Merge branch 'master' into add_description

cBioPortal · Sep 24, 2024 · 436787d · 436787d
2 parents 83ecece + 1dd45af
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diff --git a/OPEN-SOURCE-DOCUMENTATION b/OPEN-SOURCE-DOCUMENTATION
@@ -49,3 +49,20 @@ Available under license:
     5. Products derived from this software may not be called
     "ColorBrewer", nor may "ColorBrewer" appear in their name, without
     prior written permission of Cynthia Brewer.
+
+* JavaScript/CSS Font Detector
+
+JavaScript/CSS Font Detector
+----------------------------
+Available under license:
+
+    JavaScript code to detect available availability of a
+    particular font in a browser using JavaScript and CSS.
+
+    Author : Lalit Patel
+    Website: http://www.lalit.org/lab/javascript-css-font-detect/
+    License: Apache Software License 2.0
+             http://www.apache.org/licenses/LICENSE-2.0
+
+
+
diff --git a/...ots/reference/initializes_as_configured_by_default_element_chrome_1600x1000.png b/...ots/reference/initializes_as_configured_by_default_element_chrome_1600x1000.png
diff --git a/..._correctly_when_clinicallist_config_present_in_url_element_chrome_1600x1000.png b/..._correctly_when_clinicallist_config_present_in_url_element_chrome_1600x1000.png
diff --git a/...hart_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png b/...hart_for_patient_who_has_significant_id_signatures_element_chrome_1600x1000.png
diff --git a/.../reference/shows_oql_structural_variant_variations_element_chrome_1600x1000.png b/.../reference/shows_oql_structural_variant_variations_element_chrome_1600x1000.png
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/...archical_sorting_when_two_tracks_have_enabled_gaps_element_chrome_1600x1000.png b/...archical_sorting_when_two_tracks_have_enabled_gaps_element_chrome_1600x1000.png
diff --git a/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png b/...mote/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png
diff --git a/.../remote/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png b/.../remote/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png
diff --git a/...ps_for_sex_track_with_correct_subgroup_percentages_element_chrome_1600x1000.png b/...ps_for_sex_track_with_correct_subgroup_percentages_element_chrome_1600x1000.png
diff --git a/...te/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png b/...te/screenshots/reference/tcga_pancancer_atlas_page_element_chrome_1600x1000.png
diff --git a/end-to-end-test/remote/specs/core/coexpression.screenshot.spec.js b/end-to-end-test/remote/specs/core/coexpression.screenshot.spec.js
@@ -1,110 +1,129 @@
-var assert = require('assert');
-var expect = require('chai').expect;
-var waitForOncoprint = require('../../../shared/specUtils').waitForOncoprint;
-var setOncoprintMutationsMenuOpen = require('../../../shared/specUtils')
-    .setOncoprintMutationsMenuOpen;
-var goToUrlAndSetLocalStorage = require('../../../shared/specUtils')
-    .goToUrlAndSetLocalStorage;
-var waitForNetworkQuiet = require('../../../shared/specUtils')
-    .waitForNetworkQuiet;
-var sessionServiceIsEnabled = require('../../../shared/specUtils')
-    .sessionServiceIsEnabled;
-var assertScreenShotMatch = require('../../../shared/lib/testUtils')
-    .assertScreenShotMatch;
-
+const {
+    getElement,
+    goToUrlAndSetLocalStorage,
+    COEXPRESSION_TIMEOUT,
+    clickElement,
+} = require('../../../shared/specUtils_Async');
 const CBIOPORTAL_URL = process.env.CBIOPORTAL_URL.replace(/\/$/, '');
-
-var { COEXPRESSION_TIMEOUT } = require('../../../shared/specUtils');
+const { assertScreenShotMatch } = require('../../../shared/lib/testUtils');
 
 describe('coexpression tab screenshot tests', function() {
-    this.retries(2);
-
-    before(function() {
-        var url = `${CBIOPORTAL_URL}/results/coexpression?tab_index=tab_visualize&cancer_study_list=coadread_tcga_pub&cancer_study_id=coadread_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&Z_SCORE_THRESHOLD=2.0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS+NRAS+BRAF&gene_set_choice=user-defined-list&Action=Submit`;
