htsworkflow/frontend/experiments/tests.py

   1 try:
   2     import json
   3 except ImportError, e:
   4     import simplejson as json
   5
   6 from django.test import TestCase
   7 from htsworkflow.frontend.experiments import models
   8 from htsworkflow.frontend.experiments import experiments
   9 from htsworkflow.frontend.auth import apidata
  10
  11 class ExperimentsTestCases(TestCase):
  12     fixtures = ['test_flowcells.json']
  13
  14     def setUp(self):
  15         pass
  16
  17     def test_flowcell_information(self):
  18         """
  19         Check the code that packs the django objects into simple types.
  20         """
  21         for fc_id in [u'303TUAAXX', u"42JTNAAXX", "42JU1AAXX"]:
  22             fc_dict = experiments.flowcell_information(fc_id)
  23             fc_django = models.FlowCell.objects.get(flowcell_id=fc_id)
  24             self.failUnlessEqual(fc_dict['flowcell_id'], fc_id)
  25             self.failUnlessEqual(fc_django.flowcell_id, fc_id)
  26             self.failUnlessEqual(fc_dict['sequencer'], fc_django.sequencer.name)
  27             self.failUnlessEqual(fc_dict['read_length'], fc_django.read_length)
  28             self.failUnlessEqual(fc_dict['notes'], fc_django.notes)
  29             self.failUnlessEqual(fc_dict['cluster_station'], fc_django.cluster_station.name)
  30
  31             for lane in fc_django.lane_set.all():
  32                 lane_dict = fc_dict['lane_set'][lane.lane_number]
  33                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  34                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  35                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  36                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  37                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  38                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  39                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  40                 self.failUnlessEqual(lane_dict['library_species'],
  41                                      lane.library.library_species.scientific_name)
  42
  43             response = self.client.get('/experiments/config/%s/json' % (fc_id,), apidata)
  44             # strptime isoformat string = '%Y-%m-%dT%H:%M:%S'
  45             fc_json = json.loads(response.content)
  46             self.failUnlessEqual(fc_json['flowcell_id'], fc_id)
  47             self.failUnlessEqual(fc_json['sequencer'], fc_django.sequencer.name)
  48             self.failUnlessEqual(fc_json['read_length'], fc_django.read_length)
  49             self.failUnlessEqual(fc_json['notes'], fc_django.notes)
  50             self.failUnlessEqual(fc_json['cluster_station'], fc_django.cluster_station.name)
  51
  52
  53             for lane in fc_django.lane_set.all():
  54                 lane_dict = fc_json['lane_set'][unicode(lane.lane_number)]
  55                 self.failUnlessEqual(lane_dict['cluster_estimate'], lane.cluster_estimate)
  56                 self.failUnlessEqual(lane_dict['comment'], lane.comment)
  57                 self.failUnlessEqual(lane_dict['flowcell'], lane.flowcell.flowcell_id)
  58                 self.failUnlessEqual(lane_dict['lane_number'], lane.lane_number)
  59                 self.failUnlessEqual(lane_dict['library_name'], lane.library.library_name)
  60                 self.failUnlessEqual(lane_dict['library_id'], lane.library.library_id)
  61                 self.failUnlessAlmostEqual(lane_dict['pM'], float(lane.pM))
  62                 self.failUnlessEqual(lane_dict['library_species'],
  63                                      lane.library.library_species.scientific_name)
  64
  65     def test_invalid_flowcell(self):
  66         """
  67         Make sure we get a 404 if we request an invalid flowcell ID
  68         """
  69         response = self.client.get('/experiments/config/nottheone/json', apidata)
  70         self.failUnlessEqual(response.status_code, 404)
  71
  72     def test_no_key(self):
  73         """
  74         Require logging in to retrieve meta data
  75         """
  76         response = self.client.get(u'/experiments/config/303TUAAXX/json')
  77         self.failUnlessEqual(response.status_code, 403)
  78
  79     def test_library_id(self):
  80         """
  81         Library IDs should be flexible, so make sure we can retrive a non-numeric ID
  82         """
  83         response = self.client.get('/experiments/config/303TUAAXX/json', apidata)
  84         self.failUnlessEqual(response.status_code, 200)
  85         flowcell = json.loads(response.content)
  86
  87         self.failUnlessEqual(flowcell['lane_set']['3']['library_id'], 'SL039')
  88
  89         response = self.client.get('/samples/library/SL039/json', apidata)
  90         self.failUnlessEqual(response.status_code, 200)
  91         library_sl039 = json.loads(response.content)
  92
  93         self.failUnlessEqual(library_sl039['library_id'], 'SL039')
  94
  95 #class RetriveConfigTestCases(TestCase):
  96 #    fixtures = ['test_flowcells.json']