Merge pull request #1163 from cBioPortal/release-1.13.0

Release 1.13.0

end-to-end-tests/specs/screenshot.spec.js

@@ -94,6 +94,27 @@ describe('result page screenshot tests', function(){
 });
 
 describe("oncoprint screenshot tests", function() {
+    it("coadread_tcga_pub with clinical and heatmap tracks", ()=>{
+        var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=coadread_tcga_pub&Z_SCORE_THRESHOLD=1&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=coadread_tcga_pub_nonhypermut&gene_list=KRAS%20NRAS%20BRAF&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=coadread_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=coadread_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=coadread_tcga_pub_rna_seq_mrna_median_Zscores&show_samples=false&clinicallist=0%2C2%2CMETHYLATION_SUBTYPE&heatmap_track_groups=coadread_tcga_pub_rna_seq_mrna_median_Zscores%2CKRAS%2CNRAS%2CBRAF&`;
+        goToUrlAndSetLocalStorage(url);
+        waitForOncoprint(10000);
+        var res = browser.checkElement('#oncoprint');
+        assertScreenShotMatch(res);
+    });
+    it("acc_tcga with clinical and heatmap tracks", ()=>{
+        var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=acc_tcga&Z_SCORE_THRESHOLD=1&RPPA_SCORE_THRESHOLD=1&data_priority=0&case_set_id=acc_tcga_all&gene_list=SOX9%20RAN%20TNK2%20EP300%20PXN%20NCOA2%20AR%20NRIP1%20NCOR1%20NCOR2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=acc_tcga_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=acc_tcga_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=acc_tcga_rna_seq_v2_mrna_median_Zscores&genetic_profile_ids_PROFILE_PROTEIN_EXPRESSION=acc_tcga_rppa_Zscores&show_samples=false&clinicallist=0%2C1%2CMETASTATIC_DX_CONFIRMED_BY&heatmap_track_groups=acc_tcga_rna_seq_v2_mrna_median_Zscores%2CSOX9%2CRAN%2CTNK2%2CEP300%2CPXN%2CNCOA2%2CAR%2CNRIP1%2CNCOR1%2CNCOR2`;
+        goToUrlAndSetLocalStorage(url);
+        waitForOncoprint(10000);
+        var res = browser.checkElement('#oncoprint');
+        assertScreenShotMatch(res);
+    });
+    it("blca_tcga with clinical and heatmap tracks", ()=>{
+        var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=blca_tcga_pub&Z_SCORE_THRESHOLD=1&RPPA_SCORE_THRESHOLD=1&data_priority=0&case_set_id=blca_tcga_pub_all&gene_list=SOX9%20RAN%20TNK2%20EP300%20PXN%20NCOA2%20AR%20NRIP1%20NCOR1%20NCOR2&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=blca_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=blca_tcga_pub_gistic&genetic_profile_ids_PROFILE_MRNA_EXPRESSION=blca_tcga_pub_rna_seq_mrna_median_Zscores&genetic_profile_ids_PROFILE_PROTEIN_EXPRESSION=blca_tcga_pub_rppa_Zscores&show_samples=false&heatmap_track_groups=blca_tcga_pub_rna_seq_mrna_median_Zscores%2CSOX9%2CRAN%2CTNK2%2CEP300%2CPXN%2CNCOA2%2CAR%2CNRIP1%2CNCOR1%2CNCOR2&clinicallist=CANCER_TYPE_DETAILED%2CMETASTATIC_SITE_OTHER%2CNEW_TUMOR_EVENT_AFTER_INITIAL_TREATMENT`;
+        goToUrlAndSetLocalStorage(url);
+        waitForOncoprint(10000);
+        var res = browser.checkElement('#oncoprint');
+        assertScreenShotMatch(res);
+    });
     it("hcc_inserm_fr_2015 with genes including TERT - it should show orange promoter mutations in TERT", function() {
         goToUrlAndSetLocalStorage(`${CBIOPORTAL_URL}/index.do?cancer_study_id=hcc_inserm_fr_2015&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=hcc_inserm_fr_2015_sequenced&gene_list=SOX9%2520RAN%2520TNK2%2520EP300%2520PXN%2520NCOA2%2520AR%2520NRIP1%2520NCOR1%2520NCOR2%2520TERT&geneset_list=+&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=hcc_inserm_fr_2015_mutations`);
         waitForOncoprint(20000);
@@ -121,6 +142,13 @@ describe("oncoprint screenshot tests", function() {
         var res = browser.checkElement("#oncoprint");
         assertScreenShotMatch(res);
     });
+    it("brca_tcga_pub with KRAS NRAS BRAF and methylation heatmap tracks", function() {
+        var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=brca_tcga_pub&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=brca_tcga_pub_cnaseq&gene_list=KRAS%2520NRAS%2520BRAF&geneset_list=%20&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=brca_tcga_pub_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=brca_tcga_pub_gistic&show_samples=false&heatmap_track_groups=brca_tcga_pub_methylation_hm27%2CKRAS%2CNRAS%2CBRAF%2CTP53%2CBRCA1%2CBRCA2`;
+        goToUrlAndSetLocalStorage(url);
+        waitForOncoprint(10000);
+        var res = browser.checkElement("#oncoprint");
+        assertScreenShotMatch(res);
+    });
 });
 
