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);
 

package.json

@@ -3,7 +3,10 @@
   "private": true,
   "version": "0.0.0",
   "workspaces": {
-    "packages": [".", "packages/*"]
+    "packages": [
+      ".",
+      "packages/*"
+    ]
   },
   "description": "",
   "scripts": {
@@ -172,7 +175,7 @@
     "node-sass": "^4.9.3",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncoprintjs": "4.0.9",
+    "oncoprintjs": "4.1.3",
     "parameter-validator": "^1.0.2",
     "pdfobject": "^2.0.201604172",
     "pegjs": "^0.10.0",

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,
@@ -1015,7 +1019,10 @@ export function transitionHeatmapTrack(
             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);

yarn.lock

@@ -15699,10 +15699,10 @@ oncokb-styles@~0.1.2:
   resolved "https://registry.yarnpkg.com/oncokb-styles/-/oncokb-styles-0.1.2.tgz#8b26c0a0829787cdc1b595d3a021b3266607102b"
   integrity sha512-tuy5s3qFxgf1ogMATQSRPNgLlAMrvOOTCAN1dm/wJ+VZoStbJ7g36/qHwc99UPfh3vrB05broLodF+k58p5tUw==
 
-oncoprintjs@4.0.9:
-  version "4.0.9"
-  resolved "https://registry.yarnpkg.com/oncoprintjs/-/oncoprintjs-4.0.9.tgz#d4b7bb673e50c571a435a4a27e82247dfd2d0249"
-  integrity sha512-T6VutMr3g+hx8e6E/873CrnuWS3s+3rfSqfU0sjgboV3N6hajU3WX/PMe3WNFBCSRHYLIi1SQV9bWcwdouZNkw==
+oncoprintjs@4.1.3:
+  version "4.1.3"
+  resolved "https://registry.yarnpkg.com/oncoprintjs/-/oncoprintjs-4.1.3.tgz#aca0528fc18d04e5c505333d603f871b1f40dec9"
+  integrity sha512-iP3mXiokJT5j1M3vsRaU9lxQUyt9zY57RSATlFa1rpegbZGyVwMwdZawZRd+Gov9P49JHNPvKeM/qagYo1Gglg==
   dependencies:
     gl-matrix "2.3.2"
     jquery "^3.0.0"