def setUp(self):
self.renderPatch = patch('clonotypes.views.render', render_echo)
self.renderPatch.start()
self.request = FakeRequestFactory()
make_fake_patient()
self.s = Sample.objects.get()
self.aa = AminoAcid.objects.get()
def test_parse_nucleotide_should_not_create_a_span_if_index_is_lt_0(self):
''' Adaptive uses -1 in the index field to represent the lack of
that element. This test makes sure rendered text does no create a span
for an empty region '''
make_fake_patient()
r = Recombination.objects.get()
r.j_start = 10
r.d_end = 9
pr = r.parsed_nucleotide()
self.assertNotIn('<span class="dj_additions"', pr)
r = Recombination.objects.get()
r.d_start = 8
r.d_end = 9
pr = r.parsed_nucleotide()
self.assertNotIn('<span class="d_gene"', pr)
r = Recombination.objects.get()
r.v_end = 6
r.d_start = 7
pr = r.parsed_nucleotide()
self.assertNotIn('<span class="vd_additions"', pr)
def test_parsed_nucleotide_should_wrap_spans_around_nucleotide_groups(self):
make_fake_patient()
r = Recombination.objects.get()
pr = r.parsed_nucleotide()
# Test v
regex = re.compile('.*<span class="v_gene">(.*?)</span>')
match = regex.match(pr)
self.assertEqual(len(match.groups()[0]), r.v_end)
# VD junction
regex = re.compile('.*<span class="vd_additions">(.*?)</span>')
match = regex.match(pr)
num_n2_additions = r.d_start - r.v_end
self.assertEqual(len(match.groups()[0]), num_n2_additions)
# D
regex = re.compile('.*<span class="d_gene">(.*?)</span>')
match = regex.match(pr)
d_length = r.d_end- r.d_start
self.assertEqual(len(match.groups()[0]), d_length)
# DJ Junction
regex = re.compile('.*<span class="dj_additions">(.*?)</span>')
match = regex.match(pr)
num_n1_additions = r.j_start - r.d_end
self.assertEqual(len(match.groups()[0]), num_n1_additions)
# J
regex = re.compile('.*<span class="j_gene">(.*?)</span>')
match = regex.match(pr)
j_length = len(r.nucleotide) - r.j_start
self.assertEqual(len(match.groups()[-1]), j_length)
def DONTtest_summary_page_shows_productivity_choices_using_form(self):
make_fake_patient()
fake_sample = Sample.objects.get()
response = self.client.get(reverse('samples.views.summary',
args=[fake_sample.id]))
self.assertTrue(isinstance(response.context['form'], FilterForm))
def setUp(self):
make_fake_patient()
self.fake_sample = Sample.objects.get()
self.aa = AminoAcid.objects.get()
def setUp(self):
make_fake_patient()
self.fake_sample = Sample.objects.get()
self.clonotype = Clonotype.objects.all()[:1].get()
self.response = self.client.get(
reverse('clonotypes.views.detail', args=[self.clonotype.id]))
def setUp(self):
make_fake_patient()
self.s = Sample.objects.get()
self.p = Patient.objects.get()
def test_parsed_nucleotide_returns_a_string(self):
make_fake_patient()
r = Recombination.objects.get()
pr = r.parsed_nucleotide()
self.assertIsInstance(pr, str)
def test_parsed_nucleotide_should_return_nucleotide_sequence(self):
make_fake_patient()
r = Recombination.objects.get()
pr = r.parsed_nucleotide()
no_html = re.sub('<[^<]+?>', '', pr)
self.assertEqual(r.nucleotide, no_html)
