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
23 # The django test runner flushes the database between test suites not cases,
24 # so to be more compatible with running via nose we flush the database tables
25 # of interest before creating our sample data.
27 Species.objects.all().delete()
28 obj.species_human = Species(
29 scientific_name = 'Homo Sapeins',
30 common_name = 'human',
32 obj.species_human.save()
33 obj.species_worm = Species(
34 scientific_name = 'C. Elegans',
37 obj.species_worm.save()
38 obj.species_phix = Species(
39 scientific_name = 'PhiX',
42 obj.species_phix.save()
44 ExperimentType.objects.all().delete()
45 obj.experiment_de_novo = ExperimentType(
48 obj.experiment_de_novo.save()
49 obj.experiment_chip_seq = ExperimentType(
52 obj.experiment_chip_seq.save()
53 obj.experiment_rna_seq = ExperimentType(
56 obj.experiment_rna_seq.save()
58 Affiliation.objects.all().delete()
59 obj.affiliation_alice = Affiliation(
62 email = 'alice@some.where.else.'
64 obj.affiliation_alice.save()
65 obj.affiliation_bob = Affiliation(
67 contact = 'Other Lab Boss',
68 email = 'bob@some.where.else',
70 obj.affiliation_bob.save()
72 Library.objects.all().delete()
73 obj.library_10001 = Library(
75 library_name = 'C2C12 named poorly',
76 library_species = obj.species_human,
77 experiment_type = obj.experiment_rna_seq,
78 creation_date = datetime.datetime.now(),
79 made_for = 'scientist unit 2007',
80 made_by = 'microfludics system 7321',
81 stopping_point = '2A',
82 undiluted_concentration = '5.01',
84 obj.library_10001.save()
85 obj.library_10002 = Library(
87 library_name = 'Worm named poorly',
88 library_species = obj.species_human,
89 experiment_type = obj.experiment_rna_seq,
90 creation_date = datetime.datetime.now(),
91 made_for = 'scientist unit 2007',
92 made_by = 'microfludics system 7321',
93 stopping_point = '2A',
94 undiluted_concentration = '5.01',
96 obj.library_10002.save()
98 class LibraryTestCase(TestCase):
102 def testOrganism(self):
103 self.assertEquals(self.library_10001.organism(), 'human')
105 def testAffiliations(self):
106 self.library_10001.affiliations.add(self.affiliation_alice)
107 self.library_10002.affiliations.add(
108 self.affiliation_alice,
111 self.failUnless(len(self.library_10001.affiliations.all()), 1)
112 self.failUnless(self.library_10001.affiliation(), 'Alice')
114 self.failUnless(len(self.library_10002.affiliations.all()), 2)
115 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
117 class SampleWebTestCase(TestCase):
119 Test returning data from our database in rest like ways.
120 (like returning json objects)
122 fixtures = ['test_samples.json']
124 def test_library_info(self):
126 for lib in Library.objects.all():
127 lib_dict = library_dict(lib.id)
128 url = '/samples/library/%s/json' % (lib.id,)
129 lib_response = self.client.get(url, apidata)
130 self.failUnlessEqual(lib_response.status_code, 200)
131 lib_json = json.loads(lib_response.content)
133 for d in [lib_dict, lib_json]:
134 # amplified_from_sample is a link to the library table,
135 # I want to use the "id" for the data lookups not
136 # the embedded primary key.
137 # It gets slightly confusing on how to implement sending the right id
138 # since amplified_from_sample can be null
139 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
140 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
141 self.failUnlessEqual(d['avg_lib_size'], lib.avg_lib_size)
142 self.failUnlessEqual(d['cell_line'], lib.cell_line.cellline_name)
143 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
144 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
145 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
146 self.failUnlessEqual(d['id'], lib.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 response = self.client.get('/samples/library/nottheone/json', apidata)
168 self.failUnlessEqual(response.status_code, 404)
171 def test_library_no_key(self):
173 Make sure we get a 302 if we're not logged in
175 response = self.client.get('/samples/library/10981/json')
176 self.failUnlessEqual(response.status_code, 403)
177 response = self.client.get('/samples/library/10981/json', apidata)
178 self.failUnlessEqual(response.status_code, 200)