def test_send_gene_request():
"""Test send request with correct params and endpoint"""
url = 'https://grch37.rest.ensembl.org/overlap/id/ENSG00000103591?feature=gene'
client = eracs.EnsemblRestApiClient()
data = client.send_request(url)
# get all gene for the ensembl gene, They should be a list of items
assert data[0]['assembly_name'] == 'GRCh37'
assert data[0]['external_name'] == 'AAGAB'
assert data[0]['start']
assert data[0]['end']
def test_send_request_wrong_url():
"""Successful requests are tested by other tests in this file.
This test will trigger errors instead.
"""
url = 'fakeyurl'
client = eracs.EnsemblRestApiClient()
data = client.send_request(url)
assert type(data) == ValueError
url = 'https://grch37.rest.ensembl.org/fakeyurl'
data = client.send_request(url)
assert type(data) == HTTPError
def test_use_api():
"""Test the use_api method of the EnsemblRestClient"""
endpoint = '/overlap/id/ENSG00000157764'
params = {'feature': 'transcript'}
client = eracs.EnsemblRestApiClient(build='38')
# get all transctipts for an ensembl gene, They should be a list of items
data = client.use_api(endpoint, params)
assert data[0]['assembly_name'] == 'GRCh38'
assert data[0]['feature_type'] == 'transcript'
assert data[0]['id']
assert data[0]['start']
assert data[0]['strand']
def test_use_api():
"""Test the use_api method of the EnsemblRestClient"""
endpoint = "/overlap/id/ENSG00000157764"
params = {"feature": "transcript"}
client = eracs.EnsemblRestApiClient(build="38")
# get all transctipts for an ensembl gene, They should be a list of items
data = client.use_api(endpoint, params)
assert data[0]["assembly_name"] == "GRCh38"
assert data[0]["feature_type"] == "transcript"
assert data[0]["id"]
assert data[0]["start"]
assert data[0]["strand"]
def test_send_gene_request():
"""Test send request with correct params and endpoint"""
url = "https://grch37.rest.ensembl.org/overlap/id/ENSG00000103591?feature=gene"
client = eracs.EnsemblRestApiClient()
try:
data = client.send_request(url)
# get all gene for the ensembl gene, They should be a list of items
assert data[0]["assembly_name"] == "GRCh37"
assert data[0]["external_name"] == "AAGAB"
assert data[0]["start"]
assert data[0]["end"]
except Exception as ex:
assert isinstance(data, HTTPError) # service is down
def ensembl_rest_client_38():
"""Return a client to the ensembl rest api, build 38"""
return ensembl_rest_clients.EnsemblRestApiClient("38")
def test_ping_ensemble_37():
"""Test ping ensembl server containing human build 37"""
client = eracs.EnsemblRestApiClient()
data = client.ping_server()
assert data == {'ping': 1}
def test_ping_ensemble_38():
"""Test ping ensembl server containing human build 38"""
client = eracs.EnsemblRestApiClient(build="38")
data = client.ping_server()
assert data == {"ping": 1}