-        goToUrlAndSetLocalStorage(url);
+    this.retries(0);
+    before(async function() {
+        const url = `${CBIOPORTAL_URL}/results/coexpression?tab_index=tab_visualize&cancer_study_list=coadread_tcga_pub&cancer_study_id=coadread_tcga_pub&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&Z_SCORE_THRESHOLD=2.0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS+NRAS+BRAF&gene_set_choice=user-defined-list&Action=Submit`;
+        await goToUrlAndSetLocalStorage(url);
     });
-    it('coexpression tab coadread_tcga_pub initial load', function() {
-        $('div[data-test="CoExpressionPlot"]').waitForExist({
+    it('coexpression tab coadread_tcga_pub initial load', async function() {
+        await getElement('div[data-test="CoExpressionPlot"]', {
             timeout: COEXPRESSION_TIMEOUT,
         }); // wait for plot to show up
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        await (await getElement('body')).moveTo({ xOffset: 0, yOffset: 0 });
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub log scale x and y mutations on', function() {
-        $(
-            'div[data-test="coExpressionTabDiv"] input[data-test="logScale"]'
+    it('coexpression tab coadread_tcga_pub log scale x and y mutations on', async function() {
+        await (
+            await getElement(
+                'div[data-test="coExpressionTabDiv"] input[data-test="logScale"]'
+            )
         ).click();
-        $('body').moveTo({ xOffset: 0, yOffset: 0 });
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        await (await getElement('body')).moveTo({ xOffset: 0, yOffset: 0 });
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub log scale x and y with regression line', function() {
-        $('input[data-test="ShowRegressionLine"]').click();
-        $('body').moveTo({ xOffset: 0, yOffset: 0 });
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+    it('coexpression tab coadread_tcga_pub log scale x and y with regression line', async function() {
+        await (
+            await getElement('input[data-test="ShowRegressionLine"]')
+        ).click();
+        await (await getElement('body')).moveTo({ xOffset: 0, yOffset: 0 });
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub loc scale x and y mutations off', function() {
-        $('input[data-test="ShowRegressionLine"]').click();
-        $(
-            'div[data-test="coExpressionTabDiv"] input[data-test="ShowMutations"]'
+    it('coexpression tab coadread_tcga_pub loc scale x and y mutations off', async function() {
+        await (
+            await getElement('input[data-test="ShowRegressionLine"]')
         ).click();
-        $('body').moveTo({ xOffset: 0, yOffset: 0 });
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        await (
+            await getElement(
+                'div[data-test="coExpressionTabDiv"] input[data-test="ShowMutations"]'
+            )
+        ).click();
+        await (await getElement('body')).moveTo({ xOffset: 0, yOffset: 0 });
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub switch tabs', function() {
-        $('#coexpressionTabGeneTabs>ul>li:nth-child(2)>a').click(); // click on NRAS
-        $('body').moveTo({ xOffset: 0, yOffset: 0 });
-        browser.pause(100); // give time to start loading
-        $('div[data-test="CoExpressionPlot"]').waitForExist({
+    it('coexpression tab coadread_tcga_pub switch tabs', async function() {
+        await (
+            await getElement('#coexpressionTabGeneTabs>ul>li:nth-child(2)>a')
+        ).click(); // click on NRAS
+        await (await getElement('body')).moveTo({ xOffset: 0, yOffset: 0 });
+        await browser.pause(100); // give time to start loading
+        await getElement('div[data-test="CoExpressionPlot"]', {
             timeout: COEXPRESSION_TIMEOUT,
         }); // wait for plot to show up
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub switch profiles', function() {
-        browser.execute(function() {
+    it('coexpression tab coadread_tcga_pub switch profiles', async function() {
