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
25 class LibraryTestCase(TestCase):
29 def testOrganism(self):
30 self.assertEquals(self.library_10001.organism(), 'human')
32 def testAffiliations(self):
33 self.library_10001.affiliations.add(self.affiliation_alice)
34 self.library_10002.affiliations.add(
35 self.affiliation_alice,
38 self.failUnless(len(self.library_10001.affiliations.all()), 1)
39 self.failUnless(self.library_10001.affiliation(), 'Alice')
41 self.failUnless(len(self.library_10002.affiliations.all()), 2)
42 self.failUnless(self.library_10001.affiliation(), 'Alice, Bob')
45 class SampleWebTestCase(TestCase):
47 Test returning data from our database in rest like ways.
48 (like returning json objects)
50 fixtures = ['test_samples.json']
52 def test_library_info(self):
54 for lib in Library.objects.all():
55 lib_dict = library_dict(lib.id)
56 url = '/samples/library/%s/json' % (lib.id,)
57 lib_response = self.client.get(url, apidata)
58 self.failUnlessEqual(lib_response.status_code, 200)
59 lib_json = json.loads(lib_response.content)
61 for d in [lib_dict, lib_json]:
62 # amplified_from_sample is a link to the library table,
63 # I want to use the "id" for the data lookups not
64 # the embedded primary key.
65 # It gets slightly confusing on how to implement sending the right id
66 # since amplified_from_sample can be null
67 #self.failUnlessEqual(d['amplified_from_sample'], lib.amplified_from_sample)
68 self.failUnlessEqual(d['antibody_id'], lib.antibody_id)
69 self.failUnlessEqual(d['cell_line_id'], lib.cell_line_id)
70 self.failUnlessEqual(d['cell_line'], unicode_or_none(lib.cell_line))
71 self.failUnlessEqual(d['experiment_type'], lib.experiment_type.name)
72 self.failUnlessEqual(d['experiment_type_id'], lib.experiment_type_id)
73 self.failUnlessEqual(d['gel_cut_size'], lib.gel_cut_size)
74 self.failUnlessEqual(d['hidden'], lib.hidden)
75 self.failUnlessEqual(d['id'], lib.id)
76 self.failUnlessEqual(d['insert_size'], lib.insert_size)
77 self.failUnlessEqual(d['library_name'], lib.library_name)
78 self.failUnlessEqual(d['library_species'], lib.library_species.scientific_name)
79 self.failUnlessEqual(d['library_species_id'], lib.library_species_id)
80 self.failUnlessEqual(d['library_type_id'], lib.library_type_id)
81 if lib.library_type_id is not None:
82 self.failUnlessEqual(d['library_type'], lib.library_type.name)
84 self.failUnlessEqual(d['library_type'], None)
85 self.failUnlessEqual(d['made_for'], lib.made_for)
86 self.failUnlessEqual(d['made_by'], lib.made_by)
87 self.failUnlessEqual(d['notes'], lib.notes)
88 self.failUnlessEqual(d['replicate'], lib.replicate)
89 self.failUnlessEqual(d['stopping_point'], lib.stopping_point)
90 self.failUnlessEqual(d['successful_pM'], lib.successful_pM)
91 self.failUnlessEqual(d['undiluted_concentration'],
92 unicode(lib.undiluted_concentration))
95 # test a case where there is no known status
96 lane_set = {u'status': u'Unknown', u'paired_end': True, u'read_length': 75, u'lane_number': 1, u'flowcell': u'303TUAAXX', u'status_code': None}
97 self.failUnlessEqual(len(d['lane_set']), 1)
98 self.failUnlessEqual(d['lane_set'][0], lane_set)
99 elif lib.id == '11016':
100 # test a case where there is a status
101 lane_set = {u'status': 'Good', u'paired_end': True, u'read_length': 75, u'lane_number': 5, u'flowcell': u'303TUAAXX', u'status_code': 2}
102 self.failUnlessEqual(len(d['lane_set']), 1)
103 self.failUnlessEqual(d['lane_set'][0], lane_set)
105 def test_invalid_library(self):
107 Make sure we get a 404 if we request an invalid library id
109 response = self.client.get('/samples/library/nottheone/json', apidata)
110 self.failUnlessEqual(response.status_code, 404)
113 def test_library_no_key(self):
115 Make sure we get a 302 if we're not logged in
117 response = self.client.get('/samples/library/10981/json')
118 self.failUnlessEqual(response.status_code, 403)
119 response = self.client.get('/samples/library/10981/json', apidata)
120 self.failUnlessEqual(response.status_code, 200)
122 # The django test runner flushes the database between test suites not cases,
123 # so to be more compatible with running via nose we flush the database tables
124 # of interest before creating our sample data.
126 Species.objects.all().delete()
127 obj.species_human = Species(
128 scientific_name = 'Homo Sapeins',
129 common_name = 'human',
131 obj.species_human.save()
132 obj.species_worm = Species(
133 scientific_name = 'C. Elegans',
134 common_name = 'worm',
136 obj.species_worm.save()
137 obj.species_phix = Species(
138 scientific_name = 'PhiX',
141 obj.species_phix.save()
143 ExperimentType.objects.all().delete()
144 obj.experiment_de_novo = ExperimentType(
147 obj.experiment_de_novo.save()
148 obj.experiment_chip_seq = ExperimentType(
151 obj.experiment_chip_seq.save()
152 obj.experiment_rna_seq = ExperimentType(
155 obj.experiment_rna_seq.save()
157 Affiliation.objects.all().delete()
158 obj.affiliation_alice = Affiliation(
160 contact = 'Lab Boss',
161 email = 'alice@some.where.else.'
163 obj.affiliation_alice.save()
164 obj.affiliation_bob = Affiliation(
166 contact = 'Other Lab Boss',
167 email = 'bob@some.where.else',
169 obj.affiliation_bob.save()
171 Library.objects.all().delete()
172 obj.library_10001 = Library(
174 library_name = 'C2C12 named poorly',
175 library_species = obj.species_human,
176 experiment_type = obj.experiment_rna_seq,
177 creation_date = datetime.datetime.now(),
178 made_for = 'scientist unit 2007',
179 made_by = 'microfludics system 7321',
180 stopping_point = '2A',
181 undiluted_concentration = '5.01',
184 obj.library_10001.save()
185 obj.library_10002 = Library(
187 library_name = 'Worm named poorly',
188 library_species = obj.species_human,
189 experiment_type = obj.experiment_rna_seq,
190 creation_date = datetime.datetime.now(),
191 made_for = 'scientist unit 2007',
192 made_by = 'microfludics system 7321',
193 stopping_point = '2A',
194 undiluted_concentration = '5.01',
197 obj.library_10002.save()