cBioPortal · inodb · Oct 11, 2018 · Oct 11, 2018 · Oct 11, 2018 · Oct 11, 2018
diff --git a/.circleci/config.yml b/.circleci/config.yml
@@ -6,7 +6,7 @@ defaults: &defaults
   working_directory: ~/repo
   docker:
     # specify the version you desire here
-    - image: circleci/node:8.9.4-browsers
+    - image: circleci/node:8.12.0-browsers
 
 version: 2
 jobs:
@@ -20,12 +20,7 @@ jobs:
             npm --version
       - checkout
       # Download and cache dependencies
-      - restore_cache:
-          keys:
-          - v1-dependencies-{{ checksum "package-lock.json" }}
-          # fallback to using the latest cache if no exact match is found
-          - v1-dependencies-
-      - run: npm install
+      - run: npm ci
       - run:
           name: "Ignore https to http switches on circleci in package lock (not sure why this happens)"
           command: "git diff --exit-code package-lock.json || sed -i 's/http:/https:/g' package-lock.json"
@@ -96,7 +91,7 @@ jobs:
           command: |
             ./node_modules/http-server/bin/http-server --cors dist/ -p 3000 & \
             cd end-to-end-tests && \
-            npm install && \
+            npm ci && \
             ./node_modules/webdriver-manager/bin/webdriver-manager update --versions.chrome '2.37' && \
             ./node_modules/webdriver-manager/bin/webdriver-manager start --versions.chrome '2.37' & \
             ./scripts/env_vars.sh && \

diff --git a/.travis.yml b/.travis.yml
diff --git a/...e/'profiled_in'_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png b/...e/'profiled_in'_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png
diff --git a/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...eference/acc_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...ference/blca_tcga_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...with_kras_nras_braf_and_methylation_heatmap_tracks_element_chrome_1600x1000.png b/...with_kras_nras_braf_and_methylation_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png b/...coadread_tcga_pub_with_clinical_and_heatmap_tracks_element_chrome_1600x1000.png
diff --git a/...ce/coexpression_tab_coadread_tcga_pub_initial_load_element_chrome_1600x1000.png b/...ce/coexpression_tab_coadread_tcga_pub_initial_load_element_chrome_1600x1000.png
diff --git a/..._coadread_tcga_pub_loc_scale_x_and_y_mutations_off_element_chrome_1600x1000.png b/..._coadread_tcga_pub_loc_scale_x_and_y_mutations_off_element_chrome_1600x1000.png
diff --git a/...b_coadread_tcga_pub_log_scale_x_and_y_mutations_on_element_chrome_1600x1000.png b/...b_coadread_tcga_pub_log_scale_x_and_y_mutations_on_element_chrome_1600x1000.png
diff --git a/...coexpression_tab_coadread_tcga_pub_switch_profiles_element_chrome_1600x1000.png b/...coexpression_tab_coadread_tcga_pub_switch_profiles_element_chrome_1600x1000.png
diff --git a/...nce/coexpression_tab_coadread_tcga_pub_switch_tabs_element_chrome_1600x1000.png b/...nce/coexpression_tab_coadread_tcga_pub_switch_tabs_element_chrome_1600x1000.png
diff --git a/...pression_tab_coadread_tcga_pub_with_a_lot_of_genes_element_chrome_1600x1000.png b/...pression_tab_coadread_tcga_pub_with_a_lot_of_genes_element_chrome_1600x1000.png
diff --git a/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png b/...nce/enrichments_tab_coadread_tcga_pub_mrna_profile_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/expression_tab_with_complex_oql_element_chrome_1600x1000.png b/...eenshots/reference/expression_tab_with_complex_oql_element_chrome_1600x1000.png
diff --git a/...-_it_should_show_orange_promoter_mutations_in_tert_element_chrome_1600x1000.png b/...-_it_should_show_orange_promoter_mutations_in_tert_element_chrome_1600x1000.png
diff --git a/...s/reference/msk_impact_2017_query_stk11:homdel_mut_element_chrome_1600x1000.png b/...s/reference/msk_impact_2017_query_stk11:homdel_mut_element_chrome_1600x1000.png
diff --git a/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...7_with_alk_and_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...pact_2017_with_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png b/...pact_2017_with_sos1_-_sos1_should_be_not_sequenced_element_chrome_1600x1000.png
diff --git a/...s1_with_cna_profile_-_sos1_should_not_be_sequenced_element_chrome_1600x1000.png b/...s1_with_cna_profile_-_sos1_should_not_be_sequenced_element_chrome_1600x1000.png
diff --git a/...reenshots/reference/no_session_cancer_type_summary_element_chrome_1600x1000.png b/...reenshots/reference/no_session_cancer_type_summary_element_chrome_1600x1000.png
diff --git a/.../screenshots/reference/no_session_coexpression_tab_element_chrome_1600x1000.png b/.../screenshots/reference/no_session_coexpression_tab_element_chrome_1600x1000.png
diff --git a/...s/screenshots/reference/no_session_enrichments_tab_element_chrome_1600x1000.png b/...s/screenshots/reference/no_session_enrichments_tab_element_chrome_1600x1000.png
diff --git a/...ests/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png b/...ests/screenshots/reference/no_session_mutation_tab_element_chrome_1600x1000.png
