def store():
client = MongoClient(username=MONGO_USERNAME, password=MONGO_PASSWORD)
try:
client.server_info()
except ServerSelectionTimeoutError as err:
print("MongoClient could not reach server, is it running ?")
raise
client_es = Elasticsearch([ES_URL], http_auth=("elastic", ES_PASSWORD))
fhirstore = FHIRStore(client, client_es, DB_NAME)
fhirstore.reset()
fhirstore.bootstrap(depth=2, resource="Patient")
fhirstore.bootstrap(depth=2, resource="Practitioner")
fhirstore.bootstrap(depth=2, resource="MedicationRequest")
return fhirstore
# uncomment the next 2 following line if you wish to activate
# the replication mode of mongo (required by monstache)
# res = client.admin.command("replSetInitiate", None)
# time.sleep(1)
store = FHIRStore(client, client_es, "fhirstore")
# uncomment the following line if mongo already has initialised
# collections and you don't want to bootstrap them all
# store.resume()
# reset collections (comment if you used `store.resume()`)
print("Dropping collections...")
start = timer()
store.reset()
end = timer()
print(end - start, "seconds")
# create collections (comment if you used `store.resume()`)
print("Creating collections...")
start = timer()
store.bootstrap(depth=3)
end = timer()
print(end - start, "seconds")
# creating document
print("Inserting documents...")
json_folder_path = os.path.join(os.getcwd(), "test/fixtures")
json_files = [
x for x in os.listdir(json_folder_path) if x.endswith(".json")