+        await browser.execute(function() {
             resultsViewCoExpressionTab.onSelectProfileX({
                 value: 'coadread_tcga_pub_mrna',
             });
         });
-        browser.execute(function() {
+        await browser.execute(function() {
             resultsViewCoExpressionTab.onSelectProfileY({
                 value: 'coadread_tcga_pub_mrna',
             });
         });
-        browser.pause(100); // give time to start loading
-        $('div[data-test="CoExpressionPlot"]').waitForExist({
+        await browser.pause(100);
+        await getElement('div[data-test="CoExpressionPlot"]', {
             timeout: COEXPRESSION_TIMEOUT,
         }); // wait for plot to show up
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub switch profiles + regression line', function() {
-        $('input[data-test="ShowRegressionLine"]').click();
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+    it('coexpression tab coadread_tcga_pub switch profiles + regression line', async function() {
+        await clickElement('input[data-test="ShowRegressionLine"]');
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub with a lot of genes', function() {
-        goToUrlAndSetLocalStorage(
+    it('coexpression tab coadread_tcga_pub with a lot of genes', async function() {
+        await goToUrlAndSetLocalStorage(
             `${CBIOPORTAL_URL}/results/coexpression?Action=Submit&RPPA_SCORE_THRESHOLD=2&Z_SCORE_THRESHOLD=2&cancer_study_id=coadread_tcga_pub&cancer_study_list=coadread_tcga_pub&case_set_id=coadread_tcga_pub_hypermut&data_priority=0&gene_list=AKR1C3%2520AR%2520CYB5A%2520CYP11A1%2520CYP11B1%2520CYP11B2%2520CYP17A1%2520CYP19A1%2520CYP21A2%2520HSD17B1%2520HSD17B10%2520HSD17B11%2520HSD17B12%2520HSD17B13%2520HSD17B14%2520HSD17B2%2520HSD17B3%2520HSD17B4%2520HSD17B6%2520HSD17B7%2520HSD17B8%2520HSD3B1%2520HSD3B2%2520HSD3B7%2520RDH5%2520SHBG%2520SRD5A1%2520SRD5A2%2520SRD5A3%2520STAR&geneset_list=%20&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&profileFilter=0&tab_index=tab_visualize`
         );
-        $('div[data-test="CoExpressionPlot"]').waitForExist({
+        await getElement('div[data-test="CoExpressionPlot"]', {
             timeout: COEXPRESSION_TIMEOUT,
         }); // wait for plot to show up
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
 
-    it('coexpression tab coadread_tcga_pub with user defined case list', function() {
-        goToUrlAndSetLocalStorage(
+    it('coexpression tab coadread_tcga_pub with user defined case list', async function() {
+        await goToUrlAndSetLocalStorage(
             `${CBIOPORTAL_URL}/results/coexpression?Action=Submit&cancer_study_list=coadread_tcga_pub&case_ids=coadread_tcga_pub%3ATCGA-A6-2672-01%2Bcoadread_tcga_pub%3ATCGA-A6-2678-01%2Bcoadread_tcga_pub%3ATCGA-A6-3809-01%2Bcoadread_tcga_pub%3ATCGA-AA-3502-01%2Bcoadread_tcga_pub%3ATCGA-AA-3510-01%2Bcoadread_tcga_pub%3ATCGA-AA-3672-01%2Bcoadread_tcga_pub%3ATCGA-AA-3673-01%2Bcoadread_tcga_pub%3ATCGA-AA-3850-01%2Bcoadread_tcga_pub%3ATCGA-AA-3852-01%2Bcoadread_tcga_pub%3ATCGA-AA-3862-01%2Bcoadread_tcga_pub%3ATCGA-AA-3877-01%2Bcoadread_tcga_pub%3ATCGA-AA-3986-01%2Bcoadread_tcga_pub%3ATCGA-AA-3989-01%2Bcoadread_tcga_pub%3ATCGA-AA-3994-01%2Bcoadread_tcga_pub%3ATCGA-AA-A00L-01%2Bcoadread_tcga_pub%3ATCGA-AA-A010-01%2Bcoadread_tcga_pub%3ATCGA-AA-A02O-01%2Bcoadread_tcga_pub%3ATCGA-CM-4748-01&case_set_id=-1&clinicallist=PROFILED_IN_coadread_tcga_pub_mutations%2CPROFILED_IN_coadread_tcga_pub_gistic&gene_list=KRAS%0AAPC&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&show_samples=false&tab_index=tab_visualize`
         );
-        $('div[data-test="CoExpressionPlot"]').waitForExist({
+        await getElement('div[data-test="CoExpressionPlot"]', {
             timeout: COEXPRESSION_TIMEOUT,
         }); // wait for plot to show up
-        var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
+        const res = await browser.checkElement(
+            'div[data-test="coExpressionTabDiv"]'
+        );
         assertScreenShotMatch(res);
     });
 });