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 # The django test runner flushes the database between test suites not cases,
  25 # so to be more compatible with running via nose we flush the database tables
  26 # of interest before creating our sample data.
  27 def create_db(obj):
  28     Species.objects.all().delete()
  29     obj.species_human = Species(
  30         scientific_name = 'Homo Sapeins',
  31         common_name = 'human',
  32     )
  33     obj.species_human.save()
  34     obj.species_worm = Species(
  35         scientific_name = 'C. Elegans',
  36         common_name = 'worm',
  37     )
  38     obj.species_worm.save()
  39     obj.species_phix = Species(
  40         scientific_name = 'PhiX',
  41         common_name = 'PhiX'
  42     )
  43     obj.species_phix.save()
  44
  45     ExperimentType.objects.all().delete()
  46     obj.experiment_de_novo = ExperimentType(
  47         name = 'De Novo',
  48     )
  49     obj.experiment_de_novo.save()
  50     obj.experiment_chip_seq = ExperimentType(
  51         name = 'ChIP-Seq'
  52     )
  53     obj.experiment_chip_seq.save()
  54     obj.experiment_rna_seq = ExperimentType(
  55         name = 'RNA-Seq'
  56     )
  57     obj.experiment_rna_seq.save()
  58
  59     Affiliation.objects.all().delete()
  60     obj.affiliation_alice = Affiliation(
  61         name = 'Alice',
  62         contact = 'Lab Boss',
  63         email = 'alice@some.where.else.'
  64     )
  65     obj.affiliation_alice.save()
  66     obj.affiliation_bob = Affiliation(
  67         name = 'Bob',
  68         contact = 'Other Lab Boss',
  69         email = 'bob@some.where.else',
  70     )
  71     obj.affiliation_bob.save()
  72
  73     Library.objects.all().delete()
  74     obj.library_10001 = Library(
  75         id = "10001",
  76         library_name = 'C2C12 named poorly',
  77         library_species = obj.species_human,
  78         experiment_type = obj.experiment_rna_seq,
  79         creation_date = datetime.datetime.now(),
  80         made_for = 'scientist unit 2007',
  81         made_by = 'microfludics system 7321',
  82         stopping_point = '2A',
  83         undiluted_concentration = '5.01',
  84     )
  85     obj.library_10001.save()
  86     obj.library_10002 = Library(
  87         id = "10002",
  88         library_name = 'Worm named poorly',
  89         library_species = obj.species_human,
  90         experiment_type = obj.experiment_rna_seq,
  91         creation_date = datetime.datetime.now(),
  92         made_for = 'scientist unit 2007',
  93         made_by = 'microfludics system 7321',
  94         stopping_point = '2A',
  95         undiluted_concentration = '5.01',
  96     )
  97     obj.library_10002.save()
  98
  99 class LibraryTestCase(TestCase):
 100     def setUp(self):
 101         create_db(self)
 102
 103     def testOrganism(self):
 104         self.assertEquals(self.library_10001.organism(), 'human')
 105
 106     def testAffiliations(self):
 107         self.library_10001.affiliations.add(self.affiliation_alice)
 108         self.library_10002.affiliations.add(
 109                 self.affiliation_alice,
 110                 self.affiliation_bob
 111         )
 112         self.failUnless(len(self.library_10001.affiliations.all()), 1)
 113         self.failUnless(self.library_10001.affiliation(), 'Alice')
 114
 115         self.failUnless(len(self.library_10002.affiliations.all()), 2)
 116         self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
 117
 118 class SampleWebTestCase(TestCase):
 119     """
 120     Test returning data from our database in rest like ways.
 121     (like returning json objects)
 122     """
 123     fixtures = ['test_samples.json']
 124
 125     def test_library_info(self):
 126
 127         for lib in Library.objects.all():
 128             lib_dict = library_dict(lib.id)
 129             url = '/samples/library/%s/json' % (lib.id,)
 130             lib_response = self.client.get(url, apidata)
 131             self.failUnlessEqual(lib_response.status_code, 200)
 132             lib_json = json.loads(lib_response.content)
 133
 134             for d in [lib_dict, lib_json]:
 135                 # amplified_from_sample is a link to the library table,
 136                 # I want to use the "id" for the data lookups not
 137                 # the embedded primary key.
 138                 # It gets slightly confusing on how to implement sending the right id
 139                 # since amplified_from_sample can be null
 140                 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
 141                 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
 142                 self.failUnlessEqual(d['avg_lib_size'], lib.avg_lib_size)
 143                 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
 144                 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
 145                 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
 146                 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
 147                 self.failUnlessEqual(d['id'], lib.id)
 148                 self.failUnlessEqual(d['library_name'], lib.library_name)
 149                 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
 150                 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
 151                 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
 152                 if lib.library_type_id is not None:
 153                     self.failUnlessEqual(d['library_type'], lib.library_type.name)
 154                 else:
 155                     self.failUnlessEqual(d['library_type'], None)
 156                     self.failUnlessEqual(d['made_for'], lib.made_for)
 157                     self.failUnlessEqual(d['made_by'], lib.made_by)
 158                     self.failUnlessEqual(d['notes'], lib.notes)
 159                     self.failUnlessEqual(d['replicate'], lib.replicate)
 160                     self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
 161                     self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
 162                     self.failUnlessEqual(d['undiluted_concentration'],
 163                                          unicode(lib.undiluted_concentration))
 164     def test_invalid_library(self):
 165         """
 166         Make sure we get a 404 if we request an invalid library id
 167         """
 168         response = self.client.get('/samples/library/nottheone/json', apidata)
 169         self.failUnlessEqual(response.status_code, 404)
 170
 171
 172     def test_library_no_key(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, 403)
 178         response = self.client.get('/samples/library/10981/json', apidata)
 179         self.failUnlessEqual(response.status_code, 200)