 describe("download tab screenshot tests", function() {

env/rc.sh

@@ -1,2 +1,2 @@
-export CBIOPORTAL_URL="http://www.cbioportal.org/beta"
-export GENOME_NEXUS_URL="https://genomenexus-rc.herokuapp.com"
+export CBIOPORTAL_URL="http://www.cbioportal.org/rc"
+export GENOME_NEXUS_URL="https://www.genomenexus.org"

package.json

@@ -52,7 +52,7 @@
     "@types/js-combinatorics": "0.5.29",
     "@types/jspdf": "^1.1.31",
     "@types/jstree": "^3.3.35",
-    "@types/lodash": "4.14.66",
+    "@types/lodash": "^4.14.104",
     "@types/lolex": "1.5.31",
     "@types/mocha": "2.2.41",
     "@types/pdfobject": "2.0.5",
@@ -204,7 +204,7 @@
     "swagger-client": "^2.1.32",
     "swagger-js-codegen": "git+https://github.com/cBioPortal/swagger-js-codegen.git#77031560146c6985c99cd40eda208b04052ab631",
     "ts-loader": "^2.0.0",
-    "typescript": "^2.6.2",
+    "typescript": "^2.7.2",
     "underscore": "^1.8.3",
     "universal-ga": "^1.2.0",
     "url": "^0.11.0",

src/globalComponents.tsx

@@ -5,6 +5,7 @@ import QueryAndDownloadTabs from "./shared/components/query/QueryAndDownloadTabs
 import {QueryStore} from "./shared/components/query/QueryStore";
 import formSubmit from "shared/lib/formSubmit";
 import {getStudySummaryUrl} from "./shared/api/urls";
+import {genes} from "shared/lib/oql/oqlfilter.js"
 
 class GlobalStores {
 
@@ -13,8 +14,12 @@ class GlobalStores {
     }
 
 }
+(window as any).frontendVars = {};
 
 (window as any).getStudySummaryUrl = getStudySummaryUrl;
+(window as any).frontendVars.oqlGenes = (oqlQuery:string)=>{
+    return genes(oqlQuery);
+};
 
 exposeComponentRenderer('renderRightBar', ()=> {
     return <RightBar store={GlobalStores.queryStore} />;

src/pages/patientView/sampleManager.tsx

@@ -70,7 +70,7 @@ export function sortSamples(samples: Array<ClinicalDataBySampleId>,
 
