Merge branch 'tests' into 'master'

Tests

See merge request !10

Dockerfile-tests

+FROM docker-test
+
+ADD . /plugin
+
+WORKDIR /plugin
+
+RUN /bin/bash tests/docker-init.sh

package.json

@@ -19,14 +19,18 @@
     "@babel/preset-env": "^7.6.2",
     "browserify": "^14.5.0",
     "browserify-css": "^0.15.0",
+    "chai": "^4.2.0",
     "core-js": "^3.2.1",
     "mkdirp": "^0.5.1",
-    "node-sass": "^4.6.1",
+    "mocha": "^7.1.1",
+    "node-sass": "^4.13.1",
     "rimraf": "latest",
-    "uglify-js": "^3.1.9"
+    "selenium-webdriver": "^4.0.0-alpha.7",
+    "uglify-js": "^3.1.9",
+    "xmlhttprequest": "^1.8.0"
   },
   "dependencies": {
     "@babel/polyfill": "^7.6.0",
-    "npm": "^6.11.3"
+    "npm": "^6.14.4"
   }
 }

src/js/index.js

@@ -2,6 +2,7 @@ require('../css/styles.css');
 
 const pluginName = 'GSEA';
 const pluginVersion = '0.9.1';
+const containerName = pluginName + '-container';
 
 const globals = {
     models: {},
@@ -56,6 +57,7 @@ const register = function (_minerva) {
         calculatePathways().then(function(){
             container.find('.gsea-pw-loading').hide();
             initMainPageStructure(container);
+            pluginContainer.find(`.${containerName}`).data("minervaProxy", minervaProxy);
         });
     });
 };
@@ -112,7 +114,7 @@ function deHighlightAll() {
 
 
 function getContainerClass() {
-    return pluginName + '-container';
+    return containerName;
 }
 
 function initMainContainer(){
@@ -135,7 +137,7 @@ function initMainContainer(){
 
 function initMainPageStructure() {
 
-    const container = $('<div class="' + pluginName + '-container"></div>').appendTo(pluginContainer);
+    const container = $("." + getContainerClass());//.appendTo(pluginContainer);
     container.append(`       
         <div class="panel card panel-primary border-primary panel-events">
             <div class="panel-heading card-header bg-primary text-light">Gene Set Enrichment Analysis</div>
@@ -304,11 +306,11 @@ function calculateGSEA() {
                 var N = globals.allProteinRnaGene.length;
                 var n = ovHgncNames.size;
 
-                // console.log('pw', pwName);
-                // console.log('m', m);
-                // console.log('k', k);
-                // console.log('N', N);
-                // console.log('n', n);
+                console.log('pw', pwName);
+                console.log('m', m);
+                console.log('k', k);
+                console.log('N', N);
+                console.log('n', n);
 
                 if (k > 0) {
                     //var px = (kcomb(m,k)*kcomb(N-m,n-k))/kcomb(N,n);

tests/docker-init.sh

+#!/bin/bash
+
+rm -r node_modules
+
+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))
+
+/usr/local/tomcat/bin/startup.sh
+sleep 15
+
+
+test 200 = $(curl -X POST -d "login=admin&password=admin" --write-out %{http_code} --silent --output /dev/null -c cookie.txt http://localhost:8080/minerva/api/doLogin)
+curl "http://localhost:8080/minerva/api/plugins/" --cookie cookie.txt --data "hash=$PLUGIN_MD5&url=http%3A%2F%2Flocalhost%3A8080%2Ftest%2F$PLUGIN_FILE&name=test&version=0.0.1&isPublic=false"
+
+npm run test
\ No newline at end of file

