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 from htsworkflow.frontend.auth import apidata
22 from htsworkflow.util.conversion import unicode_or_none
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.
28 Species.objects.all().delete()
29 obj.species_human = Species(
30 scientific_name = 'Homo Sapeins',
31 common_name = 'human',
33 obj.species_human.save()
34 obj.species_worm = Species(
35 scientific_name = 'C. Elegans',
38 obj.species_worm.save()
39 obj.species_phix = Species(
40 scientific_name = 'PhiX',
43 obj.species_phix.save()
45 ExperimentType.objects.all().delete()
46 obj.experiment_de_novo = ExperimentType(
49 obj.experiment_de_novo.save()
50 obj.experiment_chip_seq = ExperimentType(
53 obj.experiment_chip_seq.save()
54 obj.experiment_rna_seq = ExperimentType(
57 obj.experiment_rna_seq.save()
59 Affiliation.objects.all().delete()
60 obj.affiliation_alice = Affiliation(
63 email = 'alice@some.where.else.'
65 obj.affiliation_alice.save()
66 obj.affiliation_bob = Affiliation(
68 contact = 'Other Lab Boss',
69 email = 'bob@some.where.else',
71 obj.affiliation_bob.save()
73 Library.objects.all().delete()
74 obj.library_10001 = Library(
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',
85 obj.library_10001.save()
86 obj.library_10002 = Library(
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',
97 obj.library_10002.save()
99 class LibraryTestCase(TestCase):
103 def testOrganism(self):
104 self.assertEquals(self.library_10001.organism(), 'human')
106 def testAffiliations(self):
107 self.library_10001.affiliations.add(self.affiliation_alice)
108 self.library_10002.affiliations.add(
109 self.affiliation_alice,
112 self.failUnless(len(self.library_10001.affiliations.all()), 1)
113 self.failUnless(self.library_10001.affiliation(), 'Alice')
115 self.failUnless(len(self.library_10002.affiliations.all()), 2)
116 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
118 class SampleWebTestCase(TestCase):
120 Test returning data from our database in rest like ways.
121 (like returning json objects)
123 fixtures = ['test_samples.json']
125 def test_library_info(self):
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)
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)
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):
166 Make sure we get a 404 if we request an invalid library id
168 response = self.client.get('/samples/library/nottheone/json', apidata)
169 self.failUnlessEqual(response.status_code, 404)
172 def test_library_no_key(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, 403)
178 response = self.client.get('/samples/library/10981/json', apidata)
179 self.failUnlessEqual(response.status_code, 200)