Merge pull request #2785 from cBioPortal/release-3.1.1

Merge Release 3.1.1

Former-commit-id: 94ff80077315e82b912c43c6243630529a2b927c

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

@@ -66,14 +66,14 @@ describe("coexpression tab screenshot tests", function() {
         var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
         assertScreenShotMatch(res);
     });
-    it('coexpression tab coadread_tcga_pub with a lot of genes', function() {
+    it.skip('coexpression tab coadread_tcga_pub with a lot of genes', function() {
         goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/results/coexpression?cancer_study_id=coadread_tcga_pub&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=coadread_tcga_pub_nonhypermut&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=+&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`);
         browser.waitForExist('div[data-test="CoExpressionPlot"]', COEXPRESSION_TIMEOUT); // wait for plot to show up
         var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');
         assertScreenShotMatch(res);
     });
 
-    it('coexpression tab coadread_tcga_pub with user defined case list', function() {
+    it.skip('coexpression tab coadread_tcga_pub with user defined case list', function() {
         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`);
         browser.waitForExist('div[data-test="CoExpressionPlot"]', COEXPRESSION_TIMEOUT); // wait for plot to show up
         var res = browser.checkElement('div[data-test="coExpressionTabDiv"]');

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

@@ -62,7 +62,7 @@ function runResultsTestSuite(prefix){
         assertScreenShotMatch(res);
     });
 
-    it(`${prefix} coexpression tab`, function(){
+    it.skip(`${prefix} coexpression tab`, function(){
         browser.click("a.tabAnchor_coexpression");
         browser.waitForVisible('div[data-test="CoExpressionPlot"]',COEXPRESSION_TIMEOUT);
         var res = browser.checkElement('[data-test="coExpressionTabDiv"]', { hide:['.qtip'] } );

end-to-end-test/remote/specs/core/studyview.spec.js

@@ -193,13 +193,13 @@ describe('study laml_tcga tests', () => {
                 const beforeClick = getNumberOfStudyViewCharts();
                 browser.click(ADD_CHART_CUSTOM_GROUPS_ADD_CHART_BUTTON);
 
-                browser.waitForVisible("[data-test='chart-container-CUSTOM_FILTERS_3']");
+                browser.waitForVisible("[data-test='chart-container-CUSTOM_FILTERS_4']");
 
                 // it should not impact any other charts
                 assert(beforeClick + 1 === getNumberOfStudyViewCharts());
 
                 // make sure the title is reflected
-                assert(getTextFromElement("[data-test='chart-container-CUSTOM_FILTERS_3'] .chartTitle") === 'Custom Chart 1');
+                assert(getTextFromElement("[data-test='chart-container-CUSTOM_FILTERS_4'] .chartTitle") === 'Custom Chart 1');
 
                 // make sure the chart is filtered
                 const res = browser.checkElement(".userSelections");
@@ -229,7 +229,7 @@ describe('add chart should not be shown in other irrelevant tabs', () => {
 describe('check the filters are working properly', ()=>{
 
