def test_import_adaptive_data_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_adaptive(s, 'clonotypes/tests/data/test_adaptive.tsv')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
def test_import_miTCR_to_database(self):
# Make a test sample
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
# Model can read in a file
Clonotype.import_mitcr(s, 'clonotypes/tests/data/test_mitcr.txt')
all_clonotypes = Clonotype.objects.all()
self.assertEquals(len(all_clonotypes), 100)
self.fail('todo')
def handle(self, *args, **options):
try:
sample_id, tsv_filename = args
# self.stdout.write(" ".join(args))
self.stdout.write(sample_id + " " + tsv_filename)
except:
raise BaseException("Incorrect number of arguments for import")
try:
sample = Sample.objects.get(id=sample_id)
except:
raise BaseException(
"Sample with sample id " + sample_id + " not found.")
Clonotype.import_mitcr(sample, tsv_filename)
def test_clonotypes_have_these_required_fields(self):
s = SampleFactory()
r = RecombinationFactory()
data = {'sample': s,
'frequency': 0.1,
'count': 1,
'recombination': r,
}
c = Clonotype()
for key, value in data.items():
setattr(c, key, value)
c.save()
c_in_db = Clonotype.objects.get()
for key, value in data.items():
self.assertEqual(
value, getattr(c_in_db, key), 'key value %s not equal' % key)
def test_create_clonotypes_for_a_sample(self):
p = Patient()
p.save()
s = Sample(patient=p)
s.save()
r = RecombinationFactory()
c = Clonotype(
sample=s,
recombination=r,
frequency=9.336458E-6,
count=2,
)
c.save()
# Get all clonotypes from database
all_clonotypes = Clonotype.objects.all()
self.assertEqual(all_clonotypes[0], c)