tests/test.js

+const {Builder, By, until} = require('selenium-webdriver');
+const chrome = require('selenium-webdriver/chrome');
+
+const assert = require('chai').assert;
+
+const XMLHttpRequest = require("xmlhttprequest").XMLHttpRequest;
+
+// Some tests need to access the MINERVA proxy to, e.g., check which elements are highlighted. However, the tests
+// do not run in the same scope as the plugin and thus they do not have access to the Proxy. Therefore, the plugin
+// exposes the proxy by attaching it as a data attribute to the main div element.
+const pluginName = 'GSEA';
+const minervaProxyContainerClass = pluginName + '-container';
+const minervaProxyCode = `$('.${minervaProxyContainerClass}').data('minervaProxy')`;
+
+
+function minervaLogin() {
+
+    const xhr = new XMLHttpRequest();
+
+    return new Promise(function (resolve, reject) {
+
+        xhr.onreadystatechange = function () {
+
+            if (xhr.readyState !== 4) return;
+
+            if (xhr.status >= 200 && xhr.status < 300) {
+                resolve(xhr);
+            } else {
+                reject({
+                    status: xhr.status,
+                    statusText: xhr.statusText
+                });
+            }
+        };
+
+        xhr.open("POST", 'http://localhost:8080/minerva/api/doLogin', false);
+        xhr.setRequestHeader("Content-Type", "application/x-www-form-urlencoded");
+        xhr.send("login=admin&password=admin");
+    });
+}
+
+async function getRequest(uri) {
+
+    const xhr = new XMLHttpRequest();
+
+    return new Promise(function (resolve, reject) {
+
+        xhr.onreadystatechange = function () {
+
+            if (xhr.readyState !== 4) return;
+
+            if (xhr.status >= 200 && xhr.status < 300) {
+                resolve(xhr);
+            } else {
+                reject({
+                    status: xhr.status,
+                    statusText: xhr.statusText
+                });
+            }
+        };
+
+        xhr.open("GET", uri);
+        xhr.send();
+    });
+}
+
+async function getPluginHash(){
+    return getRequest('http://localhost:8080/minerva/api/plugins/').then(function (pluginsResponse) {
+        return JSON.parse(pluginsResponse.responseText).filter(plugin => plugin.name === pluginName && plugin.isPublic)[0].hash;
+    });
+}
+
+describe('GSEA plugin', async function() {
+
+    //Some functions can take a lot of time as they need, for isntance, start MINERVA interface
+    this.timeout(20000);
+
+    let driver;
+    let minervaProxy;
+    let pluginContainer;
+
+    function wait(timeInMs) {
+        return driver.executeAsyncScript(`
+            const callback = arguments[arguments.length - 1];
+            setTimeout(()=>callback(), ${timeInMs})`);
+    }
+
+    function deHighlightAll(){
+        return driver.executeScript(`minervaProxy = ${minervaProxyCode}; minervaProxy.project.map.getHighlightedBioEntities().then( highlighted => minervaProxy.project.map.hideBioEntity(highlighted) )`);
+    }
+
+    async function countHighlighted(){
+        return driver.executeAsyncScript(`
+                    var callback = arguments[arguments.length - 1];
+                    ${minervaProxyCode}.project.map.getHighlightedBioEntities().then(highlighted => callback(highlighted));                    
+                `);
+    }
+
+    before(async function () {
+        const opts = new chrome.Options().addArguments('--no-sandbox', '--headless', '--remote-debugging-port=9222');
+        driver = await new Builder().setChromeOptions(opts).forBrowser('chrome').build();
+        // driver = await new Builder().forBrowser('chrome').build();
+
+        await driver.manage().window().maximize();
+
+        const loginResponse = await minervaLogin();
+        const minervaToken = JSON.parse(loginResponse.responseText).token;
+
+        await driver.get('http://localhost:8080');
+        await driver.manage().addCookie({name: 'MINERVA_AUTH_TOKEN', value: minervaToken});
+        const pluginHash = await getPluginHash();
+
+        await driver.get(`http://localhost:8080/minerva/index.xhtml?id=single-map&plugins=${pluginHash}`);
+
+        pluginContainer = await driver.wait(until.elementLocated(By.css(`.${minervaProxyContainerClass}`)),10000);
+        minervaProxy = await driver.executeScript(`return $('.${minervaProxyContainerClass}').data('minervaProxy')`);
+
+        await driver.executeScript(function () {
+            $('td:contains("Sorted-by-species")').parent().find("input").click();
+        });
+
+        await wait(500);
+    });
+
+    describe("show enriched pathways", function () {
+        before(async function () {
+            await driver.executeScript(function () {
+                $('.gsea-buttons .btn-calc').click();
+            });
+
+            await driver.wait(until.elementLocated(By.css(`.gsea-results button`)),5000);
+        });
+
+        let elPanelTitle;
+        it('should have one record in the table being the main map', async function () {
+            const panels = await driver.findElements(By.css('.gsea-pw-results-panel'));
+            assert.equal(panels.length, 1);
+
+            elPanelTitle = panels[0].findElement(By.css('.panel-title'));
+            assert.equal(await elPanelTitle.getText(), 'Main map');
+        });
+
+        describe("clicking reset", function () {
+
+            before(async function () {
+
+                await driver.executeScript(function () {
+                    $('.gsea-buttons .btn-reset').click();
+                });
+
+                await driver.wait(until.stalenessOf(elPanelTitle),1000);
+            });
+
+            it("should reset results", async function () {
+                const cnt = await driver.executeScript(function () {
+                    return $('.gsea-results').children().length;
+
+                });
+                assert.equal(cnt, 0);
+            })
+        })
+    });
+
+    after(async function finishWebDriver() {
+        await driver.quit();
+    });
+});
\ No newline at end of file