cBioPortal · alisman · Nov 20, 2023 · Aug 16, 2023 · Aug 18, 2023 · Sep 7, 2023
diff --git a/...nshots/reference/oncoprint_reflects_default_colors_element_chrome_1600x1000.png b/...nshots/reference/oncoprint_reflects_default_colors_element_chrome_1600x1000.png
diff --git a/.../reference/oncoprint_reflects_user_selected_colors_element_chrome_1600x1000.png b/.../reference/oncoprint_reflects_user_selected_colors_element_chrome_1600x1000.png
diff --git a/...ault_background_for_glyphs_when_option_not_toggled_element_chrome_1600x1000.png b/...ault_background_for_glyphs_when_option_not_toggled_element_chrome_1600x1000.png
diff --git a/...es_white_background_for_glyphs_when_option_toggled_element_chrome_1600x1000.png b/...es_white_background_for_glyphs_when_option_toggled_element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/resultsOncoprintColorConfig.spec.js b/end-to-end-test/remote/specs/core/resultsOncoprintColorConfig.spec.js
@@ -0,0 +1,190 @@
+var assertScreenShotMatch = require('../../../shared/lib/testUtils')
+    .assertScreenShotMatch;
+var assert = require('assert');
+var waitForOncoprint = require('../../../shared/specUtils').waitForOncoprint;
+var goToUrlAndSetLocalStorage = require('../../../shared/specUtils')
+    .goToUrlAndSetLocalStorage;
+var getNthOncoprintTrackOptionsElements = require('../../../shared/specUtils')
+    .getNthOncoprintTrackOptionsElements;
+var getTextInOncoprintLegend = require('../../../shared/specUtils')
+    .getTextInOncoprintLegend;
+var {
+    checkOncoprintElement,
+    getElementByTestHandle,
+} = require('../../../shared/specUtils.js');
+
+const ONCOPRINT_TIMEOUT = 60000;
+const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
+
+describe('oncoprint colors', () => {
+    describe('clinical tracks color configuration', () => {
+        before(function() {
+            goToUrlAndSetLocalStorage(
+                `${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=gbm_tcga&case_set_id=gbm_tcga_all&data_priority=0&gene_list=EGFR%250APTEN%250AIDH1%250ATP53&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=gbm_tcga_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=gbm_tcga_mrna_median_all_sample_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=gbm_tcga_mutations&hide_unprofiled_samples=false&profileFilter=0&tab_index=tab_visualize&show_samples=false`
+            );
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+        });
+
+        it('color configuration modal reflects user selected colors', () => {
+            // add "Mutation spectrum" track
+            const $tracksDropdown = $('#addTracksDropdown');
+            $tracksDropdown.click();
+            getElementByTestHandle(
+                'add-chart-option-mutation-spectrum'
+            ).waitForDisplayed();
+            getElementByTestHandle('add-chart-option-mutation-spectrum')
+                .$('label')
+                .click();
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+            // check that mutation spectrum is added to the oncoprint
+            let legendText = getTextInOncoprintLegend();
+            assert(legendText.indexOf('Mutation spectrum') > -1);
+
+            $tracksDropdown.waitForDisplayed();
+            $tracksDropdown.click();
+
+            var trackOptionsElts = getNthOncoprintTrackOptionsElements(5);
+            // open menu
+            $(trackOptionsElts.button_selector).click();
+            $(trackOptionsElts.dropdown_selector).waitForDisplayed({
+                timeout: 1000,
+            });
+            // click "Edit Colors" to open modal
+            $(trackOptionsElts.dropdown_selector + ' li:nth-child(8)').click();
+            browser.pause(1000);
+
+            // select new colors for track values
+            getElementByTestHandle('color-picker-icon').click();
+            $('.circle-picker').waitForDisplayed({ timeout: 1000 });
+            $('.circle-picker [title="#990099"]').click();
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            getElementByTestHandle('color-picker-icon').waitForDisplayed();
+            getElementByTestHandle('color-picker-icon').click();
+            $('.circle-picker').waitForDisplayed({ reverse: true });
+
+            $$('[data-test="color-picker-icon"]')[1].click();
+            $('.circle-picker').waitForDisplayed({ timeout: 1000 });
+            $('.circle-picker [title="#109618"]').click();
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+            getElementByTestHandle('color-picker-icon').waitForDisplayed();
+            $$('[data-test="color-picker-icon"]')[1].click();
+            $('.circle-picker').waitForDisplayed({ reverse: true });
+
+            $$('[data-test="color-picker-icon"]')[2].click();
+            $('.circle-picker').waitForDisplayed({ timeout: 1000 });
+            $('.circle-picker [title="#8b0707"]').click();
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+            assert.strictEqual(
+                $('[data-test="color-picker-icon"] rect').getAttribute('fill'),
