Here is the result of this example - parsing the 15MB file with 500,000 lines in your browser.
1) Installing a npm dependency
As we want to download data, we need a request package.
In npm this is very easy, just run.
npm install nets --save
What does --save mean? Help
2) Require a dependency
var request = require("nets");
A sample request might look like this.
request('https://raw.githubusercontent.com/biojs-edu/biojs-io-snipspector/master/test/test.file', function (error, response, body) {
if (!error && response.statusCode == 200) {
console.log(body) // Prints the reponse body
}
})
manny.dummy only contains the first 50 lines. We will use the whole file with 500.000 lines later in this tutorial.
- Install the
netspackage - Create a sample file (e.g.
foo.js) - Download
https://raw.githubusercontent.com/biojs-edu/biojs-io-snipspector/master/test/test.fileand print it to the screen
Run a file: node foo.js
Solution
var request = require("nets");
request('https://raw.githubusercontent.com/biojs-edu/biojs-io-snipspector/master/test/test.file', function (error, response, body) {
if (!error && response.statusCode == 200) {
console.log(body) // Prints the reponse body
}
})3) Download the real data
snipspector.read = function(url, callback) {
// TODO
}
Create the read method in the graduate object which takes a url and a callback as input
and calls the callback with the parsed data.
Using callbacks is just one of multiple ways (but probably the easiest to understand). Another very popular one is to use promises.
You can need to remove the static data object in the parse method.
Put this data into your unit test.
Solution - if you have troubles: write the unit test first, before you look at this solution.
lib/index.js
var request = require("nets");
var snipspector = {};
snipspector.read = function(url, callback) {
request(url, function (error, response, body) {
if (!error && response.statusCode == 200) {
callback(snipspector.parse(body));
}
})
}
snipspector.parse = function(data) {
if(data.indexOf('\n') >= 0 ){
data = data.split('\n');
}
var chromosomes = [];
// analyze snippets
// homo(zygous): AA
// hetero(zygous): AC
// del(etion): A-, -A or --
var chr = null;
for (var i = 0; i < data.length; i++) {
// ignore empty rows or comments
if(data[i].length == 0 || data[i][0] === "#"){
continue;
}
var row = data[i].split(/\s+/);
var chrName = row[1];
// new chromosome begins
if( chr == null || chrName !== chr.name) {
// ignore the first time
if( chr != null ){
chromosomes.push(chr);
}
chr = {homo: 0, hetero: 0, del: 0};
chr.name = chrName;
}
var genotype = row[3];
if( genotype.length == 2){
// ignore MT
if(genotype[0] == genotype[1] && genotype[0] != "-"){
// homo
chr.homo = chr.homo + 1;
} else if( genotype[0] !== "-" && genotype[1] !== "-"){
// hetero
chr.hetero = chr.hetero + 1;
}else{
// del
chr.del = chr.del + 1;
}
}
}
// push the last item
chromosomes.push(chr);
return chromosomes;
}
//Should print [{name: "20", homo: 2, hetero: 1, del: 0,
// {name: "21", homo: 1, hetero: 1, del: 1},
// {name: "22", homo 1, hetero: 1, del: 0 }]
module.exports = snipspector; // Export the object for other components4) Test with live data (mocking)
4.1) Mocking the backend
npm install nock --save-dev
Why did we use --save-dev?
Nock allows us to mock a backend, in this example http://an.url/list
All you need to do is to add this block before your mocha tests run
(i.e. before the describe method).
var nock = require('nock')
var testURL = 'http://an.url/'
var scope = nock(testURL)
.get('/list')
.replyWithFile(200, __dirname + '/test.file');
__dirname is the current directory of an script (here: test).
Now you only need to create the dummy file with which Nock should reply.
test/test.file
rs5747620 20 15412698 TT
rs9605903 20 15434720 CC
rs2236639 20 15452483 GC
rs5747999 21 15455353 AA
rs11089263 21 15467656 A-
rs2096537 21 15474749 AC
rs9604959 22 15479107 CG
rs9604967 22 15492342 CC
(this is the same file from the package basics tutorial
For the beginning we use a small file for testing, so it is easier to debug.
4.2) Asynchronous testing
Now before you write your second unit test, there is a small thing to which you should pay attention.
XHR requests are asynchronous, that means you have to stop the test suite and wait until you have received the request.
In Mocha this is incredible easy.
it('should work with live data', function(done){
done(); // call the mocha callback and resume the test suite
});
Passing an argument to an Mocha test will automatically let the test suite run your test asynchronously - the argument is your callback. More info.
Write a second unit test that calls our mocked URL and test whether snipspector.read(<url>, <callback>) works.
5) Solution
no please do not have a look at our solution, if your unit test is green - your solution is correct!
test/simple.js
var assert = require("chai").assert;
var snip = require("../");
// you can find more docu about mocha here
// https://visionmedia.github.io/mocha/
var nock = require('nock')
var testURL = 'http://an.url/'
var scope = nock(testURL)
.get('/list')
.replyWithFile(200, __dirname + '/test.file');
var dummyObj = [{name: "20", homo: 2, hetero: 1, del: 0},
{name: "21", homo: 1, hetero: 1, del: 1},
{name: "22", homo: 1, hetero: 1, del: 0 }];
describe('Snipspector', function(){
// do any init stuff here
beforeEach(function(){
});
describe('parse', function(){
it('should return match with default object', function(){
var data = ["rs5747620 20 15412698 TT",
"rs9605903 20 15434720 CC",
"rs2236639 20 15452483 GC",
"rs5747999 21 15455353 AA",
"rs11089263 21 15467656 A-",
"rs2096537 21 15474749 AC",
"rs9604959 22 15479107 CG",
"rs9604967 22 15492342 CC"];
assert.deepEqual(snip.parse(data), dummyObj);
});
});
it('should work with live data', function(done){
snip.read(testURL + "list", function(parsed){
// the dummy file contains exactly this obj
assert.deepEqual(parsed, dummyObj);
done(); // you need to call the done callback to resume mocha
});
});
});