     sampleOrder = _.orderBy(sampleOrder, ['eventOrdering', 'sampleTypeIndex', 'naturalSortIndex'], ['asc','asc','asc']);
     let sampleOrderMap = _.fromPairs(sampleOrder.map((so, i) => [so.id, i]));
-    return _.sortBy(samples, (sample) => {
+    return _.sortBy<ClinicalDataBySampleId>(samples, (sample) => {
         return sampleOrderMap[sample.id];
     });
 }

src/pages/resultsView/ResultsViewPage.tsx

@@ -24,6 +24,7 @@ import OverlappingStudiesWarning from "../../shared/components/overlappingStudie
 import CNSegments from "./cnSegments/CNSegments";
 import './styles.scss';
 import {genes} from "shared/lib/oql/oqlfilter.js";
+import oql_parser from "shared/lib/oql/oql-parser.js";
 
 (Chart as any).plugins.register({
     beforeDraw: function(chartInstance:any) {
@@ -49,7 +50,7 @@ function initStore(queryStore: QueryStore) {
 
     const oqlQuery = serverVars.theQuery;
 
-    const parsedOQL = (window as any).oql_parser.parse(oqlQuery);
+    const parsedOQL = oql_parser.parse(oqlQuery);
 
     const genesetIds = (serverVars.genesetIds.length
         ? serverVars.genesetIds.split(/\s+/)
@@ -103,6 +104,7 @@ function initStore(queryStore: QueryStore) {
     resultsViewPageStore.zScoreThreshold = serverVars.zScoreThreshold;
     resultsViewPageStore.oqlQuery = oqlQuery;
     resultsViewPageStore.queryStore = queryStore;
+    resultsViewPageStore.cohortIdsList = serverVars.cohortIdsList;
 
     return resultsViewPageStore;
 
@@ -143,17 +145,29 @@ export default class ResultsViewPage extends React.Component<IResultsViewPagePro
 
         // hide mutex tab
         $(document).ready(()=>{
-            if (genes((window as any).serverVars.theQuery).length <= 1) {
+            if (!(window as any).serverVars.theQuery.trim().length || genes((window as any).serverVars.theQuery).length <= 1) {
                 $('a#mutex-result-tab').parent().hide();
             }
+            //hide gene-specific tabs when we only query gene sets (and no genes are queried)
+            // TODO: this should probably be changed once we have single page
+            // app
+            if (!(window as any).serverVars.theQuery.trim().length || genes((window as any).serverVars.theQuery).length == 0) {
+                $('a#cancer-types-result-tab').parent().hide();
+                $('a#plots-result-tab').parent().hide();
+                $('a#mutation-result-tab').parent().hide();
+                $('a#coexp-result-tab').parent().hide();
+                $('a#enrichments-result-tab').parent().hide();
+                $('a#survival-result-tab').parent().hide();
+                $('a#network-result-tab').parent().hide();
+                $('a#igv-result-tab').parent().hide();
+                $('a#data-download-result-tab').parent().hide();
+            }
 
             if (win.cancerStudyIdList !== 'null') {
                 getGAInstance().event('results view', 'show', { eventLabel: win.cancerStudyIdList  });
             } else if (_.includes(['all','null'],win.cancerStudyId) === false) {
                 getGAInstance().event('results view', 'show', { eventLabel: win.cancerStudyId  });
             }
-
-
         });
     }
 
@@ -272,7 +286,7 @@ export default class ResultsViewPage extends React.Component<IResultsViewPagePro
                                     samplesExtendedWithClinicalData={this.resultsViewPageStore.samplesExtendedWithClinicalData.result!}
                                     alterationsByGeneBySampleKey={this.resultsViewPageStore.alterationsByGeneBySampleKey.result!}
                                     studies={this.resultsViewPageStore.studies.result!}
-                                    studyMap={this.resultsViewPageStore.studyMap}
+                                    studyMap={this.resultsViewPageStore.physicalStudySet}
                                   />
                             </div>)
                         } else if (isPending) {