htsworkflow/frontend/samples/tests.py

   1 import datetime
   2 import unittest
   3
   4 try:
   5     import json
   6 except ImportError, e:
   7     import simplejson as json
   8
   9 from django.test import TestCase
  10
  11 from htsworkflow.frontend.samples.models import \
  12         Affiliation, \
  13         ExperimentType, \
  14         Species, \
  15         Library
  16
  17 from htsworkflow.frontend.samples.views import \
  18      library_dict, \
  19      library_json
  20
  21 from htsworkflow.frontend.auth import apidata
  22 from htsworkflow.util.conversion import unicode_or_none
  23
  24
  25 class LibraryTestCase(TestCase):
  26     def setUp(self):
  27         create_db(self)
  28
  29     def testOrganism(self):
  30         self.assertEquals(self.library_10001.organism(), 'human')
  31
  32     def testAffiliations(self):
  33         self.library_10001.affiliations.add(self.affiliation_alice)
  34         self.library_10002.affiliations.add(
  35                 self.affiliation_alice,
  36                 self.affiliation_bob
  37         )
  38         self.failUnless(len(self.library_10001.affiliations.all()), 1)
  39         self.failUnless(self.library_10001.affiliation(), 'Alice')
  40
  41         self.failUnless(len(self.library_10002.affiliations.all()), 2)
  42         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
  43
  44
  45 class SampleWebTestCase(TestCase):
  46     """
  47     Test returning data from our database in rest like ways.
  48     (like returning json objects)
  49     """
  50     fixtures = ['test_samples.json']
  51
  52     def test_library_info(self):
  53
  54         for lib in Library.objects.all():
  55             lib_dict = library_dict(lib.id)
  56             url = '/samples/library/%s/json' % (lib.id,)
  57             lib_response = self.client.get(url, apidata)
  58             self.failUnlessEqual(lib_response.status_code, 200)
  59             lib_json = json.loads(lib_response.content)
  60
  61             for d in [lib_dict, lib_json]:
  62                 # amplified_from_sample is a link to the library table,
  63                 # I want to use the "id" for the data lookups not
  64                 # the embedded primary key.
  65                 # It gets slightly confusing on how to implement sending the right id
  66                 # since amplified_from_sample can be null
  67                 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
  68                 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
  69                 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
  70                 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
  71                 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
  72                 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
  73                 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
  74                 self.failUnlessEqual(d['hidden'], lib.hidden)
  75                 self.failUnlessEqual(d['id'], lib.id)
  76                 self.failUnlessEqual(d['insert_size'], lib.insert_size)
  77                 self.failUnlessEqual(d['library_name'], lib.library_name)
  78                 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
  79                 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
  80                 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
  81                 if lib.library_type_id is not None:
  82                     self.failUnlessEqual(d['library_type'], lib.library_type.name)
  83                 else:
  84                     self.failUnlessEqual(d['library_type'], None)
  85                     self.failUnlessEqual(d['made_for'], lib.made_for)
  86                     self.failUnlessEqual(d['made_by'], lib.made_by)
  87                     self.failUnlessEqual(d['notes'], lib.notes)
  88                     self.failUnlessEqual(d['replicate'], lib.replicate)
  89                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
  90                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
  91                     self.failUnlessEqual(d['undiluted_concentration'],
  92                                          unicode(lib.undiluted_concentration))
  93                 # some specific tests
  94                 if lib.id == '10981':
  95                     # test a case where there is no known status
  96                     lane_set = {u'status': u'Unknown', u'paired_end': True, u'read_length': 75, u'lane_number': 1, u'flowcell': u'303TUAAXX', u'status_code': None}
  97                     self.failUnlessEqual(len(d['lane_set']), 1)
  98                     self.failUnlessEqual(d['lane_set'][0], lane_set)
  99                 elif lib.id == '11016':
 100                     # test a case where there is a status
 101                     lane_set = {u'status': 'Good', u'paired_end': True, u'read_length': 75, u'lane_number': 5, u'flowcell': u'303TUAAXX', u'status_code': 2}
 102                     self.failUnlessEqual(len(d['lane_set']), 1)
 103                     self.failUnlessEqual(d['lane_set'][0], lane_set)
 104
 105     def test_invalid_library(self):
 106         """
 107         Make sure we get a 404 if we request an invalid library id
 108         """
 109         response = self.client.get('/samples/library/nottheone/json', apidata)
 110         self.failUnlessEqual(response.status_code, 404)
 111
 112
 113     def test_library_no_key(self):
 114         """
 115         Make sure we get a 302 if we're not logged in
 116         """
 117         response = self.client.get('/samples/library/10981/json')
 118         self.failUnlessEqual(response.status_code, 403)
 119         response = self.client.get('/samples/library/10981/json', apidata)
 120         self.failUnlessEqual(response.status_code, 200)
 121
 122 # The django test runner flushes the database between test suites not cases,
 123 # so to be more compatible with running via nose we flush the database tables
 124 # of interest before creating our sample data.
 125 def create_db(obj):
 126     Species.objects.all().delete()
 127     obj.species_human = Species(
 128         scientific_name = 'Homo Sapeins',
 129         common_name = 'human',
 130     )
 131     obj.species_human.save()
 132     obj.species_worm = Species(
 133         scientific_name = 'C. Elegans',
 134         common_name = 'worm',
 135     )
 136     obj.species_worm.save()
 137     obj.species_phix = Species(
 138         scientific_name = 'PhiX',
 139         common_name = 'PhiX'
 140     )
 141     obj.species_phix.save()
 142
 143     ExperimentType.objects.all().delete()
 144     obj.experiment_de_novo = ExperimentType(
 145         name = 'De Novo',
 146     )
 147     obj.experiment_de_novo.save()
 148     obj.experiment_chip_seq = ExperimentType(
 149         name = 'ChIP-Seq'
 150     )
 151     obj.experiment_chip_seq.save()
 152     obj.experiment_rna_seq = ExperimentType(
 153         name = 'RNA-Seq'
 154     )
 155     obj.experiment_rna_seq.save()
 156
 157     Affiliation.objects.all().delete()
 158     obj.affiliation_alice = Affiliation(
 159         name = 'Alice',
 160         contact = 'Lab Boss',
 161         email = 'alice@some.where.else.'
 162     )
 163     obj.affiliation_alice.save()
 164     obj.affiliation_bob = Affiliation(
 165         name = 'Bob',
 166         contact = 'Other Lab Boss',
 167         email = 'bob@some.where.else',
 168     )
 169     obj.affiliation_bob.save()
 170
 171     Library.objects.all().delete()
 172     obj.library_10001 = Library(
 173         id = "10001",
 174         library_name = 'C2C12 named poorly',
 175         library_species = obj.species_human,
 176         experiment_type = obj.experiment_rna_seq,
 177         creation_date = datetime.datetime.now(),
 178         made_for = 'scientist unit 2007',
 179         made_by = 'microfludics system 7321',
 180         stopping_point = '2A',
 181         undiluted_concentration = '5.01',
 182         hidden = False,
 183     )
 184     obj.library_10001.save()
 185     obj.library_10002 = Library(
 186         id = "10002",
 187         library_name = 'Worm named poorly',
 188         library_species = obj.species_human,
 189         experiment_type = obj.experiment_rna_seq,
 190         creation_date = datetime.datetime.now(),
 191         made_for = 'scientist unit 2007',
 192         made_by = 'microfludics system 7321',
 193         stopping_point = '2A',
 194         undiluted_concentration = '5.01',
 195         hidden = False,
 196     )
 197     obj.library_10002.save()
 198