fix minor issues

package.json

@@ -9,7 +9,8 @@
     "build-css": "node-sass --include-path src/css src/css/styles.scss src/css/styles.css",
     "build": "mkdirp dist && npm run build-css && npm run babel && browserify -t browserify-css __tmp_minerva_plugin/js/index.js | uglifyjs --compress --mangle > dist/plugin.js && npm run clean-babel",
     "build-debug": "mkdirp dist && npm run build-css  && npm run babel && browserify -t browserify-css __tmp_minerva_plugin/js/index.js > dist/plugin.js && npm run clean-babel",
-    "clean": "rimraf dist && npm run clean-babel"
+    "clean": "rimraf dist && npm run clean-babel",
+    "test": "mocha tests"
   },
   "author": "Marek Ostaszewski, David Hoksza",
   "license": "MIT",

src/js/index.js

@@ -301,10 +301,10 @@ function calculateGSEA() {
                 //calculate intersect
                 const isect = [...ovHgncNames].filter(name => mpHgncNames.has(name));
 
-                var m = mpHgncNames.size;
-                var k = isect.length;
-                var N = globals.allProteinRnaGene.length;
-                var n = ovHgncNames.size;
+                var m = mpHgncNames.size; //number of entities in the pathway (with HGNC_SYMBOL)
+                var k = isect.length; //number of entities in both pathway and overlay (with HGNC_SYMBOL)
+                var N = globals.allProteinRnaGene.length; // number of all entities (with HGNC_SYMBOL)
+                var n = ovHgncNames.size; //number of entities in the overlay (with HGNC_SYMBOL)
 
                 console.log('pw', pwName);
                 console.log('m', m);

tests/test.js

@@ -9,6 +9,7 @@ const XMLHttpRequest = require("xmlhttprequest").XMLHttpRequest;
 // 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 pluginLabel = 'GSEA';
 const minervaProxyContainerClass = pluginName + '-container';
 const minervaProxyCode = `$('.${minervaProxyContainerClass}').data('minervaProxy')`;
 
@@ -66,14 +67,19 @@ async function getRequest(uri) {
 
 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;
+        let hashes = JSON.parse(pluginsResponse.responseText).filter(plugin => plugin.name === pluginLabel);
+        if (hashes.length === 0){
+            // when tested withing CI there is only one plugin, the current one and it's name is test
+            hashes = JSON.parse(pluginsResponse.responseText);
+        }
+        return hashes[hashes.length -1].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);
+    this.timeout(40000);
 
     let driver;
     let minervaProxy;
@@ -128,7 +134,7 @@ describe('GSEA plugin', async function() {
                 $('.gsea-buttons .btn-calc').click();
             });
 
-            await driver.wait(until.elementLocated(By.css(`.gsea-results button`)),5000);
+            await driver.wait(until.elementLocated(By.css(`.gsea-results button`)));
         });
 
         let elPanelTitle;