     before(function() {
-        const url = `${CBIOPORTAL_URL}/study?id=laml_tcga&filters=%7B%2522clinicalDataEqualityFilters%2522:%5B%7B%2522attributeId%2522:%2522SEX%2522,%2522clinicalDataType%2522:%2522PATIENT%2522,%2522values%2522:%5B%2522Female%2522%5D%7D%5D,%2522clinicalDataIntervalFilters%2522:%5B%7B%2522attributeId%2522:%2522AGE%2522,%2522clinicalDataType%2522:%2522PATIENT%2522,%2522values%2522:%5B%7B%2522start%2522:25,%2522end%2522:30%7D,%7B%2522start%2522:30,%2522end%2522:35%7D,%7B%2522start%2522:35,%2522end%2522:40%7D,%7B%2522start%2522:40,%2522end%2522:45%7D,%7B%2522start%2522:45,%2522end%2522:50%7D,%7B%2522start%2522:50,%2522end%2522:55%7D,%7B%2522start%2522:55,%2522end%2522:60%7D,%7B%2522start%2522:60,%2522end%2522:65%7D,%7B%2522start%2522:65,%2522end%2522:70%7D,%7B%2522start%2522:70,%2522end%2522:75%7D,%7B%2522start%2522:75,%2522end%2522:80%7D%5D%7D%5D,%2522mutatedGenes%2522:%5B%7B%2522entrezGeneIds%2522:%5B2322,4869%5D%7D%5D,%2522cnaGenes%2522:%5B%7B%2522alterations%2522:%5B%7B%2522alteration%2522:-2,%2522entrezGeneId%2522:60412%7D,%7B%2522alteration%2522:2,%2522entrezGeneId%2522:84435%7D%5D%7D%5D%7D`;
+        const url = `${CBIOPORTAL_URL}/study?id=laml_tcga&filters=%7B%2522clinicalDataEqualityFilters%2522:%5B%7B%2522attributeId%2522:%2522SEX%2522,%2522clinicalDataType%2522:%2522PATIENT%2522,%2522values%2522:%5B%2522Female%2522%5D%7D%5D,%2522clinicalDataIntervalFilters%2522:%5B%7B%2522attributeId%2522:%2522AGE%2522,%2522clinicalDataType%2522:%2522PATIENT%2522,%2522values%2522:%5B%7B%2522start%2522:25,%2522end%2522:30%7D,%7B%2522start%2522:30,%2522end%2522:35%7D,%7B%2522start%2522:35,%2522end%2522:40%7D,%7B%2522start%2522:40,%2522end%2522:45%7D,%7B%2522start%2522:45,%2522end%2522:50%7D,%7B%2522start%2522:50,%2522end%2522:55%7D,%7B%2522start%2522:55,%2522end%2522:60%7D,%7B%2522start%2522:60,%2522end%2522:65%7D,%7B%2522start%2522:65,%2522end%2522:70%7D,%7B%2522start%2522:70,%2522end%2522:75%7D,%7B%2522start%2522:75,%2522end%2522:80%7D%5D%7D%5D,%2522mutatedGenes%2522:%5B%7B%2522entrezGeneIds%2522:%5B2322,4869%5D%7D%5D,%2522cnaGenes%2522:%5B%7B%2522alterations%2522:%5B%7B%2522alteration%2522:-2,%2522entrezGeneId%2522:2521%7D,%7B%2522alteration%2522:2,%2522entrezGeneId%2522:4297%7D%5D%7D%5D%7D`;
         goToUrlAndSetLocalStorage(url);
         waitForNetworkQuiet(60000);
     });
@@ -248,17 +248,17 @@ describe('check the filters are working properly', ()=>{
         // Remove bar chart filter
         browser.elements("[data-test='pill-tag-delete']").value[0].click();
         waitForStudyViewSelectedInfo();
-        assert(getTextFromElement(SELECTED_PATIENTS) === '6');
-        assert(getTextFromElement(SELECTED_SAMPLES) === '6');
+        assert(getTextFromElement(SELECTED_PATIENTS) === '5');
+        assert(getTextFromElement(SELECTED_SAMPLES) === '5');
 
 
         // Remove mutated genes filter
         browser.elements("[data-test='pill-tag-delete']").value[0].click();
         waitForStudyViewSelectedInfo();
         browser.elements("[data-test='pill-tag-delete']").value[0].click();
         waitForStudyViewSelectedInfo();
-        assert(getTextFromElement(SELECTED_PATIENTS) === '9');
-        assert(getTextFromElement(SELECTED_SAMPLES) === '9');
+        assert(getTextFromElement(SELECTED_PATIENTS) === '13');
+        assert(getTextFromElement(SELECTED_SAMPLES) === '13');
 
