added tests for util class and color handler class

bhofmei · Jun 23, 2017 · e4013b3 · e4013b3
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diff --git a/.bowerrc b/.bowerrc
@@ -0,0 +1,3 @@
+{
+ "directory": "test"
+}
diff --git a/.gitignore b/.gitignore
@@ -0,0 +1,7 @@
+.DS_Store
+test/*
+!test/index.html
+!test/spec
+!test/run-jasmine.js
+!test/data
+built
diff --git a/.travis.yml b/.travis.yml
@@ -0,0 +1,16 @@
+language: node_js
+node_js:
+ - 7
+sudo: false
+cache:
+ directories:
+ - $HOME/.cache/bower
+before_install:
+ - pip install --user RangeHTTPServer
+ - npm install -g bower
+install:
+ - bower install
+before_script:
+ - python -m RangeHTTPServer &
+script:
+ - phantomjs test/run-jasmine.js http:https://localhost:8000/test/
diff --git a/bower.json b/bower.json
@@ -0,0 +1,23 @@
+{
+ "name": "jbplugin-nucdens",
+ "homepage": "https://github.com/bhofmei/jbplugin-nucdens#readme",
+ "description": "JBrowse plugin for viewing nucleotide density",
+ "main": "js/main.js",
+ "keywords": [
+ "jbrowse",
+ "jbrowse-plugin",
+ "nucelotide density"
+ ],
+ "license": "MIT",
+ "ignore": [
+ "**/.*",
+ "node_modules",
+ "bower_components",
+ "src",
+ "test"
+ ],
+ "devDependencies": {
+ "jasmine-core": "jasmine#^2.4.1",
+ "jbrowse": "git:https://github.com/GMOD/jbrowse.git#master"
+ }
+}
diff --git a/package.json b/package.json
@@ -0,0 +1,32 @@
+{
+ "name": "jbplugin-smallrna",
+ "version": "1.3.1",
+ "description": "JBrowse plugin for viewing small RNA alignments",
+ "main": "js/main.js",
+ "scripts": {
+ "test": "echo \"Error: no test specified\" && exit 1"
+ },
+
+ "repository": {
+ "type": "git",
+ "url": "git+https://github.com/bhofmei/jbplugin-smallrna.git"
+ },
+ "keywords": [
+ "jbrowse",
+ "jbrowse-plugin",
+ "small rna"
+ ],
+ "author": "Brigitte Hofmeister",
+ "license": "MIT",
+ "bugs": {
+ "url": "https://github.com/bhofmei/jbplugin-smallrna/issues"
+ },
+ "ignore": [
+ "node_modules",
+ "test"
+ ],
+ "directories": {
+ "test": "test"
+ },
+ "homepage": "https://github.com/bhofmei/jbplugin-smallrna#readme"
+}
diff --git a/test/index.html b/test/index.html
@@ -0,0 +1,47 @@
+<!DOCTYPE HTML PUBLIC "-//W3C//DTD HTML 4.01 Transitional//EN"
+ "http:https://www.w3.org/TR/html4/loose.dtd">
+<html>
+<head>
+ <meta charset="utf-8">
+ <title>Jasmine Spec Runner</title>
+
+ <link rel="stylesheet" href="jasmine-core/lib/jasmine-core/jasmine.css">
+ <script src="jasmine-core/lib/jasmine-core/jasmine.js"></script>
+ <script src="jasmine-core/lib/jasmine-core/jasmine-html.js"></script>
+ <script src="jasmine-core/lib/jasmine-core/boot.js"></script>
+ <!--<script src ="jasmine-jquery/lib/jasmine-jquery.js"></script>
+ <script src="jquery/src/jquery.js"></script>-->
+
+ <!-- include source files here... -->
+ <script type="text/javascript" src="dojo/dojo.js" data-dojo-config="async: 1" ></script>
+
+ <script type="text/javascript">
+ require( { baseUrl: '.',
+ packages: [
+ 'dojo',
+ 'dijit',
+ 'dojox',
+ 'jszlib',
+ { name: 'lazyload', location: 'lazyload', main: 'lazyload' },
+ 'dgrid',
+ 'xstyle',
+ 'put-selector',
+ 'FileSaver',
+ { name: 'jDataView', location: 'jDataView/src', main: 'jdataview' },
+ { name: 'JBrowse', location: 'jbrowse/src/JBrowse' },
+ { name: 'NucleotideDensityPlugin', location: '../js' }
+ ]
+ },
+ ['dojo/ready','JBrowse/Browser','NucleotideDensityPlugin/View/Track/NucleotideDensity', 'NucleotideDensityPlugin/View/ColorHandler'],
+ function( ready,Browser,NucleotideDensity, colorHandler ) {
+ });
+ </script>
+ <script type="text/javascript" src="spec/NucleotideDensityPlugin.spec.js"></script>
+
+
+</head>
+<body>
+ <div id="sandbox" style="overflow:hidden; height:1px;"></div>
+
+</body>
+</html>
diff --git a/test/run-jasmine.js b/test/run-jasmine.js
@@ -0,0 +1,92 @@
+"use strict";
+var system = require('system');
+
+/**
+ * Wait until the test condition is true or a timeout occurs. Useful for waiting
+ * on a server response or for a ui change (fadeIn, etc.) to occur.
