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
t = tqdm(total=total_size,
unit='B',
unit_scale=True,
desc="Downloading example resources")
with open('benchmark/examples.zip', 'wb') as f:
for data in r.iter_content(block_size):
t.update(len(data))
f.write(data)
t.close()
else:
print("Using cached resources")
download_resources()
client = MongoClient()
store = FHIRStore(client, "benchmark")
store.resume()
# store.reset()
# store.bootstrap(depth=3)
examples = tqdm(iter_examples(),
total=count_examples(),
desc="Running write benchmark")
stats = {}
inserted = []
for example, data in examples:
if not data.get('id'):
data["id"] = str(uuid4())
start = timer()
res = store.create(data)
end = timer()
from elasticsearch import Elasticsearch
from fhirstore import FHIRStore
if __name__ == '__main__':
client = MongoClient(username="******", password="******")
client_es = Elasticsearch(['http://localhost:9200'],
http_auth=("elastic", "SuperSecurePassword2019"))
# 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()
