htsworkflow/frontend/experiments/tests.py

   1 import re
   2 from BeautifulSoup import BeautifulSoup
   3 try:
   4     import json
   5 except ImportError, e:
   6     import simplejson as json
   7 import sys
   8
   9 from django.core import mail
  10 from django.test import TestCase
  11 from htsworkflow.frontend.experiments import models
  12 from htsworkflow.frontend.experiments import experiments
  13 from htsworkflow.frontend.auth import apidata
  14
  15 LANE_SET = range(1,9)
  16
  17 class ExperimentsTestCases(TestCase):
  18     fixtures = ['test_flowcells.json']
  19
  20     def setUp(self):
  21         pass
  22
  23     def test_flowcell_information(self):
  24         """
  25         Check the code that packs the django objects into simple types.
  26         """
  27         for fc_id in [u'303TUAAXX', u"42JTNAAXX", "42JU1AAXX"]:
  28             fc_dict = experiments.flowcell_information(fc_id)
  29             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
  30             self.failUnlessEqual(fc_dict['flowcell_id'], fc_id)
  31             self.failUnlessEqual(fc_django.flowcell_id, fc_id)
  32             self.failUnlessEqual(fc_dict['sequencer'], fc_django.sequencer.name)
  33             self.failUnlessEqual(fc_dict['read_length'], fc_django.read_length)
  34             self.failUnlessEqual(fc_dict['notes'], fc_django.notes)
  35             self.failUnlessEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
  36
  37             for lane in fc_django.lane_set.all():
  38                 lane_dict = fc_dict['lane_set'][lane.lane_number]
  39                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  40                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  41                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  42                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  43                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  44                 self.failUnlessEqual(lane_dict['library_id'], lane.library.id)
  45                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  46                 self.failUnlessEqual(lane_dict['library_species'],
  47                                      lane.library.library_species.scientific_name)
  48
  49             response = self.client.get('/experiments/config/%s/json' % (fc_id,), apidata)
  50             # strptime isoformat string = '%Y-%m-%dT%H:%M:%S'
  51             fc_json = json.loads(response.content)
  52             self.failUnlessEqual(fc_json['flowcell_id'], fc_id)
  53             self.failUnlessEqual(fc_json['sequencer'], fc_django.sequencer.name)
  54             self.failUnlessEqual(fc_json['read_length'], fc_django.read_length)
  55             self.failUnlessEqual(fc_json['notes'], fc_django.notes)
  56             self.failUnlessEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
  57
  58
  59             for lane in fc_django.lane_set.all():
  60                 lane_dict = fc_json['lane_set'][unicode(lane.lane_number)]
  61                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  62                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  63                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  64                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  65                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  66                 self.failUnlessEqual(lane_dict['library_id'], lane.library.id)
  67                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  68                 self.failUnlessEqual(lane_dict['library_species'],
  69                                      lane.library.library_species.scientific_name)
  70
  71     def test_invalid_flowcell(self):
  72         """
  73         Make sure we get a 404 if we request an invalid flowcell ID
  74         """
  75         response = self.client.get('/experiments/config/nottheone/json', apidata)
  76         self.failUnlessEqual(response.status_code, 404)
  77
  78     def test_no_key(self):
  79         """
  80         Require logging in to retrieve meta data
  81         """
  82         response = self.client.get(u'/experiments/config/303TUAAXX/json')
  83         self.failUnlessEqual(response.status_code, 403)
  84
  85     def test_library_id(self):
  86         """
  87         Library IDs should be flexible, so make sure we can retrive a non-numeric ID
  88         """
  89         response = self.client.get('/experiments/config/303TUAAXX/json', apidata)
  90         self.failUnlessEqual(response.status_code, 200)
  91         flowcell = json.loads(response.content)
  92
  93         self.failUnlessEqual(flowcell['lane_set']['3']['library_id'], 'SL039')
  94
  95         response = self.client.get('/samples/library/SL039/json', apidata)
  96         self.failUnlessEqual(response.status_code, 200)
  97         library_sl039 = json.loads(response.content)
  98
  99         self.failUnlessEqual(library_sl039['library_id'], 'SL039')
 100
 101     def test_raw_id_field(self):
 102         """
 103         Test ticket:147
 104
 105         Library's have IDs, libraries also have primary keys,
 106         we eventually had enough libraries that the drop down combo box was too
 107         hard to filter through, unfortnately we want a field that uses our library
 108         id and not the internal primary key, and raw_id_field uses primary keys.
 109
 110         This tests to make sure that the value entered in the raw library id field matches
 111         the library id looked up.
 112         """
 113         expected_ids = [u'10981',u'11016',u'SL039',u'11060',
 114                         u'11061',u'11062',u'11063',u'11064']
 115         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
 116         response = self.client.get('/admin/experiments/flowcell/153/')
 117         soup = BeautifulSoup(response.content)
 118         for i in range(0,8):
 119             input_field = soup.find(id='id_lane_set-%d-library' % (i,))
 120             library_field = input_field.findNext('strong')
 121             library_id, library_name = library_field.string.split(':')
 122             # strip leading '#' sign from name
 123             library_id = library_id[1:]
 124             self.failUnlessEqual(library_id, expected_ids[i])
 125             self.failUnlessEqual(input_field['value'], library_id)
 126
 127 class TestEmailNotify(TestCase):
 128     fixtures = ['test_flowcells.json']
 129
 130     def test_started_email_not_logged_in(self):
 131         response = self.client.get('/experiments/started/153/')
 132         self.failUnlessEqual(response.status_code, 302)
 133
 134     def test_started_email_logged_in_user(self):
 135         self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 136         response = self.client.get('/experiments/started/153/')
 137         self.failUnlessEqual(response.status_code, 302)
 138
 139     def test_started_email_logged_in_staff(self):
 140         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 141         response = self.client.get('/experiments/started/153/')
 142         self.failUnlessEqual(response.status_code, 200)
 143
 144     def test_started_email_send(self):
 145         self.client.login(username='admintest', password='BJOKL5kAj6aFZ6A5')
 146         response = self.client.get('/experiments/started/153/')
 147         self.failUnlessEqual(response.status_code, 200)
 148
 149         self.failUnless('pk1@example.com' in response.content)
 150         self.failUnless('Lane #8 : (11064) Paired ends 104' in response.content)
 151
 152         response = self.client.get('/experiments/started/153/', {'send':'1','bcc':'on'})
 153         self.failUnlessEqual(response.status_code, 200)
 154         self.failUnlessEqual(len(mail.outbox), 4)
 155         for m in mail.outbox:
 156             self.failUnless(len(m.body) > 0)
 157
 158     def test_email_navigation(self):
 159         """
 160         Can we navigate between the flowcell and email forms properly?
 161         """
 162         self.client.login(username='supertest', password='BJOKL5kAj6aFZ6A5')
 163         response = self.client.get('/experiments/started/153/')
 164         self.failUnlessEqual(response.status_code, 200)
 165         self.failUnless(re.search('Flowcell 303TUAAXX', response.content))
 166         # require that navigation back to the admin page exists
 167         self.failUnless(re.search('<a href="/admin/experiments/flowcell/153/">[^<]+</a>', response.content))
 168