Merge pull request #1555 from inodb/upgrade-npm

Upgrade to node LTS 8.12.0 / npm 6.4.1

Former-commit-id: 41c305e7492a6dacdc06458846e2a4e1af5bb675

.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 && \

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);