+                '#990099'
+            );
+            assert.strictEqual(
+                $$('[data-test="color-picker-icon"] rect')[1].getAttribute(
+                    'fill'
+                ),
+                '#109618'
+            );
+            assert.strictEqual(
+                $$('[data-test="color-picker-icon"] rect')[2].getAttribute(
+                    'fill'
+                ),
+                '#8b0707'
+            );
+        });
+
+        it('oncoprint reflects user selected colors', () => {
+            // close modal
+            $('a.tabAnchor_oncoprint').click();
+            var res = checkOncoprintElement();
+            assertScreenShotMatch(res);
+        });
+
+        it('reset colors button is visible when default colors not used', () => {
+            // click "Edit Colors" to open modal and check "Reset Colors" button in modal
+            var trackOptionsElts = getNthOncoprintTrackOptionsElements(5);
+            $(trackOptionsElts.button_selector).click();
+            $(trackOptionsElts.dropdown_selector).waitForDisplayed({
+                timeout: 1000,
+            });
+            $(trackOptionsElts.dropdown_selector + ' li:nth-child(8)').click();
+            getElementByTestHandle('resetColors').waitForDisplayed();
+        });
+
+        it('color configuration modal reflects default colors', () => {
+            // click "Reset Colors" track
+            getElementByTestHandle('resetColors').click();
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+
+            assert.strictEqual(
+                $('[data-test="color-picker-icon"] rect').getAttribute('fill'),
+                '#3d6eb1'
+            );
+            assert.strictEqual(
+                $$('[data-test="color-picker-icon"] rect')[1].getAttribute(
+                    'fill'
+                ),
+                '#8ebfdc'
+            );
+            assert.strictEqual(
+                $$('[data-test="color-picker-icon"] rect')[2].getAttribute(
+                    'fill'
+                ),
+                '#dff1f8'
+            );
+        });
+
+        it('oncoprint reflects default colors', () => {
+            // close modal
+            $('a.tabAnchor_oncoprint').click();
+            var res = checkOncoprintElement();
+            assertScreenShotMatch(res);
+        });
+
+        it('reset colors button is hidden when default colors are used', () => {
+            // click "Edit Colors" to open modal and check "Reset Colors" button in modal
+            var trackOptionsElts = getNthOncoprintTrackOptionsElements(5);
+            $(trackOptionsElts.button_selector).click();
+            $(trackOptionsElts.dropdown_selector).waitForDisplayed({
+                timeout: 1000,
+            });
+            $(trackOptionsElts.dropdown_selector + ' li:nth-child(8)').click();
+            getElementByTestHandle('resetColors').waitForDisplayed({
+                reverse: true,
+            });
+        });
+    });
+
+    describe('enable white background for glyphs', () => {
+        before(function() {
+            goToUrlAndSetLocalStorage(
+                `${CBIOPORTAL_URL}/results/oncoprint?Action=Submit&RPPA_SCORE_THRESHOLD=2.0&Z_SCORE_THRESHOLD=2.0&cancer_study_list=gbm_tcga&case_set_id=gbm_tcga_all&data_priority=0&gene_list=EGFR%250APTEN%250AIDH1%250ATP53&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=gbm_tcga_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=gbm_tcga_mrna_median_all_sample_Zscores&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=gbm_tcga_mutations&hide_unprofiled_samples=false&profileFilter=0&tab_index=tab_visualize&show_samples=false`
+            );
+            waitForOncoprint(ONCOPRINT_TIMEOUT);
+        });
+        it('oncoprint uses white background for glyphs when option toggled', () => {
+            // toggle on white backgrounds for glyphs
+            const $viewDropdown = $('#viewDropdownButton');
+            $viewDropdown.click();
+            waitForOncoprint(2000);
+            getElementByTestHandle('toggleWhiteBackgroundForGlyphs').click();
+            $viewDropdown.click();
+
+            var res = checkOncoprintElement();
+            assertScreenShotMatch(res);
+        });
+
+        it('oncoprint uses default background for glyphs when option not toggled', () => {
+            // toggle off white backgrounds for glyphs
+            const $viewDropdown = $('#viewDropdownButton');
+            $viewDropdown.click();
+            waitForOncoprint(2000);
+            getElementByTestHandle('toggleWhiteBackgroundForGlyphs').click();
+            $viewDropdown.click();
+
+            var res = checkOncoprintElement();
+            assertScreenShotMatch(res);
+        });
+    });
+});
diff --git a/src/pages/resultsView/ResultsViewPageStore.ts b/src/pages/resultsView/ResultsViewPageStore.ts
@@ -304,6 +304,7 @@ import {
     ONCOKB_DEFAULT_INFO,
     USE_DEFAULT_PUBLIC_INSTANCE_FOR_ONCOKB,
 } from 'react-mutation-mapper';
+import { RGBAColor } from 'oncoprintjs';
 
