7 import simplejson as json
9 from django.test import TestCase
11 from htsworkflow.frontend.samples.models import \
17 from htsworkflow.frontend.samples.views import \
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.
25 Species.objects.all().delete()
26 obj.species_human = Species(
27 scientific_name = 'Homo Sapeins',
28 common_name = 'human',
30 obj.species_human.save()
31 obj.species_worm = Species(
32 scientific_name = 'C. Elegans',
35 obj.species_worm.save()
36 obj.species_phix = Species(
37 scientific_name = 'PhiX',
40 obj.species_phix.save()
42 ExperimentType.objects.all().delete()
43 obj.experiment_de_novo = ExperimentType(
46 obj.experiment_de_novo.save()
47 obj.experiment_chip_seq = ExperimentType(
50 obj.experiment_chip_seq.save()
51 obj.experiment_rna_seq = ExperimentType(
54 obj.experiment_rna_seq.save()
56 Affiliation.objects.all().delete()
57 obj.affiliation_alice = Affiliation(
60 email = 'alice@some.where.else.'
62 obj.affiliation_alice.save()
63 obj.affiliation_bob = Affiliation(
65 contact = 'Other Lab Boss',
66 email = 'bob@some.where.else',
68 obj.affiliation_bob.save()
70 Library.objects.all().delete()
71 obj.library_10001 = Library(
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',
82 obj.library_10001.save()
83 obj.library_10002 = Library(
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',
94 obj.library_10002.save()
96 class LibraryTestCase(TestCase):
100 def testOrganism(self):
101 self.assertEquals(self.library_10001.organism(), 'human')
103 def testAffiliations(self):
104 self.library_10001.affiliations.add(self.affiliation_alice)
105 self.library_10002.affiliations.add(
106 self.affiliation_alice,
109 self.failUnless(len(self.library_10001.affiliations.all()), 1)
110 self.failUnless(self.library_10001.affiliation(), 'Alice')
112 self.failUnless(len(self.library_10002.affiliations.all()), 2)
113 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
115 class SampleWebTestCase(TestCase):
117 Test returning data from our database in rest like ways.
118 (like returning json objects)
120 fixtures = ['test_samples.json']
122 def test_library_info(self):
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)
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)
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):
165 Make sure we get a 404 if we request an invalid library id
167 self.client.login(username='test', password='BJOKL5kAj6aFZ6A5')
168 response = self.client.get('/samples/library/nottheone/json')
169 self.failUnlessEqual(response.status_code, 404)
172 def test_library_not_logged_in(self):
174 Make sure we get a 302 if we're not logged in
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)