oncoprint - allow adding gaps to string-valued clinical tracks

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

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

@@ -11,6 +11,21 @@ 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 +108,22 @@ describe("oncoprint screenshot tests", function() {
         var res = checkOncoprintElement('.oncoprintContainer');
         assertScreenShotMatch(res);
     });
+    it("coadread_tcga_pub with column gaps inserted based on clinical track", function() {
+        goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/results?Z_SCORE_THRESHOLD=2.0&cancer_study_id=coadread_tcga_pub&cancer_study_list=coadread_tcga_pub&case_ids=&case_set_id=coadread_tcga_pub_nonhypermut&clinicallist=CANCER_TYPE_DETAILED&gene_list=KRAS%20NRAS%20BRAF&gene_set_choice=user-defined-list&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&oncoprint_cluster_profile=&oncoprint_sortby=`);
+        waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+        // open minimap just to see how it doesnt reflect the column gaps
+        browser.waitForExist('[data-test="ShowMinimapButton"]');
+        browser.click('[data-test="ShowMinimapButton"]');
+
+        const cancerTypeDetailedElements = getNthTrackOptionsElements(1);
+        setDropdownOpen(true, cancerTypeDetailedElements.button_selector, cancerTypeDetailedElements.dropdown_selector, "Failed to open cancer type detailed track menu");
+        browser.click(`${cancerTypeDetailedElements.dropdown_selector} li:nth-child(9)`); // Click "show gaps"
+        browser.pause(100); // give time to sort and insert gaps
+
+        const res = checkOncoprintElement('.oncoprintContainer');
+        assertScreenShotMatch(res);
+    });
 });
 
 describe("track group headers", function() {
@@ -153,21 +184,6 @@ 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

@@ -154,7 +154,7 @@
     "node-sass": "^4.9.3",
     "numeral": "^2.0.6",
     "object-sizeof": "^1.2.0",
-    "oncoprintjs": "4.0.8",
+    "oncoprintjs": "4.1.0",
     "parameter-validator": "^1.0.2",
     "pdfobject": "^2.0.201604172",
     "pegjs": "^0.10.0",

src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx

@@ -220,13 +220,13 @@ export default class Oncoprinter extends React.Component<IOncoprinterProps, {}>
                 }
             },
             onSetHorzZoom:(z:number)=>{
-                this.oncoprint.setHorzZoom(z);
+                this.oncoprint.setHorzZoomCentered(z);
             },
             onClickZoomIn:()=>{
-                this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()/0.7);
+                this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()/0.7);
             },
             onClickZoomOut:()=>{
-                this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()*0.7);
+                this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()*0.7);
             }
         };
     }

src/shared/components/oncoprint/DeltaUtils.ts

@@ -785,7 +785,7 @@ function transitionClinicalTrack(
         rule_set_params.legend_label = nextSpec.label;
         rule_set_params.exclude_from_legend = !nextProps.showClinicalTrackLegends;
         rule_set_params.na_legend_label = nextSpec.na_legend_label;
-        const clinicalTrackParams = {
+        const clinicalTrackParams:UserTrackSpec<any> = {
             rule_set_params,
             data: nextSpec.data,
             data_id_key: "uid",
@@ -804,7 +804,8 @@ function transitionClinicalTrack(
             init_sort_direction: 0 as 0,
             target_group: CLINICAL_TRACK_GROUP_INDEX,
             onSortDirectionChange: nextProps.onTrackSortDirectionChange,
-            custom_track_options: nextSpec.custom_options
+            custom_track_options: nextSpec.custom_options,
+            track_can_show_gaps: nextSpec.datatype === "string"
         };
         trackSpecKeyToTrackId[nextSpec.key] = oncoprint.addTracks([clinicalTrackParams])[0];
     } else if (nextSpec && prevSpec) {

src/shared/components/oncoprint/ResultsViewOncoprint.tsx

@@ -659,13 +659,13 @@ export default class ResultsViewOncoprint extends React.Component<IResultsViewOn
                 }
             },
             onSetHorzZoom:(z:number)=>{
-                this.oncoprint.setHorzZoom(z);
+                this.oncoprint.setHorzZoomCentered(z);
             },
             onClickZoomIn:()=>{
-                this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()/0.7);
+                this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()/0.7);
             },
             onClickZoomOut:()=>{
-                this.oncoprint.setHorzZoom(this.oncoprint.getHorzZoom()*0.7);
+                this.oncoprint.setHorzZoomCentered(this.oncoprint.getHorzZoom()*0.7);
             }
         };
     }

src/shared/components/oncoprint/controls/OncoprintControls.tsx

@@ -1279,6 +1279,7 @@ export default class OncoprintControls extends React.Component<
                         onClick={this.toggleShowMinimap}
                     >
                         <img
+                            data-test="ShowMinimapButton"
                             src={require('./toggle-minimap.svg')}
                             alt="icon"
                             style={{ width: 15, height: 15 }}

yarn.lock

@@ -10715,10 +10715,10 @@ oncokb-styles@~0.1.0:
   resolved "https://registry.yarnpkg.com/oncokb-styles/-/oncokb-styles-0.1.0.tgz#3a67a03dbdf6ebdde497c77451fef167afe00c4f"
   integrity sha512-4vhF2Q5hAbOyKWlstA/AItd33cnXbp/Z1Zluxnlc7u0Dz6GnqnrZFK/upUleT4CTES6k5+QWT4Zv95+l5FL0hg==
 
-oncoprintjs@4.0.8:
-  version "4.0.8"
-  resolved "https://registry.yarnpkg.com/oncoprintjs/-/oncoprintjs-4.0.8.tgz#03d586ea45c415805d952ddeb6fc5399a9e4737b"
-  integrity sha512-wSl9je+fEgitLRydOKae1gftKCB0XRv5oqbNYE9+Y1inLYj7RUVqDKTBS+HaYaAFD+vmEVoTPTtboRpiE5obQw==
+oncoprintjs@4.1.0:
+  version "4.1.0"
+  resolved "https://registry.yarnpkg.com/oncoprintjs/-/oncoprintjs-4.1.0.tgz#7f253f6235b1523e3ada8bb8960ad545696203af"
+  integrity sha512-RHJDoWOsfFt39j/bUidRARqMbGy9MJXN3Z7SaSl1oDE5E0VNwhBeZbCSuakTZJjTJkGeqqhqr30QhPDfrEHkJA==
   dependencies:
     gl-matrix "2.3.2"
     jquery "^3.0.0"