def test_send_request_timout():
"""This test will trigge a timout error."""
# GIVEN a request and a request that timouts
url = "http://www.badurl.com"
responses.add(
responses.GET,
url,
body=requests.exceptions.Timeout(),
)
# WHEN requesting
with pytest.raises(requests.exceptions.Timeout):
# THEN assert that the a Timeout is raised
scout_requests.get_request(url)
def test_get_request():
"""Test functions that accepts an url and returns decoded data from it"""
# test function with url that exists
url = "http://www.github.com"
decoded_resp = get_request(url)
assert "<!DOCTYPE html>" in decoded_resp
def load_panel_app(adapter, panel_id=None, institute="cust000"):
"""Load PanelApp panels into scout database
If no panel_id load all PanelApp panels
Args:
adapter(scout.adapter.MongoAdapter)
panel_id(str): The panel app panel id
"""
base_url = "https://panelapp.genomicsengland.co.uk/WebServices/{0}/"
hgnc_map = adapter.genes_by_alias()
if panel_id:
panel_ids = [panel_id]
if not panel_id:
LOG.info("Fetching all panel app panels")
data = get_request(base_url.format("list_panels"))
json_lines = json.loads(data)
panel_ids = [panel_info["Panel_Id"] for panel_info in json_lines["result"]]
for panel_id in panel_ids:
panel_data = get_request(base_url.format("get_panel") + panel_id)
parsed_panel = parse_panel_app_panel(
panel_info=json.loads(panel_data)["result"],
hgnc_map=hgnc_map,
institute=institute,
)
parsed_panel["panel_id"] = panel_id
if len(parsed_panel["genes"]) == 0:
LOG.warning(
"Panel {} is missing genes. Skipping.".format(
parsed_panel["display_name"]
)
)
continue
try:
adapter.load_panel(parsed_panel=parsed_panel)
except Exception as err:
raise err
def test_get_request_bad_url():
"""Test functions that accepts an url and returns decoded data from it"""
# test function with a url that is not valid
url = "fakeyurl"
with pytest.raises(ValueError) as err:
# function should raise error
assert get_request(url)
def test_get_request_bad_url():
"""Test function that accepts an url and returns decoded data from it"""
# test function with a url that is not valid
url = "fakeyurl"
with pytest.raises(requests.exceptions.MissingSchema):
# function should raise error
assert scout_requests.get_request(url)
def test_get_request():
"""Test functions that accepts an url and returns decoded data from it"""
# GIVEN an URL
url = "http://www.github.com"
responses.add(
responses.GET,
url,
status=200,
)
# WHEN requesting
response = scout_requests.get_request(url)
# THEN assert that the reponse is correct
assert response.status_code == 200
def test_get_request_bad_request():
"""Test functions that accepts an url and returns decoded data from it"""
# GIVEN an URL
url = "http://www.badurl.com"
responses.add(
responses.GET,
url,
status=404,
)
# WHEN requesting
with pytest.raises(requests.exceptions.HTTPError):
response = scout_requests.get_request(url)
# THEN assert that the a httperror is raised
assert response.status_code == 404
