def test_browse(self):
p = Protein(**test_protein_data())
db.session.add(p)
response = self.client.get('/protein/browse', follow_redirects=True)
assert response.status_code == 200
def test_sites(self):
p = Protein(**test_protein_data())
sites = [
Site(position=3, residue='R', type='phosphorylation'),
Site(position=4, residue='T', type='methylation')
]
db.session.add(p)
p.sites = sites
response = self.client.get('/protein/sites/NM_000123')
assert response.status_code == 200
assert response.content_type == 'application/json'
assert len(response.json) == 2
phospo_site_repr = None
for site_repr in response.json:
if site_repr['type'] == 'phosphorylation':
phospo_site_repr = site_repr
assert phospo_site_repr
def test_mutation(self):
p = Protein(**test_protein_data())
p.mutations = create_test_mutations()
db.session.add(p)
queries = {
'/protein/mutation/NM_000123/1/K': 1,
'/protein/mutation/NM_000123/1/K?filters=Mutation.sources:in:MC3':
1,
'/protein/mutation/NM_000123/2/K': 1,
}
for query, expected_results_cnt in queries.items():
response = self.client.get(query)
assert len(response.json) == expected_results_cnt
response = self.client.get(
'/protein/mutation/NM_000123/2/K?filters=Mutation.sources:in:MC3')
assert 'Warning: There is a mutation, but it does not satisfy given filters' in response.json
response = self.client.get('/protein/mutation/NM_000123/2/K')
mut = response.json.pop()
assert mut['ref'] == 'A'
assert mut['pos'] == 2
assert mut['alt'] == 'K'
assert mut['protein'] == 'NM_000123'
def test_known_mutations(self):
p = Protein(**test_protein_data())
p.mutations = create_test_mutations()
db.session.add(p)
response = self.client.get('/protein/known_mutations/NM_000123')
muts = response.json
assert len(muts) == 4
def test_redirect(self):
p = Protein(**test_protein_data())
db.session.add(p)
response = self.client.get(
'/protein/show/NM_000123?filters=Mutation.sources:in:MC3')
assert response.status_code == 302
assert relative_location(
response
) == '/sequence/show/NM_000123?filters=Mutation.sources:in:MC3'