def run():
body = request.get_json()
# Get credentials if given in request
if "credentialId" not in body:
raise OperationOutcome("credentialId is required to run fhirpipe.")
credential_id = body.pop("credentialId")
try:
credentials = get_pyrog_client().get_credentials(credential_id)
except OperationOutcome as e:
raise OperationOutcome(
f"Error while fetching credientials for DB: {e}.")
# Merge body with default_params to get parameters to use
params = {**default_params, **body}
try:
# Connect to DB and run
fp_run(**params,
credentials=credentials,
pyrog_client=get_pyrog_client())
except Exception as e:
# If something went wrong
raise OperationOutcome(e)
return jsonify(success=True)
def run_graphql_query(self,
graphql_query,
variables=None,
auth_required=True):
"""
This function queries a GraphQL endpoint
and returns a json parsed response.
"""
PYROG_URL = fhirpipe.global_config["graphql"]["server"]
if not PYROG_URL:
raise OperationOutcome("PYROG_URL is missing from environment")
try:
response = requests.post(
PYROG_URL,
headers=self.get_headers(auth_required),
json={
"query": graphql_query,
"variables": variables
},
)
except requests.exceptions.ConnectionError:
raise OperationOutcome("Could not connect to the Pyrog service")
if response.status_code != 200:
raise Exception("Graphql query failed with returning code "
f"{response.status_code}\n{response.json()}.")
body = response.json()
if "errors" in body:
raise Exception(
f"GraphQL query failed with errors: {body['errors']}.")
return body
def get_resource_from_id(self, resource_id):
resp = self.run_graphql_query(resource_from_id_query,
variables={"resourceId": resource_id})
resource = resp["data"]["resource"]
if not resource:
raise OperationOutcome(
f"Resource with id {resource_id} does not exist")
return resource
def get_credentials(self, credential_id):
resp = self.run_graphql_query(
credential_query, variables={"credentialId": credential_id})
credentials = resp["data"]["credential"]
if not credentials:
raise OperationOutcome(
f"Database using credentials ID {credential_id} does not exist"
)
return credentials
def preview(resource_id, primary_key_value):
resource_mapping = get_pyrog_client().get_resource_from_id(resource_id)
# Get credentials if given in request
if not resource_mapping["source"]["credential"]:
raise OperationOutcome("credentialId is required to run fhirpipe.")
credentials = resource_mapping["source"]["credential"]
try:
# Connect to DB and run
fhir_objects, errors = fp_preview(resource_id, [primary_key_value],
credentials,
pyrog_client=get_pyrog_client())
except Exception as e:
# If something went wrong
raise OperationOutcome(e)
return jsonify({"preview": fhir_objects[0], "errors": errors})
def get_headers(self, auth_required=True):
if auth_required and not self.token:
raise OperationOutcome(
"PyrogClient is not authenticated (login has probably failed, check your logs)"
)
headers = {"content-type": "application/json"}
if auth_required:
headers["Authorization"] = f"Bearer {self.token}"
return headers
def login(self):
PYROG_LOGIN = fhirpipe.global_config["graphql"]["login"]
PYROG_PASSWORD = fhirpipe.global_config["graphql"]["password"]
if not PYROG_LOGIN or not PYROG_PASSWORD:
raise OperationOutcome(
"graphql.login and graphql.password must be set in fhirpipe config"
)
resp = self.run_graphql_query(
login_mutation,
variables={
"email": PYROG_LOGIN,
"password": PYROG_PASSWORD
},
auth_required=False,
)
data = resp["data"]
if not data:
raise OperationOutcome(
f"Could not login to pyrog (email={PYROG_LOGIN}): {resp['errors'][0]['message']}"
)
return data["login"]["token"]
def fetch(concept_map_id: str) -> T:
api_url = fhirpipe.global_config["fhir-api"]["url"]
try:
response = requests.get(f"{api_url}/ConceptMap/{concept_map_id}")
except requests.exceptions.ConnectionError as e:
raise OperationOutcome(
f"Could not connect to the fhir-api service: {e}")
if response.status_code != 200:
raise Exception(
f"Error while fetching concept map {concept_map_id}: {response.text}."
)
return response.json()