         // Remove cna genes filter
         browser.elements("[data-test='pill-tag-delete']").value[0].click();
@@ -270,6 +270,27 @@ describe('check the filters are working properly', ()=>{
     });
 });
 
+// This needs to be done separately due to leak of data in the other tests
+describe('check the fusion filter is working properly', ()=>{
+
+    before(function() {
+        const url = `${CBIOPORTAL_URL}/study/summary?filters=%7B%2522fusionGenes%2522%3A%5B%7B%2522entrezGeneIds%2522%3A%5B2313%5D%7D%5D%7D&id=es_dfarber_broad_2014`;
+        goToUrlAndSetLocalStorage(url);
+        waitForNetworkQuiet(60000);
+    });
+    it('fusion filter filter study from url', function() {
+        const res = checkElementWithMouseDisabled('#mainColumn');
+        assertScreenShotMatch(res);
+    });
+
+    it('fusion filter removing filters are working properly', function() {
+        // Remove cna genes filter
+        browser.elements("[data-test='pill-tag-delete']").value[0].click();
+        waitForStudyViewSelectedInfo();
+        assert(getTextFromElement(SELECTED_PATIENTS) === '103');
+        assert(getTextFromElement(SELECTED_SAMPLES) === '107');
+    });
+});
 
 describe('cancer gene filter', () => {
     before(() => {

env/release-3.1.1.sh

@@ -0,0 +1,2 @@
+export CBIOPORTAL_URL="https://master.cbioportal.org"
+export GENOME_NEXUS_URL="https://www.genomenexus.org"

src/config/serverConfigDefaults.ts

@@ -116,6 +116,7 @@ const ServerConfigDefaults: Partial<IServerConfig> = {
             DFS_SURVIVAL: 300,
             MUTATION_COUNT_CNA_FRACTION: 200,
             MUTATED_GENES_TABLE: 90,
+            FUSION_GENES_TABLE: 85,
             CNA_GENES_TABLE: 80,
             CANCER_STUDIES: 70,
             SEQUENCED: 60,

src/pages/studyView/StudyViewConfig.ts

@@ -65,6 +65,7 @@ export enum ChartTypeEnum {
     TABLE = 'TABLE',
     SCATTER = 'SCATTER',
     MUTATED_GENES_TABLE = 'MUTATED_GENES_TABLE',
+    FUSION_GENES_TABLE = 'FUSION_GENES_TABLE',
     CNA_GENES_TABLE = 'CNA_GENES_TABLE',
     NONE = 'NONE'
 }
@@ -76,6 +77,7 @@ export enum ChartTypeNameEnum {
     TABLE = 'table',
     SCATTER = 'density plot',
     MUTATED_GENES_TABLE = 'table',
+    FUSION_GENES_TABLE = 'table',
     CNA_GENES_TABLE = 'table',
     NONE = 'none'
 }
@@ -98,6 +100,7 @@ const studyViewFrontEnd = {
         "DFS_SURVIVAL": 300,
         "MUTATION_COUNT_CNA_FRACTION": 200,
         "MUTATED_GENES_TABLE": 90,
+        "FUSION_GENES_TABLE": 85,
         "CNA_GENES_TABLE": 80,
         "CANCER_STUDIES": 70,
         "SEQUENCED": 60,
@@ -170,6 +173,10 @@ const studyViewFrontEnd = {
                 w: 2,
                 h: 2
             },
+            [ChartTypeEnum.FUSION_GENES_TABLE]: {
+                w: 2,
+                h: 2
+            },
             [ChartTypeEnum.CNA_GENES_TABLE]: {
                 w: 2,
                 h: 2
@@ -196,4 +203,4 @@ const studyViewFrontEnd = {
     }
 };
 
-export const STUDY_VIEW_CONFIG: StudyViewConfig = _.assign(studyViewFrontEnd, AppConfig.serverConfig.study_view);
+export const STUDY_VIEW_CONFIG: StudyViewConfig = _.assign(studyViewFrontEnd, AppConfig.serverConfig.study_view);