def test_SampleToAmino_amino_acids_returns_list_of_keys_if_amino_acids_exist_when_created(self):
make_fake_patient_with_3_clonotypes()
s = Sample.objects.get()
s2a = SampleToAmino(sample=s)
s2a.save()
aa_keys = [aa.id for aa in AminoAcid.objects.all()]
self.assertEquals(aa_keys, s2a.amino_acids)
def test_create_samples_for_a_patient(self):
make_fake_patient_with_3_clonotypes()
# Try retreiving the sample from the database
s = Sample.objects.get()
all_samples = Sample.objects.all()
self.assertEqual(len(all_samples), 1)
# Check to see if the attributes have been saved
# Make sure the sample is linked to the patient
self.assertEqual(all_samples[0].patient, s.patient)
def test_SampleToAmino_update_stores_amino_acid_keys_as_json_in_db(self):
make_fake_patient_with_3_clonotypes()
s = Sample.objects.get()
s2a = SampleToAmino(sample=s)
s2a.save()
self.assertEquals('[1, 2, 3]', s2a._amino_acids)
def setUp(self):
make_fake_patient_with_3_clonotypes()
def setUp(self):
self.renderPatch = patch('clonotypes.views.render', render_echo)
self.renderPatch.start()
self.request = FakeRequestFactory()
make_fake_patient_with_3_clonotypes()
def test_j_gene_names_returns_list_of_distinct_j_gene_names(self):
make_fake_patient_with_3_clonotypes()
self.assertIsInstance(Recombination.j_gene_names(), list)
self.assertEqual(
[u'TRBJ1-1', u'TRBJ2-4'], Recombination.j_gene_names())
def test_functionality_states_returns_list_of_all_functionality_states_in_db(self):
make_fake_patient_with_3_clonotypes()
self.assertIsInstance(Recombination.functionality_states(), list)
self.assertEqual([u'Productive', u'Out of frame'],
Recombination.functionality_states())
def setUp(self):
make_fake_patient_with_3_clonotypes()
self.s = Sample.objects.get()
def setUp(self):
make_fake_patient_with_3_clonotypes()
self.s = Sample.objects.get()
self.f = ClonoFilter(sample=self.s)
self.f.save()
def test_samples_have_a_draw_date(self):
make_fake_patient_with_3_clonotypes()
# Retrieve the sample from the db
all_samples = Sample.objects.all()
# make sure the draw dates are equal
self.assertTrue(all_samples[0].draw_date)