 type Optional<T> =
     | { isApplicable: true; value: T }
@@ -493,6 +494,15 @@ export class ResultsViewPageStore extends AnalysisStore
                 }
             )
         );
+
+        const clinicalTracksColorConfig = localStorage.getItem(
+            'clinicalTracksColorConfig'
+        );
+        if (clinicalTracksColorConfig !== null) {
+            this._userSelectedStudiesToClinicalTracksColors = JSON.parse(
+                clinicalTracksColorConfig
+            );
+        }
     }
 
     destroy() {
@@ -525,6 +535,10 @@ export class ResultsViewPageStore extends AnalysisStore
     get cancerStudyIds() {
         return this.urlWrapper.query.cancer_study_list.split(',');
     }
+    @computed
+    get cancerStudyListSorted() {
+        return this.cancerStudyIds.sort().join(',');
+    }
 
     @computed
     get rppaScoreThreshold() {
@@ -573,6 +587,14 @@ export class ResultsViewPageStore extends AnalysisStore
 
     @observable queryFormVisible: boolean = false;
 
+    @observable _userSelectedStudiesToClinicalTracksColors: {
+        [studies: string]: {
+            [label: string]: {
+                [value: string]: RGBAColor;
+            };
+        };
+    } = { global: {} };
+
     @computed get doNonSelectedDownloadableMolecularProfilesExist() {
         return (
             this.nonSelectedDownloadableMolecularProfilesGroupByName.result &&
@@ -586,6 +608,48 @@ export class ResultsViewPageStore extends AnalysisStore
         | ModifyQueryParams
         | undefined = undefined;
 
+    @action.bound
+    public setUserSelectedClinicalTrackColor(
+        label: string,
+        value: string,
+        color: RGBAColor | undefined
+    ) {
+        // if color is undefined, delete color from userSelectedClinicalAttributeColors if exists
+        // else, set the color in userSelectedClinicalAttributeColors
+        if (
+            !color &&
+            this._userSelectedStudiesToClinicalTracksColors['global'][label] &&
+            this._userSelectedStudiesToClinicalTracksColors['global'][label][
+                value
+            ]
+        ) {
+            delete this._userSelectedStudiesToClinicalTracksColors['global'][
+                label
+            ][value];
+        } else if (color) {
+            if (
+                !this._userSelectedStudiesToClinicalTracksColors['global'][
+                    label
+                ]
+            ) {
+                this._userSelectedStudiesToClinicalTracksColors['global'][
+                    label
+                ] = {};
+            }
+            this._userSelectedStudiesToClinicalTracksColors['global'][label][
+                value
+            ] = color;
+        }
+        localStorage.setItem(
+            'clinicalTracksColorConfig',
+            JSON.stringify(this._userSelectedStudiesToClinicalTracksColors)
+        );
+    }
+
+    @computed get userSelectedStudiesToClinicalTracksColors() {
+        return this._userSelectedStudiesToClinicalTracksColors;
+    }
+
     @action.bound
     public setOncoprintAnalysisCaseType(e: OncoprintAnalysisCaseType) {
         this.urlWrapper.updateURL({

diff --git a/src/pages/resultsView/ResultsViewURLWrapper.ts b/src/pages/resultsView/ResultsViewURLWrapper.ts
@@ -77,6 +77,7 @@ export enum ResultsViewURLQueryEnum {
     geneset_list = 'geneset_list',
     generic_assay_groups = 'generic_assay_groups',
     show_samples = 'show_samples',
+    enable_white_background_for_glyphs = 'enable_white_background_for_glyphs',
     heatmap_track_groups = 'heatmap_track_groups',
     oncoprint_sortby = 'oncoprint_sortby',
     oncoprint_cluster_profile = 'oncoprint_cluster_profile',
@@ -127,6 +128,7 @@ export type ResultsViewURLQuery = {
 const shouldForceRemount: { [prop in keyof ResultsViewURLQuery]: boolean } = {
     clinicallist: false,
     show_samples: false,
+    enable_white_background_for_glyphs: false,
     heatmap_track_groups: false,
     oncoprint_sortby: false,
     oncoprint_cluster_profile: false,
@@ -181,6 +183,7 @@ const propertiesMap = _.mapValues(
         // oncoprint props
         clinicallist: { isSessionProp: false },
         show_samples: { isSessionProp: false },
+        enable_white_background_for_glyphs: { isSessionProp: false },
         heatmap_track_groups: { isSessionProp: false },
         oncoprint_sortby: { isSessionProp: false },
         oncoprint_cluster_profile: { isSessionProp: false },