+ *
+ * @param testFx javascript condition that evaluates to a boolean,
+ * it can be passed in as a string (e.g.: "1 == 1" or "$('#bar').is(':visible')" or
+ * as a callback function.
+ * @param onReady what to do when testFx condition is fulfilled,
+ * it can be passed in as a string (e.g.: "1 == 1" or "$('#bar').is(':visible')" or
+ * as a callback function.
+ * @param timeOutMillis the max amount of time to wait. If not specified, 3 sec is used.
+ */
+function waitFor(testFx, onReady, timeOutMillis) {
+ var maxtimeOutMillis = timeOutMillis ? timeOutMillis : 3001, //< Default Max Timeout is 3s
+ start = new Date().getTime(),
+ condition = false,
+ interval = setInterval(function() {
+ if ( (new Date().getTime() - start < maxtimeOutMillis) && !condition ) {
+ // If not time-out yet and condition not yet fulfilled
+ condition = (typeof(testFx) === "string" ? eval(testFx) : testFx()); //< defensive code
+ } else {
+ if(!condition) {
+ // If condition still not fulfilled (timeout but condition is 'false')
+ console.log("'waitFor()' timeout");
+ phantom.exit(1);
+ } else {
+ typeof(onReady) === "string" ? eval(onReady) : onReady(); //< Do what it's supposed to do once the condition is fulfilled
+ clearInterval(interval); //< Stop this interval
+ }
+ }
+ }, 100); //< repeat check every 100ms
+};
+
+
+if (system.args.length !== 2) {
+ console.log('Usage: run-jasmine2.js URL');
+ phantom.exit(1);
+}
+
+var page = require('webpage').create();
+
+// Route "console.log()" calls from within the Page context to the main Phantom context (i.e. current "this")
+page.onConsoleMessage = function(msg) {
+ console.log(msg);
+};
+
+page.open(system.args[1], function(status){
+ if (status !== "success") {
+ console.log("Unable to access network");
+ phantom.exit();
+ } else {
+ waitFor(function(){
+ return page.evaluate(function(){
+ return (document.body.querySelector('.symbolSummary .pending') === null &&
+ document.body.querySelector('.jasmine-duration') !== null);
+ });
+ }, function(){
+ var exitCode = page.evaluate(function(){
+ console.log('');
+
+ var title = 'Jasmine';
+ var version = document.body.querySelector('.jasmine-version').innerText;
+ var duration = document.body.querySelector('.jasmine-duration').innerText;
+ var banner = title + ' ' + version + ' ' + duration;
+ console.log(banner);
+
+ var list = document.body.querySelectorAll('.jasmine-results > .jasmine-failures > .jasmine-spec-detail.jasmine-failed');
+ if (list && list.length > 0) {
+ console.log('');
+ console.log(list.length + ' test(s) FAILED:');
+ for (i = 0; i < list.length; ++i) {
+ var el = list[i],
+ desc = el.querySelector('.jasmine-description'),
+ msg = el.querySelector('.jasmine-messages > .jasmine-result-message');
+ console.log('');
+ console.log(desc.innerText);
+ console.log(msg.innerText);
+ console.log('');
+ }
+ return 1;
+ } else {
+ console.log(document.body.querySelector('.jasmine-alert > .jasmine-bar,.jasmine-passed > .bar.skipped').innerText);
+ return 0;
+ }
+ });
+ phantom.exit(exitCode);
+ });
+ }
+});
diff --git a/test/spec/NucleotideDensityPlugin.spec.js b/test/spec/NucleotideDensityPlugin.spec.js
@@ -0,0 +1,112 @@
+require([
+ 'dojo/_base/declare',
+ 'dojo/_base/array',
+ 'JBrowse/Browser',
+ 'NucleotideDensityPlugin/View/ColorHandler',
+ 'NucleotideDensityPlugin/View/Track/NucleotideDensity',
+ 'NucleotideDensityPlugin/Store/SeqFeature/NucDensity',
