johngrimes

#!/usr/bin/env python3
import click
import os
from pathling._version import (
    __java_version__,
    __scala_version__,
    __delta_version__,
    __hadoop_version__,
)

johngrimes

{
  "resourceType": "Condition",
  "id": "1",
  "clinicalStatus": {
    "coding": [
      {
        "system": "http://terminology.hl7.org/CodeSystem/condition-clinical",
        "code": "active"
      }
    ]

johngrimes

import requests


def get_oauth2_token(client_id, client_secret, token_url):
    """
    Obtain an OAuth2 token using client credentials grant.

    :param client_id: OAuth2 Client ID
    :param client_secret: OAuth2 Client Secret
    :param token_url: OAuth2 Token Endpoint URL

johngrimes

johngrimes

Dependencies

• jq
• Pathling Python library

Step 1

bash get-codings.sh fhir/*.json >codings.ndjson

johngrimes

import json
import multiprocessing as mp
import sys
from math import floor
from time import time

import requests


def update_resource(file):

johngrimes

import multiprocessing as mp
import sys
from time import time

import requests


def upload_bundle(file):
    with open(file) as bundle:
        data = bundle.read()

johngrimes

import json
import sys

input_bundle = json.load(sys.stdin)

output_bundle = {
    "resourceType": "Bundle",
    "type": "transaction",
    "entry": [
        {

johngrimes

johngrimes

jq -r ".expansion.contains[] | { system: .system, code: .code, display: .display } | map(values) | @csv" ~/Desktop/source.ValueSet.json >~/Desktop/target.csv