diff --git a/...d-tests/screenshots/reference/no_session_mutex_tab_element_chrome_1600x1000.png b/...d-tests/screenshots/reference/no_session_mutex_tab_element_chrome_1600x1000.png
diff --git a/...tests/screenshots/reference/no_session_network_tab_element_chrome_1600x1000.png b/...tests/screenshots/reference/no_session_network_tab_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/no_session_render_the_oncoprint_element_chrome_1600x1000.png b/...eenshots/reference/no_session_render_the_oncoprint_element_chrome_1600x1000.png
diff --git a/...ests/screenshots/reference/no_session_survival_tab_element_chrome_1600x1000.png b/...ests/screenshots/reference/no_session_survival_tab_element_chrome_1600x1000.png
diff --git a/...eference/plots_tab_clinical_vs_clinical_table_plot_element_chrome_1600x1000.png b/...eference/plots_tab_clinical_vs_clinical_table_plot_element_chrome_1600x1000.png
diff --git a/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png b/.../reference/plots_tab_clinical_vs_molecular_boxplot_element_chrome_1600x1000.png
diff --git a/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png b/...eenshots/reference/plots_tab_clinical_vs_molecular_element_chrome_1600x1000.png
diff --git a/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png b/...molecular_vs_clinical_boxplot,_mutation_search_off_element_chrome_1600x1000.png
diff --git a/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png b/..._tab_molecular_vs_molecular_same_gene_changed_gene_element_chrome_1600x1000.png
diff --git a/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png b/...ference/plots_tab_molecular_vs_molecular_same_gene_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png b/...screenshots/reference/plots_tab_mutation_type_view_element_chrome_1600x1000.png
diff --git a/..._in_tracks_in_msk_impact_with_3_not_profiled_genes_element_chrome_1600x1000.png b/..._in_tracks_in_msk_impact_with_3_not_profiled_genes_element_chrome_1600x1000.png
diff --git a/...nce/profiled_in_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png b/...nce/profiled_in_tracks_in_multiple_study_with_sos1_element_chrome_1600x1000.png
diff --git a/.../screenshots/reference/session_cancer_type_summary_element_chrome_1600x1000.png b/.../screenshots/reference/session_cancer_type_summary_element_chrome_1600x1000.png
diff --git a/...sts/screenshots/reference/session_coexpression_tab_element_chrome_1600x1000.png b/...sts/screenshots/reference/session_coexpression_tab_element_chrome_1600x1000.png
diff --git a/...ests/screenshots/reference/session_enrichments_tab_element_chrome_1600x1000.png b/...ests/screenshots/reference/session_enrichments_tab_element_chrome_1600x1000.png
diff --git a/...d-tests/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png b/...d-tests/screenshots/reference/session_mutation_tab_element_chrome_1600x1000.png
diff --git a/...-end-tests/screenshots/reference/session_mutex_tab_element_chrome_1600x1000.png b/...-end-tests/screenshots/reference/session_mutex_tab_element_chrome_1600x1000.png
diff --git a/...nd-tests/screenshots/reference/session_network_tab_element_chrome_1600x1000.png b/...nd-tests/screenshots/reference/session_network_tab_element_chrome_1600x1000.png
diff --git a/...screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png b/...screenshots/reference/session_render_the_oncoprint_element_chrome_1600x1000.png
diff --git a/...d-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png b/...d-tests/screenshots/reference/session_survival_tab_element_chrome_1600x1000.png
diff --git a/end-to-end-tests/specs/screenshot.spec.js b/end-to-end-tests/specs/screenshot.spec.js
@@ -181,14 +181,14 @@ describe("oncoprint screenshot tests", function() {
         var res = browser.checkElement("#oncoprint");
         assertScreenShotMatch(res);
     });
-    it("'profiled in' tracks in msk impact with 3 n/p genes", function() {
+    it("profiled in tracks in msk impact with 3 not profiled genes", function() {
         var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=msk_impact_2017&Z_SCORE_THRESHOLD=2.0&RPPA_SCORE_THRESHOLD=2.0&data_priority=0&case_set_id=msk_impact_2017_cnaseq&gene_list=AKR1C1%2520AKR1C2%2520AKR1C4&geneset_list=+&tab_index=tab_visualize&Action=Submit&genetic_profile_ids_PROFILE_MUTATION_EXTENDED=msk_impact_2017_mutations&genetic_profile_ids_PROFILE_COPY_NUMBER_ALTERATION=msk_impact_2017_cna`;
         goToUrlAndSetLocalStorage(url);
         waitForOncoprint(20000);
         var res = browser.checkElement("#oncoprint");
         assertScreenShotMatch(res);
     });
-    it("'profiled in' tracks in multiple study with SOS1", function() {
+    it("profiled in tracks in multiple study with SOS1", function() {
         var url = `${CBIOPORTAL_URL}/index.do?cancer_study_id=all&Z_SCORE_THRESHOLD=2&RPPA_SCORE_THRESHOLD=2&data_priority=0&case_set_id=all&gene_list=SOS1&geneset_list=%20&tab_index=tab_visualize&Action=Submit&cancer_study_list=msk_impact_2017%2Cbrca_bccrc&show_samples=false&clinicallist=CANCER_STUDY%2CPROFILED_IN_MUTATION_EXTENDED%2CPROFILED_IN_msk_impact_2017_cna#summary`;
         goToUrlAndSetLocalStorage(url);
         waitForOncoprint(20000);