How to authenticate Supertest requests with Passport?

You should use superagent for that. It is lower level module and used by supertest. Take a look at the section Persisting an agent:

var request = require('superagent');
var user1 = request.agent();
user1
  .post('http://localhost:4000/signin')
  .send({ user: '[email protected]', password: 'password' })
  .end(function(err, res) {
    // user1 will manage its own cookies
    // res.redirects contains an Array of redirects
  });

Now you can use user1 to make authenticated requests.

As zeMirco points out, the underlying superagent module supports sessions, automatically maintaining cookies for you. However, it is possible to use the superagent.agent() functionality from supertest, through an undocumented feature.

Simply use require('supertest').agent('url') instead of require('supertest')('url'):

var request = require('supertest');
var server = request.agent('http://localhost:3000');

describe('GET /api/getDir', function(){
    it('login', loginUser());
    it('uri that requires user to be logged in', function(done){
    server
        .get('/api/getDir')                       
        .expect(200)
        .end(function(err, res){
            if (err) return done(err);
            console.log(res.body);
            done()
        });
    });
});


function loginUser() {
    return function(done) {
        server
            .post('/login')
            .send({ username: 'admin', password: 'admin' })
            .expect(302)
            .expect('Location', '/')
            .end(onResponse);

        function onResponse(err, res) {
           if (err) return done(err);
           return done();
        }
    };
};

Try this,

  var request=require('supertest');
  var cookie;
  request(app)
  .post('/login')
  .send({ email: "[email protected]", password:'password' })
  .end(function(err,res){
    res.should.have.status(200);
    cookie = res.headers['set-cookie'];
    done();        
  });

  //
  // and use the cookie on the next request
  request(app)
  .get('/v1/your/path')
  .set('cookie', cookie)
  .end(function(err,res){  
    res.should.have.status(200);
    done();        
  });