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()
panel_ids = [panel_id]
if not panel_id:
LOG.info("Fetching all panel app panels")
json_lines = fetch_resource(base_url.format("list_panels"), json=True)
panel_ids = [
panel_info["Panel_Id"] for panel_info in json_lines["result"]
]
for _panel_id in panel_ids:
json_lines = fetch_resource(base_url.format("get_panel") + _panel_id,
json=True)
parsed_panel = parse_panel_app_panel(panel_info=json_lines["result"],
hgnc_map=hgnc_map,
institute=institute)
parsed_panel["panel_id"] = _panel_id
if len(parsed_panel["genes"]) == 0:
LOG.warning("Panel %s is missing genes. Skipping.",
parsed_panel["display_name"])
continue
try:
adapter.load_panel(parsed_panel=parsed_panel)
except Exception as err:
raise err
def test_fetch_resource():
"""Test fetch resource"""
# GIVEN an URL
url = "http://www.github.com"
content = "Some things\n That are not so\ninteresting"
responses.add(
responses.GET,
url,
body=content,
status=200,
)
# WHEN fetching the resource
data = scout_requests.fetch_resource(url)
# THEN assert that a list of lines are returned
assert isinstance(data, list)
def test_fetch_resource_json():
"""Test fetch resource"""
# GIVEN an URL
url = "http://www.github.com"
content = [{"first": "second"}]
responses.add(
responses.GET,
url,
json=content,
status=200,
)
# WHEN fetching the resource
data = scout_requests.fetch_resource(url, json=True)
# THEN assert that a list of lines are returned
assert isinstance(data, list)
assert data[0]["first"] == "second"
def test_fetch_resource_gzipped(variant_clinical_file):
"""Test fetch resource"""
# GIVEN an URL
url = "http://www.github.com/things.txt.gz"
with open(variant_clinical_file, "rb") as zipped_file:
content = zipped_file.read()
responses.add(
responses.GET,
url,
body=content,
status=200,
)
# WHEN fetching the resource
data = scout_requests.fetch_resource(url)
# THEN assert that a list of lines are returned
assert isinstance(data, list)
# THEN assert that the vcf header is there
assert "##fileformat" in data[0]