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

johngrimes

johngrimes

SCTID,FSN,Body,External,Nature
100051000032108,Bat scratch (event),0,1,0
100071000032104,Bat scratch injury (disorder),0,0,1
10050004,Contusion of chest (disorder),0,0,1
10061007,Brain stem contusion without open intracranial wound AND with prolonged loss of consciousness (more than 24 hours) AND return to pre-existing conscious level (disorder),0,0,1
10065003,Excoriated acne (disorder),0,0,1
10070005,Poisoning caused by quinoline AND/OR hydroxyquinoline derivative (disorder),0,1,0
10132008,Burns of multiple sites (disorder),1,0,0
10186000,Toxic effect of selenium compound (disorder),0,1,0
10217006,Third degree perineal laceration (disorder),0,0,1