htsworkflow/frontend/experiments/tests.py

   1 import re
   2 try:
   3     import json
   4 except ImportError, e:
   5     import simplejson as json
   6 import sys
   7
   8 from django.core import mail
   9 from django.test import TestCase
  10 from htsworkflow.frontend.experiments import models
  11 from htsworkflow.frontend.experiments import experiments
  12 from htsworkflow.frontend.auth import apidata
  13
  14 class ExperimentsTestCases(TestCase):
  15     fixtures = ['test_flowcells.json']
  16
  17     def setUp(self):
  18         pass
  19
  20     def test_flowcell_information(self):
  21         """
  22         Check the code that packs the django objects into simple types.
  23         """
  24         for fc_id in [u'303TUAAXX', u"42JTNAAXX", "42JU1AAXX"]:
  25             fc_dict = experiments.flowcell_information(fc_id)
  26             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
  27             self.failUnlessEqual(fc_dict['flowcell_id'], fc_id)
  28             self.failUnlessEqual(fc_django.flowcell_id, fc_id)
  29             self.failUnlessEqual(fc_dict['sequencer'], fc_django.sequencer.name)
  30             self.failUnlessEqual(fc_dict['read_length'], fc_django.read_length)
  31             self.failUnlessEqual(fc_dict['notes'], fc_django.notes)
  32             self.failUnlessEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
  33
  34             for lane in fc_django.lane_set.all():
  35                 lane_dict = fc_dict['lane_set'][lane.lane_number]
  36                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  37                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  38                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  39                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  40                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  41                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  42                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  43                 self.failUnlessEqual(lane_dict['library_species'],
  44                                      lane.library.library_species.scientific_name)
  45
  46             response = self.client.get('/experiments/config/%s/json' % (fc_id,), apidata)
  47             # strptime isoformat string = '%Y-%m-%dT%H:%M:%S'
  48             fc_json = json.loads(response.content)
  49             self.failUnlessEqual(fc_json['flowcell_id'], fc_id)
  50             self.failUnlessEqual(fc_json['sequencer'], fc_django.sequencer.name)
  51             self.failUnlessEqual(fc_json['read_length'], fc_django.read_length)
  52             self.failUnlessEqual(fc_json['notes'], fc_django.notes)
  53             self.failUnlessEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
  54
  55
  56             for lane in fc_django.lane_set.all():
  57                 lane_dict = fc_json['lane_set'][unicode(lane.lane_number)]
  58                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  59                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  60                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  61                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  62                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  63                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  64                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  65                 self.failUnlessEqual(lane_dict['library_species'],
  66                                      lane.library.library_species.scientific_name)
  67
  68     def test_invalid_flowcell(self):
  69         """
  70         Make sure we get a 404 if we request an invalid flowcell ID
  71         """
  72         response = self.client.get('/experiments/config/nottheone/json', apidata)
  73         self.failUnlessEqual(response.status_code, 404)
  74
  75     def test_no_key(self):
  76         """
  77         Require logging in to retrieve meta data
  78         """
  79         response = self.client.get(u'/experiments/config/303TUAAXX/json')
  80         self.failUnlessEqual(response.status_code, 403)
  81
  82     def test_library_id(self):
  83         """
  84         Library IDs should be flexible, so make sure we can retrive a non-numeric ID
  85         """
  86         response = self.client.get('/experiments/config/303TUAAXX/json', apidata)
  87         self.failUnlessEqual(response.status_code, 200)
  88         flowcell = json.loads(response.content)
  89
  90         self.failUnlessEqual(flowcell['lane_set']['3']['library_id'], 'SL039')
  91
  92         response = self.client.get('/samples/library/SL039/json', apidata)
  93         self.failUnlessEqual(response.status_code, 200)
  94         library_sl039 = json.loads(response.content)
  95
  96         self.failUnlessEqual(library_sl039['library_id'], 'SL039')
  97
  98 class TestEmailNotify(TestCase):
  99     fixtures = ['test_flowcells.json']
 100
 101     def test_started_email_not_logged_in(self):
 102         response = self.client.get('/experiments/started/153/')
 103         self.failUnlessEqual(response.status_code, 302)
 104
 105     def test_started_email_logged_in_user(self):
 106         self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 107         response = self.client.get('/experiments/started/153/')
 108         self.failUnlessEqual(response.status_code, 302)
 109
 110     def test_started_email_logged_in_staff(self):
 111         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 112         response = self.client.get('/experiments/started/153/')
 113         self.failUnlessEqual(response.status_code, 200)
 114
 115     def test_started_email_send(self):
 116         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 117         response = self.client.get('/experiments/started/153/')
 118         self.failUnlessEqual(response.status_code, 200)
 119
 120         self.failUnless('pk1@example.com' in response.content)
 121         self.failUnless('Lane #8 : (11064) Paired ends 104' in response.content)
 122
 123         response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
 124         self.failUnlessEqual(response.status_code, 200)
 125         self.failUnlessEqual(len(mail.outbox), 4)
 126         for m in mail.outbox:
 127             self.failUnless(len(m.body) > 0)
 128
 129     def test_email_navigation(self):
 130         """
 131         Can we navigate between the flowcell and email forms properly?
 132         """
 133         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
 134         response = self.client.get('/experiments/started/153/')
 135         self.failUnlessEqual(response.status_code, 200)
 136         self.failUnless(re.search('Flowcell 303TUAAXX', response.content))
 137         # require that navigation back to the admin page exists
 138         self.failUnless(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
 139