tests + ci

.gitlab-ci.yml

@@ -5,6 +5,7 @@ before_script:
 
 stages:
   - build
+  - test
   - deploy
 
 build:
@@ -30,3 +31,69 @@ deploy:
     - echo "mkdir plugins-www/disease-associations" | sftp -P 8022 gitlab-ci@10.240.6.160
     - echo "put dist/plugin.js plugins-www/disease-associations/" | sftp -P 8022 gitlab-ci@10.240.6.160
 
+test:
+  image: tomcat:9-jdk11
+
+  stage: test
+
+  script:
+  - apt-get update
+  - wget https://dl.google.com/linux/direct/google-chrome-stable_current_amd64.deb
+  - DEBIAN_FRONTEND=noninteractive apt install -y ./google-chrome-stable_current_amd64.deb
+
+  - DEBIAN_FRONTEND=noninteractive apt-get install -y maven curl unzip
+  - curl -sL https://deb.nodesource.com/setup_12.x | bash -
+  - DEBIAN_FRONTEND=noninteractive apt-get install -y nodejs
+
+  - wget https://chromedriver.storage.googleapis.com/2.41/chromedriver_linux64.zip
+  - unzip chromedriver_linux64.zip
+  - mv chromedriver /usr/bin/chromedriver
+  - chown root:root /usr/bin/chromedriver
+  - chmod +x /usr/bin/chromedriver
+
+  - npm install
+  - npm run build
+  - mkdir /usr/local/tomcat/webapps/test
+  - cp dist/plugin.js /usr/local/tomcat/webapps/test/
+  - PLUGIN_FILE=plugin.js
+  - PLUGIN_MD5=($(md5sum dist/plugin.js))
+  - echo $PLUGIN_FILE $PLUGIN_MD5
+
+  - PLUGIN_DIR=`pwd`
+
+  - mkdir /etc/minerva/
+  - mkdir /etc/minerva/test
+
+  #configure database
+  - echo "database.driver=org.hsqldb.jdbcDriver" >>/etc/minerva/db.properties
+  - echo "database.dialect=org.hibernate.dialect.HSQLDialect" >>/etc/minerva/db.properties
+  - echo "database.uri=jdbc:hsqldb:mem:dapi" >>/etc/minerva/db.properties
+  - echo "database.username=sa" >>/etc/minerva/db.properties
+  - echo "database.password=" >>/etc/minerva/db.properties
+  - echo "database.connectionQuery=SELECT 1 FROM INFORMATION_SCHEMA.SYSTEM_USERS" >>/etc/minerva/db.properties
+  - echo "database.pathToDataScripts=/etc/minerva/test" >>/etc/minerva/db.properties
+
+  #download test data (database and images)
+  - wget https://git-r3lab.uni.lu/ewa.smula/testing/raw/master/testData/generated_test_data.zip
+  - unzip generated_test_data.zip
+  - mv *.sql /etc/minerva/test
+  - mv map_images /usr/local/tomcat/webapps/
+
+  #fetch latest minerva (from master branch)
+  - cd /
+  - git clone -b 1016-refactor-test-framework --single-branch https://git-r3lab.uni.lu/minerva/core.git
+  - cd core
+  #build minerva and deploy it
+  - mvn -Dmaven.test.skip=true clean install -pl web -am
+  - mv web/target/*.war /usr/local/tomcat/webapps/minerva.war
+  - /usr/local/tomcat/bin/startup.sh
+  - sleep 15
+
+  - curl -X POST -d "login=admin&password=admin" --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin
+  - curl "http://localhost:8080/minerva/api/plugins/" --cookie cookie.txt --data "hash=$PLUGIN_MD5&url=http%3A%2F%2Flocalhost%3A8080%2Ftest%2F$PLUGIN_FILE&name=test&version=0.0.1&isPublic=false"
+
+  #run test
+  - cd ${PLUGIN_DIR}
+  - npm run test
+
+

tests/test.js

@@ -117,7 +117,7 @@ describe("disease-association plugin", async function() {
         await driver.wait(until.elementLocated(By.css(`.disease-input-group .input-disease`)),5000);
     });
 
-    describe("Parkinson's disease", function () {
+    describe("Parkinson's disease by EFO", function () {
         before(async function () {
             const input = driver.findElement(By.css('.disease-input-group .input-disease'));
             input.sendKeys('parkinson');
@@ -205,12 +205,38 @@ describe("disease-association plugin", async function() {
                     assert.equal(cnt, 2);
                 });
             });
+        })
 
 
+    });
 
-        })
-
+    describe("Parkinson's disease by OMIM", function () {
+        before(async function () {
+            await driver.executeScript(function(){
+                $('.disease-input-group input.omim').click();
+            });
+            await wait(500);
+            await driver.executeScript(function(){
+                $('.disease-input-group .input-disease').val('');
+            });
+            await wait(100);
+            driver.findElement(By.css('.disease-input-group .input-disease')).sendKeys('168601');
+            await wait(500);
+            driver.executeScript(function () {
+                $('.disease-associations-container button.btn-search').click();
+            });
+            await driver.wait(until.elementLocated(By.css('.associations-content .bootstrap-table td')), 10000);
+            await wait(500);
+        });
 
+        describe("variation", function () {
+            it("should have SNCA associated", async function () {
+                const cnt = await driver.executeScript(function () {
+                    return $('table.variation-table td:contains("SNCA")').length
+                });
+                assert.equal(cnt, 1);
+            });
+        });
     });
 
     after(async function finishWebDriver() {