifNotDefined(nextSpec.sortDirectionChangeable, true),
             sortCmpFn: heatmapTrackSortComparator,

src/shared/components/oncoprint/Oncoprint.tsx

@@ -120,7 +120,6 @@ export interface IBaseHeatmapTrackSpec {
 export interface IHeatmapTrackSpec extends IBaseHeatmapTrackSpec {
     data: IBaseHeatmapTrackDatum[]; // can be IGeneHeatmapTrackDatum or ITreatmentHeatmapTrackDatum
     naLegendLabel?:string;
-    onRemove?: () => void;
     info?: string;
     labelColor?: string;
     labelCircleColor?: string;
@@ -131,6 +130,8 @@ export interface IHeatmapTrackSpec extends IBaseHeatmapTrackSpec {
     movable?:boolean;
     sortDirectionChangeable?:boolean; // never updated
     trackLinkUrl?: string | undefined;
+    onRemove?:()=>void;
+    onClickRemoveInTrackMenu?: ()=>void;
     molecularProfileName?: string;
     pivotThreshold?: number;
     sortOrder?: string;

src/shared/components/oncoprint/OncoprintUtils.ts

@@ -714,7 +714,7 @@ export function makeHeatmapTracksMobxPromise(oncoprint:ResultsViewOncoprint, sam
                         data
                     ),
                     trackGroupIndex: molecularProfileIdToHeatmapTracks[molecularProfileId].trackGroupIndex,
-                    onRemove:action(()=>{
+                    onClickRemoveInTrackMenu:action(()=>{
                         const trackGroup = oncoprint.molecularProfileIdToHeatmapTracks[molecularProfileId];
                         if (trackGroup) {
                             const newEntities = _.keys(trackGroup.entities).filter((entity)=>entity!==gene);
@@ -799,8 +799,7 @@ export function makeTreatmentProfileHeatmapTracksMobxPromise(oncoprint:ResultsVi
                     sortOrder: sortOrder,
                     trackLinkUrl: treatmentLinkMap[treatmentId],
                     trackGroupIndex: molecularProfileIdToHeatmapTracks[molecularProfileId]!.trackGroupIndex,
-                    onRemove:action(()=>{
-
+                    onClickRemoveInTrackMenu:action(()=>{
                         const trackGroup = oncoprint.molecularProfileIdToHeatmapTracks[molecularProfileId]!;
                         if (trackGroup){
                             const newEntities = _.keys(trackGroup.entities).filter((entity)=>entity!==treatmentId);