htsworkflow/frontend/experiments/tests.py

   1 try:
   2     import json
   3 except ImportError, e:
   4     import simplejson as json
   5 import sys
   6
   7 from django.core import mail
   8 from django.test import TestCase
   9 from htsworkflow.frontend.experiments import models
  10 from htsworkflow.frontend.experiments import experiments
  11 from htsworkflow.frontend.auth import apidata
  12
  13 class ExperimentsTestCases(TestCase):
  14     fixtures = ['test_flowcells.json']
  15
  16     def setUp(self):
  17         pass
  18
  19     def test_flowcell_information(self):
  20         """
  21         Check the code that packs the django objects into simple types.
  22         """
  23         for fc_id in [u'303TUAAXX', u"42JTNAAXX", "42JU1AAXX"]:
  24             fc_dict = experiments.flowcell_information(fc_id)
  25             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
  26             self.failUnlessEqual(fc_dict['flowcell_id'], fc_id)
  27             self.failUnlessEqual(fc_django.flowcell_id, fc_id)
  28             self.failUnlessEqual(fc_dict['sequencer'], fc_django.sequencer.name)
  29             self.failUnlessEqual(fc_dict['read_length'], fc_django.read_length)
  30             self.failUnlessEqual(fc_dict['notes'], fc_django.notes)
  31             self.failUnlessEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
  32
  33             for lane in fc_django.lane_set.all():
  34                 lane_dict = fc_dict['lane_set'][lane.lane_number]
  35                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  36                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  37                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  38                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  39                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  40                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  41                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  42                 self.failUnlessEqual(lane_dict['library_species'],
  43                                      lane.library.library_species.scientific_name)
  44
  45             response = self.client.get('/experiments/config/%s/json' % (fc_id,), apidata)
  46             # strptime isoformat string = '%Y-%m-%dT%H:%M:%S'
  47             fc_json = json.loads(response.content)
  48             self.failUnlessEqual(fc_json['flowcell_id'], fc_id)
  49             self.failUnlessEqual(fc_json['sequencer'], fc_django.sequencer.name)
  50             self.failUnlessEqual(fc_json['read_length'], fc_django.read_length)
  51             self.failUnlessEqual(fc_json['notes'], fc_django.notes)
  52             self.failUnlessEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
  53
  54
  55             for lane in fc_django.lane_set.all():
  56                 lane_dict = fc_json['lane_set'][unicode(lane.lane_number)]
  57                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  58                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  59                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  60                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  61                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  62                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  63                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  64                 self.failUnlessEqual(lane_dict['library_species'],
  65                                      lane.library.library_species.scientific_name)
  66
  67     def test_invalid_flowcell(self):
  68         """
  69         Make sure we get a 404 if we request an invalid flowcell ID
  70         """
  71         response = self.client.get('/experiments/config/nottheone/json', apidata)
  72         self.failUnlessEqual(response.status_code, 404)
  73
  74     def test_no_key(self):
  75         """
  76         Require logging in to retrieve meta data
  77         """
  78         response = self.client.get(u'/experiments/config/303TUAAXX/json')
  79         self.failUnlessEqual(response.status_code, 403)
  80
  81     def test_library_id(self):
  82         """
  83         Library IDs should be flexible, so make sure we can retrive a non-numeric ID
  84         """
  85         response = self.client.get('/experiments/config/303TUAAXX/json', apidata)
  86         self.failUnlessEqual(response.status_code, 200)
  87         flowcell = json.loads(response.content)
  88
  89         self.failUnlessEqual(flowcell['lane_set']['3']['library_id'], 'SL039')
  90
  91         response = self.client.get('/samples/library/SL039/json', apidata)
  92         self.failUnlessEqual(response.status_code, 200)
  93         library_sl039 = json.loads(response.content)
  94
  95         self.failUnlessEqual(library_sl039['library_id'], 'SL039')
  96
  97 class TestEmailNotify(TestCase):
  98     fixtures = ['test_flowcells.json']
  99
 100     def test_started_email_not_logged_in(self):
 101         response = self.client.get('/experiments/started/153/')
 102         self.failUnlessEqual(response.status_code, 302)
 103
 104     def test_started_email_logged_in_user(self):
 105         self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 106         response = self.client.get('/experiments/started/153/')
 107         self.failUnlessEqual(response.status_code, 302)
 108
 109     def test_started_email_logged_in_staff(self):
 110         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 111         response = self.client.get('/experiments/started/153/')
 112         self.failUnlessEqual(response.status_code, 200)
 113
 114     def test_started_email_send(self):
 115         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 116         response = self.client.get('/experiments/started/153/')
 117         self.failUnlessEqual(response.status_code, 200)
 118
 119         self.failUnless('pk1@example.com' in response.content)
 120         self.failUnless('Lane #8 : (11064) Paired ends 104' in response.content)
 121
 122         response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
 123         self.failUnlessEqual(response.status_code, 200)
 124         self.failUnlessEqual(len(mail.outbox), 4)
 125         for m in mail.outbox:
 126             self.failUnless(len(m.body) > 0)