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 # The django test runner flushes the database between test suites not cases,
  22 # so to be more compatible with running via nose we flush the database tables
  23 # of interest before creating our sample data.
  24 def create_db(obj):
  25     Species.objects.all().delete()
  26     obj.species_human = Species(
  27         scientific_name = 'Homo Sapeins',
  28         common_name = 'human',
  29     )
  30     obj.species_human.save()
  31     obj.species_worm = Species(
  32         scientific_name = 'C. Elegans',
  33         common_name = 'worm',
  34     )
  35     obj.species_worm.save()
  36     obj.species_phix = Species(
  37         scientific_name = 'PhiX',
  38         common_name = 'PhiX'
  39     )
  40     obj.species_phix.save()
  41
  42     ExperimentType.objects.all().delete()
  43     obj.experiment_de_novo = ExperimentType(
  44         name = 'De Novo',
  45     )
  46     obj.experiment_de_novo.save()
  47     obj.experiment_chip_seq = ExperimentType(
  48         name = 'ChIP-Seq'
  49     )
  50     obj.experiment_chip_seq.save()
  51     obj.experiment_rna_seq = ExperimentType(
  52         name = 'RNA-Seq'
  53     )
  54     obj.experiment_rna_seq.save()
  55
  56     Affiliation.objects.all().delete()
  57     obj.affiliation_alice = Affiliation(
  58         name = 'Alice',
  59         contact = 'Lab Boss',
  60         email = 'alice@some.where.else.'
  61     )
  62     obj.affiliation_alice.save()
  63     obj.affiliation_bob = Affiliation(
  64         name = 'Bob',
  65         contact = 'Other Lab Boss',
  66         email = 'bob@some.where.else',
  67     )
  68     obj.affiliation_bob.save()
  69
  70     Library.objects.all().delete()
  71     obj.library_10001 = Library(
  72         library_id = 10001,
  73         library_name = 'C2C12 named poorly',
  74         library_species = obj.species_human,
  75         experiment_type = obj.experiment_rna_seq,
  76         creation_date = datetime.datetime.now(),
  77         made_for = 'scientist unit 2007',
  78         made_by = 'microfludics system 7321',
  79         stopping_point = '2A',
  80         undiluted_concentration = '5.01',
  81     )
  82     obj.library_10001.save()
  83     obj.library_10002 = Library(
  84         library_id = 10002,
  85         library_name = 'Worm named poorly',
  86         library_species = obj.species_human,
  87         experiment_type = obj.experiment_rna_seq,
  88         creation_date = datetime.datetime.now(),
  89         made_for = 'scientist unit 2007',
  90         made_by = 'microfludics system 7321',
  91         stopping_point = '2A',
  92         undiluted_concentration = '5.01',
  93     )
  94     obj.library_10002.save()
  95
  96 class LibraryTestCase(TestCase):
  97     def setUp(self):
  98         create_db(self)
  99
 100     def testOrganism(self):
 101         self.assertEquals(self.library_10001.organism(), 'human')
 102
 103     def testAffiliations(self):
 104         self.library_10001.affiliations.add(self.affiliation_alice)
 105         self.library_10002.affiliations.add(
 106                 self.affiliation_alice,
 107                 self.affiliation_bob
 108         )
 109         self.failUnless(len(self.library_10001.affiliations.all()), 1)
 110         self.failUnless(self.library_10001.affiliation(), 'Alice')
 111
 112         self.failUnless(len(self.library_10002.affiliations.all()), 2)
 113         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
 114
 115 class SampleWebTestCase(TestCase):
 116     """
 117     Test returning data from our database in rest like ways.
 118     (like returning json objects)
 119     """
 120     fixtures = ['test_samples.json']
 121
 122     def test_library_info(self):
 123
 124         for lib in Library.objects.all():
 125             lib_dict = library_dict(lib.library_id)
 126             self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 127             url = '/samples/library/%s/json' % (lib.library_id,)
 128             lib_response = self.client.get(url)
 129             self.failUnlessEqual(lib_response.status_code, 200)
 130             lib_json = json.loads(lib_response.content)
 131
 132             for d in [lib_dict, lib_json]:
 133                 # amplified_from_sample is a link to the library table,
 134                 # I want to use the "library_id" for the data lookups not
 135                 # the embedded primary key.
 136                 # It gets slightly confusing on how to implement sending the right id
 137                 # since amplified_from_sample can be null
 138                 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
 139                 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
 140                 self.failUnlessEqual(d['avg_lib_size'], lib.avg_lib_size)
 141                 self.failUnlessEqual(d['cell_line'], lib.cell_line.cellline_name)
 142                 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
 143                 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
 144                 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
 145                 self.failUnlessEqual(d['id'], lib.id)
 146                 self.failUnlessEqual(d['library_id'], lib.library_id)
 147                 self.failUnlessEqual(d['library_name'], lib.library_name)
 148                 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
 149                 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
 150                 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
 151                 if lib.library_type_id is not None:
 152                     self.failUnlessEqual(d['library_type'], lib.library_type.name)
 153                 else:
 154                     self.failUnlessEqual(d['library_type'], None)
 155                     self.failUnlessEqual(d['made_for'], lib.made_for)
 156                     self.failUnlessEqual(d['made_by'], lib.made_by)
 157                     self.failUnlessEqual(d['notes'], lib.notes)
 158                     self.failUnlessEqual(d['replicate'], lib.replicate)
 159                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
 160                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
 161                     self.failUnlessEqual(d['undiluted_concentration'],
 162                                          unicode(lib.undiluted_concentration))
 163     def test_invalid_library(self):
 164         """
 165         Make sure we get a 404 if we request an invalid library id
 166         """
 167         self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 168         response = self.client.get('/samples/library/nottheone/json')
 169         self.failUnlessEqual(response.status_code, 404)
 170
 171
 172     def test_library_not_logged_in(self):
 173         """
 174         Make sure we get a 302 if we're not logged in
 175         """
 176         response = self.client.get('/samples/library/10981/json')
 177         self.failUnlessEqual(response.status_code, 302)
 178         self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
 179         response = self.client.get('/samples/library/10981/json')
 180         self.failUnlessEqual(response.status_code, 200)