main.py

import os
import json
from timeit import default_timer as timer
from pymongo import MongoClient
from elasticsearch import Elasticsearch

from fhirstore import FHIRStore

MONGO_USERNAME = os.getenv("MONGO_USERNAME")
MONGO_PASSWORD = os.getenv("MONGO_PASSWORD")

ES_USERNAME = os.getenv("ES_USERNAME", "elastic")
ES_PASSWORD = os.getenv("ES_PASSWORD")
ES_HOST = os.getenv("ES_HOST", "localhost")
ES_PORT = os.getenv("ES_PORT", 9200)
ES_URL = f"http://{ES_USERNAME}{':'+ES_PASSWORD if ES_PASSWORD else ''}@{ES_HOST}:{ES_PORT}"

if __name__ == "__main__":
    client = MongoClient(username=MONGO_USERNAME, password=MONGO_PASSWORD)
    client_es = Elasticsearch([ES_URL])
    # 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()
    res = store.db["Practitioner"].find_one(
        {
            "identifier.value": "161765",
            "identifier.system": "http://terminology.arkhn.org/ck8oojkbu27044kp4od9c3pmz/ck8oojkec27414kp4n4dxkrw5",
        }
    )
    print(res)
    exit(0)
    res = [r for r in res]
    print(res[0] if len(res) > 0 else "", len(res))
    exit(0)

    # 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")]
    total = 0
    for json_file in json_files:
        json_file_path = os.path.join(json_folder_path, json_file)
        with open(json_file_path, "r") as f:
            data = json.load(f)
            start = timer()
            print("Creating", json_file_path, "...")
            try:
                store.create(data)
            except Exception as e:
                print(e)
            end = timer()
            print(end - start, "seconds")
            total += end - start
    print(f"Inserted {len(json_files)} documents in {total} seconds")
    # srch = store.search(resource='patient',params="male")
    # print(srch)

    client.close()