+ 'NucleotideDensityPlugin/Store/Util'
+ ], function(
+ declare,
+ array,
+ Browser,
+ ColorHandler,
+ nucDensTrack,
+ nucDensStore,
+ nucDensUtil
+ ) {
+
+ describe( 'Initial test', function() {
+ var test = true;
+ it('jasmine is working', function() {
+ expect(test).toBe(true);
+ });
+ }); // end initial test
+
+ describe( 'Test degenerate nucleotide utilities', function(){
+ it('non-degenerate test, forward only', function(){
+ var cgAr = nucDensUtil.getPossibilities('CG',false);
+ var gttAr = nucDensUtil.getPossibilities('GTT',false);
+ expect(cgAr.length).toBe(1);
+ expect(gttAr.length).toBe(1);
+ });
+
+ it('non-degenerate test, both strands', function(){
+ var cgAr = nucDensUtil.getPossibilities('CG',true);
+ var gttAr = nucDensUtil.getPossibilities('GTT',true);
+ expect(cgAr.length).toBe(2);
+ expect(gttAr.length).toBe(2);
+ });
+
+ it('degenerate test, forward only', function(){
+ var cnAr = nucDensUtil.getPossibilities('CN',false);
+ var chhAr = nucDensUtil.getPossibilities('CHH',false);
+ var gbrAr = nucDensUtil.getPossibilities('GBR',false);
+ var nnAr = nucDensUtil.getPossibilities('NN',false);
+ var nnnAr = nucDensUtil.getPossibilities('NNN',false);
+ expect(cnAr.length).toBe(4);
+ expect(chhAr.length).toBe(9);
+ expect(gbrAr.length).toBe(6);
+ expect(nnAr.length).toBe(16);
+ expect(nnnAr.length).toBe(64);
+ });
+
+ it('degenerate test, both strands', function(){
+ var cnAr = nucDensUtil.getPossibilities('CN',true);
+ var chhAr = nucDensUtil.getPossibilities('CHH',true);
+ var gbrAr = nucDensUtil.getPossibilities('GBR',true);
+ var nnAr = nucDensUtil.getPossibilities('NN',true);
+ expect(cnAr.length).toBe(8);
+ expect(chhAr.length).toBe(18);
+ expect(gbrAr.length).toBe(12);
+ expect(nnAr.length).toBe(32);
+ });
+ }); // end test util
+
+ describe('test color handler utility', function(){
+ it('generate n colors', function(){
+ var clr5 = ColorHandler.generateNColors(5);
+ expect(clr5.length).toBe(5);
+ expect(clr5).toEqual(["#ff00a2", "#ea8500", "#00bb20", "#00c2ff", "#0097ff"]);
+ });
+
+ it('generate random colors', function(){
+ var clr2 = ColorHandler.generateRandomColors(["CG","CH"]);
+ expect(clr2).toEqual({CG:"#ff00a2",CH:'#00c29b'});
+ });
+
+ it('get font color', function(){
+ var cr1 = ColorHandler.getFontColor('#284996');
+ expect(cr1).toBe('#F0F0F0');
+ var cr2 = ColorHandler.getFontColor('#f1b982');
+ expect(cr2).toBe('#010101');
+ });
+
+ it('get color from list', function(){
+ var colorList = ['blue','red','pink','purple']
+
+ var clr2 = ColorHandler.intToColorFromList(1, colorList, true);
+ expect(clr2).toBe('red');
+
+ var clr2 = ColorHandler.contextToColorFromList('CN', ['TA','WCN','CN','NY'],['blue','red','pink','purple'], true);
+ expect(clr2).toBe('pink');
+ });
+
+ it('get color from list not defined', function(){
+ var un = ColorHandler.contextToColorFromList('NN',['NH','GT','AC'],['blue','red','pink'], false);
+ expect(un).not.toBeDefined()
+ });
+
+ it('get color from repeatable list', function(){
+ var colorList = ['blue','red','pink'];
+ var ctxList = ['AA','AC','AT','CC','CG','CT','GA','GC','TT'];
+
+ var clr1 = ColorHandler.contextToColorFromList('CC',ctxList, colorList, true);
+ expect(clr1).toBe('blue');
+ var clr2 = ColorHandler.contextToColorFromList('TT',ctxList, colorList, true);
+ expect(clr2).toBe('pink');
+ });
+ }); // end test color handler
+
+});
+