def trigger_refresh():
"""Triggers refresh in the CCDH model."""
logger.info('Requesting refresh of CCDH Model.')
token: str = get_settings().docker_user_token_limited
if not token:
logger.error(
'Error: Attempted to trigger update in CCDH Model repository, '
'but "DOCKER_USER_TOKEN_LIMITED" was not found in environment.',
file=sys.stderr)
else:
r = requests.post(
'https://api.github.com/repos/cancerDHC/ccdhmodel/dispatches',
headers={
"Accept": "application/vnd.github.v3+json",
"Content-Type": "application/json",
"Authorization": "Bearer " + token
},
json={"event_type": "refreshModel"})
if r.status_code >= 400: # errors defined as codes 400 and above
logger.error(
'Error: Triggering update in CCDH Model repository failed.\n',
'Status code: ',
r.status_code, '\n'
'Reason: ',
r.reason, '\n'
'Response text: ',
r.text,
file=sys.stderr)
else:
logger.info('Success.')
async def startup():
"""Start up FastAPI server"""
settings = get_settings()
app.state.graph = TccmGraph(settings)
app.state.graph.connect()
redis = aioredis.from_url(url=settings.redis_url,
encoding="utf8",
decode_responses=True)
FastAPICache.init(backend=RedisBackend(redis), prefix="fastapi-cache")
def neo4j_graph(docker_ip, docker_services):
settings = get_settings()
port = docker_services.port_for('ccdh-neo4j', 7474)
url = f'http://{docker_ip}:{port}'
docker_services.wait_until_responsive(timeout=60.0,
pause=0.1,
check=lambda: is_responsive(url))
bolt_port = docker_services.port_for('ccdh-neo4j', 7687)
bolt_url = f'bolt://{docker_ip}:{bolt_port}'
graph = Graph(bolt_url,
auth=(settings.neo4j_username, settings.neo4j_password))
yield graph
def read_ccdh_model_yaml():
"""Read model yaml from CCDH Model GH repository"""
branch = get_settings().ccdhmodel_branch
yaml_url = f'https://raw.githubusercontent.com/cancerDHC/ccdhmodel/{branch}/model/schema/crdch_model.yaml'
# to-do: Remove old yaml url when done w/ debugging:
# Old yaml_url for debugging purposes (-jef 2021/11/19):
# yaml_url = 'https://raw.githubusercontent.com/cancerDHC/ccdhmodel/253fdbc48f2d3df809f79356cbde6d449306e84f/model/schema/crdch_model.yaml' # 2021/09/23
logger.info("Retrieving CCDH Model YAML: " + yaml_url)
r = requests.get(yaml_url)
if r.status_code == 200:
return r.content
else:
logger.info(f"Failed to Retrieving CCDH Model YAML: {r.status_code}")
logger.info(r.content)
raise ValueError('Failed to fetch yaml from ' + yaml_url)
"""Wrapper around the FastApiCache-2 library"""
from fastapi_cache.decorator import cache
from ccdh.config import get_settings
# Note: args and kwargs left here because they are used by...
# ...`fastapi_cache.decorator.cache`
# noinspection PyUnusedLocal
def nocache(*args, **kwargs):
"""Wrapper func"""
def decorator(func):
"""Decorator"""
return func
return decorator
if get_settings().environment_name == 'production':
cache = cache
else:
cache = nocache
def test_config():
settings = get_settings()
assert settings.neo4j_bolt_port is not None