oncoprint - allow adding gaps to string-valued clinical tracks

Signed-off-by: Abeshouse, Adam A./Sloan Kettering Institute <[email protected]>
cBioPortal · Feb 10, 2020 · b33a3cf · b33a3cf
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Showing 15 changed files with 47 additions and 7 deletions.
diff --git a/..._with_column_gaps_inserted_based_on_clinical_track_element_chrome_1600x1000.png b/..._with_column_gaps_inserted_based_on_clinical_track_element_chrome_1600x1000.png
diff --git a/...oprinter_example_data,_dont_color_by_driver_vs_vus_element_chrome_1600x1000.png b/...oprinter_example_data,_dont_color_by_driver_vs_vus_element_chrome_1600x1000.png
diff --git a/...oprinter_example_data,_dont_color_by_mutation_type_element_chrome_1600x1000.png b/...oprinter_example_data,_dont_color_by_mutation_type_element_chrome_1600x1000.png
diff --git a/...shots/reference/oncoprinter_example_data,_hide_vus_element_chrome_1600x1000.png b/...shots/reference/oncoprinter_example_data,_hide_vus_element_chrome_1600x1000.png
diff --git a/...ta,_start_by_set_gene_order,_then_set_sample_order_element_chrome_1600x1000.png b/...ta,_start_by_set_gene_order,_then_set_sample_order_element_chrome_1600x1000.png
diff --git a/...ta,_start_by_set_sample_order,_then_set_gene_order_element_chrome_1600x1000.png b/...ta,_start_by_set_sample_order,_then_set_gene_order_element_chrome_1600x1000.png
diff --git a/...ple_data,_then_set_gene_order,_including_all_genes_element_chrome_1600x1000.png b/...ple_data,_then_set_gene_order,_including_all_genes_element_chrome_1600x1000.png
diff --git a/...data,_then_set_gene_order,_not_including_all_genes_element_chrome_1600x1000.png b/...data,_then_set_gene_order,_not_including_all_genes_element_chrome_1600x1000.png
diff --git a/...data,_then_set_sample_order,_including_all_samples_element_chrome_1600x1000.png b/...data,_then_set_sample_order,_including_all_samples_element_chrome_1600x1000.png
diff --git a/...ote/screenshots/reference/oncoprinter_example_data_element_chrome_1600x1000.png b/...ote/screenshots/reference/oncoprinter_example_data_element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/oncoprint.screenshot.spec.js b/end-to-end-test/remote/specs/core/oncoprint.screenshot.spec.js
@@ -139,6 +139,36 @@ 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(
+            `${CBIOPORTAL_URL}/results?Z_SCORE_THRESHOLD=2.0&cancer_study_id=coadread_tcga_pub&cancer_study_list=coadread_tcga_pub&case_ids=&case_set_id=coadread_tcga_pub_nonhypermut&clinicallist=CANCER_TYPE_DETAILED&gene_list=KRAS%20NRAS%20BRAF&gene_set_choice=user-defined-list&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&oncoprint_cluster_profile=&oncoprint_sortby=`
+        );
+        waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+        const cancerTypeDetailedElements = getNthTrackOptionsElements(1);
+        setDropdownOpen(
+            true,
+            cancerTypeDetailedElements.button_selector,
+            cancerTypeDetailedElements.dropdown_selector,
+            'Failed to open cancer type detailed track menu'
+        );
+        browser.click(
+            `${cancerTypeDetailedElements.dropdown_selector} li:nth-child(9)`
+        ); // Click "show gaps"
+        browser.pause(100); // give time to sort and insert gaps
+
+        // open minimap
+        browser.waitForExist('[data-test="ShowMinimapButton"]');
+        browser.click('[data-test="ShowMinimapButton"]');
+
+        // zoom to fit
+        browser.waitForVisible('.oncoprint-zoomtofit-btn');
+        browser.click('.oncoprint-zoomtofit-btn');
+        browser.pause(100); // give time to rezoom
+
+        const res = checkOncoprintElement('.oncoprintContainer');
+        assertScreenShotMatch(res);
+    });
 });
 
 describe('track group headers', function() {

diff --git a/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx b/src/pages/staticPages/tools/oncoprinter/Oncoprinter.tsx
@@ -285,13 +285,17 @@ export default class Oncoprinter extends React.Component<
                 }
             },
             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
+                );
             },
             onClickNGCHM: () => {}, // do nothing in oncoprinter mode
         };

diff --git a/src/shared/components/oncoprint/DeltaUtils.ts b/src/shared/components/oncoprint/DeltaUtils.ts
@@ -1172,7 +1172,7 @@ 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',
@@ -1199,6 +1199,7 @@ function transitionClinicalTrack(
             target_group: CLINICAL_TRACK_GROUP_INDEX,
             onSortDirectionChange: nextProps.onTrackSortDirectionChange,
             custom_track_options: nextSpec.custom_options,
+            track_can_show_gaps: nextSpec.datatype === 'string',
         };
         trackSpecKeyToTrackId[nextSpec.key] = oncoprint.addTracks([
             clinicalTrackParams,

diff --git a/src/shared/components/oncoprint/ResultsViewOncoprint.tsx b/src/shared/components/oncoprint/ResultsViewOncoprint.tsx
@@ -882,13 +882,17 @@ export default class ResultsViewOncoprint extends React.Component<
                 }
             },
             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
+                );
             },
         };
     }

diff --git a/src/shared/components/oncoprint/controls/OncoprintControls.tsx b/src/shared/components/oncoprint/controls/OncoprintControls.tsx
@@ -1401,6 +1401,7 @@ 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 }}